Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange.

ABSTRACT: Genetic variants causing underlying pharmacogenetic and disease phenotypes have been used as the basis for clinical decision-making. However, due to the lack of standards for next-generation sequencing (NGS) pipelines, reproducing genetic variants among institutions is still difficult. The aim of this study is to show how many important variants for clinical decisions can be individually detected using different pipelines. Genetic variants were derived from 105 breast cancer patient target DNA sequences via three different variant-calling pipelines. HaplotypeCaller, Mutect2 tumor-only mode in the Genome Analysis ToolKit (GATK), and VarScan were used in variant calling from the sequence read data processed by the same NGS preprocessing tools using Variant Effect Predictor. GATK HaplotypeCal

SUBMITTER: Lee JH 

PROVIDER: S-EPMC7838410 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature