-
Je něco špatně v tomto záznamu ?
A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
W. Jones, B. Gong, N. Novoradovskaya, D. Li, R. Kusko, TA. Richmond, DJ. Johann, H. Bisgin, SME. Sahraeian, PR. Bushel, M. Pirooznia, K. Wilkins, M. Chierici, W. Bao, LS. Basehore, AB. Lucas, D. Burgess, DJ. Butler, S. Cawley, CJ. Chang, G. Chen,...
Jazyk angličtina Země Velká Británie
Typ dokumentu časopisecké články, práce podpořená grantem
NLK
BioMedCentral
od 2001
Directory of Open Access Journals
od 2000
PubMed Central
od 2001
ProQuest Central
od 2015-01-01
Open Access Digital Library
od 2000-01-01
Open Access Digital Library
od 2000-01-01
Medline Complete (EBSCOhost)
od 2011-02-01
Health & Medicine (ProQuest)
od 2015-01-01
ROAD: Directory of Open Access Scholarly Resources
od 2001
Springer Nature OA/Free Journals
od 2000-02-01
- MeSH
- alely * MeSH
- frekvence genu * MeSH
- genetická heterogenita MeSH
- genetická variace * MeSH
- genetické testování metody normy MeSH
- genomika metody normy MeSH
- lidé MeSH
- nádorové biomarkery * MeSH
- nádorové buněčné linie MeSH
- nádory diagnóza genetika MeSH
- průběh práce MeSH
- variabilita počtu kopií segmentů DNA MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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.
Agilent Technologies 11011 N Torrey Pines Rd La Jolla CA 92037 USA
Agilent Technologies 1834 State Hwy 71 West Cedar Creek TX 78612 USA
Agilent Technologies 5301 Stevens Creek Blvd Santa Clara CA 95051 USA
Bioinformatics Integrated DNA Technologies Inc 1710 Commercial Park Coralville IA 52241 USA
Bioinformatics Research Institute of Molecular Biotechnology Boku University Vienna Vienna Austria
College of Chemistry Sichuan University Chengdu 610064 Sichuan China
Department of Biotechnology Boku University Vienna Austria
Department of Epidemiology School of Public Health Fudan University Shanghai China
Fondazione Bruno Kessler 38123 Trento Italy
Fudan Gospel Joint Research Center for Precision Medicine Fudan University Shanghai 200438 China
Human Phenome Institute Fudan University Shanghai 201203 China
Illumina Inc 5200 Illumina Way San Diego CA 92122 USA
Immuneering Corporation One Broadway 14th Floor Cambridge MA 02142 USA
Institute for Molecular Medicine Finland Helsinki Finland
JMP Life Sciences SAS Institute Inc Cary NC 27519 USA
Kelly Government Solutions Inc Research Triangle Park NC 27709 USA
Małopolska Centre of Biotechnology Jagiellonian University Krakow Poland
Marketing Integrated DNA Technologies Inc 1710 Commercial Park Coralville IA 52241 USA
Massachusetts General Hospital Harvard Medical School Boston MA 02114 USA
National Institute of Environmental Health Sciences Research Triangle Park Durham NC 27709 USA
Q2 Solutions EA Genomics 5927 S Miami Blvd Morrisville NC 27560 USA
Research and Development Burning Rock Biotech Shanghai 201114 China
Research and Development QIAGEN Sciences Inc Frederick MD 21703 USA
Research and Development Roche Sequencing Solutions Inc 500 South Rosa Rd Madison WI 53719 USA
Stanford Genome Technology Center Stanford University Palo Alto CA 94304 USA
Thermo Fisher Scientific 110 Miller Ave Ann Arbor MI 48104 USA
University of Arkansas at Little Rock Little Rock AR 72204 USA
University of North Carolina Health 101 Manning Drive Chapel Hill NC 27514 USA
University of Texas Southwestern Medical Center 2330 Inwood Rd Dallas TX 75390 USA
Citace poskytuje Crossref.org
- 000
- 00000naa a2200000 a 4500
- 001
- bmc22012470
- 003
- CZ-PrNML
- 005
- 20220506130321.0
- 007
