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Award Information
Proposal Number: 1011114
Proposal Title: Utility of Next Generation Sequencing Data for Rare Variant Detection and Identification in a Bacterial Sample
Topic Number: H-SB010.1-002
Phase: Phase I
Topic Title: Rare Variant Detection Using Next Generation Sequencing Technology
Organization: Eureka Genomics
Address: 750 Alfred Nobel Drive, #108
hercules, CA 94547-1387  
Abstract: The long-term objective is to develop a statistically sound rare variant (SNPs) detection and SNP profile comparison method, based on high throughput sequencing (HTS) and advanced bioinformatics, that is capable of detecting a mutations present in as low as 1/5000 bacterial cells in the sample. This will be accomplished in five tasks: (1) Develop and test a statistical model to predict sample coverage required to detect SNPs in a strain of given rarity with pre-specified level of confidence. (2) Determine the ability to use HTS reads to assign SNPs to correct rare variants (3) Quantify the effect of limitations of the sequencing platform on rare variant detection (4) Develop a statistical framework to compare SNP profiles, (5) Develop a research plan for phase II. Rare variant detection and matching will be important for prosecution of bioterrorism attacks or attempts. The commercial opportunity of the forensic application is unknown, but commercial applications in clinical diagnostics associated with the detection of drug resistant variants are extensive. There is an urgent need (estimated 100M USD US market annually) for a diagnostic test to identify the presence of multi- or extensively- drug resistant tuberculosis present in 1 percent or less of the sample.
Award/Contract Number: N10PC20199
Period of Performance: 05/17/2010 - 11/30/2010
Award/Contract Value: $100,000.00
Award/Obligated Amount: $100,000.00