Amplicon Sequencing, Deep Sequencing, Targeted Resequencing & SNP Genotyping

NeoGenomics provides targeted sequencing services and genomic enrichment using the customizable targeted amplicon workflows of Illumina TruSeq™ and Life Technologies' Ion AmpliSeq™ as well as the leading Target Capture technologies. Customers can select their genes, exons or regions of interest or take advantage of the various gene panels offered. Leveraging these technologies, deep sequence coverage can be obtained within your regions of interest, allowing you to maximize platform throughput. These technologies enhance variant detection or SNP genotyping capabilities while maximizing cost-efficiency.

Please contact us to discuss your project needs and receive a recommendation on which technology is optimal for your project.

Amplicon Sequencing Workflow:

Choose Amplion for Sequencing
Multiplex Samples. Barcode Library Prep
Pool Sequence  and Data Analysis
Variant Detection

Next Generation Platforms Compatible With our Amplicon Sequencing:

  • Illumina MiSeq™
  • Illumina HiSeq
  • Ion Torrent Proton
  • Ion Torrent PGM™

Each of the above systems has strengths which lend themselves to certain types of projects. Please contact one of our representativesand provide them with the details of your project so that we may recommend a solution which will achieve your goals in the most efficient manner possible.


The applications of cutting-edge amplicon sequencing technology combined with next generation genomics are as broad as they are powerful. They enable the average researcher to take on projects from multifactorial diseases studies to the analysis of multiple gene sets involved in specific disease-relevant pathways. General applications of these technologies include:

  • Resequencing of Exonic Regions
  • Polygenic Disease Studies
  • Genetic Marker Development
  • Large Genomic Loci Resequencing
  • Resequencing of Candidate Gene Sets
  • Metabolic Pathway Studies
  • SNP Genotyping
    • Detection of low-frequency mutations comprising as low as 5% of the population without subcloning
    • Mixtures with mutations below 5% can be detected using subcloning strategies
    • DNA extraction from paraffin-embedded tissue
    • Detection and de-convolution of hetero-indel profiles*
    • Whole Genome Amplification (WGA) for low sample quantities
    • CLIA certified for handling patient samples

*Heterozygote insertion-deletions (indels) are detected by a data frame-shift and the loss of signal quality at the mutation boundary. The 5% threshold applies. The de-convoluted hetero-indel peak profiles are included in the final report.

Bioinformatics and Deliverables

Identifying sequence variants (SNPs and InDels) is very important for clinicians to make decisions regarding the diagnosis of patients with genetic disease. NeoGenomics can use a variety of open source software such as SAMTOOLS and snpEff to identify and annotate variants in captured DNA sequences. Along with its targeted resequencing capabilities and amplicon sequencing services, NeoGenomics can provide its customers with industry-leading DNA capture technologies as well as comprehensive bioinformatics support. With all of these tools in hand, our customers can focus on using their results to identify variations related to disease-causing protein structural and functional changes. The following files will be provided with your DNA-Seq project:

  • Sorted-NoDup.bam: This file contains information about sequence alignment
  • Sorted-NoDup.bam.bai: This is the index file for sorted.bam. Users can load both the sorted.bam and sorted.bam.bai files into software such as Integrative Genomic View to view the variants detected.
  • Var.vcf: This file contains all the variants and their annotations. The file is in standard Variant Call Format (.vcf). Users can open this file with WordPad

 More info on Bioinformatics and Data Analysis