ArticleGenome biology2021
A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency.
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Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36citing papers in PubMed
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Who cites it
36 citing papers in PubMed.
- Liquid biopsy in modern medicine: advancing diagnostics from molecular insights to clinical practice.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Review
- Tumor-naïve ctDNA detection with deep learning-enhanced error suppression for sensitive mutation calling.Genome medicine · 2026Article
- Characterization of subclonal variants in HG002 Genome in a Bottle reference material as a resource for benchmarking variant callers.Cell genomics · 2026Article
- Comprehensive benchmarking of methods for mutation calling in circulating tumor DNA.Nature communications · 2025Article
- Evaluation of false positive and false negative errors in targeted next generation sequencing.Genome biology · 2025Article
- Multi-omics strategies for biomarker discovery and application in personalized oncology.Molecular biomedicine · 2025Review
- Implementation of an ISO 15189 accredited next generation sequencing service for cell-free total nucleic acid (cfTNA) analysis to facilitate driver mutation reporting in blood: the experience of a clinical diagnostic laboratory.Journal of clinical pathology · 2025Article
- Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.Scientific data · 2025Article
- Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.bioRxiv : the preprint server for biology · 2025Article
- Augmenting precision medicine via targeted RNA-Seq detection of expressed mutations.NPJ precision oncology · 2025Article
- Multi-omics Quality Assessment in Personalized Medicine Through European Infrastructure for Translational Medicine (EATRIS): An Overview.Phenomics (Cham, Switzerland) · 2025Review
- Evaluative Methodology for HRD Testing: Development of Standard Tools for Consistency Assessment.Genomics, proteomics & bioinformatics · 2025Article
- Improvement of the sensitivity of circulating tumor DNA-based liquid biopsy: current approaches and future perspectives.Exploration of targeted anti-tumor therapy · 2025Review
- A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.bioRxiv : the preprint server for biology · 2024Article
- NCI workshop on ctDNA in cancer treatment and clinical care.Journal of the National Cancer Institute · 2024Article
- Reference Materials for Improving Reliability of Multiomics Profiling.Phenomics (Cham, Switzerland) · 2024Review
- Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing.Scientific data · 2024Article
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials.Nature biotechnology · 2024Article
- Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA.Scientific reports · 2024Article
- Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project.Scientific reports · 2024Article
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Authors and funding
74 authors.
Wendell JonesQ2 Solutions - EA Genomics, 5927 S Miami Blvd., Morrisville, NC, 27560, USA. Wendell.Jones@q2labsolutions.com.ORCID 0000-0002-9676-5387
Binsheng GongDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Natalia NovoradovskayaAgilent Technologies, 11011 N Torrey Pines Rd., La Jolla, CA, 92037, USA.
Dan LiDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Rebecca KuskoImmuneering Corporation, One Broadway, 14th Floor, Cambridge, MA, 02142, USA.
Todd A RichmondMarket & Application Development Bioinformatics, Roche Sequencing Solutions Inc., 4300 Hacienda Dr., Pleasanton, CA, 94588, USA.
Donald J JohannWinthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W Markham St., Little Rock, AR, 72205, USA.
Halil BisginDepartment of Computer Science, Engineering and Physics, University of Michigan-Flint, Flint, MI, 48502, USA.
Sayed Mohammad Ebrahim SahraeianBioinformatics Research & Early Development, Roche Sequencing Solutions Inc., 1301 Shoreway Rd., Suite 7 #300, Belmont, CA, 94002, USA.
Pierre R BushelNational Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, 27709, USA.
Mehdi PiroozniaBioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Katherine WilkinsAgilent Technologies, 5301 Stevens Creek Blvd., Santa Clara, CA, 95051, USA.
Marco ChiericiFondazione Bruno Kessler, 38123, Trento, Italy.
Wenjun BaoJMP Life Sciences, SAS Institute Inc., Cary, NC, 27519, USA.
Lee Scott BasehoreAgilent Technologies, 11011 N Torrey Pines Rd., La Jolla, CA, 92037, USA.
Anne Bergstrom LucasAgilent Technologies, 5301 Stevens Creek Blvd., Santa Clara, CA, 95051, USA.
Daniel Burgess(formerly) Research and Development, Roche Sequencing Solutions Inc., 500 South Rosa Rd., Madison, WI, 53719, USA.
Daniel J ButlerDepartment of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA.
Simon Cawley(formerly) Clinical Sequencing Division, Thermo Fisher Scientific, 180 Oyster Point Blvd., South San Francisco, CA, 94080, USA.
Chia-Jung ChangStanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA.
Guangchun ChenDepartment of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, 5323 Harry Hine Blvd., Dallas, TX, 75390, USA.
