Displaying 1 - 290 of 290 tests
1p/19q Deletions for GliomaProbes: 1p36/1q25 |19q13/19p13
Disease(s): Oligodendroglioma
Ratios of p:q signals are determined for each chromosome to account for sectioning artifact. Deletion status is reported for each chromosome.
FISH
AACT

This antibody labels the cytoplasm of histiocytes and neoplasms of histiocytic origin, as well as monocytes and macrophages of human colon, tonsil and skin.

Immunohistochemistry (IHC)
AATAlpha-1-Antitrypsin (AAT) is useful in the study of inherited AAT deficiency, benign and malignant hepatic tumors and yolk sac carcinoma. Sensitivity and specificity of the results have made this antibody a useful tool in the screening of patients with cryptogenic cirrhosis or other forms of liver disease with portal fibrosis of uncertain etiology. Immunohistochemistry (IHC)
ACTHAnti-adrenocorticotropic hormone (ACTH) is a useful marker in the classification of pituitary tumors and the study of pituitary disease. It reacts with ACTH-producing cells (corticotrophs). It also may react with other tumors (e.g., some small cell carcinomas of the lung) causing paraneoplastic syndromes by secreting ACTH. Immunohistochemistry (IHC)
AFBSpecial stain. Ziehl-Neelsen Acid-Fast Bacilli Stain is used to detect the presence of acid-fast mycobacteria in tissue sections. Acid-fast techniques are of value in the detection of mycobacteria, rod-shaped organisms that sometimes exhibit filamentous (fungus-like) growth. The most significant disease-producing mycobacteria are Mycobacterium tuberculosis and Mycobacterium leprae. Immunohistochemistry (IHC)
AFPAlpha-1-fetoprotein (AFP) is a 64 kD tumor-associated embryonal antigen produced by fetal liver, hepatocellular carcinoma, yolk sac tumor and several germ cell tumors of testicular and ovarian origin. Most non-seminomatous germ cell tumors produce AFP. AFP is of importance in diagnosing hepatocellular carcinoma. Immunohistochemistry (IHC)
Alcian BlueSpecial stain. Alcian blue is intended to identify weakly sulfated mucins in tissue samples. Immunohistochemistry (IHC)
ALK (D5F3)

VENTANA FDA approved ALK (D5F3) CDx Assay is intended for the qualitative detection of the anaplastic lymphoma kinase (ALK) protein in formalin-fixed, paraffin-embedded (FFPE) non-small cell lung carcinoma (NSCLC) tissue stained with a BenchMark XT or BenchMark ULTRA automated staining instrument. It is indicated as an aid in identifying patients eligible for treatment with XALKORI® (crizotinib) or ZYKADIA® (ceritinib).

Immunohistochemistry (IHC)
ALK for NSCLCProbes: ALK (2p23)
Disease(s): Non-small cell lung carcinoma (NSCLC)
FISH
ALK Mutation Analysis

Bi-directional Sanger sequencing of ALK is performed using PCR primers designed to target hotspot mutations in exons 23 and 25.

Molecular
ALK-1 (for heme cases)The ALK1 (ALK1 cline) antibody labels normal human ALK protein and the NPM-ALK chimeric protein, and is a useful tool for the identification of the subgroup of anaplastic large-cell lymphomas (ALCL) that are ALK positive. Immunohistochemistry (IHC)
Amyloid A & Amyloid PAmyloid A and P react with amyloid deposits in many tissues. When accompanied by Congo Red, Amyloid A and P can be used to distinguish primary and secondary amyloidosis. Because these stains are interpreted in context of each other and Congo Red, testing options available to global and tech-only clients differ. Immunohistochemistry (IHC)
Androgen Receptor Mutation AnalysisBi-directional Sanger sequencing of the gene Androgen Receptor is performed using PCR primers designed to target hotspot mutations in exons 4, 5 and 8. Molecular
ARAndrogen receptor (AR) is responsible for the regulation of the growth of the prostate epithelial cells. In untreated prostate carcinoma, AR positive cells are more likely to be responsive to hormonal therapy. In patients with hormone refractory prostate carcinoma, the presence of AR has a negative prognostic impact. It is also commonly expressed in salivary duct carcinoma. Immunohistochemistry (IHC)
Arginase 1Arginase 1 (ARG1), also known as liver arginase, is a binuclear manganese metalloenzyme. ARG1 is abundantly expressed in liver and represents a sensitive and specific marker of benign and malignant hepatocytes that may be a useful diagnostic tool in routine surgical pathology practice. Immunohistochemistry (IHC)
ATRX

ATRX mutations predominantly occur in grade II/III astrocytoma and secondary glioblastoma multiforme (GBM) brain tumors. ATRX loss defines a subgroup of astrocytic tumors with a favorable prognosis.

Immunohistochemistry (IHC)
ATRX Mutation Analysis

Bi-directional Sanger sequencing of ATRX is performed using PCR primers designed to target hotspot mutations in exons 8-10, 12-15, 17, 18, 21, 22, 26, 30-32, and 35.

Molecular
BAP1

BAP1 IHC stain is a tool for detection of BAP1 mutations with subsequent inactivation. Loss of BAP1 by IHC is 100% specific for malignant mesothelioma in the context of mesothelioma vs. mesothelial hyperplasia. Loss of BAP1 may be seen in other neoplasms.

Immunohistochemistry (IHC)
BCA-225This antibody recognizes a human breast carcinoma associated glycoprotein BCA-225 (220-225kD). This protein differs in size and distribution from other breast carcinoma antigens. It does not react with benign or malignant gastrointestinal tissues. It can be used to identify skin carcinomas with sweat gland and sebaceous differentiation. Immunohistochemistry (IHC)
BCL10

BCL-10 is an N-terminal CARD (Caspase Recruitment Domain) containing protein that is involved in the adaptive immune response. It is also a substrate for MALT1. Mutations in the gene can lead to lymphoma, mucosa-associated lymphoid type. It is useful in the assessment of pancreatic tumors to distinguish acinar cell carcinoma from primitive neuroectodermal tumor (PNET), solid pseudopapillary tumor (SPT) and pancreatic blastoma (PB).

Immunohistochemistry (IHC)
BCL2B-cell lymphoma 2 (BCL2) was the first of the translocation-associated proteins to be identified in lymphoma. Most cases of follicular lymphoma have a [t(14;18)] translocation, resulting in BCL2 overexpression. Overexpression of BCL2 in activated diffuse B-cell lymphoma may predict disease progression. BCL2 is also expressed in a wide range of other neoplasms. Immunohistochemistry (IHC)
BerEP4Ber-EP4 recognizes two glycoproteins of 34 and 49 kDa present on the surface and the cytoplasm of all epithelial cells except the superficial layers of squamous epithelial, hepatocytes and parietal cells. It does not label mesothelial cells and rarely marks mesotheliomas. It shows a broad spectrum of reactivity with human epithelial cells including simple epithelia and basal layers of stratified non-keratinized squamous epithelium and epidermis. Ber-EP4 reportedly distinguishes adenocarcinomas from pleural mesotheliomas. Immunohistochemistry (IHC)
Beta CateninBeta-catenin is an important regulator of cell–cell adhesion and embryogenesis. Mutations of beta-catenin could lead to some human cancers. Normal cells show membrane staining for beta-catenin, while cytoplasmic and/or nuclear staining is abnormal. Dysregulation of beta-catenin occurs in Gardner syndrome, where it leads to both familial adenomatous polyposis and fibromatosis. Nuclear location of beta-catenin also occurs in colon and endometrioid ovarian carcinomas as well as in synovial sarcoma, osteosarcoma, liposarcoma, palisaded myofibroblastoma, and other sarcomas. Immunohistochemistry (IHC)
BG8This antibody is specific for the Lewis Y (Type 2 Chain) carbohydrate antigen. Lewis Y has been evaluated as a clinical marker for the diagnosis and prognosis of cholangiocarcinoma, hepatocellular carcinoma and breast cancer. It was also shown that BG8 reacts predominantly with lung adenocarcinomas and is negative focally or weakly positive in epithelial mesotheliomas. Immunohistochemistry (IHC)
Bladder Cancer

Probes: +3 (Cen 3) | +7 (Cen 7) | p16 (9p21) | +17 (Cen 17)
Disease(s): Bladder cancer

FISH
BRAF Mutation Analysis

Bi-directional sequencing of exon 15 of the BRAF gene, which includes qualitative detection of V600 mutations E, K, D, and others, plus other significant exon 15 mutations.  For solid tumors, tumor enrichment is performed before extraction. Expanded coverage for BRAF exons 11 & 15 is available in the RAS/RAF Panel. Testing is available separately or in combination with HRAS, KRAS, and NRAS in the RAS/RAF Panel. Testing is approved for specimens from the state of New York. 

Molecular
BRAF Rearrangement

Probes: BRAF (7q34)
Disease(s): Brain cancer, thyroid cancer, melanoma

FISH
BRAF V600EA monoclonal antibody (VE1) against mutant BRAF (V600E) permits fast assessment of the mutant protein expression throughout a tumor sample in hairy cell leukemia, some melanomas, and some thyroid carcinomas. BRAF mutation is a strong molecular marker of poor prognosis in colorectal carcinoma (CRC), and can be used as evidence of a sporadic mechanism of mismatch repair deficiency. Immunohistochemistry (IHC)
Breast Triple Stain (CK5 + p63 + CK 8/18)The combination of CK5 + P63 + CK8/18 (Breast Triple Stain) can be useful in distinguishing ductal carcinoma in situ (DCIS) from microinvasive breast carcinoma. This multiplex can decipher between a radial scar and infiltrating carcinoma. P63 (nuclear brown) and CK5/6 (cytoplasmic brown) stain myoepithelial cells, whereas CK8/18 labels the cytoplasm (red) of all ductal or lobular epithelium. Immunohistochemistry (IHC)
CA125CA125 reacts with most epithelial ovarian neoplasms of serous, endometrioid, clear cell and undifferentiated types. CA125 is a useful tumor marker for ovarian carcinomas; however, CA125 has also been described in other neoplasms such as seminal vesicle and anaplastic lymphomas. No reactivity has been shown for mucinous ovarian tumors. It reacts with both normal tissues and neoplasms of fallopian tube, endometrium, endocervix and mesothelioma. It does not react with colon cancer. Normal tissues such as breast, liver, skin, kidney and spleen are negative. Immunohistochemistry (IHC)
CA19.9In normal tissues, the CA19.9 antigen has been demonstrated in ductal epithelium of the breast, kidney, salivary gland, sweat glands, respiratory epithelium of the lung, colon epithelium, pancreatic acini and ducts, biliary epithelium in the liver and prostate epithelium. Gastrointestinal carcinomas are positive, as well as transitional cell carcinomas of the bladder, endometrial adenocarcinomas, thyroid papillary, gallbladder carcinomas and lung carcinomas, including adenocarcinomas, bronchoalveolar cell carcinomas, squamous and small cell carcinomas. Immunohistochemistry (IHC)
CalcitoninCalcitonin is secreted by thyroidal parafollicular cells of neuroectodermal origin, probably in response to hypercalcemia. The IHC demonstration of calcitonin is important: (1) For identification of early or microscopic medullary thyroid cancer (MTC), (2) To identify an MTC in the absence of amyloid deposits, (3) To distinguish non-typical forms of MTC (e.g., predominantly spindle cell or small cell patterns) from anaplastic carcinoma or malignant lymphoma, (4) To differentiate MTC with microfollicular or papillary patterns from thyroid follicular and papillary neoplasms and (5) To identify C-cell hyperplasia in association with hypercalcemia of diverse etiologies. Immunohistochemistry (IHC)
CaldesmonCaldesmon is a developmentally regulated protein involved in smooth muscle and non-muscle contraction. Two closely related variants of human caldesmon have been identified. The h-caldesmon variant (120-150kDa) is predominantly expressed in smooth muscle and a subset of myoepithelial cells, whereas l-caldesmon (70-80kDa) is found in non-muscle tissue and cells. Neither of the two variants has been detected in skeletal muscle. Immunohistochemistry (IHC)
Calretinin

Calretinin is the most specific and reproducible positive marker of epithelial mesothelioma. Calretinin is a calcium-binding protein similar to S100 protein. It is found in the central and peripheral nervous system and in a wide spectrum of non-neural cells, including steroid-producing cells of ovaries and testes, fat cells, renal tubular epithelial cells, eccrine glands, thymic epithelial cells and mesothelial cells. Calretinin immunostaining is found in most epithelial mesotheliomas.

Immunohistochemistry (IHC)
CAM 5.2Anti-Cytokeratin (CAM 5.2) has a primary reactivity with human keratin proteins that correspond to Moll`s peptides #7 and #8, Mr 48 and 52 Kd. Cytokeratin 8 is present on secretory epithelia of normal human tissue but not on stratified squamous epithelium. CAM 5.2 stains most epithelial derived tissue, including liver, renal tubular epithelium, hepatocellular and renal cell carcinomas. CAM 5.2 may not react with some squamous cell carcinomas. Immunohistochemistry (IHC)
CancerTYPE ID® with reflex to NeoTYPE® Cancer Profile

CancerTYPE ID is a proprietary molecular cancer classifier used to identify unknown or unclear tumor types and subtypes in patients with metastatic cancer. When ordered through NeoGenomics, classification with CancerTYPE ID is followed by tumor profiling for actionable biomarkers using the NeoTYPE® Cancer Profile most appropriate for the tumor type identified by Cancer TYPE ID. Tech-only options for FISH and IHC within the NeoTYPE Cancer Profile are available.

CancerTYPE ID is performed and billed separately by NeoGenomics’ contracted reference laboratory, Biotheranostics, Inc., an independent CLIA-licensed and CAP-accredited reference laboratory. The test uses quantitative RT-PCR to measure the expression of 92 genes in the patient’s specimen and classifies the tumor by matching the gene expression profile to a database of more than 2000 known tumor types and subtypes. Using this technology, CancerTYPE ID can identify 50 different tumor types and subtypes, covering >95% of all solid tumors based on incidence.1 The test reports a main cancer type with the highest probability, as well as a list of tumor types that may be ruled out with 95% confidence. 

CancerTYPE ID may be ordered as a stand-alone test directly from Biotheranostics, Inc. Please see www.cancertypeid.com.   

Molecular
Carbonic Anhydrase IX (CA IX)Carbonic anhydrase IX (CAIX) is a cell surface transmembrane protein, which is predominantly found in the gastrointestinal tract and gall bladder. The glandular regions of normal colon are reported to be negative, but in the case of adenocarcinoma, the glands are positive. CAIX is also expressed in common epithelial tumors such as carcinomas of the esophagus, lung, colon, kidney, cervix, and non-small cell lung carcinoma (NSCLC). In breast carcinomas, CAIX expression is associated with malignant tissue. Expression of CAIX is absent in normal kidney, chromophobe carcinomas or oncocytomas; however, it is specifically expressed in clear cell renal carcinomas. Immunohistochemistry (IHC)
CD10CD10, also known as Common Acute Lymphocytic Leukemia Antigen (CALLA), is expressed in early lymphoid progenitors and normal germinal center cells. It is almost always present on the surface of precursor B-lymphoblastic and Burkitt lymphomas and much less frequently on precursor T-lymphoblastic leukemia-lymphoma. Many follicular lymphoma and some diffuse large B-cell lymphomas, along with multiple myeloma are positive. CD10 is also present on breast myoepithelial cells, bile canaliculi, fibroblasts and with especially high expression on the brush border of kidney and gut epithelial cells. CD10 is also a good marker of endometrial stomal sarcoma. Immunohistochemistry (IHC)
CD163CD163 antigen is restricted in its expression to the monocytic/macrophage lineage. It is present on all circulating monocytes and most tissue macrophages except those found in the mantle zone and germinal centers of lymphoid follicles, interdigitating reticulum cells and Langerhans cells. Immunohistochemistry (IHC)
CD31CD31 is a 130kDa transmembrane glycoprotein that is shared by vascular lining cells, megakaryocytes and platelets. This marker is highly restricted to endothelial neoplasms among all tumors of the soft tissue and its sensitivity is excellent. 100% of angiosarcomas and hemangiomas are CD31 positive. However, Kaposi’s sarcoma (KS) is labeled more consistently by CD34 than by CD31. CD31 has also been used as a prognostic marker measuring tumor angiogenesis. CD31 also stains histiocytes. Immunohistochemistry (IHC)
CD34CD34, a single chain transmembrane glycoprotein, is selectively expressed on human lymphoid and myeloid hematopoietic progenitor cells and endothelial cells. CD34 antibody labels many gastrointestinal stromal tumors (GIST), dermatofibrosarcoma protuberans, solitary fibrous tumor and a subset of sarcomas. CD34 staining has been also used to measure angiogenesis. Immunohistochemistry (IHC)
CD4CD4, a single chain transmembrane glycoprotein, is found on a T-cell subset (helper/inducer). It is also present on a variety of monocyte-derived cells, including Langerhans and other dendritic cells. The CD4 epitope is absent from immature thymocytes and is expressed during T-cell development. Precursor T-lymphoblastic lymphomas are therefore variable in their expression of CD4, but most mature T-cell lymphomas are positive, with the exception of aggressive NK-cell leukemia, extranodal NK-cell lymphoma, gamma delta T-cell lymphomas, and enteropathy-type T-cell lymphoma. Immunohistochemistry (IHC)
CD44The CD44 family of glycoproteins exists in a number of variant isoforms, including hematopoietic variant (CD44s) and epithelial cells variant (CD44v). While many human tumors express CD44, a positive correlation between increased CD44 expression and tumor progression has been demonstrated in only some. The most practical application of CD44 immunostaining at present is the discrimination of urothelial transitional call carcinoma-in-situ from non-neoplastic changes in the urothelium. Immunohistochemistry (IHC)
CD68CD68 is an antibody directed against lysosomes. It is important for identifying macrophages in tissue sections. It stains macrophages in a wide variety of human tissues, including Kupffer cells and macrophages in the red pulp of the spleen, lamina propria of the gut, lung alveoli, and bone marrow. This antibody reacts with myeloid precursors and peripheral blood granulocytes. It shows strong granular cytoplasmic staining of chronic and acute myeloid leukemia and also reacts with true histiocytic neoplasia. It also stains granular cell tumors and some cases of melanoma, renal cell carcinoma, and pleomorphic sarcoma. Tumors of lymphoid origin are usually not stained. Immunohistochemistry (IHC)
CD99CD99 (MIC2 gene product, E2) antigen is strongly expressed by Ewing sarcoma cells, primitive peripheral neuroectodermal tumors, and lymphoblastic leukemia/lymphoma. Immunohistochemistry (IHC)
CDK4Among cyclin/CDK proteins, CDK4 and cyclin D1 are the most frequently activated by somatic genetic alterations in multiple tumor types. CDK4 antibody assists in distinguishing atypical lipomatous tumor well-differentiated liposarcoma (WDL) (positive) from benign adipocytic neoplasms (negative). Immunohistochemistry (IHC)
CDKN2A (p16) Deletion for Mesothelioma

