Evidence map›Paper›PMID 33863344›Full record

ArticleGenome biology2021

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions.

Binsheng Gong, Dan Li, Rebecca Kusko, Natalia Novoradovskaya, Yifan Zhang, Shangzi Wang, Carlos Pabón-Peña, Zhihong Zhang, Kevin Lai, Wanshi Cai and 141 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

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 23 papers.

0numbers the graph read from it
0cells of the map it votes in
23citing papers in PubMed
3.0field-weighted citation impact, top 7% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

23 citing papers in PubMed, 38 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

151 authors at 20 institutions in 14 countries.

Binsheng Gong *Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Dan Li *Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Rebecca Kusko *Immuneering Corporation, One Broadway, 14th Floor, Cambridge, MA, 02142, USA.
Natalia NovoradovskayaAgilent Technologies, 11011 N Torrey Pines Rd, La Jolla, CA, 92037, USA.
Yifan ZhangDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Shangzi WangState Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China.
Carlos Pabón-PeñaAgilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, CA, 95051, USA.
Zhihong ZhangResearch and Development, Burning Rock Biotech, Shanghai, 201114, China.
Kevin LaiBioinformatics, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA.
Wanshi CaiiGeneTech, 8 Shengmingyuan Rd., Zhongguancun Life Science Park, Changping District, Beijing, 100080, China.
Jennifer S LoCocoIllumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA.
Eric LaderResearch and Development, QIAGEN Sciences Inc., Frederick, MD, 21703, USA.
Todd A RichmondMarket & Application Development Bioinformatics, Roche Sequencing Solutions Inc., 4300 Hacienda Dr, Pleasanton, CA, 94588, USA.
Vinay K MittalThermo Fisher Scientific, 110 Miller Ave, Ann Arbor, MI, 48104, USA.
Liang-Chun LiuClinical Diagnostic Division, Thermo Fisher Scientific, 46500 Kato Rd, Fremont, CA, 94538, USA.
Donald J JohannWinthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, 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.
Pierre R BushelNational Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.
Ying YuState Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China.
Chang XuResearch and Development, QIAGEN Sciences Inc., Frederick, MD, 21703, USA.
Guangchun ChenDepartment of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, 5323 Harry Hine Blvd, Dallas, TX, 75390, USA.
Daniel BurgessResearch and Development, Roche Sequencing Solutions Inc., 500 South Rosa Rd, Madison, WI, 53719, USA.
Simon CawleyClinical Sequencing Division, Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA, 94080, USA.
Kristina GiordaMarketing, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA.
Nathan HaseleyIllumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA.
Fujun QiuResearch and Development, Burning Rock Biotech, Shanghai, 201114, China.
Katherine WilkinsAgilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, CA, 95051, USA.
Hanane AribIcahn Institute and Dept. of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA.
Claire AttwoollIllumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA.
Kevin BabsonGreenwood Genetic Center, 106 Gregor Mendel Circle, Greenwood, SC, 29646, USA.
Longlong BaoDepartment of Pathology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
Wenjun BaoJMP Life Sciences, SAS Institute Inc., Cary, NC, 27519, USA.
Anne Bergstrom LucasAgilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, CA, 95051, USA.
Hunter BestDepartments of Pathology and Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA.
Ambica BhandariResearchDx, Inc., 5 Mason, Irvine, CA, 92618, USA.
Halil BisginDepartment of Computer Science, Engineering and Physics, University of Michigan-Flint, Flint, MI, 48502, USA.
James BlackburnGarvan Institute of Medical Research, Sydney, NSW, Australia.
Thomas M BlomquistDepartment of Pathology, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, 43614, USA.
Lisa BoardmanDivision of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA.
Blake BurgherOmniSeq, Inc. 700 Ellicott St, Buffalo, NY, 14203, USA.
Daniel J ButlerDepartment of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA.
Chia-Jung ChangStanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA.
Alka ChaubeyGreenwood Genetic Center, 106 Gregor Mendel Circle, Greenwood, SC, 29646, USA.
Tao ChenDivision of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Marco ChiericiFondazione Bruno Kessler, 38123, Trento, Italy.
Christopher R ChinDepartment of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA.
Devin CloseR&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT, 84108, USA.
Jeffrey ConroyOmniSeq, Inc. 700 Ellicott St, Buffalo, NY, 14203, USA.
Jessica Cooley ColemanGreenwood Genetic Center, 106 Gregor Mendel Circle, Greenwood, SC, 29646, USA.
