PSST: A tool for detecting multiple SNPs in NGS datasets

Authors

• A Vohra
• S La
• C Mashayamombe
• E Marte
• D Thompson
• B Busby

Abstract

SNPs are short -- less than 50 -- nucleotide variations. Some SNPs or combinations thereof cause or predispose individuals to disease. The relationship between highly penetrant SNPs and disease is somewhat straightforward to elucidate, and many independent assertions have been reported in the ClinVar database at NCBI, among others. Relationships between combinations of SNPs and disease are much more difficult to understand, and more technically difficult to define. We have developed Polygenic SNP Search Tool (PSST), software that determines multiple SNPs associated with diseases, including variants that modify the penetrance of others. PSST finds SNP IDs associated with the disease, extracts the flanking sequences, creates BLAST database for those sequences, runs Magic-BLAST into the individual runs in the Sequence Read Archive -- a store of 4 Pb of genomic data -- and calls variants without dumping data. This software can be used for any disease where known variants have been established and there are NGS datasets available. As a proof of principle, we show repeated combinations of variants in breast cancer and age-related macular degeneration. We think this may help to illuminate the relationship between complex variants and human disease.

Scientific Focus Area: Computational Biology

This page was last updated on Friday, March 26, 2021