{"entity": "researcher", "timestamp": "2026-09-23T21:55:18.821Z", "family": "Trent", "given": "Jeffrey", "initials": "J", "orcid": "0000-0003-0183-4202", "affiliations": ["Translational Genomics Research Institute, Phoenix, AZ, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7944971712140458e7b8e87c6a9e47b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7944971712140458e7b8e87c6a9e47b"}}, "publications": [{"entity": "publication", "iuid": "69cd66b0d0fa42a1b63182230aa42e3e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/69cd66b0d0fa42a1b63182230aa42e3e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/69cd66b0d0fa42a1b63182230aa42e3e"}}, "title": "Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.", "authors": [{"family": "Fang", "given": "Li Tai", "initials": "LT", "orcid": "0000-0003-3201-5162", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e8580485571444697c60fe584e885d9.json"}}, {"family": "Zhu", "given": "Bin", "initials": "B", "orcid": "0000-0003-0172-5516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9f8dd1f641e44c5a15fead6f95ad052.json"}}, {"family": "Zhao", "given": "Yongmei", "initials": "Y", "orcid": "0000-0003-0800-4658", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/835069a0dd69421e820eed56607eb6c7.json"}}, {"family": "Chen", "given": "Wanqiu", "initials": "W", "orcid": "0000-0003-3706-7834", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5885e8c00cf449b5a85bf62a1075ee68.json"}}, {"family": "Yang", "given": "Zhaowei", "initials": "Z", "orcid": "0000-0002-1805-4360", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06f50b137284428ba566c6c6f99b8d3f.json"}}, {"family": "Kerrigan", "given": "Liz", "initials": "L"}, {"family": "Langenbach", "given": "Kurt", "initials": "K"}, {"family": "de Mars", "given": "Maryellen", "initials": "M"}, {"family": "Lu", "given": "Charles", "initials": "C"}, {"family": "Idler", "given": "Kenneth", "initials": "K"}, {"family": "Jacob", "given": "Howard", "initials": "H"}, {"family": "Zheng", "given": "Yuanting", "initials": "Y"}, {"family": "Ren", "given": "Luyao", "initials": "L"}, {"family": "Yu", "given": "Ying", "initials": "Y"}, {"family": "Jaeger", "given": "Erich", "initials": "E"}, {"family": "Schroth", "given": "Gary P", "initials": "GP", "orcid": "0000-0002-3055-056X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/130bab49ad08489584a9d1ac9870d28a.json"}}, {"family": "Abaan", "given": "Ogan D", "initials": "OD"}, {"family": "Talsania", "given": "Keyur", "initials": "K"}, {"family": "Lack", "given": "Justin", "initials": "J"}, {"family": "Shen", "given": "Tsai-Wei", "initials": "TW", "orcid": "0000-0001-9644-1748", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c2a7f2752bc84ee79fd835eb8b79d939.json"}}, {"family": "Chen", "given": "Zhong", "initials": "Z", "orcid": "0000-0003-2444-8216", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/529afc6dc35a4ece827b6d412bf74855.json"}}, {"family": "Stanbouly", "given": "Seta", "initials": "S"}, {"family": "Tran", "given": "Bao", "initials": "B"}, {"family": "Shetty", "given": "Jyoti", "initials": "J"}, {"family": "Kriga", "given": "Yuliya", "initials": "Y"}, {"family": "Meerzaman", "given": "Daoud", "initials": "D"}, {"family": "Nguyen", "given": "Cu", "initials": "C"}, {"family": "Petitjean", "given": "Virginie", "initials": "V"}, {"family": "Sultan", "given": "Marc", "initials": "M"}, {"family": "Cam", "given": "Margaret", "initials": "M"}, {"family": "Mehta", "given": "Monika", "initials": "M", "orcid": "0000-0003-3928-3733", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04bb9ec9701c4e0482c27e8c5faead15.json"}}, {"family": "Hung", "given": "Tiffany", "initials": "T"}, {"family": "Peters", "given": "Eric", "initials": "E"}, {"family": "Kalamegham", "given": "Rasika", "initials": "R"}, {"family": "Sahraeian", "given": "Sayed Mohammad Ebrahim", "initials": "SME"}, {"family": "Mohiyuddin", "given": "Marghoob", "initials": "M"}, {"family": "Guo", "given": "Yunfei", "initials": "Y"}, {"family": "Yao", "given": "Lijing", "initials": "L"}, {"family": "Song", "given": "Lei", "initials": "L"}, {"family": "Lam", "given": "Hugo Y