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Gong B, Li D, Zhang Y, Kusko R, Lababidi S, Cao Z, Chen M, Chen N, Chen Q, Chen Q, Dai J, Gan Q, Gao Y, Guo M, Hariani G, He Y, Hou W, Jiang H, Kushwaha G, Li JL, Li J, Li Y, Liu LC, Liu R, Liu S, Meriaux E, Mo M, Moore M, Moss TJ, Niu Q, Patel A, Ren L, Saremi NF, Shang E, Shang J, Song P, Sun S, Urban BJ, Wang D, Wang S, Wen Z, Xiong X, Yang J, Yin L, Zhang C, Zhang R, Bhandari A, Cai W, Eterovic AK, Megherbi DB, Shi T, Suo C, Yu Y, Zheng Y, Novoradovskaya N, Sears RL, Shi L, Jones W, Tong W, Xu J. Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project. Sci Rep 2024; 14:7028. [PMID: 38528062 DOI: 10.1038/s41598-024-57439-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 03/18/2024] [Indexed: 03/27/2024] Open
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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Affiliation(s)
- Binsheng Gong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Dan Li
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Yifan Zhang
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Rebecca Kusko
- Cellino Bio, 750 Main Street, Cambridge, MA, 02143, USA
| | - Samir Lababidi
- 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
| | - Zehui Cao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Mingyang Chen
- Human Phenome Institute, Fudan University, Shanghai, 201203, China
| | - Ning Chen
- iGeneTech Bioscience Co., Ltd., 8 Shengmingyuan Rd., Changping, Beijing, China
| | - Qiaochu Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Jiacheng Dai
- Human Phenome Institute, Fudan University, Shanghai, 201203, China
| | - Qiang Gan
- Clinical Diagnostics Division, Thermo Fisher Scientific, 46500 Kato Rd., Fremont, CA, 94538, USA
| | - Yuechen Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Mingkun Guo
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China
| | - Gunjan Hariani
- Q squared Solutions Genomics, 2400 Ellis Road, Durham, NC, 27703, USA
| | - Yujie He
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Garima Kushwaha
- Guardant Health, Inc., 505 Penobscot Drive, Redwood City, CA, 94063, USA
| | - Jian-Liang Li
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Jianying Li
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Yulan Li
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Liang-Chun Liu
- Clinical Diagnostics Division, Thermo Fisher Scientific, 46500 Kato Rd., Fremont, CA, 94538, USA
| | - Ruimei Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Shiming Liu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Edwin Meriaux
- CMINDS Research Center, University of Massachusetts, Lowell, MA, 01854, USA
| | - Mengqing Mo
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200032, China
| | | | - Tyler J Moss
- Eurofins Viracor, LLC, 18000 W 99th St., Lenexa, KS, 66219, USA
| | - Quanne Niu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Ananddeep Patel
- Eurofins Viracor Biopharma Services, Inc., 18000 W 99th St., Lenexa, KS, 66219, USA
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Nedda F Saremi
- Agilent Technologies, Inc., 11011 N Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Erfei Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Jun Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Ping Song
- Cancer Genomics Laboratory, Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Siqi Sun
- ResearchDx, Irvine, CA, 92618, USA
| | - Brent J Urban
- Eurofins Viracor Biopharma Services, Inc., 18000 W 99th St., Lenexa, KS, 66219, USA
| | - Danke Wang
- Human Phenome Institute, Fudan University, Shanghai, 201203, China
| | - Shangzi Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Zhining Wen
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China
| | - Xiangyi Xiong
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Lihui Yin
- PathGroup, Nashville, TN, 37217, USA
| | - Chao Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Ruolan Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | | | - Wanshi Cai
- iGeneTech Bioscience Co., Ltd., 8 Shengmingyuan Rd., Changping, Beijing, China
| | - Agda Karina Eterovic
- Eurofins Viracor Biopharma Services, Inc., 18000 W 99th St., Lenexa, KS, 66219, USA
| | - Dalila B Megherbi
- CMINDS Research Center, University of Massachusetts, Lowell, MA, 01854, USA
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Chen Suo
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200032, China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | | | - Renee L Sears
- Velsera, 6 Cityplace Dr Suite 550, Creve Coeur, MO, 63141, USA
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Wendell Jones
- Q squared Solutions Genomics, 2400 Ellis Road, Durham, NC, 27703, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
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Dobromyslin VI, Megherbi DB. Augmenting Imaging Biomarker Performance with Blood-Based Gene Expression Levels for Predicting Alzheimer’s Disease Progression. J Alzheimers Dis 2022; 87:583-594. [DOI: 10.3233/jad-215640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background: Structural brain imaging metrics and gene expression biomarkers have previously been used for Alzheimer’s disease (AD) diagnosis and prognosis, but none of these studies explored integration of imaging and gene expression biomarkers for predicting mild cognitive impairment (MCI)-to-AD conversion 1-2 years into the future. Objective: We investigated advantages of combining gene expression and structural brain imaging features for predicting MCI-to-AD conversion. Selection of the differentially expressed genes (DEGs) for classifying cognitively normal (CN) controls and AD patients was benchmarked against previously reported results. Methods: The current work proposes integrating brain imaging and blood gene expression