- ta
- 008
- 220425s2021 xxk f 000 0|eng||
- 009
- AR
- 024 7_
- $a 10.1186/s13059-021-02316-z $2 doi
- 035 __
- $a (PubMed)33863366
- 040 __
- $a ABA008 $b cze $d ABA008 $e AACR2
- 041 0_
- $a eng
- 044 __
- $a xxk
- 100 1_
- $a Jones, Wendell $u Q2 Solutions - EA Genomics, 5927 S Miami Blvd., Morrisville, NC, 27560, USA. Wendell.Jones@q2labsolutions.com $1 https://orcid.org/0000000296765387
- 245 12
- $a A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency / $c W. Jones, B. Gong, N. Novoradovskaya, D. Li, R. Kusko, TA. Richmond, DJ. Johann, H. Bisgin, SME. Sahraeian, PR. Bushel, M. Pirooznia, K. Wilkins, M. Chierici, W. Bao, LS. Basehore, AB. Lucas, D. Burgess, DJ. Butler, S. Cawley, CJ. Chang, G. Chen, T. Chen, YC. Chen, DJ. Craig, A. Del Pozo, J. Foox, M. Francescatto, Y. Fu, C. Furlanello, K. Giorda, KP. Grist, M. Guan, Y. Hao, S. Happe, G. Hariani, N. Haseley, J. Jasper, G. Jurman, DP. Kreil, P. Łabaj, K. Lai, J. Li, QZ. Li, Y. Li, Z. Li, Z. Liu, MS. López, K. Miclaus, R. Miller, VK. Mittal, M. Mohiyuddin, C. Pabón-Peña, BL. Parsons, F. Qiu, A. Scherer, T. Shi, S. Stiegelmeyer, C. Suo, N. Tom, D. Wang, Z. Wen, L. Wu, W. Xiao, C. Xu, Y. Yu, J. Zhang, Y. Zhang, Z. Zhang, Y. Zheng, CE. Mason, JC. Willey, W. Tong, L. Shi, J. Xu
- 520 9_
- $a BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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.
- 650 12
- $a alely $7 D000483
- 650 12
- $a nádorové biomarkery $7 D014408
- 650 _2
- $a nádorové buněčné linie $7 D045744
- 650 _2
- $a variabilita počtu kopií segmentů DNA $7 D056915
- 650 12
- $a frekvence genu $7 D005787
- 650 _2
- $a genetická heterogenita $7 D018740
- 650 _2
- $a genetické testování $x metody $x normy $7 D005820
- 650 12
- $a genetická variace $7 D014644
- 650 _2
- $a genomika $x metody $x normy $7 D023281
- 650 _2
- $a lidé $7 D006801
- 650 _2
- $a nádory $x diagnóza $x genetika $7 D009369
- 650 _2
- $a průběh práce $7 D057188
- 655 _2
- $a časopisecké články $7 D016428
- 655 _2
- $a práce podpořená grantem $7 D013485
- 700 1_
- $a Gong, Binsheng $u Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
- 700 1_
- $a Novoradovskaya, Natalia $u Agilent Technologies, 11011 N Torrey Pines Rd., La Jolla, CA, 92037, USA
- 700 1_
- $a Li, Dan $u Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
- 700 1_
- $a Kusko, Rebecca $u Immuneering Corporation, One Broadway, 14th Floor, Cambridge, MA, 02142, USA
- 700 1_
- $a Richmond, Todd A $u Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., 4300 Hacienda Dr., Pleasanton, CA, 94588, USA
- 700 1_
- $a Johann, Donald J $u Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W Markham St., Little Rock, AR, 72205, USA
- 700 1_
- $a Bisgin, Halil $u Department of Computer Science, Engineering and Physics, University of Michigan-Flint, Flint, MI, 48502, USA
- 700 1_
- $a Sahraeian, Sayed Mohammad Ebrahim $u Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., 1301 Shoreway Rd., Suite 7 #300, Belmont, CA, 94002, USA
- 700 1_
- $a Bushel, Pierre R $u National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, 27709, USA
- 700 1_
- $a Pirooznia, Mehdi $u Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- 700 1_
- $a Wilkins, Katherine $u Agilent Technologies, 5301 Stevens Creek Blvd., Santa Clara, CA, 95051, USA
- 700 1_
- $a Chierici, Marco $u Fondazione Bruno Kessler, 38123, Trento, Italy
- 700 1_
- $a Bao, Wenjun $u JMP Life Sciences, SAS Institute Inc., Cary, NC, 27519, USA
- 700 1_
