Literature DB >> 27311679

Comparison of genome sequencing and clinical genotyping for pharmacogenes.

W Yang1, G Wu2, U Broeckel3, C A Smith1, V Turner4, C E Haidar1, S Wang2, R Carter2, S E Karol1, G Neale5, K R Crews1, J J Yang1, C G Mullighan4, J R Downing4, W E Evans1, M V Relling6.   

Abstract

We compared whole exome sequencing (WES, n = 176 patients) and whole genome sequencing (WGS, n = 68) and clinical genotyping (DMET array-based approach) for interrogating 13 genes with Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines. We focused on 127 CPIC important variants: 103 single nucleotide variations (SNV), 21 insertion/deletions (Indel), HLA-B alleles, and two CYP2D6 structural variations. WES and WGS provided interrogation of nonoverlapping sets of 115 SNV/Indels with call rate >98%. Among 68 loci interrogated by both WES and DMET, 64 loci (94.1%, confidence interval [CI]: 85.6-98.4%) showed no discrepant genotyping calls. Among 66 loci interrogated by both WGS and DMET, 63 loci (95.5%, CI: 87.2-99.0%) showed no discrepant genotyping calls. In conclusion, even without optimization to interrogate pharmacogenetic variants, WES and WGS displayed potential to provide reliable interrogation of most pharmacogenes and further validation of genome sequencing in a clinical lab setting is warranted.
© 2016 American Society for Clinical Pharmacology and Therapeutics.

Entities:  

Mesh：

Year:  2016        PMID： 27311679      PMCID： PMC5684873          DOI： 10.1002/cpt.411

Source DB:  PubMed          Journal:  Clin Pharmacol Ther        ISSN： 0009-9236            Impact factor:   6.875


  45 in total

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10.  Genome sequencing as a platform for pharmacogenetic genotyping: a pediatric cohort study.

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