Probes: CDKN2A (p16) (9p21) | Centromere 9
Disease(s):  Mesothelioma

FISH
CDX2CDX2 is an intestine specific transcription factor that regulates both the proliferation and differentiation of intestinal epithelial cells. It is expressed in the nuclei of epithelial cells throughout the intestine, from duodenum to rectum. The CDX2 protein is expressed in primary and metastatic colorectal carcinomas and has also been demonstrated in the intestinal metaplasia of the stomach and intestinal-type gastric cancer. It is not expressed in the normal gastric mucosa. CDX2 may be used in identifying metastatic carcinoma of colonic or other gastrointestinal tract origin in the setting of an unknown primary tumor. Immunohistochemistry (IHC)
CEA (Mono)Carcinoembryonic antigen (CEA) is usually demonstrated as a linear labeling of the apical poles of cells lining the glandular lumen and occasionally as weak staining near the apex of normal colonic epithelial cells. Tumors tend to display an increased cytoplasmic staining. In specific cases, CEA can be useful in tumor diagnosis. Pancreatic carcinomas, testicular tumors, gallbladder neoplasms and granular cell myoblastomas all stain positive for CEA, while malignant tumors of brain, prostate, skin, lymphoreticular tissues, hepatocellular carcinomas, esophageal squamous cell carcinomas and mesothelioma fail to stain for CEA. Immunohistochemistry (IHC)
CEA (Poly)Polyclonal carcinoembryonic antigen (CEA) antibody stains a larger percentage of cholangiocarcinomas compared to hepatocellular carcinomas. Approximately 95% of olangiocarcinomas are stained diffusely and strongly with polyclonal CEA, whereas show a canalicular staining pattern with this antibody. Immunohistochemistry (IHC)
Chromogranin AChromogranin is present in several elements of the diffuse neuroendocrine system (DNES), including anterior pituitary, thyroid perifollicular C cells, parathyroid chief cells, pancreatic islet cells, intestinal enterochromaffin cells and tumors derived from these cells. Chromogranin immunoreactivity was also seen in thymus, spleen, lymph nodes, fetal liver, neurons, the inner segment of rods and cones, the submandibullar gland and the central nervous system. This marker is useful in evaluating neuroendocrine tumors. Immunohistochemistry (IHC)
Chromosome Analysis

A wide variety of abnormalities can be identified, providing both diagnostic and prognostic information. Acute leukemias, lymphomas and chronic myeloid and lymphoid disorders are examined cytogenetically in order to establish the exact nature of the acquired genetic change. Rearrangements, also known as translocations, inversions, and deletions, can usually be detected under a light microscope. In most leukemias and lymphomas, changes in chromosome number (ploidy) or chromosome structure (rearrangements) are often observed.
 

Cytogenetics
CK HMW (CK903/34BE12)CK903 (34betaE12) is a high molecular weight cytokeratin present in all squamous epithelium and their carcinomas. This antibody recognizes cytokeratins 1, 5, 10 and 14 that are found in complex epithelia. There has been no reactivity with cells derived from simple epithelia, mesenchymal tumors, lymphomas, melanomas, neural tumors and neuroendocrine tumors. One useful application is the identification of the basal cell layer in prostate tissue in the determination of carcinoma. Immunohistochemistry (IHC)
CK OSCARAnti-cytokeratin clone OSCAR (CK OSCAR) demonstrates a broad spectrum of cytokeratin reactivity. In normal tissues, OSCAR is reactive with most epithelial types, including bile ducts and hepatocytes in liver, bladder epithelium, breast ducts, bronchial epithelium, endometrium, intestinal epithelium of stomach, duodenum, ileum, colon, rectum, pancreas, ovarian epithelium, pancreatic acini, pituitary acini, pneumocytes, prostate, thyroid, skin (positive on the basal layer and negative on the superficial layers of squamous epithelium), and apocrine and sweat glands. In tumors, OSCAR is reactive with most carcinomas, including breast, transitional cell (TCC), renal cell (RCC), lung adenocarcinoma, lung small cell, lung squamous cell, endometrial, prostate, ovarian, hepatocellular (HCC), colorectal CA, stomach and thyroid. It is negative in certain normal tissues, including brain, lymphocytes and all cells of hematolymphoid origin, muscle, brain, nerves, endothelium and in certain tumors including most melanomas, sarcomas, lymphomas, primitive neuroectodermal tumors (PNET)/Ewings and gastrointestinal stromal tumors (GIST). Positivity has been seen on some dendritic cells in lymph nodes, some endothelia, and some muscle cells. Immunohistochemistry (IHC)
CK17Cytokeratin 17 (CK17) is an effective marker to distinguish myoepithelial cells from luminal epithelium of various glands (mammary, sweat, salivary, bronchial, tracheal, laryngeal, esophageal) and benign from malignant forms of tumors, e.g. mammary gland tumors. Predominant expression of CK17 is the characteristic feature of basal cell carcinomas. It is often positive in carcinomas of pancreatic or biliary origin. Immunohistochemistry (IHC)
CK19Cytokeratin 19 (CK19) is a member of the type I acidic subfamily of keratins. It is expressed in various different human tissues. CK19 labels ductal and glandular epithelia, prostatic epithelia, and non-keratinizing squamous epithelia. This antibody is useful in the diagnosis of breast and cervical carcinoma. CK19 is not expressed in hepatocytes, therefore, antibody to CK19 is also useful in the distinction of liver metastasis from hepatocellular carcinomas. Immunohistochemistry (IHC)
CK20Cytokeratin 20 (CK20) positivity is seen in the majority of adenocarcinomas of the colon, mucinous ovarian carcinomas, transitional cell, and Merkel cell carcinomas, and frequently in adenocarcinomas of the stomach, bile system and pancreas. CK7/CK20 immunostaining patterns may be helpful in separating pulmonary from colonic adenocarcinomas. Immunohistochemistry (IHC)
CK5/6D5/16 B4 clone of CK5/6 antibody reacts strongly with cytokeratins 5 and 6. Cytokeratin 5/6 have been found valuable for the distinction between low differentiated squamous cell carcinoma and adenocarcinoma. It labels mesothelioma, and epithelial basal cells in prostate and tonsil. No reactivity with other mesodermally derived tissues, such as muscle and connective tissues, has been observed. Anti-CK 5/6 has also been found useful in the differential diagnosis of atypical proliferations of the breast. Immunohistochemistry (IHC)
CK7Cytokeratin 7 (CK7) antibody reacts with proteins that are found in most ductal, glandular and transitional epithelium of the urinary tract and bile duct epithelial cells. CK7 distinguishes between lung and breast epithelium that stain positive, and colon and prostate epithelial cells that are negative. It also reacts with many benign and malignant epithelial lesions, e.g. adenocarcinomas of the ovary, breast and lung. Transitional cell carcinomas are positive and most prostate cancers are negative. This antibody does not recognize other intermediate filament proteins. Immunohistochemistry (IHC)
cMETThe cMET tyrosine kinase receptor, normally expressed by epithelial cells, is overexpressed and amplified in a variety of human tumors, including non-small cell lung carcinoma (NSCLC). High levels of intratumor cMET expression have been associated with a more aggressive biology and a worse prognosis in NSCLC. Engelman et al. reported that cMET amplification induced resistance to gefitinib in a gefitinib-sensitive lung cancer cell line. Moreover, cMET inhibition with a cMET tyrosine kinase inhibitor (PHA-665,752) restored gefitinib sensitivity. Immunohistochemistry (IHC)
CMV

In situ hybridization for detection of cytomegalovirus (CMV) RNA.

In Situ Hybridization (ISH)
Collagen IVCollagen IV is a major constituent of the basement membranes along with laminins and enactins. In kidney, the antibody reacts with glomerular and tubular basement membranes, parts of the mesenchymal matrix, and the Bowman’s capsule. It also reacts with the basal lamina of capillaries and basement membranes in a variety of tissues. Antibody to collagen IV is useful in evaluating neural neoplasms. Immunohistochemistry (IHC)
Copper StainSpecial stain. Immunohistochemistry (IHC)
COX2Cyclooxygenase-2 (COX-2) plays a role in tumorigenesis through stimulating epithelial cell proliferation, inhibiting apoptosis, stimulating angiogenesis, enhancing cell invasiveness, mediating immune suppression, and by increasing the production of mutagens. COX-2 is expressed in breast cancer, transitional cell carcinoma of the bladder, high-grade endometrioid carcinoma, and ovarian cancer. Overexpression of COX-2 is associated with poor prognosis in cervical cancers after radiation and concurrent chemotherapy. Immunohistochemistry (IHC)
D240D2 40 identifies a 40kDa O-linked sialoglycoprotein expressed by a variety of tissues, including fetal testes and testicular germ cell tumors. Anti-D2 40 has also been demonstrated to label lymphatic endothelium whereas it is unreactive with vascular endothelium. In neoplastic tissue, immunostaining of lymphatic endothelium by anti-D2 40 can be useful in identifying lymphatic invasion of primary tumors. It is also often positive on sarcomatoid malignant mesothelioma. Immunohistochemistry (IHC)
DDIT3 (CHOP)Probes: DDIT3 (CHOP) (12q13)
Disease(s): Myxoid-round cell liposarcoma (M/RCLS)
FISH
DesminDesmin is an intermediate filament protein of both smooth and striated muscles. Antibody to desmin reacts with striated (skeletal and cardiac) as well as smooth muscle cells. Anti-desmin antibody is useful in identification of tumors of myogenic origin. It reacts with leiomyosarcomas (smooth muscle) as well as rhabdomyosarcomas (striated muscle). Immunohistochemistry (IHC)
DNA Ploidy/Cell Cycle Analysis – POC/Solid Tumors

Available as a global test only. DNA stain propidium iodide (PI) is used to determine S-phase cell cycle fraction and DNA index as indicators of DNA ploidy. Products of conception (POC) and solid tumors are accepted for this test. Please see DNA Ploidy/Cell Cycle Analysis – Heme for other indications.

Flow Cytometry
DNMT3A Mutation Analysis

Bi-directional sequencing of exon 26, a mutation hotspot region containing R882 and other mutations. In hematological disease, testing may be performed on plamsa to increase sensitivity. For solid tumors, tumor enrichment is performed before extraction.

Molecular
DOG1DOG1 is a cell surface protein of unknown function selectively expressed in gastrointestinal stromal tumors (GIST). Among GIST cases with Kit mutations the DOG1 antibody identified 11% more cases than c-Kit antibody. DOG1 identifies the vast majority of both cKIT negative and Platelet-derived Growth Factor Receptor Alpha (PDGFRA) mutated GIST cases that may still benefit from imatinib mesylate (Gleevec®), an inhibitor of the Kit tyrosine kinase. In addition, DOG1 immunoreactivity is seen in fewer cases of mesanchymal, epithelial tumors and melanomas when compared with cKIT. The use of this highly sensitive and specific novel marker will increase the accuracy of GIST diagnosis. Immunohistochemistry (IHC)
DPC4The gene DPC4 (deleted in pancreatic carcinoma 4, also called SMAD4) was identified in 18q21.3 This gene is frequently mutated and deleted in pancreatic carcinomas (55%) and less frequently (20 - 22%) in colon carcinomas. Loss of expression is specific for pancreatic malignancy (in-situ or invasive) vs. benign process, particularly helpful in biopsies. Immunohistochemistry (IHC)
E-CadherinE Cadherin is an adhesion protein that is expressed in cells of epithelial lineage. It stains positively in glandular epithelium, as well as adenocarcinomas of the lung, G.I. tract and ovary. It is useful in distinguishing adenocarcinoma from mesothelioma. It is also positive in some thyroid carcinomas. Breast carcinomas with ductal and lobular features show two staining patterns: (1) complete or almost complete lack of membrane staining in lobular carcinomas and (2) uniform membrane expression throughout the tumor in ductal carcinomas. Immunohistochemical detection of ECadherin expression can be a useful diagnostic tool for the differentiation of ductal and lobular carcinomas of the breast. Immunohistochemistry (IHC)
EBER

This probe set labels all latent EBV-infected cells, including EBV-positive lymphoblastoid cell lines and EBV infected B-cell immunoblasts in infectious mononucleosis. It also reacts with EBV-associated undifferentiated nasopharyngeal carcinomas and with Reed-Sternberg cells in almost all EBV-associated Hodgkin lymphoma cases. Global interpretation is available on head and neck specimens only; tech-only testing is available for all samples.

In Situ Hybridization (ISH)
EGFREpidermal Growth Factor Receptor (EGFR) overexpression can occur in a variety of tumor types, including breast, prostate, ovarian, brain, lung and predominantly squamous cell carcinomas. Tumors that express EGFR are associated with a poor prognosis and a shorter disease-free survival. Most colon carcinomas will show expression of EGFR in more than 1% of the invasive tumor cells. Patients whose tumor expresses EGFR are eligible for cetuximab therapy although the response to therapy is independent of the intensity or percentage of cells staining. Immunohistochemistry (IHC)
EGFR (E746-A750del specific)Epidermal Growth Factor Receptor (EGFR) is a 170 kDa transmembrane receptor tyrosine kinase that belongs to the HER/ErbB protein family. Somatic mutations in the tyrosine kinase domain of EGFR are present in a subset of lung adenocarcinomas. Two types of mutations account for approximately 90% of mutated cases: a specific point mutation, L858R, which occurs in exon 21 and short in-frame deletions in exon 19. A common lesion in exon 19 is the deletion of E746-A750, although other variants occur. IHC-based EGFR E746-A750del specific antibody is designed to detect deletion of E746-A750 in exon 19. Deletion in exon 19 is associated with response of non-small cell lung carcinoma (NSCLC) to gefitinib or erlotinib monotherapy. Immunohistochemistry (IHC)
EGFR (L858R mutant specific)Epidermal Growth Factor Receptor (EGFR) is a 170 kDa transmembrane receptor tyrosine kinase that belongs to the HER/ErbB protein family. Somatic mutations in the tyrosine kinase domain of EGFR are present in a subset of lung adenocarcinomas. Two types of mutations account for approximately 90% of mutated cases: a specific point mutation (L858R) which occurs in exon 21 and short in-frame deletions in exon 19. IHC-based EGFR L858R mutant specific antibody is designed to detect the L858R missense mutation associated with response of non-small cell lung carcinoma (NSCLC) to gefitinib or erlotinib monotherapy. Immunohistochemistry (IHC)
EGFR AmplificationProbes: EGFR (7p11.2) | Centromere 7
Disease(s): Brain, lung, colorectal, gastric, breast cancers
FISH
EGFR Mutation Analysis

Bi-directional sequencing of exons 18-21 of the EGFR gene for detection of EGFR-activating mutations and TKI resistance mutations (including T790M) in these exons. Tumor enrichment is performed before extraction. Testing is approved for specimens from the state of New York.