- $a Basehore, Lee Scott $u Agilent Technologies, 11011 N Torrey Pines Rd., La Jolla, CA, 92037, USA
- 700 1_
- $a Lucas, Anne Bergstrom $u Agilent Technologies, 5301 Stevens Creek Blvd., Santa Clara, CA, 95051, USA
- 700 1_
- $a Burgess, Daniel $u (formerly) Research and Development, Roche Sequencing Solutions Inc., 500 South Rosa Rd., Madison, WI, 53719, USA
- 700 1_
- $a Butler, Daniel J $u Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
- 700 1_
- $a Cawley, Simon $u (formerly) Clinical Sequencing Division, Thermo Fisher Scientific, 180 Oyster Point Blvd., South San Francisco, CA, 94080, USA
- 700 1_
- $a Chang, Chia-Jung $u Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA
- 700 1_
- $a Chen, Guangchun $u Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, 5323 Harry Hine Blvd., Dallas, TX, 75390, USA
- 700 1_
- $a Chen, Tao $u University of Texas Southwestern Medical Center, 2330 Inwood Rd., Dallas, TX, 75390, USA
- 700 1_
- $a Chen, Yun-Ching $u Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- 700 1_
- $a Craig, Daniel J $u Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, 43614, USA
- 700 1_
- $a Del Pozo, Angela $u Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, CIBERER Instituto de Salud Carlos III, 28046, Madrid, Spain
- 700 1_
- $a Foox, Jonathan $u Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
- 700 1_
- $a Francescatto, Margherita $u Fondazione Bruno Kessler, 38123, Trento, Italy
- 700 1_
- $a Fu, Yutao $u Thermo Fisher Scientific, 110 Miller Ave., Ann Arbor, MI, 48104, USA
- 700 1_
- $a Furlanello, Cesare $u Fondazione Bruno Kessler, 38123, Trento, Italy
- 700 1_
- $a Giorda, Kristina $u Marketing, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
- 700 1_
- $a Grist, Kira P $u Q2 Solutions - EA Genomics, 5927 S Miami Blvd., Morrisville, NC, 27560, USA
- 700 1_
- $a Guan, Meijian $u JMP Life Sciences, SAS Institute Inc., Cary, NC, 27519, USA
- 700 1_
- $a Hao, Yingyi $u College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China
- 700 1_
- $a Happe, Scott $u Agilent Technologies, 1834 State Hwy 71 West, Cedar Creek, TX, 78612, USA
- 700 1_
- $a Hariani, Gunjan $u Q2 Solutions - EA Genomics, 5927 S Miami Blvd., Morrisville, NC, 27560, USA
- 700 1_
- $a Haseley, Nathan $u Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
- 700 1_
- $a Jasper, Jeff $u Q2 Solutions - EA Genomics, 5927 S Miami Blvd., Morrisville, NC, 27560, USA
- 700 1_
- $a Jurman, Giuseppe $u Fondazione Bruno Kessler, 38123, Trento, Italy
- 700 1_
- $a Kreil, David Philip $u Bioinformatics Research, Institute of Molecular Biotechnology, Boku University Vienna, Vienna, Austria
- 700 1_
- $a Łabaj, Paweł $u Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland $u Department of Biotechnology, Boku University, Vienna, Austria
- 700 1_
- $a Lai, Kevin $u Bioinformatics, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
- 700 1_
- $a Li, Jianying $u Kelly Government Solutions, Inc., Research Triangle Park, NC, 27709, USA
- 700 1_
- $a Li, Quan-Zhen $u Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, 5323 Harry Hine Blvd., Dallas, TX, 75390, USA
- 700 1_
- $a Li, Yulong $u Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
- 700 1_
- $a Li, Zhiguang $u Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
- 700 1_
- $a Liu, Zhichao $u Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
- 700 1_
- $a López, Mario Solís $u Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, CIBERER Instituto de Salud Carlos III, 28046, Madrid, Spain $u EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- 700 1_
