|Title||PGRNseq: a targeted capture sequencing panel for pharmacogenetic research and implementation.|
|Publication Type||Journal Article|
|Year of Publication||2016|
|Authors||Gordon, AS, Fulton, RS, Qin, X, Mardis, ER, Nickerson, DA, Scherer, SE|
|Date Published||2016 Jan 5|
OBJECTIVES: Although the costs associated with whole-genome and whole-exome next-generation sequencing continue to decline, they remain prohibitively expensive for large-scale studies of genetic variation. As an alternative, custom-target sequencing has become a common methodology on the basis of its favorable balance between cost, throughput, and deep coverage.
METHODS: We have developed PGRNseq, a custom-capture panel of 84 genes with associations to pharmacogenetic phenotypes, as a tool to explore the relationship between drug response and genetic variation, both common and rare. We utilized a set of 32 diverse HapMap trios and two clinical cohorts to assess platform performance, accuracy, and ability to discover novel variation.
RESULTS: We found that PGRNseq generates ultra-deep coverage data (mean=496×) that are over 99.8% concordant with orthogonal datasets. In addition, in our testing sets, PGRNseq identified many novel, rare variants of interest, underscoring its value in both research and clinical settings.
CONCLUSION: PGRNseq is an ideal platform for carrying out sequencing-based analyses of pharmacogenetic variation in large cohorts. In addition, the high accuracy associated with genotypes from PGRNseq highlight its utility as a clinical test.
|Alternate Journal||Pharmacogenet. Genomics|
|PubMed Central ID||PMC4935646|
|Grant List||U19 GM061388 / GM / NIGMS NIH HHS / United States |
U01 GM061388 / GM / NIGMS NIH HHS / United States
U19 HL069757 / HL / NHLBI NIH HHS / United States
R43 HL069579 / HL / NHLBI NIH HHS / United States
U01 HL069757 / HL / NHLBI NIH HHS / United States
U01 GM097119 / GM / NIGMS NIH HHS / United States