Molecular
EGFR T790M Germline Mutation Analysis

Bidirectional sequence analysis of EGFR exon 20 in peripheral blood for detection of T790M germline mutation. Note: Patient and physician or genetic counselor signatures on the NeoGenomics Consent for Hereditary Cancer Genetic Testing form are required. Testing will be put on hold until signatures are received.

Molecular
EGFRvIII Analysis

The EGFRvIII Analysis test is a real-time RT-PCR assay that is capable of detecting the EGFRvIII mutation that results from an inframe deletion of 801 base pairs spanning exons 2-7 of the coding sequence. 

Molecular
EMAEpithelial Membrane Antigen (EMA) antibody stains normal and neoplastic cells from various tissues, including mammary epithelium, sweat glands and squamous epithelium. Hepatocellular carcinoma, adrenal carcinoma and embryonal carcinomas are consistently EMA negative, therefore, keratin positivity with negative EMA favors one of these tumors. EMA is frequently positive in meningioma, which can be useful when distinguishing it from other intracranial neoplasms, e.g. Schwannomas. The absence of EMA can also be of value since negative EMA is characteristic of tumors such as adrenal carcinoma, seminomas, paraganglioma and hepatoma. Immunohistochemistry (IHC)
EREstrogen Receptor (ER) belongs to a superfamily of nuclear hormone receptors and is expressed in about 85% of invasive breast cancers. There are two known isoforms of estrogen receptor, ERα and ERß. It is a weak prognostic factor but a strong predictive factor for response to endocrine therapies, both in adjuvant and metastatic settings. The primary indication to assess ER in breast cancer is to predict response to hormonal therapies such as tamoxifen, other selective estrogen receptor modulators (SERMs) and aromatase inhibitors. In univariate analysis, moderate to strong staining in even 1% of the invasive tumor cells is associated with significant improvement in disease-free survival compared to those patients whose tumor lacks ER expression. Immunohistochemistry (IHC)
ERCC1The Excision Repair Cross-Complementing Rodent Repair Deficiency, Complementation Group 1 (ERCC1) polypeptide is required for nucleotide excision repair (NER) of damaged DNA. Elevated levels of ERCC1 have also been reported in cisplatin-resistant cells. Immunohistochemistry (IHC)
ERGERG oncoprotein expression has been shown to be a highly specific marker for prostate cancer. Given the lack of ERG expression in a wide variety of normal epithelial tissues and tumors, detection of ERG by IHC is a valuable tool for diagnosing prostate cancer or determining prostatic origin. ERG is also a highly specific and sensitive marker of endothelial cells and vascular tumors. Immunohistochemistry (IHC)
EWSR1

Probes: EWSR1 (22q12)
Disease(s): Ewing sarcoma, primitive neuroectodermal tumor (PNET)

FISH
Extended Leukemia/Lymphoma Panel - 31 markers

Available as global and tech-only. Markers are CD2, CD3, CD4, CD5, CD7, CD8, CD10, CD11b, CD11c, CD13, CD14, CD15, CD16, CD19, CD20, CD23, CD33, CD34, CD38, CD41, CD45, CD56, CD64, CD71, CD117, CD138, CD235a, FMC-7, HLA-DR, kappa, and lambda.

Flow Cytometry
Factor VIII RAFactor VIII-related antigen is a component of Factor VIII complex. Factor VIII-related antigen is one of the available immunohistochemical markers of endothelial cells. It has also been demonstrated in platelets and megakaryocytes. IHC staining of Factor VIII-related antigen is useful for diagnosis of vascular neoplasms and for identification of vascular invasion by neoplasms. Immunohistochemistry (IHC)
Factor XIIIaFactor XIIIa is a dermal dendrocyte marker and shows variable reaction with these types of tumors. It can be used for histiocytic phenotyping and has been reported to mark capillary hemangiomas and tumors of the central nervous system. Factor XIIIa has also been used with CD34 to differentiate between dermatofibroma and dermatofibrosarcoma protuberans. Immunohistochemistry (IHC)
FLi-1Friend leukemia integration (FLI1) is a nuclear transcription factor and has been reported as the first nuclear marker of endothelial differentiation. FLI1 labels hemangiomas, angiosarcomas, Kaposis sarcoma, Ewings and Merkel cell carcinoma.

FLI1 is expressed in normal endothelial cells, megakaryocytes, normal breast epithelia.

Immunohistochemistry (IHC)
FOXP3FOX P3 is expressed at a high level in CD25 positive/CD4 positive regulatory T cells, at a low level in CD4 positive/CD25 negative cells, and is absent in CD4 negative/CD8 positive T cells. FOX P3 may be a master regulatory gene and a more specific marker of regulatory T cells than other T cells. Immunohistochemistry (IHC)
FSHFollicle Stimulating Hormone (FSH) is a pituitary hormone involved in the maturation of ovarian follicles and estrogen secretion in females. In the pituitary gland, FSH is produced by gonadotrophs. In males, FSH stimulates the secretion of testosterone. This antibody is used in the identification of FSH in pituitary adenomas. Immunohistochemistry (IHC)
Galectin 3Galectins are a structurally-related family of proteins; 14 different galectins have been characterized. They are cytoplasmic proteins and can be translocated into the nucleus. Gal-3 has been found overexpressed in most malignant thyroid neoplasms. However, it was not detectable in normal and non-malignant tissue. Galactin 3 is a useful marker to differentiate benign from malignant (Calactin-3 positive) thyroid neoplasms. Immunohistochemistry (IHC)
GastrinGastrin, a polypeptide hormone, occurs naturally in three forms: gastrin-14, gastrin-17 and gastrin-34. This antibody labels gastrin or gastrin-analogue producing cells in gastrin-secreting tumors and G cell hyperplasia. Immunohistochemistry (IHC)
GATA3GATA3 (GATA binding protein 3) is a member of the GATA family of transcription factors. Among several other roles, GATA3 is involved in luminal cell differentiation in the mammary gland and appears to control a set of genes involved in the differentiation and proliferation of breast cancer. The expression of GATA3 is associated with the expression of estrogen receptor-alpha (ER) in breast cancer. GATA3 has been shown to be a novel marker for bladder cancer. GATA3 stains almost all of urothelial carcinomas, but stained no prostate or renal carcinomas. Immunohistochemistry (IHC)
GCDFP15This antibody is specific to a 15kDa monomer protein called Gross Cystic Disease Fluid Protein-15 (GCDFP-15). GCDFP15 is expressed in apocrine epithelia, lacrimal, ceruminous and Moll’s glands, as well as in numerous serous cells of the submandibular, tracheal, bronchial, sublingual and minor salivary glands. It can be of use in the identification of breast carcinoma, salivary duct carcinoma and apocrine epithelia. Immunohistochemistry (IHC)
GFAPGlial Fibrillary Acidic Protein (GFAP) is the major protein found in astrocytes and its expression is evidence of astroglial origin and differentiation. Gliomas are the most common cerebral neoplasm in adults and include astrocytomas, oligodendrogliomas and glioblastomas. It can also be demonstrated in ependymal cells, ependymomas, subependyomas, glioblastomas, mixed central nervous system neoplasms and gangliomas. It is detected in immature but not mature oligodendrocytes and neurons. Anti-GFAP antibodies do not cross-react with neurons, fibroblasts or muscle cells. Anti-GFAP antibodies are useful in differentiating primary gliomas from metastatic lesions in the brain and for documenting astrocytic differentiation in tumors outside the central nervous system. Immunohistochemistry (IHC)
GH

Growth Hormone (GH) is produced by the somatotroph cells in the pituitary. This marker is a useful in classification of pituitary tumors and the study of pituitary disease (acromegaly).

Immunohistochemistry (IHC)
GlucagonGlucagon antibody is used for the identification of tumors and hyperplasias of pancreatic islets. This antibody labels A cells of the endocrine mammalian pancreas. It reacts with glucagon in a large number of mammalian species. Immunohistochemistry (IHC)
GLUT1Glucose transporter 1 (GLUT1) facilitates the transport of glucose across the plasma membranes of mammalian cells. GLUT-1 is expressed in many human tissues including those of the colon, lung, stomach, esophagus and breast. Overexpression of GLUT1 is associated with aggressive behavior in some cancers, including breast, renal, and bladder carcinoma. Expression of GLUT1 can help distinguish malignant mesothelioma from reactive mesotholial proliferations. Immunohistochemistry (IHC)
Glutamine Synthetase

Glutamine synthetase (GS) is strongly expressed in a majority of hepatocellular carcinoma, including cases of early HCC and low grade HCC.

Immunohistochemistry (IHC)
Glypican-3A useful marker to differentiate between benign (negative) and malignant (positive) liver diseases (HCCs). Immunohistochemistry (IHC)
GNAS Mutation Analysis

Bi-directional sequencing of exons 8 and 9 of the GNAS gene to detect mutation hot spots in codons R201 and Q227.

Molecular
H. PyloriThis antibody reacts with H. pylori on the surface and in the cytoplasm of epithelial cells of stomach biopsies. Studies have shown that H. pylori plays an important role in the etiology of chronic active gastritis and the development of peptic ulcer disease. Immunohistochemistry can provide rapid detection of this bacterium. Immunohistochemistry (IHC)
HBME1HBME1 is an anti-mesothelial monoclonal antibody that recognizes an unknown antigen on the microvilli of mesothelioma cells. It stains normal mesothelial cells as well as epithelial mesotheliomas in a thick membrane pattern. This antibody also reacts with some carcinomas showing cytoplasmic immunostaining. Immunohistochemistry (IHC)
Hepatitis B Core AntigenHepatitis B virus belongs to the hepatovirus family and causes type B hepatitis. Hepatitis B virus is spherical in shape with a diameter of 42 nm. Core antigens are localized within the nuclei, whereas the surface antigens are present in the cytoplasm of the infected cells. Antibodies to surface antigens appear in circulation at an early stage of infection, whereas the antibodies to the core antigens are detected in blood after several weeks. Hepatitis B core antibody targets Hepatitis B Virus Core Antigen in IHC applications. Immunohistochemistry (IHC)
Hepatitis B Surface AntigenHepatitis B virus, belongs to the hepatovirus family, and causes type B hepatitis. It is spherical in shape with a diameter of 42 nm. It contains a 27 nm partially double stranded DNA core enclosed within a lipoprotein coat. The antigens in the outer surface are called hepatitis B virus surface antigens. Antibodies to surface antigens appear in circulation at an early stage of infection, whereas the antibodies to the core antigens are detected in blood after several weeks. Hepatitis B surface antibody targets Hepatitis B Virus Surface Antigen in IHC applications. Immunohistochemistry (IHC)
HepPar1Anti-Hepatocyte Specific Antigen (HepPar1) recognizes both benign and malignant liver derived tumors such as hepatoblastoma, hepatocellular carcinoma and hepatic adenoma. It recognizes both adult and fetal liver tissue. The typical pattern is a granular cytoplasmic staining. This antibody is useful in differentiating hepatocellular carcinomas from adenocarcinomas, either primary or metastatic. HepPar1 also can be used in differential diagnostic separation of hepatoblastoma versus other small round cell tumors. HepPar1 is also expressed in a subset of gastric carcinoma. Immunohistochemistry (IHC)
HER2 Breast

This test uses the Ventana PATHWAY anti-HER-2/neu antibody (clone 4B5) for the semi-quantitative detection of HER-2 antigen in sections of FFPE normal and neoplastic tissue. The test is FDA-approved with the indication as an aid in the assessment of breast cancer patients for whom Herceptin treatment is considered. Staining is performed according to the package insert. Scoring for breast cases is performed according to ASCO/CAP 2013 guidelines. Scoring for gastroesophageal and other tissues is according to the 2010 ToGA trial standards.
HER2 is an oncogene that is over-expressed in a variety of cancers including some breast carcinomas. The expected breast cancer overexpression rate varies based on the grade and type of cancer. Known artifacts, such as edge artifact, tissue retraction and tissue crush may give the false impression of overexpression. Care should be taken to avoid assessing these areas, especially in needle core biopsies that generally harbor all of these artifacts.

Immunohistochemistry (IHC)
HER2 Breast Cancer

Probes: HER2 (17q11.2-q12) | 17 (Cen 17
Disease(s): Breast cancer

FISH
HER2 Breast Equivocal FISH Panel

Probes: TP53 (17p13.1) | SMS Critical Region (SMSCR) (17p11.2) | Centromere 17 | RARA (17q21.1
Disease(s): Breast cancer
Testing is performed only on a global basis at this time.

FISH
HER2 Dual ISHThe FDA approved Ventana Medical Systems’ (Ventana) INFORM HER2 Dual ISH DNA Probe set is intended to determine HER2 gene status by enumeration of the ratio of theHER2 gene to Chromosome 17 in formalin-fixed, paraffin-embedded human breast cancer tissue specimens. The INFORM HER2 Dual ISH DNA Probe set is indicated as an aid in the assessment of patients for whom Herceptin (trastuzumab) treatment is being considered. In Situ Hybridization (ISH)
HER2 Gastric & Non-Breast

Probes: HER2 (17q11.2-q12) | 17 (Cen 17)
Disease(s): Gastric cancer, gastroesophageal junction (GEJ) cancer, esophageal adenocarcinoma, and others

FISH
Hereditary Cancer Comprehensive Panel

Next-gen sequencing of all coding regions and intron-exon boundaries is performed concurrently for the following 73 genes: AKT1, APC, ATM, ATR, BAP1, BARD1, BMPR1A, BRCA1, BRCA2, BRIP1, CDH1, CDK4, CDKN2A, CEBPA, CHEK1, CHEK2, CTNNA1, EPCAM, ETV6, FAM175A, GALNT12, GATA2, GEN1, GREM1, HOXB13, KLLN, MEN1, MLH1, MRE11A, MSH2, MSH6, MUTYH, MYH1, MYH2, MYH3, MYH4, MYH6, MYH7, MYH8, MYH9, MYH10, MYH11, MYH13, MYH14, MYH15, NBN, NTRK1, PALB2, PIK3CA, PMS2, POLD1, POLE, PPM1D, PRSS1, PTEN, RAD50, RAD51, RAD51C, RAD51D, RET, RUNX1, SDHB, SDHC, SDHD, SMAD4, STK11, TERC, TERT, TP53, TP53BP1, VHL, WT1, and XRCC2. Note: Patient and physician or genetic counselor signatures on the NeoGenomics Consent for Hereditary Cancer Genetic Testing form are required. Testing will be put on hold until signatures are received.

Molecular
Hereditary Cancer Susceptibility for Pediatrics

The Hereditary Cancer Susceptibility for Pediatrics panel is a sequencing based assay that can detect mutations in the entire coding region of the following genes listed. ALK, APC, BRCA1, BRCA2, CDH1, KRAS, MSH2, MSH6, NF1, NF2, NRAS, PALB2, PMS2, PTCH1, RB1, RET, RUNX1, SDHA, SDHB, TP53, and VHL. Note: Parent and physician or genetic counselor signatures on the NeoGenomics Consent for Hereditary Cancer Genetic Testing form are required. Testing will be put on hold until signatures are received.

Molecular
Hereditary DNA Repair Panel for Prostate Cancer

The Hereditary DNA Repair Panel for Prostate Cancer is a sequencing based assay that can detect mutations in the entire coding region of the following genes listed. ATM, ATR, BAP1, BARD1, BRCA1, BRCA2, BRIP1, CHEK2, FAM175A, GEN1, MLH1, MRE11A, MSH2, MSH6, NBN, PALB2, PMS2, RAD51C, RAD51D, and XRCC2. Note: Patient and physician or genetic counselor signatures on the NeoGenomics Consent for Hereditary Cancer Genetic Testing form are required. Testing will be put on hold until signatures are received.

Molecular
HHV8Human Herpes Virus (HHV) 8 is the likely etiological agent of Kaposi’s sarcoma (KS), and is present in all cases. HHV 8 encodes a latent nuclear antigen (LANA) that is the product of the viral gene of 73. HHV8 has also been identified in multicentric Castleman disease (MCD), and primary effusion lymphoma (PEL). Immunohistochemistry (IHC)
HMB45Antibody clone HMB45 recognizes a melanoma-specific antigen by reacting with melanoma cells, nevus cells and neonatal melanocytes. HMB45 is expressed on the majority of malignant melanoma cases as well as on tumors of melanocytic differentiation. Immunohistochemistry (IHC)
HOXB13 Genotyping

This test is performed on a patient's blood specimen to look for germline genetic variants. The method is bi-directional sequencing of exons 1 and 2 of the HOXB13 gene for detection of the G84E mutation and other variants of significance to prostate cancer risk. Note: Patient and physician or genetic counselor signatures on the NeoGenomics Consent for Hereditary Cancer Genetic Testing form are required. Testing will be put on hold until signatures are received.

