絞り込み

16735

広告

VarCover: Allele Min-Set Cover Software.

著者 Scott ER , Bansal V , Meacham C , Scott SA
J Mol Diagn.2019 Nov 18 ; ():.
この記事をPubMed上で見るPubMedで表示
この記事をGoogle翻訳上で見る Google翻訳で開く

スターを付ける スターを付ける     (2view , 0users)

Full Text Sources

To facilitate reference material selection for clinical genetic testing laboratories, we developed VarCover, open-source software hosted on GitHub, which accepts a file of variants (rsIDs or VCF) and returns an approximately minimal set of samples covering the targeted alleles. VarCover employs the SetCoverPy package, sample weights, and pre-selection of singleton-possessing samples to efficiently solve the min-set cover problem. As a test case, we attempted to find a minimal set of 1000 Genomes (1KG) Project reference samples to cover 237 putatively pathogenic variants (of which 12 were pathogenic or likely pathogenic) in the original 56 medically actionable genes recommended by the American College of Medical Genetics and Genomics (ACMG). The number of samples, number of alleles, and processing time was measured for subsets of the 237 target alleles. VarCover identified 140 reference material 1KG samples covering the 237 alleles in the 56 ACMG genes. Sample weights derived from the minor allele frequency spectrum increased the number of alleles in the solution set. Pre-selection of samples possessing singleton target alleles reduced computational processing time when the target set size exceeded 100 alleles. VarCover provides a simple programmatic interface to identify an approximately minimal set of reference samples thereby reducing clinical laboratory effort and molecular genetic test validation costs.
PMID: 31751680 [PubMed - as supplied by publisher]
印刷用ページを開く Endnote用テキストダウンロード