- $a Miclaus, Kelci $u JMP Life Sciences, SAS Institute Inc., Cary, NC, 27519, USA
- 700 1_
- $a Miller, Raymond $u Agilent Technologies, 5301 Stevens Creek Blvd., Santa Clara, CA, 95051, USA
- 700 1_
- $a Mittal, Vinay K $u Thermo Fisher Scientific, 110 Miller Ave., Ann Arbor, MI, 48104, USA
- 700 1_
- $a Mohiyuddin, Marghoob $u Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., 1301 Shoreway Rd., Suite 7 #300, Belmont, CA, 94002, USA
- 700 1_
- $a Pabón-Peña, Carlos $u Agilent Technologies, 5301 Stevens Creek Blvd., Santa Clara, CA, 95051, USA
- 700 1_
- $a Parsons, Barbara L $u Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
- 700 1_
- $a Qiu, Fujun $u Research and Development, Burning Rock Biotech, Shanghai, 201114, China
- 700 1_
- $a Scherer, Andreas $u EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands $u 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
- 700 1_
- $a Shi, Tieliu $u 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
- 700 1_
- $a Stiegelmeyer, Suzy $u University of North Carolina Health, 101 Manning Drive, Chapel Hill, NC, 27514, USA
- 700 1_
- $a Suo, Chen $u Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
- 700 1_
- $a Tom, Nikola $u EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands $u Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- 700 1_
- $a Wang, Dong $u Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
- 700 1_
- $a Wen, Zhining $u College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China
- 700 1_
- $a Wu, Leihong $u Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
- 700 1_
- $a Xiao, Wenzhong $u Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA $u Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- 700 1_
- $a Xu, Chang $u Research and Development, QIAGEN Sciences Inc., Frederick, MD, 21703, USA
- 700 1_
- $a Yu, Ying $u State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China
- 700 1_
- $a Zhang, Jiyang $u State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China
- 700 1_
- $a Zhang, Yifan $u University of Arkansas at Little Rock, Little Rock, AR, 72204, USA
- 700 1_
- $a Zhang, Zhihong $u Research and Development, Burning Rock Biotech, Shanghai, 201114, China
- 700 1_
- $a Zheng, Yuanting $u Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA $u State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China
- 700 1_
- $a Mason, Christopher E $u Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
- 700 1_
- $a Willey, James C $u 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
- 700 1_
- $a Tong, Weida $u Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
- 700 1_
- $a Shi, Leming $u State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China $u Human Phenome Institute, Fudan University, Shanghai, 201203, China $u Fudan-Gospel Joint Research Center for Precision Medicine, Fudan University, Shanghai, 200438, China
- 700 1_
- $a Xu, Joshua $u Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA. Joshua.xu@fda.hhs.gov
- 773 0_
- $w MED00006605 $t Genome biology $x 1474-760X $g Roč. 22, č. 1 (2021), s. 111
- 856 41
- $u https://pubmed.ncbi.nlm.nih.gov/33863366 $y Pubmed
- 910 __
- $a ABA008 $b sig $c sign $y p $z 0
- 990 __
- $a 20220425 $b ABA008
- 991 __
- $a 20220506130313 $b ABA008
- 999 __
- $a ok $b bmc $g 1789887 $s 1163671
- BAS __
- $a 3
- BAS __
- $a PreBMC
- BMC __
- $a 2021 $b 22 $c 1 $d 111 $e 20210416 $i 1474-760X $m Genome biology $n Genome Biol $x MED00006605
- LZP __
- $a Pubmed-20220425