data from two public datasets (ADNI and ANM) to predict MCI-to-AD conversion. A novel pipeline for combining gene expression data from multiple platforms is proposed and evaluated in the two independents patient cohorts. Results: Combining DEGs and imaging biomarkers for predicting MCI-to-AD conversion yielded 0.832-0.876 receiver operating characteristic (ROC) area under the curve (AUC), which exceeded the 0.808-0.840 AUC from using the imaging features alone. With using only three DEGs, the CN versus AD predictive model achieved 0.718, 0.858, and 0.873 cross-validation AUC for the ADNI, ANM1, and ANM2 datasets. Conclusion: For the first time we show that combining gene expression and imaging biomarkers yields better predictive performance than using imaging metrics alone. A novel pipeline for combining gene expression data from multiple platforms is proposed and evaluated to produce consistent results in the two independents patient cohorts. Using an improved feature selection, we show that predictive models with fewer gene expression probes can achieve competitive performance.
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Affiliation(s)
- Vitaly I. Dobromyslin
- Center for Computer Machine/Human Intelligence Networking and Distributed Systems, University of Massachusetts, Lowell, MA, USA
| | - Dalila B. Megherbi
- Center for Computer Machine/Human Intelligence Networking and Distributed Systems, University of Massachusetts, Lowell, MA, USA
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3
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Foox J, Nordlund J, Lalancette C, Gong T, Lacey M, Lent S, Langhorst BW, Ponnaluri VKC, Williams L, Padmanabhan KR, Cavalcante R, Lundmark A, Butler D, Mozsary C, Gurvitch J, Greally JM, Suzuki M, Menor M, Nasu M, Alonso A, Sheridan C, Scherer A, Bruinsma S, Golda G, Muszynska A, Łabaj PP, Campbell MA, Wos F, Raine A, Liljedahl U, Axelsson T, Wang C, Chen Z, Yang Z, Li J, Yang X, Wang H, Melnick A, Guo S, Blume A, Franke V, Ibanez de Caceres I, Rodriguez-Antolin C, Rosas R, Davis JW, Ishii J, Megherbi DB, Xiao W, Liao W, Xu J, Hong H, Ning B, Tong W, Akalin A, Wang Y, Deng Y, Mason CE. The SEQC2 epigenomics quality control (EpiQC) study. Genome Biol 2021; 22:332. [PMID: 34872606 PMCID: PMC8650396 DOI: 10.1186/s13059-021-02529-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA's Epigenomics Quality Control Group. RESULTS Each sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms. CONCLUSIONS The data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.
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Affiliation(s)
- Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Jessica Nordlund
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Claudia Lalancette
- BRCF Epigenomics Core, University of Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Ting Gong
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | | | - Samantha Lent
- AbbVie Genomics Research Center, 1 N. Waukegan Rd, North Chicago, IL, 60036, USA
| | | | | | | | | | - Raymond Cavalcante
- BRCF Epigenomics Core, University of Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Anders Lundmark
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Justin Gurvitch
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - John M Greally
- Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Masako Suzuki
- Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Mark Menor
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | - Masaki Nasu
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | - Alicia Alonso
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Caroline Sheridan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
- Division of Hematology/Oncology, Department of Medicine, Epigenomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Andreas Scherer
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Gosia Golda
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Agata Muszynska
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Paweł P Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Frank Wos
- New York Genome Center, New York, NY, 10013, USA
| | - Amanda Raine
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Ulrika Liljedahl
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Tomas Axelsson
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Zhong Chen
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Zhaowei Yang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jing Li
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaopeng Yang
- Department of Neurology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China
| | - Hongwei Wang
- Development of Medicine, the University of Chicago, Chicago, IL, 60637, USA
| | - Ari Melnick
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Shang Guo
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China
| | - Alexander Blume
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Vedran Franke
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Inmaculada Ibanez de Caceres
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Carlos Rodriguez-Antolin
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Rocio Rosas
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Justin Wade Davis
- AbbVie Genomics Research Center, 1 N. Waukegan Rd, North Chicago, IL, 60036, USA
| | | | - Dalila B Megherbi
- CMINDS Research Center, Francis College of Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Wenming Xiao
- Center for Devices and Radiological Health, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - Will Liao
- New York Genome Center, New York, NY, 10013, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Baitang Ning
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Yunliang Wang
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China.
