Greg Cooper, PhD, Faculty Investigator at HudsonAlpha, received a grant to build a variant catalog from tens of thousands of human genomes. Genome sequencing identifies millions of variants in each person, including many extremely rare variants. Most of these have little to no impact on phenotype. As such, identification of rare, highly penetrant variants that underlie any given Mendelian disease within any given patient is challenging, as many variants must be considered. However, catalogs of variation from unrelated individuals can be used to improve variant interpretation, as any variant at a population frequency that is too high can be filtered away. Dr. Cooper and his team have designed a scalable Mongo database and added allele counts for all variants observed in 6,000 human genomes sequenced by HudsonAlpha’s Genome Sequencing Laboratory. They also developed a pipeline to define a genomic “fingerprint” for each sample to prevent duplicates or closely related samples. Dr. Cooper proposed to expand this pipeline by thousands of genomes sequenced by the GSL, establish a process for regular updates and enable output files.
Dr. Cooper will be supported by computational biologists from HudsonAlpha’s Genome Sequencing Laboratory and David Gray in his laboratory.