机构：[1]Q2 Solutions - EA Genomics, 5927 S Miami Blvd., Morrisville, NC 27560, USA.[2]Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.[3]Agilent Technologies, 11011 N Torrey Pines Rd., La Jolla, CA 92037, USA.[4]Immuneering Corporation, One Broadway, 14th Floor, Cambridge, MA 02142, USA.[5]Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., 4300 Hacienda Dr., Pleasanton, CA 94588, USA.[6]Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W Markham St., Little Rock, AR 72205, USA.[7]Department of Computer Science, Engineering and Physics, University of Michigan-Flint, Flint, MI 48502, USA.[8]Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., 1301 Shoreway Rd., Suite 7 #300, Belmont, CA 94002, USA.[9]National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA.[10]Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.[11]Agilent Technologies, 5301 Stevens Creek Blvd., Santa Clara, CA 95051, USA.[12]Fondazione Bruno Kessler, 38123 Trento, Italy.[13]JMP Life Sciences, SAS Institute Inc., Cary, NC 27519, USA.[14](formerly) Research and Development, Roche Sequencing Solutions Inc., 500 South Rosa Rd., Madison, WI 53719, USA.[15]Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.[16](formerly) Clinical Sequencing Division, Thermo Fisher Scientific, 180 Oyster Point Blvd., South San Francisco, CA 94080, USA.[17]Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA.[18]Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, 5323 Harry Hine Blvd., Dallas, TX 75390, USA.[19]University of Texas Southwestern Medical Center, 2330 Inwood Rd., Dallas, TX 75390, USA.[20]Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA.[21]Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, CIBERER Instituto de Salud Carlos III, 28046 Madrid, Spain.[22]Thermo Fisher Scientific, 110 Miller Ave., Ann Arbor, MI 48104, USA.[23]Marketing, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA.[24]College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.[25]Agilent Technologies, 1834 State Hwy 71 West, Cedar Creek, TX 78612, USA.[26]Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA.[27]Bioinformatics Research, Institute of Molecular Biotechnology, Boku University Vienna, Vienna, Austria.[28]Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.[29]Department of Biotechnology, Boku University, Vienna, Austria.[30]Bioinformatics, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA.[31]Kelly Government Solutions, Inc., Research Triangle Park, NC 27709, USA.[32]Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China.[33]EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands[34]Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.[35]Research and Development, Burning Rock Biotech, Shanghai 201114, China.[36]Institute for Molecular Medicine Finland (FIMM), Nordic EMBL Partnership for Molecular Medicine, HiLIFE Unit, Biomedicum Helsinki 2U (D302b), FI-00014 University of Helsinki, P.O. Box 20 (Tukholmankatu 8), Helsinki, Finland.[37]Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai 200241, China.[38]University of North Carolina Health, 101 Manning Drive, Chapel Hill, NC 27514, USA.[39]Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.[40]Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.[41]Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.[42]Research and Development, QIAGEN Sciences Inc., Frederick, MD 21703, USA.[43]State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai 200438, China.[44]University of Arkansas at Little Rock, Little Rock, AR 72204, USA.[45]Departments of Medicine, Pathology, and Cancer Biology, College of Medicine and Life Sciences, University of Toledo Health Sciences Campus, 3000 Arlington Ave, Toledo, OH 43614, USA.[46]Human Phenome Institute, Fudan University, Shanghai 201203, China.[47]Fudan-Gospel Joint Research Center for Precision Medicine, Fudan University, Shanghai 200438, China.
Oncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference samples having a suitably large number of pre-identified variants for properly assessing oncopanel assay analytical quality and performance. The FDA-led Sequencing and Quality Control Phase 2 (SEQC2) consortium analyze ten diverse cancer cell lines individually and their pool, termed Sample A, to develop a reference sample with suitably large numbers of coding positions with known (variant) positives and negatives for properly evaluating oncopanel analytical performance.
In reference Sample A, we identify more than 40,000 variants down to 1% allele frequency with more than 25,000 variants having less than 20% allele frequency with 1653 variants in COSMIC-related genes. This is 5-100× more than existing commercially available samples. We also identify an unprecedented number of negative positions in coding regions, allowing statistical rigor in assessing limit-of-detection, sensitivity, and precision. Over 300 loci are randomly selected and independently verified via droplet digital PCR with 100% concordance. Agilent normal reference Sample B can be admixed with Sample A to create new samples with a similar number of known variants at much lower allele frequency than what exists in Sample A natively, including known variants having allele frequency of 0.02%, a range suitable for assessing liquid biopsy panels.
These new reference samples and their admixtures provide superior capability for performing oncopanel quality control, analytical accuracy, and validation for small to large oncopanels and liquid biopsy assays.
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外文
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出版当年[2021]版：
大类|1 区生物学
小类|1 区生物工程与应用微生物1 区遗传学
最新[2023]版：
大类|1 区生物学
小类|1 区生物工程与应用微生物1 区遗传学
第一作者：
第一作者机构：[1]Q2 Solutions - EA Genomics, 5927 S Miami Blvd., Morrisville, NC 27560, USA.
通讯作者：
推荐引用方式(GB/T 7714)：
Wendell Jones,Binsheng Gong,Natalia Novoradovskaya,et al.A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency.[J].Genome biology.2021,22(1):111.doi:10.1186/s13059-021-02316-z.
APA：
Wendell Jones,Binsheng Gong,Natalia Novoradovskaya,Dan Li,Rebecca Kusko...&Joshua Xu.(2021).A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency..Genome biology,22,(1)
MLA：
Wendell Jones,et al."A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency.".Genome biology 22..1(2021):111
生物学