Molecular
HPLHuman Placental Lactogen (HPL) is a polypeptide hormone synthesized in syncytiotrophoblastic cells of placenta and has been used as a tissue marker for certain trophoblastic tumors. Immunohistochemistry (IHC)
HPV DNA Tissue TestingHPV DNA Tissue Testing is peformed on FFPE tissue. It uses PCR and fragment analysis for qualitative detection and genotyping of human papillomavirus (HPV) low risk types 6/11 and high risk types 16, 18, 31, 33, 45, and 58. When detected, specific genotypes are identified except for 6 and 11 which cannot be distinguished from each other and are reported as positive for the combination 6/11. Molecular
HRAS Mutation Analysis

Bi-directional sequencing of HRAS exons 2 and 3 which includes sites of common activating mutations in codons 12, 13, 59 and 61.

Molecular
HSD3B1 Genotyping

Bi-directional Sanger sequencing is performed to detect the HSD3B1 (1245A>C) single nucleotide polymorphism (SNP). Inheritance of the HSD3B1 (1245C) allele, which enhances dihydrotestosterone synthesis, is associated with prostate cancer resistance to androgen deprivation therapy (ADT).

Molecular
HSV I/II

This antibody cocktail reacts with Herpes Simplex Virus (HSV) type 1- or type 2-specific antigens and with antigens common to both types. The antibodies react with all the major glycoproteins present in the viral envelope and at least one core protein as determined by crossed immunoelectrophoresis. Neither antibody cross-reacts with cytomegalovirus or Epstein-Barr virus. The cocktail is well suited for the detection of HSV in human cellular material obtained from superficial lesions or biopsies and for the early identification of HSV in infected tissue cultures.

Immunohistochemistry (IHC)
IDH1

IDH1 mutations are frequent genetic alterations in low-grade diffuse gliomas and secondary glioblastoma (70%). This alteration is observed in fewer than 10% of primary GBM cases. IDH1 IHC antibody is a diagnostic tool in assessing the IDH1 R132H mutational status and differentiating primary GBM tumors from the others.

Immunohistochemistry (IHC)
IDH1 & IDH2 Mutation Analysis

Bi-directional sequencing of the exon 4 mutation hotspot regions in both the IDH1 and IDH2 genes. IDH1 and IDH2 are analyzed concurrently. In hematological disease, testing may be performed on plasma to increase sensitivity. For solid tumors, tumor enrichment is performed before extraction.

Molecular
InhibinAnti-Inhibin alpha is an antibody against a peptide hormone which has a demonstrated utility in differentiating between adrenocortical tumors and renal cell carcinoma. This antibody stains most adrenal tumors but no cases of renal cell carcinomas (RCC). Sex cord stromal tumors of the ovary, as well as trophoblastic tumors, also demonstrate cytoplasmic positivity with this antibody. Immunohistochemistry (IHC)
INI1

Lack of nuclear expression of INI1 is characteristic of malignant rhabdoid tumors and epithelioid sarcomas.

Immunohistochemistry (IHC)
INSM1

INSM1 is a transcription factor that is a sensitive and specific marker for neuroendocrine tumors.  It is a nuclear stain, and is as good if not better than synaptophysin and is superior to chromogranin. It is rarely expressed on adenocarcinoma or squamous cell carcinomas without neuroendocrine differentiation. 

Immunohistochemistry (IHC)
InsulinInsulin is composed of a and b chains connected through the C-peptide. The main storage site for insulin is the pancreatic islets. Antibodies to insulin are important as a marker of islet cell tumor of pancreas (insulinoma). Immunohistochemistry (IHC)
Ki67

Ki67 is a nuclear protein that is expressed in proliferating cells. Ki67 is preferentially expressed during late G1, S, M, and G2 phases of the cell cycle, while cells in the G0 (quiescent) phase are negative for this protein. Increased proliferative activity is associated with more aggressive tumor and decreased disease-free survival period.
Note: Computer-assisted image analysis for Ki-67 is only validated for breast cancer and neuroendocrine carcinoma.

Immunohistochemistry (IHC)
KIT (c-KIT) Mutation Analysis

Bi-directional sequencing of KIT exons 8, 9, 11, 13 and 17 for detection of activating mutations including the common mutation D816V. For solid tumors, tumor enrichment is performed before extraction. In hematological disease, testing may be performed on plasma to increase sensitivity.

Molecular
KRAS Exon 4 Mutation Analysis

Bi-directional sequencing of exon 4 of the KRAS gene corresponding to amino acids  R97 through Q150.  Codon 117 and 146 mutations are detected. For solid tumors, tumor enrichment is performed before extraction.  This test may be ordered separately or by reflex after standard KRAS Mutation Analysis. Testing is available separately or in combination with BRAF, HRAS and NRAS in the RAS/RAF Panel. Testing is approved for specimens from the state of New York.

Molecular
KRAS Mutation Analysis

Bi-directional sequencing of exons 2 and 3 of the KRAS gene. High-sensitivity sequencing is used for enhanced detection of mutations in codons 12, 13, 59, and 61.  For solid tumors, tumor enrichment is performed before extraction. Testing is available separately or in combination with BRAF, HRAS and NRAS in the RAS/RAF Panel. Testing is approved for specimens from the state of New York.  

Molecular
LHLuteinizing Hormone (LH) is a tropic hormone that modulates the secretory activity of other endocrine glands. It is produced in the anterior hypophysis of the pituitary gland. LH antibody is useful for the labeling of normal gonadotropic cells of the pituitary and also for the classification of pituitary adenomas, as well as in the differential diagnosis of primary and metastatic tumors of the pituitary. Immunohistochemistry (IHC)
MammaglobinMammaglobin is a breast-associated glycoprotein. In normal breast tissue, this antibody labels breast ductal and lobular epithelial cells. In tumor cells, they are reactive with all types of breast adenocarcinoma regardless of tumor differentiation and type. Adenocarcinomas from other organs rarely express mammaglobin. Mammaglobin can help in the identification of primary sites of carcinomas. Immunohistochemistry (IHC)
MDM2Probes: MDM2 (12q15) | Centromere 12
Disease(s): Liposarcoma
FISH
MDM2 by IHC Immunohistochemistry (IHC)
Melan A (Mart1)Melan A (Mart1, Melanoma Antigen Recognized by T-cells 1), is a differentiation antigen that is expressed in melanocytes, most melanomas. Melan A recognizes a subcellular fraction found in melanosomes. Melan A is a useful addition to melanoma panels since it is specific for melanocytic lesions. Both HMB 45 and Melan A are co-expressed in the majority of melanomas, as well as uniquely expressed in certain cases. Melan A antibody, A103 clone labels the tumor cells of a subset of adrenocortical carcinomas and sex cord tumors of the gonads. Immunohistochemistry (IHC)
MesothelinMesothelin is a 40kDa cell surface glycoprotein selectively expressed by mesothelial cells and malignant mesotheliomas, as well as by non-mucinous ovarian carcinomas, breast carcinomas, pancreatic carcinomas, and squamous tumors of the esophagus and cervix. Immunohistochemistry (IHC)
MET (c-MET) Mutation Analysis

Bi-directional Sanger sequencing of MET is performed using PCR primers designed to target hotspot mutations in exons 14, 16, 17 and 19.

Molecular
MET Exon 14 Deletion Analysis

MET Exon 14 Deletion Analysis is performed by real-time RT-PCR. The assay is designed to detect alternative splice junctions that lead to exon-skipping (deletion) of exon 14 of the gene MET. Note: Available as stand-alone test or as part of the NeoTYPE® Lung Tumor Profile.

Molecular
MET FISHProbes: MET (7q31) | Centromere 7
Disease(s): Multiple solid tumor cancers including lung (NSCLC), gastric, esophageal, endometrial
FISH
MGMTMGMT (O-6-methylguanine-DNA methyltransferase) is a DNA repair enzyme. MGMT protects cells from alkylating toxins, and is an important factor in drug resistance to alkylating therapeutic agents. It is expressed in normal human tissues and is overexpressed in many types of tumors, but epigenetically silenced in other tumors. MGMT silencing is a marker associated with poor prognosis, but is a good predictive marker for response to alkylating agent chemotherapy. MGMT overexpression is associated with BCNU (carmustine) resistance in malignant gliomas. Immunohistochemistry (IHC)
MGMT Promoter Methylation Analysis

Bisulfite modification of tumor DNA and real-time PCR are used to quantify CpG methylation within the MGMT gene promoter. Percentage of methylated DNA (compared to total DNA) is reported for positive results.

Molecular
Microsatellite Instability Analysis (MSI)

PCR and fragment analysis of paired normal and tumor tissue to determine microsatellite instability (MSI) at the standard five NCI-recommended loci. Positive results are reported as MSI-high (at least two markers are unstable) or MSI-low (one marker is unstable).

Molecular
MLH1MLH1, a mismatch repair protein involved in maintaining the integrity of genetic information, alongside MSH2, MSH6 and PMS2. During DNA replication, strand misalignment can occur resulting in alterations to microsatellite repeats, often referred to as microsatellite instability (MSI). These defects in DNA repair pathways have been linked to human carcinogenesis. Mutations in the MLH1 gene have been reported to be found in tumors with MSI, such as some forms of colon cancer eg. Hereditary nonpolyposis colon cancer (HNPCC), a subset of sporadic carcinomas and breast cancer. Loss of expression of MLH1 has also been reported in acute lymphoblastic leukemia, endometrial carcinoma, gastric carcinoma and ovarian carcinoma. Immunohistochemistry (IHC)
MLH1 Promoter Methylation Analysis

This assay is performed on tumor tissue to detect hypermethylation of the MLH1 gene promoter. Bisulfite modification of tumor DNA and real-time PCR are used to quantify CpG methylation within the promoter. Percentage of methylated DNA (compared to total DNA) is reported for positive results. Analysis should be considered in combination with IHC, BRAF, and/or MSI.

Molecular
MMR Panel by IHC (MLH1, MSH2, MSH6, PMS2)

A well-defined subtype of colorectal cancer (CRC) is characterized by deficiencies in the mismatch repair (MMR) pathway. MMR status may impact prognosis and benefit of adjuvant chemotherapy. MLH1, MSH2, MSH6, and PMS2 protein expression (as assessed by IHC) and microsatellite instability analysis (MSI) assessed by PCR are well-established tools to screen for Lynch syndrome (LS), and such testing is recommended for all new colorectal cancer diagnoses. MMR IHC and molecular MSI testing also serve as companion diagnostic tests in a wide range of solid tumors for selection of certain immuno-oncology therapies.

Immunohistochemistry (IHC)
MOC31Monoclonal antibody MOC31 recognizes a membrane glycoprotein of 40kDa present on epithelial cells but not on mesothelial cells. MOC31 reacts with most adenocarcinomas of various origins, typically with strong staining pattern. Only rare cases of mesotheliomas show focal or weak staining. MOC31 antibody does not label liver as well as hepatocellular carcinoma, therefore, it will be helpful in the differential diagnosis of liver metastases versus hepatocellular carcinomas. Immunohistochemistry (IHC)
MSAMuscle Specific Actin (MSA) antibody recognizes the alpha and gamma isotypes of skeletal, cardiac, and smooth muscle cells. It is non-reactive with other mesenchymal cells and all epithelial cells except for myoepithelium. This antibody is useful in the identification of tumors with muscle differentiation and detection of myoepithelial cells. Immunohistochemistry (IHC)
MSH2Human mismatch repair protein 2 (MSH2) is involved in the initial recognition of mismatched nucleotides during the post replication mismatch repair process. Loss of MSH2 function leads to the accumulation of replication errors, which in turn may be responsible for the multiple mutations required for multistage carcinogenesis. Mutations in MSH2 gene is linked to hereditary nonpolyposis colon cancer and to sporadic cancers which exhibit microsatellite instability. Immunohistochemistry (IHC)
MSH6Mismatch repair (MMR) genes results in failure to repair errors in repetitive sequences that occur during DNA replication. The defects in DNA repair pathways have been related to tumor carcinogenesis. MSH6 mutations appear to be associated with atypical HNPCC and in particular with development of endometrial carcinoma or atypical endometrial hyperplasia, the presumed precursor of endometrial cancer. Defects in MSH6 are also found in familial colorectal cancers (suspected or incomplete HNPCC). Immunohistochemistry (IHC)
MUC1

Mucin 1 (MUC1) is a high molecular weight glycoprotein that is found on the apical surface of many glandular epithelia, including the gastrointestinal, respiratory, urinary, reproductive tracts and some hematopoietic cell lineages. MUC1 has been implicated in progression of numerous types of cancer, including breast, colon, lung, gastric and pancreatic cancers. MUC1 expression in tumors is greatly increased and accompanied by altered aberrant expression patterns that become more diffuse when compared to the normal apically restricted pattern.

Immunohistochemistry (IHC)
MUC2Mucin 2 (MUC2) expression is detected in human tissues such as normal colon, breast, prostate, and salivary gland, as well as in gastrointestinal, colonic, breast and prostate neoplasia. This antibody labels MUC2 in normal colon and colonic carcinomas where it produces intense perinuclear staining in goblet cells. Immunohistochemistry (IHC)
MUC4MUC4 is useful in the identification of low-grade fibromyxoid sarcoma (LGFMS) and sclerosing epithelioid fibrosarcoma. Immunohistochemistry (IHC)
MUC5Mucin 5 (MUC5) is expressed in gastric mucosa, and in gall bladder epithelium. MUC5 antibody is recommended for use as part of a panel of antibodies for the characterization of mucin expression and in differentiation of intestinal metaplasia as well as gastric and pancreaticobiliary carcinomas. Immunohistochemistry (IHC)
MUC6MUC6 is expressed mucopeptic neck cells and pyloric glands of the gastric mucosa. MUC6 antibody is recommended for use as part of a panel of antibodies in differentiation of gastric cancer. Immunohistochemistry (IHC)
MucicarmineSpecial stain. Mucicarmine staining is used to identify epithelial mucins, namely acid mucopolysaccharides. Staining is useful to distinguishing mucin negative undifferentiated squamous cell lesions from mucin positive adenocarcinomas. In addition, this product will stain the mucopolysaccharide capsule of Cryptococcus neoformans. Immunohistochemistry (IHC)
MYCN (n-MYC) Amplification

Probes: MYCN (2p24.3) | Centromere 2
Disease(s): Brain cancer, neuroblastoma, alveolar rhabdomyosarcoma, small-cell lung cancer, prostate cancer.

FISH
MyoD1Nuclear expression of myogenic differentiation 1 (MyoD1) is restricted to skeletal muscle tissue and has been demonstrated to be a sensitive marker of myogenic differentiation. The antibody strongly labels the nuclei of myoblasts in developing skeletal muscle tissue, whereas the majority of adult skeletal muscle is negative. MyoD1 immunostaining has been demonstrated in the majority of rhabdomyosarcomas of various histological subtypes. Immunohistochemistry (IHC)
MyogeninExpression of myogenin is restricted to cells of skeletal muscle origin. It is a useful marker for tumors of the muscle lineage, being strongly expressed in alveolar rhabdomyosarcomas. Immunohistochemistry (IHC)
MyoglobinMyoglobin is found in skeletal and cardiac muscle but not in smooth muscle. Because myoglobin appears relatively late in the maturational sequence of striated muscle, it is typically undetectable immunohistologically in embryonic neoplasms that show differentiation toward that tissue. Accordingly, pleomorphic “adult”-type rhabdomyosarcoma and rhabdomyoma are the soft tissue tumors in which myoglobin is identified most often. Immunohistochemistry (IHC)
Napsin ANapsin A has a specific function in normal alveolar epithelium and is proposed to play a role in the proteolytic processing of surfactant precursors. Napsin A is reported to be predominantly expressed in lamellar bodies of type II pneumocytes, secondary lysosomes of alveolar macrophages, respiratory epithelium of terminal and respiratory bronchioles, plasma cells, and within a subset of lymphocytes in normal lung as well as in epithelial cells of renal tubules in normal kidney. It is weakly expressed in normal spleen. Past studies have also reported that Napsin A is expressed in most primary lung adenocarcinomas. Napsin A expression may also be seen in renal carcinoma. Immunohistochemistry (IHC)
NeoARRAY™ SNP/Cytogenetic Profile

The NeoARRAY SNP/Cytogenetic Profile is available for hematological, solid tumor, and pregnancy loss indications. With the best genome-wide coverage available, this test employs an enhanced SNP microarray with over 2.6 million SNP and non-polymorphic markers for detection of copy number variants (deletions, duplications, and amplifications) and loss of heterozygosity or uniparental disomy (LOH or UPD) in any chromosome. Sensitivity and specificity for detection of copy number variants >400 kb is >99%. Testing may not reliably detect abnormalities present in less than 20% of the cells tested. Balanced rearrangements, including translocations and inversions, are not detectable by this method. Clients may request NeoARRAY on POC as the sole test, or they may order POC cytogenetics with reflex to NeoARRAY if the POC culture fails or if cytogenetic results are normal. For reflex orders, if there is no cell attachment or growth after 14 days in culture, a cytogenetics failure report will be issued and NeoARRAY will be performed. If there is limited cell attachment after 14 days in culture, NeoGenomics will contact the client for instructions. When array testing is not performed, a fee will be charged for DNA extraction (which is performed upon specimen receipt).