Daniel J CraigDepartment of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, 43614, USA.
Erin CrawfordDepartment 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.
Ira W DevesonKinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.
Daniel DuncanCancer Genetics Inc, 201 Route 17 N, Meadows Office Building, Rutherford, NJ, 07070, USA.
Agda Karina EterovicInstitute for Personalized Cancer Therapy, MD Anderson Cancer Center, 6565 MD Anderson Blvd, Houston, TX, 77030, USA.
Xiaohui FanPharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
Jonathan FooxDepartment of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA.
Cesare FurlanelloFondazione Bruno Kessler, 38123, Trento, Italy.
Abhisek GhosalResearchDx, Inc., 5 Mason, Irvine, CA, 92618, USA.
Sean GlennOmniSeq, Inc. 700 Ellicott St, Buffalo, NY, 14203, USA.
Meijian GuanJMP Life Sciences, SAS Institute Inc., Cary, NC, 27519, USA.
Christine HaagMolecular Laboratory, Prof. F. Raue, Im Weiher 12, Heidelberg, Germany.
Xinyi HangiGeneTech, 8 Shengmingyuan Rd., Zhongguancun Life Science Park, Changping District, Beijing, 100080, China.
Scott HappeAgilent Technologies, 1834 State Hwy 71 West, Cedar Creek, TX, 78612, USA.
Brittany HenniganGreenwood Genetic Center, 106 Gregor Mendel Circle, Greenwood, SC, 29646, USA.
Jennifer HippDepartment of Pathology, Strata Oncology, Inc., Ann Arbor, MI, 48103, USA.
Huixiao HongDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Kyle HorvathResearchDx, Inc., 5 Mason, Irvine, CA, 92618, USA.
Jianhong HuHuman Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
Li-Yuan HungMassachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
Mirna JaroszNGS Products and Services, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA.
Jennifer KerkhofMolecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, 800 Commissioners Rd E, London, Ontario, N6A5W9, Canada.
Benjamin KippDivision of Anatomic Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
David Philip KreilBioinformatics Research, Institute of Molecular Biotechnology, Boku University Vienna, Vienna, Austria.
Paweł ŁabajMałopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
Pablo LapunzinaEATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands.
Peng LiMassachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, 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.
Weihua LiDepartment of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China.
Zhiguang LiCenter of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, Liaoning, China.
Yu LiangGeneis, 5 Guangshun North St., Chaoyang District, Beijing, 100102, China.
Shaoqing LiuGeneSmile Ltd Co., Jiangsu Cancer Hospital, 42 Baiziting St., Xuanwu District, Nanjing, 210009, Jiangsu, China.
Zhichao LiuDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Charles MaCancer Genetics Inc, 201 Route 17 N, Meadows Office Building, Rutherford, NJ, 07070, USA.
Narasimha MarellaCancer Genetics Inc, 201 Route 17 N, Meadows Office Building, Rutherford, NJ, 07070, USA.
Rubén Martín-ArenasGenycell Biotech España, Calle Garrido Atienza, 18320 Santa Fe, Granada, Spain.
Dalila B MegherbiCMINDS Research Center, Department of Electrical and Computer Engineering, College of Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, USA.
Qingchang MengHuman Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
Piotr A MieczkowskiDepartment of Genetics, University of North Carolina, 250 Bell Tower Drive, Chapel Hill, NC, 27599, USA.
Tom MorrisonAccugenomics, Inc., 1410 Commonwealth Drive, Suite 105, Wilmington, NC, 20403, USA.
Donna MuznyHuman Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
Baitang NingDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Barbara L ParsonsDivision of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Cloud P PaweletzTranslational Research Laboratory, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, 360 Longwood Ave, Boston, MA, 02215, USA.
Mehdi PiroozniaBioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Wubin QuiGeneTech, 8 Shengmingyuan Rd., Zhongguancun Life Science Park, Changping District, Beijing, 100080, China.
Amelia RaymondAstrazeneca Pharmaceuticals, 35 Gatehouse Dr, Waltham, MA, 02451, USA.
Paul RindlerR&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT, 84108, USA.
Rebecca RinglerResearchDx, Inc., 5 Mason, Irvine, CA, 92618, USA.
Bekim SadikovicMolecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, 800 Commissioners Rd E, London, Ontario, N6A5W9, Canada.
Andreas SchererEATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands.
Egbert SchulzeLaboratory for Molecular Genetics, Endocrine Practice, Im Weiher 12, 69121, Heidelberg, Germany.
Robert SebraIcahn Institute and Dept. of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA.
Rita ShaknovichCancer Genetics Inc, 201 Route 17 N, Meadows Office Building, Rutherford, NJ, 07070, USA.
Qiang ShiDivision of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
