Internet Archive Scholar

Whole Genome and Exome Sequencing Reference Datasets from A Multi-center and Cross-platform Benchmark Study [article]

Yongmei Zhao, Li Tai Fang, Tsai-Wei Shen, Sulbha Choudhari, Keyur Talsania, Jack Chen, Jyoti Shetty, Yuliya Kriga, Bao Tran, Bin Zhu, Zhong Chen, Wanqiu Chen (+23 others)
2021 bioRxiv   pre-print

Preserved Fulltext

fulltext thumbnail
Web Archive Capture PDF (6.7 MB)
https://web.archive.org/web/20210717173116/https://www.biorxiv.org/content/biorxiv/early/2021/03/06/2021.02.27.433136.full.pdf

A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL. The file type is application/pdf.

With the rapid advancement of sequencing technologies in the past decade, next generation sequencing (NGS) analysis has been widely applied in cancer genomics research. More recently, NGS has been adopted in clinical oncology to advance personalized medicine. Clinical applications of precision oncology require accurate tests that can distinguish tumor-specific mutations from errors or artifacts introduced during NGS processes or data analysis. Therefore, there is an urgent need to develop best
more » ... ractices in cancer mutation detection using NGS and the need for standard reference data sets for systematically benchmarking sequencing platforms, library protocols, bioinformatics pipelines and for measuring accuracy and reproducibility across platforms and methods. Within the SEQC2 consortium context, we established paired tumor-normal reference samples, a human triple-negative breast cancer cell line and a matched normal cell line derived from B lymphocytes. We generated whole-genome (WGS) and whole-exome sequencing (WES) data using 16 NGS library preparation protocols, seven sequencing platforms at six different centers. We systematically interrogated somatic mutations in the paired reference samples to identify factors affecting detection reproducibility and accuracy in cancer genomes. These large cross-platform/site WGS and WES datasets using well-characterized reference samples will represent a powerful resource for benchmarking NGS technologies, bioinformatics pipelines, and for the cancer genomics studies.
doi:10.1101/2021.02.27.433136 fatcat:xy5whi7z6jhk7ibaids65sfy5e
Citation

Yongmei Zhao, Li Tai Fang, Tsai-Wei Shen, Sulbha Choudhari, Keyur Talsania, Jack Chen, Jyoti Shetty, Yuliya Kriga, Bao Tran, Bin Zhu, Zhong Chen, Wanqiu Chen, Charles Wang, Erich Jaeger, Daoud Meerzaman, Charles Lu, Kenneth Idler, Yuanting Zheng, Leming Shi, Virginie Petitjean, Marc Sultan, Tiffany Hung, Eric Peters, Jiri Drabek, Petr Vojta, Roberta Maestro, Daniela Gasparotto, Sulev Koks, Ene Reimann, Andreas Scherer, Jessica Nordlund, Ulrika Liljedahl, Jonathan Foox, Christopher Mason, Wenming Xiao. "Whole Genome and Exome Sequencing Reference Datasets from A Multi-center and Cross-platform Benchmark Study." bioRxiv (2021)