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

Bohu Pan; Luyao Ren; Vitor Onuchic; Meijian Guan; Rebecca Kusko; Steve Bruinsma; Len Trigg; Andreas Scherer; Baitang Ning; Chaoyang Zhang; Christine Glidewell-Kenney; Chunlin Xiao; Eric Donaldson; Fritz J Sedlazeck; Gary Schroth; Gokhan Yavas; Haiying Grunenwald; Haodong Chen; Heather Meinholz; Joe Meehan; Jing Wang; Jingcheng Yang; Jonathan Foox; Jun Shang; Kelci Miclaus; Lianhua Dong; Leming Shi; Marghoob Mohiyuddin; Mehdi Pirooznia; Ping Gong; Rooz Golshani; Russ Wolfinger; Samir Lababidi; Sayed Mohammad Ebrahim Sahraeian; Steve Sherry; Tao Han; Tao Chen; Tieliu Shi; Wanwan Hou; Weigong Ge; Wen Zou; Wenjing Guo; Wenjun Bao; Wenzhong Xiao; Xiaohui Fan; Yoichi Gondo; Ying Yu; Yongmei Zhao; Zhenqiang Su; Zhichao Liu; Weida Tong; Wenming Xiao; Justin M Zook; Yuanting Zheng; Huixiao Hong

doi:10.1186/s13059-021-02569-8

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

Genome Biol. 2022 Jan 3;23(1):2. doi: 10.1186/s13059-021-02569-8.

Authors

Bohu Pan^#¹, Luyao Ren^#^{2

3}, Vitor Onuchic^#⁴, Meijian Guan^#⁵, Rebecca Kusko^#⁶, Steve Bruinsma⁴, Len Trigg⁷, Andreas Scherer^{8

9}, Baitang Ning¹, Chaoyang Zhang¹⁰, Christine Glidewell-Kenney⁴, Chunlin Xiao¹¹, Eric Donaldson¹², Fritz J Sedlazeck¹³, Gary Schroth⁴, Gokhan Yavas¹, Haiying Grunenwald⁴, Haodong Chen¹⁴, Heather Meinholz⁴, Joe Meehan¹, Jing Wang¹⁵, Jingcheng Yang^{2

3}, Jonathan Foox¹⁶, Jun Shang^{2

3}, Kelci Miclaus⁵, Lianhua Dong¹⁵, Leming Shi^{2

3}, Marghoob Mohiyuddin¹⁷, Mehdi Pirooznia¹⁸, Ping Gong¹⁹, Rooz Golshani⁴, Russ Wolfinger⁵, Samir Lababidi²⁰, Sayed Mohammad Ebrahim Sahraeian¹⁷, Steve Sherry¹¹, Tao Han¹, Tao Chen¹, Tieliu Shi²¹, Wanwan Hou^{2

3}, Weigong Ge¹, Wen Zou¹, Wenjing Guo¹, Wenjun Bao⁵, Wenzhong Xiao²², Xiaohui Fan²³, Yoichi Gondo²⁴, Ying Yu^{2

3}, Yongmei Zhao²⁵, Zhenqiang Su²⁶, Zhichao Liu¹, Weida Tong¹, Wenming Xiao²⁷, Justin M Zook²⁸, Yuanting Zheng^{29

30}, Huixiao Hong³¹

Affiliations

¹ Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
² State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.
³ Human Phenome Institute, Fudan University, Shanghai, 200438, China.
⁴ Illumina Inc., San Diego, CA, 92122, USA.
⁵ SAS Institute Inc., Cary, NC, 27513, USA.
⁶ Immuneering Corporation, Cambridge, MA, 02142, USA.
⁷ Real Time Genomics, Hamilton, New Zealand.
⁸ Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
⁹ EATRIS ERIC- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands.
¹⁰ School of Computing Sciences and Computer Engineering, University of Southern Mississippi, Hattiesburg, MS, 39406, USA.
¹¹ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
¹² Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA.
¹³ Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
¹⁴ Sentieon Inc., San Jose, CA, 95134, USA.
¹⁵ Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China.
¹⁶ Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.
¹⁷ Roche Sequencing Solutions, Santa Clara, CA, 95050, USA.
¹⁸ Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
¹⁹ Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, 39180, USA.
²⁰ Office of Health Informatics, Office of the Commissioner, US Food and Drug Administration, Silver Spring, MD, 20993, USA.
²¹ The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
²² Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA, 94305, USA.
²³ Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
²⁴ Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, 259-1193, Japan.
²⁵ CCR-SF Bioinformatics Group, Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA.
²⁶ Takeda Pharmaceuticals, Cambridge, MA, 02139, USA.
²⁷ Division of Molecular Genetics and Pathology, Center for Device and Radiological Health, US Food and Drug Administration, Silver Spring, MD, 20993, USA.
²⁸ Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA. justin.zook@nist.gov.
²⁹ State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China. zhengyuanting@fudan.edu.cn.
³⁰ Human Phenome Institute, Fudan University, Shanghai, 200438, China. zhengyuanting@fudan.edu.cn.
³¹ Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA. huixiao.hong@fda.hhs.gov.

^# Contributed equally.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Genome, Human*
High-Throughput Nucleotide Sequencing
Humans
INDEL Mutation
Polymorphism, Single Nucleotide*
Reproducibility of Results
Whole Genome Sequencing

Grants and funding

UM1 HG008898/HG/NHGRI NIH HHS/United States