Cytogenetics
NeoARRAY™ SNP/Cytogenetic Profile

The NeoARRAY SNP/Cytogenetic Profile is available for hematological, solid tumor, and pregnancy loss indications. With the best genome-wide coverage available, this test employs an enhanced SNP microarray with over 2.6 million SNP and non-polymorphic markers for detection of copy number variants (deletions, duplications, and amplifications) and loss of heterozygosity or uniparental disomy (LOH or UPD) in any chromosome. Sensitivity and specificity for detection of copy number variants >400 kb is >99%. Testing may not reliably detect abnormalities present in less than 20% of the cells tested. Balanced rearrangements, including translocations and inversions, are not detectable by this method. Clients may request NeoARRAY on POC as the sole test, or they may order POC cytogenetics with reflex to NeoARRAY if the POC culture fails or if cytogenetic results are normal. For reflex orders, if there is no cell attachment or growth after 14 days in culture, a cytogenetics failure report will be issued and NeoARRAY will be performed. If there is limited cell attachment after 14 days in culture, NeoGenomics will contact the client for instructions. When array testing is not performed, a fee will be charged for DNA extraction (which is performed upon specimen receipt).

Molecular
NeoLAB™ EGFR T790M - Liquid Biopsy

The NeoLAB EGFR T790M - Liquid Biopsy test is a sequencing based assay that can detect the EGFR T790M mutation in plasma with high sensitivity (0.1%) using cell-free circulating tumor DNA (cfDNA).

Molecular
NeoLAB™ Solid Tumor Monitor - Liquid Biopsy

The NeoLAB™ Solid Tumor Monitor is a blood test that uses cell-free circulating tumor DNA (ctDNA) or RNA in combination with next-generation sequencing (NGS) to detect mutations in the following 48 genes: ABL1, AKT1, ALK, APC, ATM, BRAF, CDH1, CDKN2A, CSF1R, CTNNB1, EGFR, ERBB2, ERBB4, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNA11, GNAQ, GNAS, HNF1A, HRAS, IDH1, JAK2, JAK3, KDR, KIT, KRAS, MET, MLH1, MPL, NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, RB1, RET, SMAD4, SMARCB1, SMO, SRC, STK11, TP53, and VHL. The EGFR T790 mutation is tested at high sensitivity (10^-4). Test orders include summary interpretation of all results together. NOTE: One-time baseline molecular testing at NeoGenomics on the solid tumor is required. Please see details in Specimen Requirements.

Molecular
NeoSITE™ BE Barrett's Esophagus FISH Panel

Probes: MYC (8q24) | p16 (CDKN2A at 9p21) | HER2 (ERBB2 at 17q12) | ZNF217 (20q13)
This 4-probe FISH assay is performed on cytology brushings from Barrett esophagus to determine patterns of chromosomal gain and loss suggestive of esophageal adenocarcinoma/high-grade dysplasia vs. low grade dyplasia/non-dysplastic tissue. Sensitivity is 86% and specificity is 67% for differentiating the high-risk from the low-risk groups. Sensitivity and specificity are higher when only nodules rather than the entire esophagus are brushed. Cells from nodular surfaces will be tested first (if available) and reported as a final result if positive, or testing will reflex to the pan brushing sample if negative.
Testing is approved for specimens from the state of New York.
Disease(s): Barrett's esophagus, esophageal adenocarcinoma.

FISH
NeoSITE™ Cervical FISH PanelProbes: TERC (3q26) | D5S630 (5p15) |CEN 7 (7p11.1-q11.1) | MYC (8q24) | ZNF217 (20q13)
Disease(s): Cervical neoplasia, ASCUS, LSIL, HSIL, CIN, cervical cancer
FISH
NeoSITE™ Melanoma

Probes: RREB1 (6p25) | MYC (8q24) | CDKN2A p16 (9p21) | Centromere 9 | CCND1 (11q13)
Disease(s): Melanoma
Read more about the NeoSITE Melanoma panel.

FISH
NeoTYPE Brain Tumor Profile

This test is performed by sequencing of the entire coding regions of the genes listed unless another method is noted. AKT1, ATRX, BRAF, CDK6, CDKN2A, CIC, CTNNB1, EGFR, EGFRvIII Analysis, ERBB2, ERBB4, FGFR1, FGFR2, FGFR3, FUBP1, H3F3A, HRAS, IDH1, IDH2, KRAS, MET, MGMT Promoter Methylation Analysis, MYC, MYCN, NF1, NF2, NRAS, PIK3CA, PTCH1, PTEN, RB1, SETD2, SMAD4, SMO, SRC, TERT Promoter, TP53, 1p/19q Deletion FISH, BRAF FISH, MET FISH, MYCN FISH, PDGFRA FISH, PTEN FISH, and PD-L1 IHC. EGFRvIII Analysis and MGMT Promoter Methylation Analysis are performed by Real-Time PCR (RT-PCR). TERT Promoter is performed by bi-directional Sanger sequencing. Tumor Mutation Burden (TMB) testing and individual genes from a validated list of genes can be added. Test orders include summary interpretation of all results together. FISH components of NeoTYPE Profiles may be ordered as “Tech-Only” by pathology clients who wish to perform the professional component.
For more information, please visit our NeoTYPE Brain Tumor Profile page

Molecular
NeoTYPE Breast Tumor Profile

This test is performed by sequencing of the entire coding regions of the genes listed unless another method is noted. AKT1, BRAF, BRCA1, BRCA2, CTNNB1, EGFR, ERBB2, ERBB4, FGFR1, FGFR2, FGFR3, HRAS, KIT, KRAS, MET, NRAS, PIK3CA, PTEN, SMAD4, SMO, SRC, TP53, HER2 FISH, MET FISH, PTEN FISH and PD-L1 IHC. Tumor Mutation Burden (TMB) testing and individual genes from a validated list of genes can be added. Test orders include summary interpretation of all results together. FISH components of NeoTYPE Profiles may be ordered as "Tech-Only" by pathology clients who wish to perform the professional component. Note - Samples with equivocal HER2 FISH results will be reflexed to the Equivocal Breast FISH Panel. BRCA1/2 testing will be performed unless opted out.

Molecular
NeoTYPE Cervical Tumor Profile

This test is performed by sequencing the entire coding regions of the genes listed unless another method is noted. AKT1, BRAF, CTNNB1, EGFR, ERBB2, ERBB4, FGFR1, FGFR2, FGFR3, HRAS, JAK3, KRAS, MET, NOTCH1, NRAS, PDGFRA, PIK3CA, PTEN, SMAD4, SMO, SRC, TP53, MET FISH, PTEN FISH and PD-L1 IHC. Tumor Mutation Burden (TMB) testing and individual genes from a validated list of genes can be added. Test orders include summary interpretation of all results together. FISH components of NeoTYPE Profiles may be ordered as "Tech-Only" by pathology clients who wish to perform the professional component.

Molecular
NeoTYPE Colorectal Tumor Profile

This test is performed by sequencing the entire coding regions of the genes listed unless another method is noted. AKT1, APC, BRAF, EGFR, ERBB2, ERBB4, FGFR1, FGFR2, FGFR3, HRAS, JAK3, KIT, KRAS, MET, Microsatellite Instability (MSI), MLH1 Promoter Methylation, NOTCH1, NRAS, PDGFRA, PIK3CA, PTEN, SMO, SRC, TP53, MET FISH, PTEN FISH and PD-L1 IHC. MSI is performed by fragment analysis and MLH1 Promoter Methylation is performed by Real-Time PCR. Tumor Mutation Burden (TMB) testing and individual genes from a validated list of genes can be added. Test orders include summary interpretation of all results together. FISH components of NeoTYPE Profiles may be ordered as "Tech-Only" by pathology clients who wish to perform the professional component.

Molecular
NeoTYPE Discovery Profile for Solid Tumors

This test is performed by sequencing the entire coding regions of the genes listed unless another method is noted. ABL1, ABL2, ACVR1B, AKT1, AKT2, AKT3, ALK, AMER1 (FAM123B), APC, AR, ARAF, ARFRP1, ARID1A, ARID1B, ARID2, ASXL1, ATM, ATR, ATRX, AURKA, AURKB, AXIN1, AXL, BAP1, BARD1, BCL2, BCL2L1, BCL2L2, BCL6, BCOR, BCORL1, BLM, BRAF, BRCA1, BRCA2, BRD4, BRIP1, BTG1, BTK, C11orf30, CARD11, CBFB, CBL, CCND1, CCND2, CCND3, CCNE1, CD274, CD79A, CD79B, CDC73, CDH1, CDK12, CDK4, CDK6, CDK8, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CDKN2C, CEBPA, CHD2, CHD4, CHEK1, CHEK2, CIC, CREBBP, CRKL, CRLF2, CSF1R, CTCF, CTNNA1, CTNNB1, CUL3, CYLD, DAXX, DDR2, DICER1, DNMT3A, DOT1L, EGFR, EP300, EPHA3, EPHA5, EPHA7, EPHB1, ERBB2, ERBB3, ERBB4, ERG, ERRF11, ESR1, EZH2, FAM46C, FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCL, FAS, FAT1, FBXW7, FGF10, FGF14, FGF19, FGF23, FGF3, FGF4, FGF6, FGFR1, FGFR2, FGFR3, FGFR4, FH, FLCN, FLT1, FLT3, FLT4, FOXL2, FOXP1, FRS2, FUBP1, GABRA6, GATA1, GATA2, GATA3, GATA4, GATA6, GID4 (C17orf39), GLI1, GNA11, GNA13, GNAQ, GNAS, GPR124, GRIN2A, GRM3, GSK3B, H3F3A, HGF, HNF1A, HRAS, HSD3B1, HSP90AA1, IDH1, IDH2, IGF1R, IGF2, IKBKE, IKZF1, IL7R, INHBA, INPP4B, IRF2, IRF4, IRS2, JAK1, JAK2, JAK3, JUN, KAT6A (MYST3), KDM5A, KDM5C, KDM6A, KDR, KEAP1, KEL, KIT, KLHL6, KMT2A (MLL), KMT2C (MLL3), KMT2D (MLL2), KRAS, LMO1, LRP1B, LYN, LZTR1, MAGI2, MAP2K1 (MEK1) , MAP2K2 (MEK2) , MAP2K4 (MEK4), MAP3K1 (MEKK) , MCL1, MDM2, MDM4, MED12, MEF2B, MEN1, MET, MITF, MLH1, MPL, MRE11A, MSH2, MSH6, MTOR, MUTYH, MYC, MYCL (MYCL1), MYCN, MYD88, NBN, NF1, NF2, NFE2L2, NFKBIA, NKX2-1, NOTCH1, NOTCH2, NOTCH3, NPM1, NRAS, NSD1, NTRK1, NTRK2, NTRK3, NUP93, PAK3, PALB2, PARK2, PAX5, PBRM1, PDCD1LG2, PDGFRA, PDGFRB, PDK1, PIK3C2B, PIK3CA, PIK3CB, PIK3CG, PIK3R1, PIK3R2, PLCG2, PMS2, POLD1, POLE, PPP2R1A, PRDM1, PREX2, PRKAR1A, PRKCI, PRKDC, PRSS8, PTCH1, PTEN, PTPN11, QKI, RAC1, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RAD54L, RAF1, RANBP2, RARA, RB1, RBM10, RET, RICTOR, RNF43, ROS1, RPTOR, RUNX1, RUNX1T1, SDHA, SDHB, SDHC, SDHD, SETD2, SF3B1, SLIT2, SMAD2, SMAD3, SMAD4, SMARCA4, SMARCB1, SMO, SNCAIP, SOCS1, SOX10, SOX2, SOX9, SPEN, SPOP, SPTA1, SRC, STAG2, STAT3, STAT4, STK11, SUFU, SYK, TAF1, TBX3, TERC, TERT, TET2, TGFBR2, TNFAIP3, TNFRSF14, TOP1, TOP2A, TP53, TSC1, TSC2, TSHR, U2AF1, VEGFA, VHL, WISP3, WT1, XPO1, ZBTB2, ZNF217, ZNF703, ALK FISH, BRAF FISH, HER2 FISH, MET FISH, c-MYC FISH, PDGFRA Amplification FISH, PTEN FISH, RET FISH, ROS1 FISH and PD-L1 IHC. Tumor Mutation Burden (TMB) testing is performed with all Discovery Profiles. Test orders include summary interpretation of all results together.

Molecular
NeoTYPE Endometrial Tumor Profile

This test is performed by sequencing the entire coding regions of the genes listed unless another method is noted. AKT1, BRAF, EGFR, FGFR1, FGFR2, FGFR3, HRAS, JAK3, KIT, KRAS, MET, Microsatellite Instability (MSI), NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, SMAD4, SMO, SRC, TP53, MET FISH, PTEN FISH and PD-L1 IHC. MSI is performed by fragment analysis. Tumor Mutation Burden (TMB) testing and individual genes from a validated list of genes can be added. Test orders include summary interpretation of all results together. FISH components of NeoTYPE Profiles may be ordered as "Tech-Only" by pathology clients who wish to perform the professional component.

Molecular
NeoTYPE Esophageal Tumor Profile

This test is performed by sequencing the entire coding regions of the genes listed unless another method is noted. AKT1, BRAF, CTNNB1, ERBB2, ERBB4, FGFR1, FGFR2, FGFR3, HRAS, JAK3, KIT, KRAS, MET, Microsatellite Instability (MSI). NOTCH1, NRAS, PDGFRA, PIK3CA, PTEN, SMAD4, SMO, SRC, TP53, HER2 FISH, MET FISH, PTEN FISH and PD-L1 IHC. MSI is performed by fragment analysis. Tumor Mutation Burden (TMB) testing and individual genes from a validated list of genes can be added. Test orders include summary interpretation of all results together. FISH components of NeoTYPE Profiles may be ordered as "Tech-Only" by pathology clients who wish to perform the professional component.

Molecular
NeoTYPE Gastric Tumor Profile

This test is performed by sequencing the entire coding regions of the genes listed unless another method is noted. AKT1, BRAF, EGFR, ERBB2, ERBB4, FGFR1, FGFR2, FGFR3, HRAS, JAK3, KIT, KRAS, MET, Microsatellite Instability (MSI), NOTCH1, NRAS, PDGFRA, PIK3CA, PTEN, SMAD4, SMO, SRC, TP53, HER2 FISH, MET FISH, PTEN FISH and PD-L1 IHC. MSI is performed by fragment analysis. Tumor Mutation Burden (TMB) testing and individual genes from a validated list of genes can be added. Test orders include summary interpretation of all results together. FISH components of NeoTYPE Profiles may be ordered as "Tech-Only" by pathology clients who wish to perform the professional component.

Molecular
NeoTYPE GI Predictive Profile

This test is performed by sequencing of select exons of the genes listed unless another method is noted: BRAF, HRAS, KRAS, Microsatellite Instability Analysis (MSI), NRAS, HER2 FISH, PD-L1 IHC. MSI is performed by fragment analysis. Tumor Mutation Burden (TMB) testing and individual genes from a validated list of genes can be added. Test orders include summary interpretation of all results together. FISH components of NeoTYPE Profiles may be ordered as "Tech-Only" by pathology clients who wish to perform the professional component.

Molecular
NeoTYPE GIST Profile

This test is performed by the sequencing of select exons of the genes listed. AKT1, BRAF, CTNNB1, ERBB2, ERBB4, FGFR1, FGFR2, FGFR3, KIT, PDGFRA, SRC and PD-L1 IHC. Tumor Mutation Burden (TMB) testing and individual genes from a validated list of solid tumor genes can be added. Test orders include summary interpretation of all results together.

Molecular
NeoTYPE Head & Neck Tumor Profile

This test is performed by sequencing the entire coding regions of the genes listed unless another method is noted. AKT1, ATM, BRAF, CDKN2A, CTNNB1, EGFR, ERBB2, ERBB4, FGFR1, FGFR2, FGFR3, HRAS, IDH1, IDH2, KRAS, MET, NOTCH1, NRAS, PIK3CA, PTEN, RB, SMO, SRC, TP53, MET FISH, PTEN FISH, PD-L1 IHC and HPV DNA Tissue Testing which is performed by fragment analysis. Tumor Mutation Burden (TMB) testing and individual genes from a validated list of genes can be added. Test orders include summary interpretation of all results together. FISH components of NeoTYPE Profiles may be ordered as "Tech-Only" by pathology clients who wish to perform the professional component.

Molecular
NeoTYPE Liposarcoma Fusion Profile

The NeoTYPE Liposarcoma Fusion Profile combines next-generation sequencing to detect translocations in the genes EWSR1, FUS, HMGA2, and PLAG1 with FISH testing for MDM2 to detect amplifications relevant in liposarcoma. FISH components of NeoTYPE Profiles may be ordered as “Tech-Only” by pathology clients who wish to perform the professional component.

