112 105

Cited 0 times in

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

Authors
 Jeong Hoon Lee  ;  Solbi Kweon  ;  Yu Rang Park 
Citation
 SCIENTIFIC REPORTS, Vol.11(1) : 2268, 2021-01 
Journal Title
SCIENTIFIC REPORTS
Issue Date
2021-01
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 HaplotypeCaller, VarScan, and MuTect2 found 25,130, 16,972, and 4232 variants, comprising 1491, 1400, and 321 annotated variants with ClinVar significance, respectively. The average number of ClinVar significant variants in the patients was 769.43, 16.50% of the variants were detected by only one variant caller. Despite variants with significant impact on clinical decision-making, the detected variants are different for each algorithm. To utilize genetic variants in the clinical field, a strict standard for NGS pipelines is essential.
Files in This Item:
T202102945.pdf Download
DOI
10.1038/s41598-021-82006-9
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Biomedical Systems Informatics (의생명시스템정보학교실) > 1. Journal Papers
Yonsei Authors
Park, Yu Rang(박유랑) ORCID logo https://orcid.org/0000-0002-4210-2094
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/184381
사서에게 알리기
  feedback

qrcode

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

Browse

Links