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Bioinformatics Services

Analysis solutions for insights from genomic data

Genomic Alterations – DNA & RNA

A comprehensive understanding of the genomic alterations found in your sample is critical to understanding your disease of interest. Q2 Solutions | EA Genomics has various solutions to help maximize the full value out of your data.

Solutions
SNPs and Indels – Germline, Tumor-normal, Tumor-only*
Copy Number Alterations – Germline, Somatic
Structural Variants
TMB
Neoantigen
Fusions
RNA SNPs and Indels – Germline and Somatic*
RNA TMB*
*Inquire on availability
  • DNA variant calling is offered across a variety of service types, ranging from small targeted panels on Thermo-Fisher sequencing instruments to Whole Genome Sequencing done on Illumina instruments.
  • Our proprietary WES TMB algorithm is one of the few in the industry that can operate with or without a matched normal pair.
  • The neoantigen pipeline provides a priority list of candidate targets, assembled by combining our high confidence variant calling with gene expression data.
  • Our proprietary Gene Fusion algorithm (STAR-SEQR) is among the most accurate and sensitive algorithms on the market.
  • We utilize novel strategies to mitigate the complications associated with RNA Seq variant calling to accurately call variants.

Sensitivity of Gene Fusion Identification

Program TP FP Sensitivity
STAR-SEQR(v0.6.3) 49 0 98%
Pizzly(v0.37.3) 45 2 90%
STAR-Fusion(v.0.8.0) 44 1 90%
JAFFA(v1.07) 43 0 86%
MapSplice(v2.2.1) 42 1 84%
FusionMap(2015-3-31) 36 0 72%
defuse(v0.6.2) 35 1 70%
FusionCatcher(v0.99.6a) 31 0 62%
STAR+OncoFuse(v1.07) 31 0 62%
Tophat-Fusion(v2.0.14) 28 1 56%
FusionHunter(v1.4) 20 6 40%
EricScript(v0.0.5) 39 0 78%

Quantification & Identification

With nearly a decade of NGS experience, Q2 Solutions | EA Genomics has developed tools and procedures for accurate identification and quantification of data.
  • Custom two group comparison methodology providing superior results in comparison to other algorithms publicly available.
  • Our Influenza Sequencing pipeline has been demonstrated to be 100% accurate in strain identification.
  • ERIC certified IgHV analysis pipeline - Q2 Solutions | EA Genomics is currently the only lab in North America with this certification.
  • HLA calling by either RNA Sequencing or DNA Sequencing with equivalent accuracy.

Solutions
Gene and Isoform Quantification
Two Group Comparisons
B-cell and T-cell Repertoire
IgHV Identification
HLA Typing
16S Microbial Sequencing
Flu Strain Identification

Customized Services and Signatures

Q2 Solutions | EA Genomics has extensive experience with custom analyses, including standard Pathway and Gene Set Enrichment Analysis all the way through Biomarker discovery.
  • We can generate customized RNA signatures or replicate published RNA Signatures upon request.
  • Our Immune Landscape Signatures characterize the activity and type of immune cell infiltrate in the tumor.
  • Analysis of treatment response and survival using multiple clinical features or using signatures such as predicted Cytotoxic Immune Infiltration.

Solutions
Biomarker Discovery
RNA signature identification and interpretation
DNA-based signatures and identification
Immune Landscape/Tumor Microenvironment signatures
Gene Set Enrichment Analysis
Pathway Analysis


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