Quick-Single Nucleotide Polymorphism (Quick-SNP)

Lynntech Inc. proposes a Phase I SBIR effort to develop Quick-Single Nucleotide Polymorphism (Quick-SNP), a forensic software tool for pedigree reconstruction. Quick-SNP will analyze naïve DNA profiles, and in the process, establish sample identities, predict familial relationships (kinship and ancestral), and ultimately provide phenotypic profiles. Lynntech will develop Quick-SNP with a computational architecture that is efficient and capable of scaling to DNA profiles created by ever-increasing deep genomic sequencing techniques. Deep-sequencing makes it possible to combine useful SNP variants, routinely used for the rapid identification of close relatedness within a database, with additional statistical information. SNPs can be used to reconstruct Identity-by-Descent (IBD) relationships in pedigree reconstructions, thus providing estimates of kinship. In discussion with the DTRA, databases will be selected that model a wide variety of regional specific SNP profiles, along with databases that can be used to model deeper IBD characteristics. In addition, detailed requirements will be established, including the criteria for ancestry-estimation, proper security procedures to be established, user interface needs, and performance, facilities and hardware requirements. At the completion of Phase I, Lynntech will provide a final report and demonstrate the preliminary architecture to the cognizant project officer. The final report will include an analysis of the architecture performance using unambiguous statistical methods, a description of the system parameterization, and a thoughtful discussion of the limitations and weaknesses of the approach. The report will also include Lynntech’s plans for the development, during Phase II, of Quick-SNP’s user interface.