Assessing reproducibility of inherited variants detected with short-read whole genome sequencing
| العنوان: | Assessing reproducibility of inherited variants detected with short-read whole genome sequencing |
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| المؤلفون: | 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 |
| المساهمون: | Institute for Molecular Medicine Finland |
| المصدر: | Genome Biology Genome Biology, Vol 23, Iss 1, Pp 1-26 (2022) |
| سنة النشر: | 2021 |
| مصطلحات موضوعية: | 11832 Microbiology and virology, 0303 health sciences, 318 Medical biotechnology, Whole Genome Sequencing, QH301-705.5, Genome, Human, Research, 1184 Genetics, developmental biology, physiology, High-Throughput Nucleotide Sequencing, Reproducibility of Results, QH426-470, CANCER, Polymorphism, Single Nucleotide, GENOTYPE, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, DATA SETS, INDEL Mutation, 030220 oncology & carcinogenesis, Genetics, Humans, Biology (General), MUTATION, 030304 developmental biology |
| الوصف: | BackgroundReproducible 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.ResultsTo 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×.ConclusionsOur findings highlight sources of variability in variant detection and the need for improvement of bioinformatics pipelines in the era of precision medicine with WGS. |
| تدمد: | 1474-760X |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5c5b8bb010c7ea9313b3fdebc37dfb06 https://pubmed.ncbi.nlm.nih.gov/34980216 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....5c5b8bb010c7ea9313b3fdebc37dfb06 |
| قاعدة البيانات: | OpenAIRE |
Find this article in full text from Springer Verlag. | تدمد: | 1474760X |
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