| | - Youping Deng
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA.
- The Feil Family Brain and Mind Research Institute, New York, New York, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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4
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Deveson IW, Gong B, Lai K, LoCoco JS, Richmond TA, Schageman J, Zhang Z, Novoradovskaya N, Willey JC, Jones W, Kusko R, Chen G, Madala BS, Blackburn J, Stevanovski I, Bhandari A, Close D, Conroy J, Hubank M, Marella N, Mieczkowski PA, Qiu F, Sebra R, Stetson D, Sun L, Szankasi P, Tan H, Tang LY, Arib H, Best H, Burgher B, Bushel PR, Casey F, Cawley S, Chang CJ, Choi J, Dinis J, Duncan D, Eterovic AK, Feng L, Ghosal A, Giorda K, Glenn S, Happe S, Haseley N, Horvath K, Hung LY, Jarosz M, Kushwaha G, Li D, Li QZ, Li Z, Liu LC, Liu Z, Ma C, Mason CE, Megherbi DB, Morrison T, Pabón-Peña C, Pirooznia M, Proszek PZ, Raymond A, Rindler P, Ringler R, Scherer A, Shaknovich R, Shi T, Smith M, Song P, Strahl M, Thodima VJ, Tom N, Verma S, Wang J, Wu L, Xiao W, Xu C, Yang M, Zhang G, Zhang S, Zhang Y, Shi L, Tong W, Johann DJ, Mercer TR, Xu J. Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology. Nat Biotechnol 2021; 39:1115-1128. [PMID: 33846644 PMCID: PMC8434938 DOI: 10.1038/s41587-021-00857-z] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/15/2021] [Indexed: 02/08/2023]
Abstract
Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation of the analytical performance of five industry-leading ctDNA assays. We evaluated each stage of the ctDNA sequencing workflow with simulations, synthetic DNA spike-in experiments and proficiency testing on standardized, cell-line-derived reference samples. Above 0.5% variant allele frequency, ctDNA mutations were detected with high sensitivity, precision and reproducibility by all five assays, whereas, below this limit, detection became unreliable and varied widely between assays, especially when input material was limited. Missed mutations (false negatives) were more common than erroneous candidates (false positives), indicating that the reliable sampling of rare ctDNA fragments is the key challenge for ctDNA assays. This comprehensive evaluation of the analytical performance of ctDNA assays serves to inform best practice guidelines and provides a resource for precision oncology.
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Affiliation(s)
- Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Binsheng Gong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Kevin Lai
- Bioinformatics, Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | - Todd A Richmond
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
| | | | - Zhihong Zhang
- Research and Development, Burning Rock Biotech, Shanghai, China
| | | | - James C Willey
- Departments of Medicine, Pathology, and Cancer Biology, College of Medicine and Life Sciences, University of Toledo Health Sciences Campus, Toledo, OH, USA
| | | | | | - Guangchun Chen
- Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bindu Swapna Madala
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - James Blackburn
- Cancer Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Igor Stevanovski
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | | | - Devin Close
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
| | | | - Michael Hubank
- NIHR Biomedical Research Centre, Royal Marsden Hospital, Sutton, Surrey, UK
| | | | | | - Fujun Qiu
- Research and Development, Burning Rock Biotech, Shanghai, China
| | - Robert Sebra
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Lihyun Sun
- Elim Biopharmaceuticals, Inc., Hayward, CA, USA
| | - Philippe Szankasi
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
| | - Haowen Tan
- Primbio Genes Biotechnology, East Lake High-tech Development Zone, Wuhan, Hubei, China
| | - Lin-Ya Tang
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA
| | - Hanane Arib
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hunter Best
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
- Departments of Pathology and Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Pierre R Bushel
- National Institute of Environmental Health Sciences, Research Triangle Park, Morrisville, NC, USA
| | - Fergal Casey
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
| | - Simon Cawley
- Clinical Sequencing Division, Thermo Fisher Scientific, South San Francisco, CA, USA
| | - Chia-Jung Chang
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Jonathan Choi