Molecular
NeoTYPE Lung Tumor Profile

The NeoTYPE Lung Tumor Profile is performed by sequencing the entire coding regions of the genes listed unless another method is noted. AKT1, BRAF, EGFR, ERBB2, ERBB4, FGFR1, FGFR2, FGFR3, KIT, KRAS, MET, MET Exon 14 Deletion Analysis, NOTCH1, NRAS, PDGFRA, PIK3CA, PTEN, SMAD4, SMO, SRC, TP53, ALK FISH, HER2 FISH, MET FISH, PTEN FISH, RET FISH, ROS1 FISH and PD-L1 IHC. MET Exon 14 Deletion Analysis is performed by Real-Time PCR. Tumor Mutation Burden (TMB) testing and individual genes from a validated list of genes can be added. Test orders include summary interpretation of all results together. FISH components of NeoTYPE Profiles may be ordered as "Tech-Only" by pathology clients who wish to perform the professional component.

Molecular
NeoTYPE Melanoma Profile

This test is performed by sequencing the entire coding regions of the genes listed. AKT1, BRAF, CTNNB1, EGFR, ERBB2, ERBB4, FGFR1, FGFR2, FGFR3, GNA11, GNAQ, KIT, NRAS, PDGFRA, PTEN, SMO, SRC, TERT Promoter, PTEN FISH and PD-L1 IHC. TERT Promoter is performed by bi-directional Sanger sequencing. Tumor Mutation Burden (TMB) testing and individual genes from a validated list of genes can be added. Test orders include summary interpretation of all results together.

Molecular
NeoTYPE Other Solid Tumor Profile

This test is performed by sequencing the entire coding regions of the genes listed unless another method is noted. AKT1, BRAF, EGFR, FGFR1, FGFR2, FGFR3, GNAS, HRAS, IDH1, IDH2, JAK3, KIT, KRAS, MET, NOTCH1, NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, SMAD4, SMO, SRC, TP53, MET FISH, PTEN FISH, and PD-L1 IHC. Tumor Mutation Burden (TMB) testing and individual genes from a validated list of genes can be added. Test orders include summary interpretation of all results together. FISH components of NeoTYPE Profiles may be ordered as "Tech-Only" by pathology clients who wish to perform the professional component.

Molecular
NeoTYPE Ovarian Tumor Profile

This test is performed by sequencing the entire coding regions of the genes listed unless another method is noted. AKT1, BRAF, BRCA1, BRCA2, CTNNB1, EGFR, ERBB2, ERBB4, FGFR1, FGFR2, FGFR3, HRAS, JAK3, KRAS, MET, NRAS, Microsatellite Instability (MSI), PIK3CA, PTEN, SMAD4, SMO, SRC, TP53, MET FISH, PTEN FISH and PD-L1 IHC. MSI is performed by fragment analysis.  Tumor Mutation Burden (TMB) testing and individual genes from a validated list of genes can be added. Test orders include summary interpretation of all results together. FISH components of NeoTYPE Profiles may be ordered as "Tech-Only" by pathology clients who wish to perform the professional component. BRCA1/2 testing will be performed unless opted out.

Molecular
NeoTYPE Pancreas Tumor Profile

The Pancreas Tumor Profile is an NGS-based assay performed by sequencing the entire coding regions of the genes listed unless other method is noted. ARID1A, BRAF, BRCA1, BRCA2, CDKN2A, EGFR, ERBB2, ERBB4, FGFR1, FGFR2, FGFR3, HRAS, KIT, KRAS, MET, Microsatellite Instability (MSI), NOTCH1, NRAS, PBRM1, PIK3CA, PTEN, SMAD4, SMO, TP53, VHL, HER2 FISH, MET FISH, PTEN FISH and PD-L1 IHC. MSI is performed by fragment analysis. Tumor Mutation Burden (TMB) testing and individual genes from a validated list of genes can be added. Test orders include summary interpretation of all results together. FISH components of NeoTYPE Profiles may be ordered as "Tech-Only" by pathology clients who wish to perform the professional component. BRCA1/2 testing will be performed unless opted out.

Molecular
NeoTYPE Precision Profile for Solid Tumors

The NeoTYPE Precision Profile for Solid Tumors utilizes next-generation sequencing to detect mutations in the following 48 genes: ABL1, AKT1, ALK, APC, ATM, BRAF, CDH1, CDKN2A, CSF1R, CTNNB1, EGFR, ERBB2, ERBB4, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNA11, GNAQ, GNAS, HNF1A, HRAS, IDH1, JAK2, JAK3, KDR, KIT, KRAS, MET, MLH1, MPL, NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, RB1, RET, SMAD4, SMARCB1, SMO, SRC, STK11, TP53, VHL and PD-L1 IHC. This test is performed by sequencing the enitre coding regions of the genes listed unless another method is noted. Tumor Mutation Burden testing can be added. Test orders include summary interpretation of all results together.

Molecular
NeoTYPE Thyroid Profile

This test is performed by sequencing the entire coding regions of the genes listed unless another method is noted. AKT1, ALK, BRAF, CTNNB1, ERBB2, ERBB4, HRAS, KRAS, MET, NRAS, PIK3CA, RET, SMAD4, SMO, SRC, TERT Promoter, MET FISH, RET FISH, PD-L1 IHC. TERT Promoter is performed by bi-directional sanger sequencing. Tumor Mutation Burden (TMB) testing and individual genes from a validated list of genes can be added. Test orders include summary interpretation of all results together. FISH components of NeoTYPE Profiles may be ordered as "Tech-Only" by pathology clients who wish to perform the professional component.

Molecular
NeoTYPE® Soft Tissue Tumor Profile

This test is performed by sequencing the entire coding regions of the genes listed unless another method is noted. AKT1, BRAF, FGFR1, FGFR2, FGFR3, GNAS, HRAS, JAK3, KIT, KRAS, MET, NRAS, PDGFRA, PIK3CA, PTEN, SMAD4, SMO, SRC, TP53, MET FISH, PTEN FISH and PD-L1 IHC. Tumor Mutation Burden (TMB) testing and individual genes from a validated list of genes can be added. Test orders include summary interpretation of all results together. FISH components of NeoTYPE Profiles may be ordered as "Tech-Only" by pathology clients who wish to perform the professional component.

Molecular
NeuNNeuN is a sensitive and specific marker of neuronal differentiation in brain tumors. Immunohistochemistry (IHC)
NF (Neurofilament)Neurofilaments (NFs) are the intermediate filaments of neurons and their processes. NFs are expressed in tumors of neural origin or tumors displaying neuronal differentiation, such as neuroblastoma, medulloblastoma and retinoblastoma. This antibody labels neurons, neuronal processes and peripheral nerves, as well as sympathetic ganglion cells and adrenal medulla. The cell body of neurons, containing the non-phosphorylated neurofilament, is weakly stained. Immunohistochemistry (IHC)
NGFRNerve Growth Factor Receptor (NGFR), also known as P75NTR or CD271, is a neurotrophin receptor belonging to the tumor necrosis factor receptor family. NGFR is expressed mainly in Schwann cells and neurons, as well as a number of other non-neuronal cell types, and functions during central and peripheral nervous system development. It is useful in the diagnosis of brain tumors, peripheral nerve sheath sarcoma, melanoma, and breast malignancy. Immunohistochemistry (IHC)
NGS ALK, NTRK, RET, ROS1 Fusion Profile

The NGS ALK, NTRK, RET, ROS1 Fusion Profile is a targeted next-generation sequencing panel that detects significant translocations in the genes ALK (fusions of exons 19-22), NTRK1 (fusions of exons 8 and 10-13), NTRK3 (fusions of exons 13-16), RET (fusions of exons 8-13) and ROS1 (fusions of exons 31-37) simultaneously. Some of the more common translocations detected include EML4-ALK, KIF5B-ALK, NPM1-ALK, TPM3-ALK, CD74-NTRK1, MPRIP-NTRK1, ETV6-NTRK3, CCD6-RET (aka RET-PTC1), ERC1-RET, HOOK3-RET, KIF5B-RET, NCOA4-RET (aka RET-PTC3), PCM1-RET, TRIM33-RET, CD74-ROS1, SLC34A2-ROS1 and TPM3-ROS1. This test detects rearrangements common in lung carcinoma, colorectal carcinoma, inflammatory myofibroblastic tumor, anaplastic large cell lymphoma as well as other tumors. ALK1 and ROS1 gene rearrangements are found in 3-5% and 1-2% of non-small cell lung carcinomas (NSCLC), respectively, and determine likelihood of response to crizotinib (Xalkori®) therapy. RET translocations detected in this test are common in papillary thyroid carcinoma and are also seen in 1-2% of NSCLC. In early clinical studies, patients with RET rearranged NSCLC show response to multi-kinase inhibitors. NTRK1 rearrangements are frequent in papillary thyroid carcinoma and reported in a small subset of patients with NSCLC; early clinical studies suggest response to tyrosine kinase inhibitors. We recommend FISH as the primary method of ALK, RET, and/or ROS1 rearrangement detection. We suggest using this test for NTRK analysis and/or cases that fail to provide conclusive FISH results.

Molecular
NGS ALK, RET, ROS1 Fusion Profile

The NGS ALK, RET, ROS1 Fusion Profile is a targeted next-generation sequencing panel that detects significant translocations in the genes ALK (fusions of exons 19-22), RET (fusions of exons 8-13) and ROS1 (fusions of exons 31-37) simultaneously. In addition, mutations related to crizotinib resistance can also be detected in the genes ALK and RET. Some of the more common translocations detected include EML4-ALK, KIF5B-ALK, NPM1-ALK, TPM3-ALK, CCD6-RET (aka RET-PTC1), ERC1-RET, HOOK3-RET, KIF5B-RET, NCOA4-RET (aka RET-PTC3), PCM1-RET, TRIM33-RET, CD74-ROS1, SLC34A2-ROS1 and TPM3-ROS1. This test detects rearrangements common in lung carcinoma, colorectal carcinoma, inflammatory myofibroblastic tumor, anaplastic large cell lymphoma as well as other tumors. ALK1 and ROS1 gene rearrangements are found in 3-5% and 1-2% of non-small cell lung carcinomas (NSCLC), respectively, and determine likelihood of response to crizotinib (Xalkori®) therapy. RET translocations detected in this test are common in papillary thyroid carcinoma and are also seen in 1-2% of NSCLC. In early clinical studies, patients with RET rearranged NSCLC show response to multi-kinase inhibitors. We recommend FISH as the primary method of ALK, RET, and ROS1 rearrangement detection and suggest this test be used in cases that fail to provide conclusive FISH results.

Molecular
NGS Comprehensive Sarcoma Fusion Profile

The NGS Comprehensive Sarcoma Fusion Profile is a targeted next-generation sequencing panel that can detect 134 different translocations relevant in sarcomas in the genes ALK, CAMTA1, CCNB3, CIC, EPC1, EWSR1, FOXO1, FUS, GLI1, HMGA2, JAZF1, MEAF6, MKL2, NCOA2, NTRK3, PDGFB, PLAG1, ROS1, SS18, STAT6, TAF15, TCF12, TFE3, TFG, USP6, and YWHAE.

Molecular
NGS Ewing Sarcoma Fusion Profile

The NGS Ewing Fusion Profile is a targeted next-generation sequencing panel that can detect various translocations relevant in Ewing's sarcoma in the gene EWSR1.

Molecular
NGS Non-Ewing Sarcoma Fusion Profile

The NGS Non-Ewing Sarcoma Fusion Profile is a targeted next-generation sequencing panel that can detect various translocations unrelated to Ewing's sarcoma in the genes ALK, CAMTA1, CCNB3, CIC, EPC1, FOXO1, FUS, GLI1, HMGA2, JAZF1, MEAF6, MKL2, NCOA2, NTRK3, PDGFB, PLAG1, STAT6, TAF15, TCF12, TFE3, TFG, USP6, and YWHAE.

Molecular
NGS Pediatric Sarcoma Fusion Profile

The NGS Pediatric Sarcoma Fusion Profile is a targeted next-generation sequencing panel that can detect various translocations related to pediatric sarcomas in the genes ALK, EWSR1, FUS, FLI1, NTRK3, and USP6.

Molecular
NGS Rhabdomyosarcoma Fusion Profile

The NGS Rhabdomyosarcoma Fusion Profile is a targeted next-generation sequencing panel that can detect various translocations related to rhabdomyosarcoma in the genes FOXO1, NCOA2, and TFE3.

Molecular
NGS Thyroid Fusion Profile

The NGS Thyroid Fusion Profile is a targeted next-generation sequencing panel that detects significant translocations in the genes NTRK1 (fusions of exons 8 and 10-13), NTRK3 (fusions of exons 13-16), and RET (fusions of exons 8-13) simultaneously. Some of the more common translocations detected include CD74-NTRK1, MPRIP-NTRK1, ETV6-NTRK3, CCD6-RET (aka RET-PTC1), ERC1-RET, HOOK3-RET, KIF5B-RET, NCOA4-RET (aka RET-PTC3), PCM1-RET, and TRIM33-RET. This test detects rearrangements common in lung and thyroid cancer as well as other tumors. RET translocations detected in this test are common in papillary thyroid carcinoma and are also seen in 1-2% of NSCLC. NTRK1 rearrangements are frequent in papillary thyroid carcinoma and reported in a small subset of patients with NSCLC. Early clinical studies suggest that tumors with NTRK1/3 rearrangements respond to tyrosine kinase inhibitors. We suggest using this test for NTRK and RET analysis and/or cases that fail to provide conclusive FISH results.

Molecular
NKX2.2Homeobox protein NKX2.2 plays a critical role in neuroendocrine/glial differentiation. The NKX2.2 gene was recently identified as a target of EWS-FLI-1, the fusion protein specific to Ewing sarcoma. NKX2.2 is a valuable marker for Ewing sarcoma with a sensitivity of 93% and a specificity of 89%, and aids in the differential diagnosis of small round cell tumors. Immunohistochemistry (IHC)
NKX3.1NKX3.1 is a protein encoded by the NKX3.1 gene located on chromosome 8. NKX3.1 protein has been found to be positive in the vast majority of primary prostatic adenocarcinomas. NKX3.1 stains nuclei in both normal and prostate cancer and along with other prostate-restricted markers, may be a valuable marker to definitively determine prostatic origin in poorly differentiated metastatic carcinomas. Immunohistochemistry (IHC)
NOTCH1 Mutation Analysis

Bi-directional sequencing of exons 26, 27, and 34 is performed for detection of sequence variant mutations. Testing can be performed on plasma when adequate leukemic cells are not available.

Molecular
NRAS Exon 4 Mutation Analysis

Bi-directional sequencing of NRAS exon 4 is performed using PCR primers designed to target hotspot mutations in codons 117 and 146, among other regions in exon 4. Testing is available separately or in combination with BRAF, KRAS and HRAS in the RAS/RAF Panel. Testing is approved for specimens from the state of New York.

Molecular
NRAS Mutation Analysis

Bi-directional sequencing of NRAS exons 2 and 3 which includes sites of common activating mutations in codons 12, 13, 59, and 61. Testing is approved for specimens from the state of New York.

Molecular
NSE (Neuron Specific Enolase)In normal tissue, most neurons and their axonal and dendritic processes stain strongly positive for Neuron Specific Enolase (NSE), with the exception of Purkinje cells. Schwann cells, cells of the adrenal medulla, and paraganglia also contain NSE. Endocrine cells of the skin (Merkel cells), respiratory and GI tract epithelium, pituitary parathyroid, and pancreatic islets and C cells of thyroid all stain positively for NSE. NSE is expressed in ganglioneuromas, neuroblastomas, Schwannomas and malignant melanomas. It is also present in pheochromocytomas and paragangliomas. Carcinoids, medullary thyroid carcinomas, pituitary adenomas and endocrine tumors of the pancreas and GI tract all show positive immunoreactivity for NSE. NSE is found in neuroendocrine carcinoma of the skin (Merkel cell tumor) and small cell carcinoma of the lung. Immunohistochemistry (IHC)
Olig2Olig2, a transcription factor, is involved in oligodendroglial specification. Olig2 expression has been reported in most glial tumors, such as oligodendrogliomas and astrocytomas. Olig2 is negative in the non-glial tumors including neuroepithelial tumors, ependymomas, subependymomas,medulloblastomas, and nonneuroepithelial tumors, such as CNS lymphomas, meningiomas, schwannomas, atypical teratoid/rhabdoid tumor, and haemangioblastomas. Immunohistochemistry (IHC)
Oncomine™ Dx Target Test

The Oncomine Dx Target Test is a next-gen sequencing assay designed to detect variants in 23 genes associated with non-small cell lung cancer (NSCLC). Abnormalities targeted are ROS1 gene fusions and 367 sequence variant "hotspot" mutations in the following genes: AKT1, ALK, BRAF, CDK4, DDR2, EGFR, ERBB2, ERBB3, FGFR2, FGFR3, HRAS, KIT, KRAS, MAP2K1 (aka MEK1), MAP2K2 (aka MEK2), MET, MTOR, NRAS, PDGFRA, PIK3CA, RAF1, RET, and ROS1.
NOTE: Not yet available for samples from New York.