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.
Juan Carlos Silla-CastroNational Centre for Cardiovascular Research (CNIC), Madrid, Spain.
Melissa SmithIcahn Institute and Dept. of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA.
Mario Solís LópezInstitute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, CIBERER Instituto de Salud Carlos III, 28046, Madrid, Spain.
Ping SongInstitute for Personalized Cancer Therapy, MD Anderson Cancer Center, 6565 MD Anderson Blvd, Houston, TX, 77030, USA.
Daniel StetsonAstrazeneca Pharmaceuticals, 35 Gatehouse Dr, Waltham, MA, 02451, USA.
Maya StrahlIcahn Institute and Dept. of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA.
Alan StuartMolecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, 800 Commissioners Rd E, London, Ontario, N6A5W9, Canada.
Julianna SuppleeTranslational Research Laboratory, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, 360 Longwood Ave, Boston, MA, 02215, USA.
Philippe SzankasiR&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT, 84108, USA.
Haowen TanPrimbio Genes Biotechnology, Building C6-501, Biolake, No.666 Gaoxin Ave., East Lake High-tech Development Zone, Wuhan, 430074, Hubei, China.
Lin-Ya TangInstitute for Personalized Cancer Therapy, MD Anderson Cancer Center, 6565 MD Anderson Blvd, Houston, TX, 77030, USA.
Yonghui TaoDepartment of Pathology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
Shraddha ThakkarDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Danielle Thierry-MiegNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA.
Jean Thierry-MiegNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA.
Venkat J ThodimaCancer Genetics Inc, 201 Route 17 N, Meadows Office Building, Rutherford, NJ, 07070, USA.
David ThomasSt Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2010, Australia.
Boris TichýEATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands.
Nikola TomEATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands.
Elena Vallespin GarciaInstitute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, CIBERER Instituto de Salud Carlos III, 28046, Madrid, Spain.
Suman VermaResearchDx, Inc., 5 Mason, Irvine, CA, 92618, USA.
Kimbley WalkerHuman Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
Charles WangCenter for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA.
Junwen WangCenter for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, 85259, USA.
Yexun WangResearch and Development, QIAGEN Sciences Inc., Frederick, MD, 21703, USA.
Zhining WenCollege of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China.
Valtteri WirtaScience for Life Laboratory, Karolinska Institutet, Tomtebodavägen 23B, 171 65, Solna, Sweden.
Leihong WuDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Chunlin XiaoNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD, 20894, USA.
Wenzhong XiaoStanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA.
Shibei XuDepartment of Biostatistics, Columbia Mailman School of Public Health, 722 West 168th St., New York, NY, 10032, USA.
Mary YangDepartment of Information Science, University of Arkansas at Little Rock, 2801 S. Univ. Ave, Little Rock, AR, 72204, USA.
Jianming YingDepartment of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China.
Shun H YipCenter for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, 85259, USA.
Guangliang ZhangClinical Laboratory, Burning Rock Biotech, Guangzhou, 510300, Guangdong, China.
Sa ZhangClinical Laboratory, Burning Rock Biotech, Guangzhou, 510300, Guangdong, China.
Meiru ZhaoGeneplus, PKUCare Industrial Park, Changping District, Beijing, 102206, China.
Yuanting ZhengState Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China.
Xiaoyan ZhouDepartment of Pathology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
Christopher E MasonDepartment of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA.
Timothy MercerAustralian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia.
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. lemingshi@fudan.edu.cn.
Wendell JonesQ2 Solutions - EA Genomics, 5927 S Miami Blvd, Morrisville, NC, 27560, USA. wendell.jones@q2labsolutions.com.
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.ORCID http://orcid.org/0000-0001-5313-5847
National Center for Toxicological Research · USAgilent Technologies (United States) · USCancer Genetics (United States) · USBaylor College of Medicine · USBurning Rock Biotech (China) · CNCornell University · USGarvan Institute of Medical Research · AUGreenwood Genetic Center · USIcahn School of Medicine at Mount Sinai · USNational Institutes of Health · USARUP Laboratories (United States) · USCourtagen Life Sciences (United States) · USFudan University Shanghai Cancer Center · CNHarvard University · USHospital Universitario La Paz · ESIllumina (United States) · USIntegrated DNA Technologies (United States) · USMayo Clinic · USShanghai Medical College of Fudan University · CNThermo Fisher Scientific (United States) · US

