Rare Variant Detection Using Next Genration Sequencing Technology

Award Information
Agency: Department of Homeland Security
Branch: N/A
Contract: D11PC20117
Agency Tracking Number: 1014004
Amount: $750,000.00
Phase: Phase II
Program: SBIR
Awards Year: 2011
Solicitation Year: 2010
Solicitation Topic Code: H-SB010.1-002
Solicitation Number: FY10.1
Small Business Information
750 Alfred Nobel Drive, #108, hercules, CA, 94547-1387
DUNS: 808461664
HUBZone Owned: N
Woman Owned: N
Socially and Economically Disadvantaged: N
Principal Investigator
 Viacheslav Fofanov
 Director of Bioinformatics
 (713) 357-9587
 viacheslav@eurekagenomics.com
Business Contact
 Didier Perez
Title: COO & CFO
Phone: (415) 269-0666
Email: didier@eurekagenomics.com
Research Institution
N/A
Abstract
The long-term objective is to develop a rare variant (SNPs) detection pipeline, based on high throughput sequencing (HTS) and advanced bioinformatics, with the goal of detecting mutations present in ratio as low as 1:1000. To achieve this goal, we propose to: (1) Develop statistical and computational approaches to evaluate the effects of sequencing platform, target genome, and mapping algorithm on the accuracy of the rare variant detection. (2) Implement and deliver rare variant detection pipeline. (3) Experimentally validate the implemented rare variant detection pipeline, culminating a full scale B. anthracis case study. (4) Develop a software application to automatically acquire defined in task 1 statistical characteristics of errors associated with instruments, platforms, library preparation protocols, and sequencing chemistry, which can affect the overall accuracy of the rare variant detection. Rare variant detection is important for prosecution of bioterrorism attacks or attempts. While, the commercial opportunity of the forensic application is unknown, the commercial applications in clinical diagnostics associated with the detection of drug resistant variants such as diagnostic test to identify the presence of multi- or extensively- drug resistant tuberculosis present in less than 1 percent of the sample are significant.

* Information listed above is at the time of submission. *

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