Molecular
p120 CateninP120 Catenin is a tyrosine kinase which binds to E-cadherin within the cell membrane. It is detectable in the cell membranes of a wide variety of cells, but predominates in virtually all types of epithelia. When E-cadherin is absent, P120ctn moves to the cell cytoplasm. P120ctn can be useful in the diagnostic distinction between lobular (cytoplasmic staining pattern) and ductal (membranous) breast neoplasia. Immunohistochemistry (IHC)
p16p16 (p16 -INK4a, p16-MTS1, inhibitor of CDK4) is the product of the CDKN2 gene. It inhibits the progression of the cell cycle through the G1 phase. p16 is a candidate tumor suppressor, whose gene is frequently deleted or mutated in tumors such as melanomas, gliomas, esophageal, pancreatic, lung, and urinary bladder carcinomas, and some types of leukemias. p16 expression is associated with high-risk human papillomavirus in cervical cancer and head and neck tumors. Immunohistochemistry (IHC)
p21p21 is a cyclin dependent protein kinase inhibitor and is a member of a family of proteins that functions to slow down cell division. p21 is found in t cells as they transitions from G1 phase to S phase. Low nuclear expression of p21 has been associated with poor prognosis in colon and prostate carcinomas. Immunohistochemistry (IHC)
p27p27 (KIP1) belongs to the family of cell cycle regulators that cause cell cycle arrest in G1 phase. p27 promotes apoptosis, plays a role in terminal differentiation of some tissues and mediates chemosensitivity in solid tumors. Decreased p27 KIP1 expression in tumors is associated with a more aggressive tumor phenotype such as poor histologic grade, presence of lymphovascular invasion and higher growth fraction. These findings have been validated on various cancers such as breast, colon, esophagus, stomach, lung and prostate. Immunohistochemistry (IHC)
p40p40 antibody recognizes ΔNp63—a p63 isoform. It is equivalent to p63 in sensitivity for squamous cell carcinoma, but it is markedly superior to p63 in specificity, which eliminates a potential pitfall of misinterpreting a p63-positive adenocarcinoma as squamous cell carcinoma. These findings strongly support the routine use of p40 for the diagnosis of pulmonary squamous cell carcinoma. Immunohistochemistry (IHC)
P501S

P501S protein, also called the prostein, is a type IIIa plasma membrane protein which is exclusively expressed in cells of normal and malignant prostate. P501S expression has not been detected in other normal or malignant glandular tissues.

Immunohistochemistry (IHC)
P504SExpression of P504S protein, or Alpha-methylacyl-CoA Racemase (AMACR), is found in prostatic adenocarcinoma but not in benign prostatic tissue. It has also been found to stain premalignant lesions of the prostate, high-grade prostatic intraepithelial neoplasia (PIN) and atypical adenomatous hyperplasia. P504S stains the vast majority of prostate cancers, and P504S has been shown to stain numerous other tumor types, such as hepatoma, breast carcinoma, pancreatic islet tumor and desmoplastic small round cell tumor. Immunohistochemistry (IHC)
p53The product of the p53 gene is a nuclear phosphoprotein that regulates cell proliferation. Excess accumulation of the mutant p53 gene product results in inactivation of its tumor suppressor function and cellular transformation. Overexpression of mutant p53 gene has also been associated with high proliferative rates and poor prognosis in breast, colon, lung, and brain cancer, as well as in some leukemias and lymphomas. Immunohistochemistry (IHC)
Pan Melanoma (S100 + Melan A + Tyrosinase)The Pan Melanoma staining combination increases sensitivity for melanomas. Since many skin biopsies are small, the triple stain conserves valuable tissue while saving time. Melan A (brown cytoplasmic) is a useful addition to melanoma panels as it is specific for melanocytic lesions. Tyrosinase (brown cytoplasmic) is a key enzyme involved in the initial stages of melanin biosynthesis. Tyrosinase is a more sensitive marker when compared to HMB45 and MART-1. It also labels a higher percentage of desmoplastic melanomas than HMB45. S100 stains Schwannomas, ependymomas, astrogliomas, almost all benign and malignant melanomas and their metastases. S100 (nuclear red) protein is also expressed in antigen presenting cells, such as the Langerhans cells in skin and interdigitating reticulum cells in the paracortex of lymph nodes. Immunohistochemistry (IHC)
Pan Melanoma/Ki67Pan Melanoma/Ki67 serves as a tool to identify the proliferation rate of melanocytic lesions. A high Ki67 rate of a melanocytic lesion raises the possibility of malignancy. Immunohistochemistry (IHC)
Pan-CytokeratinMonoclonal antibodies AE1 and AE3 recognize the acidic and basic subfamilies of cytokeratin, respectively, thus the combination of these two antibodies can be used to detect almost all human epithelia. In surgical pathology, it is an important marker for carcinoma as well as some special tumor types which have an epithelial component or differentiation. This cocktail has been used to differentiate epithelial from non-epithelial tumors. Immunohistochemistry (IHC)
PAX8The PAX8 gene is a member of the paired box (PAX) family of transcription factors. This family plays critical roles during fetal development and cancer growth. PAX8 is involved in kidney cell differentiation, and thyroid development. PAX8 has been shown to be expressed in three of the most common types of renal cell carcinoma including clear cell, chromophobe and papillary carcinoma. PAX8 stains nuclei exclusively and performs well in formalin-fixed paraffin-embedded (FFPE) tissues. PAX8 has been shown to be positive in thyroid and ovarian carcinomas. Immunohistochemistry (IHC)
PD-L1 22C3 FDA (KEYTRUDA®) for Cervical

PD-L1 IHC 22C3 pharmDx is a qualitative immunohistochemical assay using Monoclonal Mouse Anti-PD-L1, Clone 22C3 intended for use in the detection of PD-L1 protein in formalin-fixed, paraffin-embedded (FFPE) cervical squamous cell carcinoma tissue using EnVision FLEX visualization system on Autostainer Link 48.

PD-L1 IHC 22C3 pharmDx is indicated as an aid in identifying patients with recurrent or metastatic cervical cancer for treatment with KEYTRUDA® (pembrolizumab).

For gastric or GEJ cancer, please order PD-L1 22C3 FDA (KEYTRUDA®) for Gastric/GEA. For urothelial (bladder) carcinoma, please order PD-L1 22C3 FDA (KEYTRUDA®) for Urothelial Carcinoma. For non-small cell lung carcinoma (NSCLC), please order PD-L1 22C3 FDA (KEYTRUDA®) for NSCLC.

Stain-only (tech-only) testing is available to clients who have completed the test kit manufacturer’s online interpretation training.

Immunohistochemistry (IHC)
PD-L1 22C3 FDA (KEYTRUDA®) for Gastric/GEA

PD-L1 IHC 22C3 pharmDx is a qualitative immunohistochemical assay using Monoclonal Mouse Anti-PD-L1, Clone 22C3 intended for use in the detection of PD-L1 protein in formalin-fixed, paraffin-embedded (FFPE) gastric or gastroesophageal junction adenocarcinoma (GEJ, GEA) tissue using EnVision FLEX visualization system on Autostainer Link 48. PD-L1 IHC 22C3 pharmDx is indicated as an aid in identifying patients with metastatic gastric or GEJ cancer for treatment with KEYTRUDA® (pembrolizumab).

For cervical cancer, please order PD-L1 22C3 FDA (KEYTRUDA®) for Cervical. For urothelial (bladder) carcinoma, please order PD-L1 22C3 FDA (KEYTRUDA®) for Urothelial Carcinoma. For non-small cell lung carcinoma (NSCLC), please order PD-L1 22C3 FDA (KEYTRUDA®) for NSCLC.

Stain-only (tech-only) testing is available to clients who have completed the test kit manufacturer’s online interpretation training.

Immunohistochemistry (IHC)
PD-L1 22C3 FDA (KEYTRUDA®) for NSCLC

PD-L1 IHC 22C3 pharmDx is a qualitative immunohistochemical assay using Monoclonal Mouse Anti-PD-L1, Clone 22C3 intended for use in the detection of PD-L1 protein in formalin-fixed, paraffin-embedded (FFPE) non-small cell lung cancer (NSCLC) tissue using EnVision FLEX visualization system on Autostainer Link 48. PD-L1 IHC 22C3 pharmDx is indicated as an aid in identifying NSCLC patients for treatment with KEYTRUDA® (pembrolizumab).

For gastric or GEJ cancer, please order PD-L1 22C3 FDA (KEYTRUDA®) for Gastric/GEA. For cervical cancer, please order PD-L1 22C3 FDA (KEYTRUDA®) for Cervical. For urothelial (bladder) carcinoma, please order PD-L1 22C3 FDA (KEYTRUDA®) for Urothelial Carcinoma

Stain-only (tech-only) testing is available to clients who have completed the test kit manufacturer’s online interpretation training.

Immunohistochemistry (IHC)
PD-L1 22C3 FDA (KEYTRUDA®) for Urothelial Carcinoma

PD-L1 IHC 22C3 pharmDx is a qualitative immunohistochemical assay using Monoclonal Mouse Anti-PD-L1, Clone 22C3 intended for use in the detection of PD-L1 protein in formalin-fixed, paraffin-embedded (FFPE) urothelial carcinoma and certain other tissues using EnVision FLEX visualization system on Autostainer Link 48. PD-L1 IHC 22C3 pharmDx is indicated as an aid in identifying urothelial carcinoma patients for treatment with KEYTRUDA® (pembrolizumab). Keytruda® is approved for use in some urothelial carcinoma patients whose tumors express PD-L1 with Combined Positive Score (CPS) ≥ 10.

For gastric or GEJ cancer, please order PD-L1 22C3 FDA (KEYTRUDA®) for Gastric/GEA. For cervical cancer, please order PD-L1 22C3 FDA (KEYTRUDA®) for Cervical. For non-small cell lung carcinoma (NSCLC), please order PD-L1 22C3 FDA (KEYTRUDA®) for NSCLC.

Stain-only (tech-only) testing is available to clients who have completed the test kit manufacturer’s online interpretation training.

Immunohistochemistry (IHC)
PD-L1 28-8 FDA (OPDIVO®)

PD-L1 IHC 28-8 pharmDx is a qualitative immunohistochemical assay using Monoclonal Rabbit Anti-PD-L1, clone 28-8 intended for use in the detection of PD-L1 protein in formalin-fixed, paraffin-embedded (FFPE) non-squamous non-small cell lung cancer (NSCLC) and melanoma tissues using EnVision FLEX visualization system on Autostainer Link 48. PD-L1 protein expression is defined as the percentage of tumor cells exhibiting positive membrane staining at any intensity.

Immunohistochemistry (IHC)
PD-L1 SP142 FDA (TECENTRIQ®) for NSCLC

The VENTANA PD-L1 (SP142) Assay is a qualitative immunohistochemical assay using rabbit monoclonal anti-PD-L1 clone SP142 intended for use in the assessment of the PD-L1 protein in formalin-fixed, paraffin-embedded (FFPE) non-small cell lung cancer (NSCLC) tissue on a VENTANA BenchMark ULTRA instrument.Evaluation is based on either the proportion of tumor area occupied by PD-L1 expressing tumor-infiltrating immune cells (% IC) of any intensity or the percentage of PD-L1 expressing tumor cells (% TC) of any intensity. Primary or metastatic NSCLC tissues may be submitted. For bladder cancer, please order PD-L1 SP142 FDA (TECENTRIQ®) for Urothelial Carcinoma.

Immunohistochemistry (IHC)
PD-L1 SP142 FDA (TECENTRIQ®) for Urothelial Carcinoma

The VENTANA PD-L1 (SP142) Assay is a qualitative immunohistochemical assay using rabbit monoclonal anti-PD-L1 clone SP142 intended for use in the assessment of the PD-L1 protein in formalin-fixed, paraffin-embedded (FFPE) urothelial carcinoma tissue on a VENTANA BenchMark ULTRA instrument. Evaluation is based on the proportion of tumor area occupied by PD-L1 expressing tumor-infiltrating immune cells (% IC) of any intensity. Primary or metastatic urothelial carcinoma (bladder cancer) Primary or metastatic NSCLC tissues may be submitted.  For non-small cell lung cancer, please order PD-L1 SP142 FDA (TECENTRIQ®) for NSCLC.

Immunohistochemistry (IHC)
PD-L1 SP263 FDA (IMFINZI™)

The VENTANA PD-L1 (SP263) assay is an FDA-approved complementary diagnostic IHC test for PD-L1 status in patients with locally advanced or metastatic urothelial carcinoma (mUC) who are being considered for treatment with  IMFINZI™ (durvalumab). This is a qualitative immunohistochemical assay using rabbit monoclonal anti-PD-L1 clone SP263 intended for use in the assessment of the PD-L1 protein in formalin-fixed, paraffin-embedded (FFPE) urothelial carcinoma tissue stained with OptiView DAB IHC Detection Kit on a VENTANA BenchMark ULTRA instrument. PD-L1 high expression status as determined by this assay was associated with increased objective response rate (ORR) in a single arm study of durvalumab.

Reference: PD-L1 SP263 Assay [package insert]. Tucson, AZ: Ventana Medical Systems, Inc.; 1014737US Rev A; 2017-04-21
Immunohistochemistry (IHC)
PDGFRA Amplification

Probes: PDGFRA (4q12) | Centromere 4
Disease(s): Brain cancer

FISH
PDGFRa Mutation Analysis

Bi-directional sequencing of exons 12 and 18 of the PDGFRA (platelet-derived growth factor alpha) gene. These exons are mutation hotspots that account for the majority of PDGFRA mutations detected in gastrointestinal stromal tumors (GISTs) including the common TKI-resistance mutation D842V. Solid tumor enrichment is performed before extraction.

Molecular
Periodic Acid Schiff (PAS)- Non HEMESpecial stain. Immunohistochemistry (IHC)
PgR

Progesterone Receptor (PR) belongs to a superfamily of nuclear hormone receptors. Estrogen Receptor (ER) induces PR expression, therefore, PR status serves as an indicator of an intact ER pathway. There are two known isoforms of PR; PRα and PRß. The current assays in clinical breast cancer measure both isoforms. PR is expressed in about 60-70% of invasive breast cancers. It is a weak prognostic factor by itself but a modest predictive factor that adds to the predictive value of ER for response to endocrine therapies, both in adjuvant and metastatic settings. The primary indication to assess PR in breast cancer is to predict response to hormonal therapies, such as tamoxifen, other selective estrogen receptor modulators (SERMs) and aromatase inhibitors.

Immunohistochemistry (IHC)
pHistone H3 (PHH3)Phosphohistone H3 (PHH3) is a marker of cells in the late G2-M phase of the cell cycle. It is not expressed in apoptotic cells which may be confused with mitotic figures on a routine H&E stained slide. PHH3 can be used as a surrogate of mitotic activity or as an independent prognostic marker in breast carcinomas. Immunohistochemistry (IHC)
PIK3CA Mutation Analysis

Bi-directional sequencing of PIK3CA exons 1, 9, and 20 which are the most commonly-mutated regions of the gene.

Molecular
PLAPNormally human Placental Alkaline Phosphatase (PLAP) is produced by syncytiotrophoblasts after the twelfth week of pregnancy. PLAP is expressed by both malignant somatic and germ cell tumors. PLAP can be useful in distinguishing seminoma and embryonal carcinomas from undifferentiated malignant tumors. Immunohistochemistry (IHC)
PMS2PMS2, also known as PMS1 protein homologue 2, is a DNA mismatch repair (MMR) protein. The PMS2 protein forms a heterodimer with the MLH1 protein which is then activated in the presence of ATP; this complex coordinates the binding of other proteins that repair DNA errors arising during cell preparation for cell division.
The loss of PMS2 expression in tumors can be helpful in identifying hMLH1 mutation carriers. PMS2 gene defects account for a small but significant proportion of colorectal cancers and for a substantial proportion of tumors with microsatellite instability.
Immunohistochemistry (IHC)
Pneumocystis Carinii ( Jiroveci)This antibody is specific to P. carinii (P. Jiroveci). It stains P. carinii distinctly. The staining pattern is visualized as homogeneous rings corresponding to individual cyst walls. In addition, free extra-cystic P. carinii (trophozoites) are stained. Immunohistochemistry (IHC)
PPM1D Mutation Analysis

PPM1D (Protein Phosphatase, Mg2+/Mn2+ Dependent 1D) Mutation Analysis is performed by next-generation sequencing (NGS) of all coding regions of the PPM1D gene. Germline and somatic mutation testing is available. Note: For germline testing (blood sample), patient and physician or genetic counselor signatures on the NeoGenomics Consent for Hereditary Cancer Genetic Testing form are required. Testing will be put on hold until signatures are received.

