Displaying 1 - 89 of 89 tests
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)
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
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)
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)
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)
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
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)
CDKN2A (p16) Deletion for Mesothelioma

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

FISH
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)
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)
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)
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)
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)
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
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 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
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)
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)
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)
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)
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)
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)
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
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
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
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)
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)
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)
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
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 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 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 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
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 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
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
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
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)
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-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)
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 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)
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
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
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)
RET FISHProbes: RET (10q11.2)
Disease(s): Lung cancer, thyroid cancer
FISH
ROS1Probes: ROS1 (6q22.1)
Disease(s): Non-small cell lung carcinoma (NSCLC)
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)
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)
STAT3 Mutation Analysis

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

Molecular
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)
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)
TP53 Mutation Analysis

Bi-directional sequencing of TP53 exons 4-9.

Molecular
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
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
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)