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Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project.
Gong, Binsheng; Li, Dan; Zhang, Yifan; Kusko, Rebecca; Lababidi, Samir; Cao, Zehui; Chen, Mingyang; Chen, Ning; Chen, Qiaochu; Chen, Qingwang; Dai, Jiacheng; Gan, Qiang; Gao, Yuechen; Guo, Mingkun; Hariani, Gunjan; He, Yujie; Hou, Wanwan; Jiang, He; Kushwaha, Garima; Li, Jian-Liang; Li, Jianying; Li, Yulan; Liu, Liang-Chun; Liu, Ruimei; Liu, Shiming; Meriaux, Edwin; Mo, Mengqing; Moore, Mathew; Moss, Tyler J; Niu, Quanne; Patel, Ananddeep; Ren, Luyao; Saremi, Nedda F; Shang, Erfei; Shang, Jun; Song, Ping; Sun, Siqi; Urban, Brent J; Wang, Danke; Wang, Shangzi; Wen, Zhining; Xiong, Xiangyi; Yang, Jingcheng; Yin, Lihui; Zhang, Chao; Zhang, Ruolan; Bhandari, Ambica; Cai, Wanshi; Eterovic, Agda Karina; Megherbi, Dalila B.
Afiliação
  • Gong B; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
  • Li D; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
  • Zhang Y; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
  • Kusko R; Cellino Bio, 750 Main Street, Cambridge, MA, 02143, USA.
  • Lababidi S; Office of Data Analytics and Research, Office of Digital Transformation, Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA.
  • Cao Z; State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
  • Chen M; Human Phenome Institute, Fudan University, Shanghai, 201203, China.
  • Chen N; iGeneTech Bioscience Co., Ltd., 8 Shengmingyuan Rd., Changping, Beijing, China.
  • Chen Q; State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
  • Chen Q; State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
  • Dai J; Human Phenome Institute, Fudan University, Shanghai, 201203, China.
  • Gan Q; Clinical Diagnostics Division, Thermo Fisher Scientific, 46500 Kato Rd., Fremont, CA, 94538, USA.
  • Gao Y; State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
  • Guo M; College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China.
  • Hariani G; Q squared Solutions Genomics, 2400 Ellis Road, Durham, NC, 27703, USA.
  • He Y; College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China.
  • Hou W; State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
  • Jiang H; State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
  • Kushwaha G; Guardant Health, Inc., 505 Penobscot Drive, Redwood City, CA, 94063, USA.
  • Li JL; Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
  • Li J; Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
  • Li Y; College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
  • Liu LC; Clinical Diagnostics Division, Thermo Fisher Scientific, 46500 Kato Rd., Fremont, CA, 94538, USA.
  • Liu R; State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
  • Liu S; Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
  • Meriaux E; CMINDS Research Center, University of Massachusetts, Lowell, MA, 01854, USA.
  • Mo M; Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200032, China.
  • Moore M; ResearchDx, Irvine, CA, 92618, USA.
  • Moss TJ; Eurofins Viracor, LLC, 18000 W 99th St., Lenexa, KS, 66219, USA.
  • Niu Q; State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
  • Patel A; Eurofins Viracor Biopharma Services, Inc., 18000 W 99th St., Lenexa, KS, 66219, USA.
  • Ren L; State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
  • Saremi NF; Agilent Technologies, Inc., 11011 N Torrey Pines Rd., La Jolla, CA, 92037, USA.
  • Shang E; State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
  • Shang J; State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
  • Song P; Cancer Genomics Laboratory, Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, 77030, USA.
  • Sun S; ResearchDx, Irvine, CA, 92618, USA.
  • Urban BJ; Eurofins Viracor Biopharma Services, Inc., 18000 W 99th St., Lenexa, KS, 66219, USA.
  • Wang D; Human Phenome Institute, Fudan University, Shanghai, 201203, China.
  • Wang S; State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China.
  • Wen Z; College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China.
  • Xiong X; College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
  • Yang J; State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
  • Yin L; PathGroup, Nashville, TN, 37217, USA.
  • Zhang C; State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
  • Zhang R; State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
  • Bhandari A; ResearchDx, Irvine, CA, 92618, USA.
  • Cai W; iGeneTech Bioscience Co., Ltd., 8 Shengmingyuan Rd., Changping, Beijing, China.
  • Eterovic AK; Eurofins Viracor Biopharma Services, Inc., 18000 W 99th St., Lenexa, KS, 66219, USA.
  • Megherbi DB; CMINDS Research Center, University of Massachusetts, Lowell, MA, 01854, USA.
Sci Rep ; 14(1): 7028, 2024 03 25.
Article em En | MEDLINE | ID: mdl-38528062
ABSTRACT
Accurate indel calling plays an important role in precision medicine. A benchmarking indel set is essential for thoroughly evaluating the indel calling performance of bioinformatics pipelines. A reference sample with a set of known-positive variants was developed in the FDA-led Sequencing Quality Control Phase 2 (SEQC2) project, but the known indels in the known-positive set were limited. This project sought to provide an enriched set of known indels that would be more translationally relevant by focusing on additional cancer related regions. A thorough manual review process completed by 42 reviewers, two advisors, and a judging panel of three researchers significantly enriched the known indel set by an additional 516 indels. The extended benchmarking indel set has a large range of variant allele frequencies (VAFs), with 87% of them having a VAF below 20% in reference Sample A. The reference Sample A and the indel set can be used for comprehensive benchmarking of indel calling across a wider range of VAF values in the lower range. Indel length was also variable, but the majority were under 10 base pairs (bps). Most of the indels were within coding regions, with the remainder in the gene regulatory regions. Although high confidence can be derived from the robust study design and meticulous human review, this extensive indel set has not undergone orthogonal validation. The extended benchmarking indel set, along with the indels in the previously published known-positive set, was the truth set used to benchmark indel calling pipelines in a community challenge hosted on the precisionFDA platform. This benchmarking indel set and reference samples can be utilized for a comprehensive evaluation of indel calling pipelines. Additionally, the insights and solutions obtained during the manual review process can aid in improving the performance of these pipelines.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Benchmarking / Sequenciamento de Nucleotídeos em Larga Escala Limite: Humans Idioma: En Revista: Sci Rep Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Benchmarking / Sequenciamento de Nucleotídeos em Larga Escala Limite: Humans Idioma: En Revista: Sci Rep Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Estados Unidos