Assessing reproducibility of inherited variants detected with short-read whole genome sequencing

Published

January 4, 2022

Author(s)

Justin Zook, Huixao Hong, Bohu Pan, Chunlin Xiao, Leming Shi

Abstract

Background Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant call quality. Systematically assessing reproducibility of inherited variants with WGS and impact of each step in the process is needed for understanding and improving quality of inherited variants from WGS. Results To dissect the impact of factors involved in detection of inherited variants with WGS, we sequence triplicates of eight DNA samples representing two populations on three short-read sequencing platforms using three library kits in six labs and call variants with 56 combinations of aligners and callers. We find that bioinformatics pipelines (callers and aligners) have a larger impact on variant reproducibility than WGS platform or library preparation. Single-nucleotide variants (SNVs), particularly outside difficult-to-map regions, are more reproducible than small insertions and deletions (indels), which are least reproducible when > 5 bp. Increasing sequencing coverage improves indel reproducibility but has limited impact on SNVs above 30×. Conclusions Our findings highlight sources of variability in variant detection and the need for improvement of bioinformatics pipelines in the era of precision medicine with WGS.

Citation

Genome Biology

Volume

23

Pub Type

Journals

Download Paper

https://doi.org/10.1186/s13059-021-02569-8

Local Download

Keywords

DNA sequencing, human genomics, interlaboratory study

Citation

Zook, J. , Hong, H. , Pan, B. , Xiao, C. and Shi, L. (2022), Assessing reproducibility of inherited variants detected with short-read whole genome sequencing, Genome Biology, [online], https://doi.org/10.1186/s13059-021-02569-8, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=930300 (Accessed October 6, 2025)