Q2-Header_1280x350_12

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 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 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 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 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

 

Q2 Solutions Paired TMB vs. TCGA Published Values
tmb-vs-tcga-published-values
Q2 Solutions calculated TMB values versus TCGA calculated values for samples across 7 indications

Submit specimens

 

Client login

Q2-Header_1280x350_13

Related Thought Leaders Insights


Bioinformatics Services

As an industry leader, Q2 Solutions offers a range of genomic services to support drug discovery, translational medicine, clinical development, and precision medicine including companion diagnostics....

Bioinformatics and Computational Solutions for Genomic Insights

With over 500 years cumulative expertise in genomics, bioinformatics, and information technologies, we provide infrastructure and consultative services to enable you with the fastest path from sample...

Translating Data into Insights with Bioinformatics

Author:Wendell Jones, Ph.D., Principal Bioinformaticist and Scientific Advisor, Q2 SolutionsBioinformatics is a cross-disciplinary area that requires skills or knowledge in molecular biology,...