Tao ChenUniversity of Texas Southwestern Medical Center, 2330 Inwood Rd., Dallas, TX, 75390, USA.
Yun-Ching ChenBioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Daniel J CraigDepartment of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, 43614, USA.
Angela Del PozoInstitute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, CIBERER Instituto de Salud Carlos III, 28046, Madrid, Spain.
Jonathan FooxDepartment of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA.
Margherita FrancescattoFondazione Bruno Kessler, 38123, Trento, Italy.
Yutao FuThermo Fisher Scientific, 110 Miller Ave., Ann Arbor, MI, 48104, USA.
Cesare FurlanelloFondazione Bruno Kessler, 38123, Trento, Italy.
Kristina GiordaMarketing, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA.
Kira P GristQ2 Solutions - EA Genomics, 5927 S Miami Blvd., Morrisville, NC, 27560, USA.
Meijian GuanJMP Life Sciences, SAS Institute Inc., Cary, NC, 27519, USA.
Yingyi HaoCollege of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China.
Scott HappeAgilent Technologies, 1834 State Hwy 71 West, Cedar Creek, TX, 78612, USA.
Gunjan HarianiQ2 Solutions - EA Genomics, 5927 S Miami Blvd., Morrisville, NC, 27560, USA.
Nathan HaseleyIllumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA.
Jeff JasperQ2 Solutions - EA Genomics, 5927 S Miami Blvd., Morrisville, NC, 27560, USA.
Giuseppe JurmanFondazione Bruno Kessler, 38123, Trento, Italy.
David Philip KreilBioinformatics Research, Institute of Molecular Biotechnology, Boku University Vienna, Vienna, Austria.
Paweł ŁabajMałopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
Kevin LaiBioinformatics, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA.
Jianying LiKelly Government Solutions, Inc., Research Triangle Park, NC, 27709, USA.
Quan-Zhen LiDepartment of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, 5323 Harry Hine Blvd., Dallas, TX, 75390, USA.
Yulong LiCenter of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China.
Zhiguang LiCenter of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China.
Zhichao LiuDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Mario Solís LópezInstitute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, CIBERER Instituto de Salud Carlos III, 28046, Madrid, Spain.
Kelci MiclausJMP Life Sciences, SAS Institute Inc., Cary, NC, 27519, USA.
Raymond MillerAgilent Technologies, 5301 Stevens Creek Blvd., Santa Clara, CA, 95051, USA.
Vinay K MittalThermo Fisher Scientific, 110 Miller Ave., Ann Arbor, MI, 48104, USA.
Marghoob MohiyuddinBioinformatics Research & Early Development, Roche Sequencing Solutions Inc., 1301 Shoreway Rd., Suite 7 #300, Belmont, CA, 94002, USA.
Carlos Pabón-PeñaAgilent Technologies, 5301 Stevens Creek Blvd., Santa Clara, CA, 95051, USA.
Barbara L ParsonsDivision of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Fujun QiuResearch and Development, Burning Rock Biotech, Shanghai, 201114, China.
Andreas SchererEATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands.
Tieliu ShiCenter 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.
Suzy StiegelmeyerUniversity of North Carolina Health, 101 Manning Drive, Chapel Hill, NC, 27514, USA.
Chen SuoDepartment of Epidemiology, School of Public Health, Fudan University, Shanghai, China.
Nikola TomEATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands.
Dong WangDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Zhining WenCollege of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China.
Leihong WuDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Wenzhong XiaoStanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA.
Chang XuResearch and Development, QIAGEN Sciences Inc., Frederick, MD, 21703, USA.
Ying YuState Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China.
Jiyang ZhangState Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China.
Yifan ZhangUniversity of Arkansas at Little Rock, Little Rock, AR, 72204, USA.
Zhihong ZhangResearch and Development, Burning Rock Biotech, Shanghai, 201114, China.
Yuanting ZhengDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Christopher E MasonDepartment of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA.
James C WilleyDepartments 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.
Weida TongDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Leming ShiState Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China.
Joshua XuDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA. Joshua.xu@fda.hhs.gov.
Funding
Microarray and Genome InformaticsZIAES102345 · NIEHS · NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES · PI BUSHEL, ROBERT · 2009 to 2021
$10.8MBioinformatics CoreZICHL006228 · NHLBI · NATIONAL HEART, LUNG, AND BLOOD INSTITUTE · PI PIROOZNIA, MEHDI · 2017 to 2021
$6.6MAbstract
backgroundOncopanel 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.
resultsIn 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.
conclusionThese 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.
Indexed as
AllelesBiomarkers, TumorGene FrequencyGenetic VariationCell Line, TumorDNA Copy Number VariationsGenetic HeterogeneityGenetic TestingGenomicsHumansNeoplasmsWorkflowBiomarkers, Tumor
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