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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.

Fang, Li Tai, Zhu, Bin, Zhao, Yongmei, Chen, Wanqiu, Yang, Zhaowei, Kerrigan, Liz, Langenbach, Kurt, de Mars, Maryellen, Lu, Charles, Idler, Kenneth, Jacob, Howard, Yu, Ying, Ren, Luyao, Zheng, Yuanting, Jaeger, Erich, Schroth, Gary, Abaan, Ogan, Lack, Justin, Shen, Tsai-Wei, Talsania, Keyur, Chen, Zhong, Stanbouly, Seta, Shetty, Jyoti, Kumar, Primal, Bettridge, John, Tran, Bao, Meerzaman, Daoud, Nguyen, Cu, Petitjean, Virginie, Sultan, Marc, Cam, Margaret, Hung, Tiffany, Peters, Eric, Kalamegham, Rasika, Sahraeian, Sayed Mohammad Ebrahim , Mohiyuddin, Marghoob, Yunfei, Guo, Yao, Liking, Song, Lei, Lam, Hugo YK, Drabek, Jiri, Maestro, Roberta, Polano, Maurizio , Kõks, Sulev , Reimann, Ene, Scherer, Andreas, Nordlund, Jessica, Liljedahl, Ulrika, Jensen, Roderick V, Pirooznia, Mehdi, Li, Zhipan, Xiao, Chunlin, Sherry, Steve , Kusko, Rebecca, Moos, Malcolm, Wang, Jing , Donaldson, Eric, Tezak, Zivana, Ning, Baitang, Tong, Weida, Li, Jing, Duerken-Hughes, Penelope, Hong, Huixiao, Shi, Leming, Wang, Charles and Xiao, Wenming (2021) Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing. Nature biotechnology, 39 (9). pp. 1151-1160. ISSN 1546-1696


The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.

Item Type: Article
Keywords: Benchmarking Breast Neoplasms Cell Line, Tumor DNA Mutational Analysis Datasets as Topic Germ Cells High-Throughput Nucleotide Sequencing Humans Mutation Reference Standards Reproducibility of Results Whole Genome Sequencing
Date Deposited: 23 Dec 2021 00:45
Last Modified: 23 Dec 2021 00:45


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