K", "initials": "HYK"}, {"family": "Drabek", "given": "Jiri", "initials": "J"}, {"family": "Vojta", "given": "Petr", "initials": "P", "orcid": "0000-0003-0036-1853", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a92f0a2adb974dd9836179661ad2ea99.json"}}, {"family": "Maestro", "given": "Roberta", "initials": "R", "orcid": "0000-0002-6642-5592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/695a16479aec4622bee3ec866cfdb65f.json"}}, {"family": "Gasparotto", "given": "Daniela", "initials": "D"}, {"family": "K\u00f5ks", "given": "Sulev", "initials": "S", "orcid": "0000-0001-6087-6643", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc9a5201963f4ad091116d98309d366e.json"}}, {"family": "Reimann", "given": "Ene", "initials": "E", "orcid": "0000-0002-5410-4433", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6726ad87a60843e79bf48d21f8293b19.json"}}, {"family": "Scherer", "given": "Andreas", "initials": "A", "orcid": "0000-0002-4254-7122", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3629fd16f1134138a13ee8ab39284794.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U"}, {"family": "Jensen", "given": "Roderick V", "initials": "RV"}, {"family": "Pirooznia", "given": "Mehdi", "initials": "M", "orcid": "0000-0002-4210-6458", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1724f814d5044e29e26553181117b04.json"}}, {"family": "Li", "given": "Zhipan", "initials": "Z"}, {"family": "Xiao", "given": "Chunlin", "initials": "C", "orcid": "0000-0001-8702-4889", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/844b21365aa74e1687aba52da231c059.json"}}, {"family": "Sherry", "given": "Stephen T", "initials": "ST"}, {"family": "Kusko", "given": "Rebecca", "initials": "R", "orcid": "0000-0001-6730-5990", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6d44ddbda74e4498b84a9ae66b6d00ab.json"}}, {"family": "Moos", "given": "Malcolm", "initials": "M"}, {"family": "Donaldson", "given": "Eric", "initials": "E"}, {"family": "Tezak", "given": "Zivana", "initials": "Z"}, {"family": "Ning", "given": "Baitang", "initials": "B"}, {"family": "Tong", "given": "Weida", "initials": "W"}, {"family": "Li", "given": "Jing", "initials": "J"}, {"family": "Duerken-Hughes", "given": "Penelope", "initials": "P"}, {"family": "Catalanotti", "given": "Claudia", "initials": "C"}, {"family": "Maheshwari", "given": "Shamoni", "initials": "S"}, {"family": "Shuga", "given": "Joe", "initials": "J"}, {"family": "Liang", "given": "Winnie S", "initials": "WS", "orcid": "0000-0002-5698-7735", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e425964ff014c80b7cb2b624810a386.json"}}, {"family": "Keats", "given": "Jonathan", "initials": "J", "orcid": "0000-0003-4375-7399", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c2bfd6746c6b46bd8a436e5fe58c5800.json"}}, {"family": "Adkins", "given": "Jonathan", "initials": "J"}, {"family": "Tassone", "given": "Erica", "initials": "E"}, {"family": "Zismann", "given": "Victoria", "initials": "V"}, {"family": "McDaniel", "given": "Timothy", "initials": "T"}, {"family": "Trent", "given": "Jeffrey", "initials": "J", "orcid": "0000-0003-0183-4202", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7944971712140458e7b8e87c6a9e47b.json"}}, {"family": "Foox", "given": "Jonathan", "initials": "J"}, {"family": "Butler", "given": "Daniel", "initials": "D"}, {"family": "Mason", "given": "Christopher E", "initials": "CE", "orcid": "0000-0002-1850-1642", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0d4b550b1cab4def9302399e8c1cb8e7.json"}}, {"family": "Hong", "given": "Huixiao", "initials": "H", "orcid": "0000-0001-8087-3968", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4674b0bb00c9404990ab4d9dd4f8d17a.json"}}, {"family": "Shi", "given": "Leming", "initials": "L", "orcid": "0000-0002-2981-4150", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a7eb9403fed44eaa67bebe95b6a5e47.json"}}, {"family": "Wang", "given": "Charles", "initials": "C"}, {"family": "Xiao", "given": "Wenming", "initials": "W", "orcid": "0000-0003-4096-9724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bfc6fcba12b54c76ad2aab40c955d2a1.json"}}, {"family": "Somatic Mutation Working Group of Sequencing Quality Control Phase II Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2021-09-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "39", "issue": "9", "pages": "1151-1160", "issn-l": "1087-0156"}, "abstract": "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.", "doi": "10.1038/s41587-021-00993-6", "pmid": "34504347", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1740806"}, {"db": "pmc", "key": "PMC8532138"}, {"db": "pii", "key": "10.1038/s41587-021-00993-6"}], "notes": [], "created": "2026-09-23T07:27:29.434Z", "modified": "2026-09-23T07:27:29.874Z"}]}