Molecular
ProlactinProlactin is a growth factor secreted by the anterior pituitary that is necessary for the proliferation and differentiation of the mammary glands. Prolactin antibody is useful in the identification of prolactin in pituitary adenomas. Immunohistochemistry (IHC)
Prostate Triple StainThe combination of p63 + CK HMW + P504S (PIN-4 cocktail) can be extremely useful for diagnosing prostatic intraepithelial neoplasia (PIN) and/or prostate carcinoma, especially in difficult cases with limited tissue. P504 stains (cytoplasm red) prostate adenocarcinoma and atypical adenomatous hyperplasia. p63 (nuclear brown) and cytokeratin high molecular weight (HMW, cytoplasmic brown) stain basal cells of all normal (negative markers) and benign prostate glands. Immunohistochemistry (IHC)
PSAProstate specific antigen (PSA) is a glycoprotein with a molecular weight of 33-34kDa. It is restricted to the cytoplasm of acinar and ductal epithelia of normal, benign or malignant prostate tissue. Furthermore, PSA from prostatic cancers has been shown to be immunologically and biochemically similar to that of normal prostate tissue. The antibody reacts against primary and metastatic prostatic neoplasms, but not against tumors of non-prostatic origin. This antibody is useful for determining if an isolated metastasis is of prostatic origin. Immunohistochemistry (IHC)
PSAP/HPAPProstate specific acid phosphatase/human prostatic acid phosphatse (PSAP/HPAP) is a 100kDa glycoprotein present in high concentration in the prostate gland and its secretions. PSAP is specific to the benign or malignant epithelial cells of the prostate gland. Prostatic stroma, urethra and the basal cells stain negatively. Also, epithelial cells injured due to inflammation, infarction, etc. and areas of squamous metaplasia of the prostatic acini show loss of PSAP activity. Nearly all metastases of prostatic carcinoma, irrespective of site, demonstrate PSAP immunoreactivity. Immunohistochemistry (IHC)
PSMAProstate specific membrane antigen (PSMA) is a 750 amino acid type II membrane glycoprotein with folate hydrolase and neuropeptidase activity. PSMA is expressed in normal and malignant prostatic epithelium and in a subset of non-prostatic tissues. In prostate cancer, PSMA expression has been shown to correlate with disease progression, with the highest levels expressed in hormone-refractory and metastatic disease. PSMA expression has also been reported on the neovasculature of a variety of non-prostatic solid tumors. Immunohistochemistry (IHC)
PTEN

Probes: PTEN (10q23) | GRID1 (10q23.2) | Centromere 10
Disease(s): Prostate cancer, melanoma, squamous cell carcinoma of the head and neck (PTEN deletions)
This test may be ordered separately or as part of the NeoTYPE Solid Tumor Profiles (Breast, Colorectal, Gastric, Lung, Other)

FISH
PTEN Mutation Analysis

Bi-directional sequencing of all exons (1-9) of the PTEN gene. For solid tumors, enrichment is performed before extraction. This assay does not detect large deletions.

Molecular
PTHParathyroid hormone (PTH) is expressed in normal parathyroid, parathyroid adenomas and primary and secondary hyperplasia of parathyroid. This antibody is useful in the differential diagnosis of autoimmune disorders involving parathyroid gland resulting in the production of anti-PTH & hypo-parathyroidism. Immunohistochemistry (IHC)
RAS/RAF Panel

The RAS/RAF Panel is an NGS-based assay performed by sequencing the entire coding region (full gene) of BRAF, HRAS, KRAS and NRAS genes. The panel reports mutations detected in the full gene including mutations in the most common hotspots, if present. The common hotspots include KRAS (exons 2-4, including codons 12, 13, 59, 61, 117, and 146), NRAS (exons 2-4, including codons 12, 13, 59, 61, 117, and 146), HRAS (exons 2-3, including codons 12, 13, 59, and 61), and BRAF (exons 11, 15 including codon V600).

Molecular
RCC1In normal kidney, renal cell carcinoma (RCC1, gp200) is localized along the brush border of the proximal tubule. In other normal tissues, RCC is also localized along the luminal surfaces of breast lobules and ducts, the luminal surface of the epididymal tubular epithelium, within the cytoplasm of parathyroid parenchymal cells and focally within the colloid of thyroid follicles. Other normal tissues do not express similar or cross-reacting antigens. RCC1 is expressed by most primary and metastatic renal cell carcinomas. Immunohistochemistry (IHC)
RET FISHProbes: RET (10q11.2)
Disease(s): Lung cancer, thyroid cancer
FISH
ROS1ROS1 gene rearrangements are reported in 1% to 2% of lung adenocarcinomas and are associated with a response to the multi-targeted tyrosine kinase inhibitor crizotinib. ROS1 rearrangement can be detected by using IHC for ROS1 protein as an alternate screening test. We recommend that any positive results be confirmed by ROS FISH studies. Immunohistochemistry (IHC)
ROS1Probes: ROS1 (6q22.1)
Disease(s): Non-small cell lung carcinoma (NSCLC)
FISH
RRM1

RRM1 is crucial for DNA synthesis and damage repair. High levels of RRM1 are associated with G2 cell cycle arrest and increased apoptosis in vitro.

Immunohistochemistry (IHC)
S100S100 belongs to the family of calcium binding proteins. Antibody to S100 stains Schwannomas, ependymomas, astrogliomas, almost all benign melanocytic lesions, melanomas and their metastases. S100 protein is also expressed in the Langerhans cells in skin and interdigitating reticulum cells in the paracortex of lymph nodes. Immunohistochemistry (IHC)
S100pExpression of S100P, a member of the S100 family, is increased in a number of tumors, including pancreas, lung, breast, and ovary carcinomas. S100P can be seen in many pancreatic ductal carcinoma, and it displays no staining in the benign pancreatic ducts and acinar glands. Immunohistochemistry (IHC)
SAT B2SATB2 stains colonic and osteogenic cells and their neoplasms. Immunohistochemistry (IHC)
SF1SF1 is expressed in all steroidogenic tissues, including the adrenal cortex, testicular Sertoli cells, and Leydig cells, ovarian theca, hypothalamus, and anterior pituitary. SF1 is highly valuable marker to determine adrenocortical origin. Immunohistochemistry (IHC)
SMMHCSmooth Muscle Myosin, Heavy Chain (SMMS-1) is an antibody to smooth muscle myosin, heavy chain that reacts with human visceral and vascular smooth muscle cells. The antibody also reacts with human myoepithelial cells. It is very helpful in distinguishing between benign sclerosing breast lesions and infiltrating carcinomas in difficult cases since it strongly stains the myoepithelial layer in the benign lesions while it is negative in the infiltrating carcinomas. Immunohistochemistry (IHC)
SmoothelinSmoothelin is a novel cytoskeletal protein that reacts with the 59 kDa and 100 kDa proteins corresponding to Smoothelin A and B, respectively, which are exclusively found in smooth muscle cells (SMC). Cells with SMC-like characteristics, such as myofibroblasts and myoepithelial cells, as well as skeletal and cardiac muscle do not contain Smoothelin. Smoothelin is exclusively expressed in fully differentiated (contractile) smooth muscle cells and could be used as a tool to differentiate muscularis propria from muscularis mucosa. Immunohistochemistry (IHC)
SomatostatinSomatostatin is a useful marker of D-cells of pancreatic islet cells. D-cells are used to identify hyperplasia of the pancreatic islets. Most of these tumors are malignant, giving rise to somatostatinomas. Somatostatin suppresses gastric acid secretion, gallbladder contractions and pancreatic insulin secretion; therefore, the most common clinical manifestations of patients with these tumors are mild diabetes. Immunohistochemistry (IHC)
SOX10SOX10 is a sensitive marker of melanoma, including conventional, spindled, and desmoplastic subtypes. It is also a useful marker in detecting both the in situ and invasive components of desmoplastic melanoma. SOX10 is diffusely expressed in schwannoma, neurofibroma, and granular cell tumor. SOX10 was not identified in any other mesenchymal and epithelial tumors except for myoepitheliomas and diffuse astrocytomas. Immunohistochemistry (IHC)
SOX2SOX2 stains all embryonal carcinomas and is highly specific for squamous cell carcinoma. Immunohistochemistry (IHC)
SS18 (SYT)Probes: SS18 (SYT) (18q11.2)
Disease(s): Synovial sarcoma
FISH
Standard Leukemia/Lymphoma Panel - 24 markers

Available as global and tech-only. Markers are CD2, CD3, CD4, CD5, CD7, CD8, CD10, CD11c, CD13, CD14, CD16, CD19, CD20, CD23, CD33, CD34, CD38, CD45, CD56, CD64, CD117, HLA-DR, kappa, and lambda.

Flow Cytometry
STAT3 Mutation Analysis

Bi-directional sequencing of STAT3 exons 13-21 encompassing the DNA binding and SH2 domains.

Molecular
STAT6STAT6 is a highly sensitive and specific immunohistochemical marker for solitary fibrous tumor (SFT) and can be helpful to distinguish this tumor type from histologic mimics. Immunohistochemistry (IHC)
SurfactantPulmonary surfactant apoproteins play essential roles in keeping alveoli from collapsing at the end of expiration. SP-A is located mainly in type II pneumocytes and has been demonstrated in bronchiolo-alveolar carcinomas and adenocarcinomas of the lung. Mesotheliomas show no positive staining with this antibody. Surfactant can be helpful in the differential diagnosis of pulmonary adenocarcinomas and mesotheliomas. Immunohistochemistry (IHC)
SynaptophysinAntibody to synaptophysin reacts with neuroendocrine neoplasms of neural as well as epithelial types. In combination with chromogranin A and NSE antibodies, the antibody to synaptophysin is very useful in the identification of normal neuroendocrine cells and neuroendocrine neoplasms. Immunohistochemistry (IHC)
TERT Promoter Mutation AnalysisBi-directional Sanger sequencing is performed using PCR primers designed to target mutations in the promoter region of TERT. Molecular
TFE3Overexpression of TFE3 is a sensitive and specific marker of Xp11 translocation in renal cell carcinomas. TFE3 is also expressed in alveolar soft part sarcoma the hallmark of which is a chromosomal rearrangement at 17q25 and Xp11.2 engendering an ASPSCR1–TFE3 fusion gene. Use of this antibody is an aid in the recognition of Xp11 translocation renal cell carcinoma and alveolar soft part sarcoma within the context of an antibody panel. Immunohistochemistry (IHC)
Thrombomodulin (TM)Thrombomodulin (TM) is a plasma membrane-related glycoprotein that has anticoagulant activity. TM antigen is found in several cell types, including megakaryocytes, mesangial cells, synovial cells, mesothelial cells, endothelial cells, and some squamous epithelial cells and their associated tumors. TM antibody labels most mesotheliomas with thick membranous staining pattern and about half of pulmonary adenocarcinomas, showing cytoplasmic immunostaining. Thrombomodulin is also a marker of urinary bladder epithelium. Immunohistochemistry (IHC)
Thyroglobulin (TGB)This antibody labels thyroglobulin (TGB) in follicular epithelial cells of the thyroid and colloid. Thyroglobulin antibody is useful in positive identification of thyroid carcinomas of the papillary and follicular types. Demonstration of thyroglobulin in a metastatic lesion establishes the thyroid origin of the tumor. Immunohistochemistry (IHC)
TLE1Expression of the transducing-like receptor (TLE) genes, TLE1, TLE2, TLE3 and TLE4, correlate with immature epithelial cells that are progressing toward a terminally differentiated state. TLE1 antibody is an excellent discriminator of synovial sarcoma from other sarcomas, including histologically similar tumors such as malignant peripheral nerve sheath tumor. Immunohistochemistry (IHC)
TOP2AProbes: TOP2A (17q21-q22) | Cen 17 (17p11.1-q11.1)
Disease(s): Breast cancer
Note: Available as a global test only.
FISH
TOPO1

Topoisomerase I (TOPO1)  is essential nuclear enzyme for replication and transcription during cell reproduction and DNA repair. Upregulation of TOPO1 increases with disease stage in colorectal and pancreatic cancers.

Immunohistochemistry (IHC)
TP53 Mutation Analysis

Bi-directional sequencing of TP53 exons 4-9.

Molecular
TrichromeSpecial stain. Trichrome stains are frequently used to differentiate between collagen and smooth muscle in tumors and to identify increases in collagenous tissue in diseases such as cirrhosis of the liver. Immunohistochemistry (IHC)
TryptaseThis antibody labels a mast cell tryptase. It will also show reactivity to basophils, but to a lesser degree. Immunohistochemistry (IHC)
TSHThyroid Stimulating Hormone (TSH) is a pituitary hormone of 28 kDa that stimulates thyroid growth and production of thyroid hormones. This antibody labels thyrotropic cells of the pituitary and may be useful in the classification of pituitary adenomas and the differential identification of primary and metastatic tumors of the pituitary. Immunohistochemistry (IHC)
TTF1Thyroid Transcription Factory (TTF1) is found only in thyroid and thyroid tumors regardless of histologic type, as well as in lung carcinomas, including adenocarcinomas, non-small cell carcinomas, neuroendocrine and small cell carcinomas, and squamous cell carcinomas. The utility of TTF1 becomes apparent in the differential diagnosis of primary versus metastatic carcinomas, especially in the lung. Immunohistochemistry (IHC)
Tumor Mutation Burden

Tumor Mutation Burden (TMB) testing at NeoGenomics measures the number of non-synonymous DNA coding sequence changes per megabase of sequenced DNA. Testing is performed routinely within the NeoTYPE™ Discovery Profile, can be added to any of the NeoTYPE Solid Tumor Profiles, and is available as a stand-alone test. Results are reported as low, high intermediate, and high upper quartile in reference to the median genomic TMB value determined across a wide variety of tumor types in an internal validation study. TMB is also called tumor mutational burden or tumor mutation load (TML). 

Molecular
TyrosinaseTyrosinase is a copper-containing metalloglycoprotein that catalyzes several steps in the melanin pigment biosynthetic pathway. Mutations of the tyrosinase gene occur in various forms of albinism. Tyrosinase is one of the targets for cytotoxic T-cell recognition in melanoma patients. Staining of melanomas with this antibody showed tyrosinase in melanotic as well as amelanotic variants. Immunohistochemistry (IHC)
UGT1A1 Genotyping

Lengths of the TA repeat polymorphism in the promoter region of the UTG1A1 gene are determined by fragment analysis using capillary electrophoresis. The alleles detected include the common normal allele *1 (with 6 TA repeats) and the common abnormal allele *28 (7 repeats). The patient's genotype is reported along with the associated high, intermediate, or low risk for toxicity from the drug irinotecan (Camptosar®).

Molecular
Universal Fusion/Expression Profile

The Universal Fusion/Expression Profile is a targeted RNA sequencing panel that utilizes next-generation sequencing (NGS) to detect all relevant fusion transcripts in 1,385 genes associated with hematologic or solid tumor cancers. It is especially useful for testing patients with rare diseases. Learn more about the Universal Fusion/Expression Profile. See the full 1,385 gene list here.

Molecular
Uroplakin IIUroplakin II is a 15 kDa protein component of urothelial plaques. Uroplakin II mRNA was found in both bladder cancer tissues and peripheral blood of patients with primary and metastatic urothelial carcinoma of the bladder. Uroplakin II antibody [BC21] is a highly specific antibody that may be useful in identifying tumors of urothelial origin. Immunohistochemistry (IHC)
VillinThis antibody recognizes villin, a cytoskeletal filament protein of 58 kDa found in human renal epithelial cells. Villin antibody is useful for the study of gastrointestinal cells in normal and tumor tissues. Immunohistochemistry (IHC)
VimentinVimentin is the major intermediate filament in a variety of mesenchymal cells, including endothelial cells, all fibroblastic cells, macrophages, Sertoli cells, melanocytes, lymphocytes and ovarian granulosa cells. Vimentin is found in all types of sarcomas and lymphomas. Positive staining for vimentin is seen in most cells of fibrosarcomas, liposarcomas, malignant fibrous histocytomas, angiosarcomas, chondrosarcomas and lymphomas. All melanomas and Schwannomas are strongly vimentin-positive. Immunohistochemistry (IHC)
Warthin StarrySpecial stain. Warthin Starry stain is intended to identify Helicobacter pylori in tissue samples. Immunohistochemistry (IHC)
WT1Wilms tumor susceptibility gene 1 protein (WT1) has diagnostic utility in the distinction of mesothelioma from adenocarcinoma in tissue sections of pleural tumors. WT1 diffusely stains most ovarian serous carcinomas and all Wilms tumors. Immunohistochemistry (IHC)
X/Y FISH for Molar Pregnancy

Probes: Centromere X | Centromere Y
Note: Testing is performed only on a global basis at this time.
Disease(s): Molar pregnancy (hydatidiform mole), partial mole, triploidy

FISH