Funding

National Biomedical Information ServicesZIHLM200888 · NLM · NATIONAL LIBRARY OF MEDICINE · PI PALTOO, DINA · 2009 to 2025
$5200.7M
Women's Cancer ProgramP30CA015083 · NCI · MAYO CLINIC ROCHESTER · PI AKHILESH PANDEY · 1985 to 2026
$151.3M
Microarray and Genome InformaticsZIAES102345 · NIEHS · NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES · PI BUSHEL, ROBERT · 2009 to 2021
$10.8M
Bioinformatics CoreZICHL006228 · NHLBI · NATIONAL HEART, LUNG, AND BLOOD INSTITUTE · PI PIROOZNIA, MEHDI · 2017 to 2021
$6.6M
DEVELOP NOVEL DEEP LEARNING AND COMBINATORIAL OPTIMIZATION METHODS TO IDENTIFY KEY DISEASE REGULATORY ELEMENTS FOR SINGLE-CELL DATAR15GM137288 · NIGMS · UNIVERSITY OF ARKANSAS AT LITTLE ROCK · PI YANG, MARY · 2020 to 2020
$444k
Developing integrative approaches for identifying disease-causing genes and dysfunctional networksR15GM114739 · NIGMS · UNIVERSITY OF ARKANSAS AT LITTLE ROCK · PI YANG, MARY · 2015 to 2015
$374k
NCI NIH HHS P30 CA015083NIGMS NIH HHS R15 GM114739NIGMS NIH HHS R15 GM137288U.S. Food and Drug Administration E0765001U.S. Food and Drug Administration E0767001
6 · The paper itself

Abstract

backgroundTargeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing.

resultsAll panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5-20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden.

conclusionThis comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.

Indexed as

Biomarkers, TumorOncogenesDNA Copy Number VariationsGenetic TestingGenomicsHumansMolecular Diagnostic TechniquesMutationNeoplasmsPolymorphism, Single NucleotideReproducibility of ResultsSensitivity and SpecificityBiomarkers, TumorAnalytical performanceMolecular diagnosticsOncopanel sequencingPrecision medicineReproducibilityTarget enrichment

Identifiers

PMID33863344
PMCPMC8051090
OpenAlexW3154107589

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.