دورية أكاديمية
Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.
| العنوان: | Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing. |
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| المؤلفون: | Fang, Li Tai, Zhu, Bin, Zhao, Yongmei, Chen, Wanqiu, Yang, Zhaowei, Kerrigan, Liz, Langenbach, Kurt, de Mars, Maryellen, Lu, Charles, Idler, Kenneth, Jacob, Howard, Zheng, Yuanting, Ren, Luyao, Yu, Ying, Jaeger, Erich, Schroth, Gary P, Abaan, Ogan D, Talsania, Keyur, Lack, Justin, Shen, Tsai-Wei, Chen, Zhong, Stanbouly, Seta, Tran, Bao, Shetty, Jyoti, Kriga, Yuliya, Meerzaman, Daoud, Nguyen, Cu, Petitjean, Virginie, Sultan, Marc, Cam, Margaret, Mehta, Monika, Hung, Tiffany, Peters, Eric, Kalamegham, Rasika, Sahraeian, Sayed Mohammad Ebrahim, Mohiyuddin, Marghoob, Guo, Yunfei, Yao, Lijing, Song, Lei, Lam, Hugo Y K, Drabek, Jiri, Vojta, Petr, Maestro, Roberta, Gasparotto, Daniela, Kõks, Sulev, Reimann, Ene, Scherer, Andreas, Nordlund, Jessica, Liljedahl, Ulrika, Jensen, Roderick V, Pirooznia, Mehdi, Li, Zhipan, Xiao, Chunlin, Sherry, Stephen T, Kusko, Rebecca, Moos, Malcolm, Donaldson, Eric, Tezak, Zivana, Ning, Baitang, Tong, Weida, Li, Jing, Duerken-Hughes, Penelope, Catalanotti, Claudia, Maheshwari, Shamoni, Shuga, Joe, Liang, Winnie S, Keats, Jonathan, Adkins, Jonathan, Tassone, Erica, Zismann, Victoria, McDaniel, Timothy, Trent, Jeffrey, Foox, Jonathan, Butler, Daniel, Mason, Christopher E, Hong, Huixiao, Shi, Leming, Wang, Charles, Xiao, Wenming |
| المصدر: | Nat Biotechnol ; ISSN:1546-1696 ; Volume:39 ; Issue:9 |
| بيانات النشر: | Nature Publishing Group |
| سنة النشر: | 2021 |
| المجموعة: | PubMed Central (PMC) |
| الوصف: | 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. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| العلاقة: | https://doi.org/10.1038/s41587-021-00993-6Test; https://pubmed.ncbi.nlm.nih.gov/34504347Test; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8532138Test/ |
| DOI: | 10.1038/s41587-021-00993-6 |
| الإتاحة: | https://doi.org/10.1038/s41587-021-00993-6Test https://pubmed.ncbi.nlm.nih.gov/34504347Test https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8532138Test/ |
| حقوق: | © 2021. This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply. |
| رقم الانضمام: | edsbas.1C30A6EE |
| قاعدة البيانات: | BASE |
| DOI: | 10.1038/s41587-021-00993-6 |
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