- Roche Sequencing Solutions, Inc., Pleasanton, CA, USA
| | - Jorge Dinis
- Roche Sequencing Solutions, Inc., Pleasanton, CA, USA
| | | | - Agda Karina Eterovic
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA
| | - Liang Feng
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
| | | | - Kristina Giorda
- Marketing, Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | | | | | | | - Li-Yuan Hung
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mirna Jarosz
- NGS Products and Services, Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Garima Kushwaha
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
| | - Dan Li
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Quan-Zhen Li
- Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhiguang Li
- Intramural Research Program, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Liang-Chun Liu
- Clinical Diagnostic Division, Thermo Fisher Scientific, Fremont, CA, USA
| | - Zhichao Liu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Charles Ma
- Cancer Genetics, Inc., Rutherford, NJ, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Dalila B Megherbi
- CMINDS Research Center, Department of Electrical and Computer Engineering, College of Engineering, University of Massachusetts Lowell, Lowell, MA, USA
| | | | | | - Mehdi Pirooznia
- Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paula Z Proszek
- NIHR Biomedical Research Centre, Royal Marsden Hospital, Sutton, Surrey, UK
| | | | - Paul Rindler
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
| | | | - Andreas Scherer
- Institute for Molecular Medicine Finland (FIMM), Nordic EMBL Partnership for Molecular Medicine, HiLIFE Unit, Biomedicum Helsinki 2U (D302b), University of Helsinki, Helsinki, Finland
- EATRIS ERIC- European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
| | | | - Tieliu Shi
- Center for Bioinformatics and Computational Biology and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Melissa Smith
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ping Song
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA
| | - Maya Strahl
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Nikola Tom
- EATRIS ERIC- European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Jiashi Wang
- Research and Development, Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Leihong Wu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Wenzhong Xiao
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Chang Xu
- Research and Development, QIAGEN Sciences, Inc., Frederick, MD, USA
| | - Mary Yang
- Department of Information Science, University of Arkansas at Little Rock, Little Rock, AR, USA
| | | | - Sa Zhang
- Clinical Laboratory, Burning Rock Biotech, Guangzhou, China
| | - Yilin Zhang
- Elim Biopharmaceuticals, Inc., Hayward, CA, USA
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
- Fudan-Gospel Joint Research Center for Precision Medicine, Fudan University, Shanghai, China
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Donald J Johann
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - Timothy R Mercer
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Queensland, QLD, Australia.
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
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5
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Gong B, Li D, Kusko R, Novoradovskaya N, Zhang Y, Wang S, Pabón-Peña C, Zhang Z, Lai K, Cai W, LoCoco JS, Lader E, Richmond TA, Mittal VK, Liu LC, Johann DJ, Willey JC, Bushel PR, Yu Y, Xu C, Chen G, Burgess D, Cawley S, Giorda K, Haseley N, Qiu F, Wilkins K, Arib H, Attwooll C, Babson K, Bao L, Bao W, Lucas AB, Best H, Bhandari A, Bisgin H, Blackburn J, Blomquist TM, Boardman L, Burgher B, Butler DJ, Chang CJ, Chaubey A, Chen T, Chierici M, Chin CR, Close D, Conroy J, Cooley Coleman J, Craig DJ, Crawford E, Del Pozo A, Deveson IW, Duncan D, Eterovic AK, Fan X, Foox J, Furlanello C, Ghosal A, Glenn S, Guan M, Haag C, Hang X, Happe S, Hennigan B, Hipp J, Hong H, Horvath K, Hu J, Hung LY, Jarosz M, Kerkhof J, Kipp B, Kreil DP, Łabaj P, Lapunzina P, Li P, Li QZ, Li W, Li Z, Liang Y, Liu S, Liu Z, Ma C, Marella N, Martín-Arenas R, Megherbi DB, Meng Q, Mieczkowski PA, Morrison T, Muzny D, Ning B, Parsons BL, Paweletz CP, Pirooznia M, Qu W, Raymond A, Rindler P, Ringler R, Sadikovic B, Scherer A, Schulze E, Sebra R, Shaknovich R, Shi Q, Shi T, Silla-Castro JC, Smith M, López MS, Song P, Stetson D, Strahl M, Stuart A, Supplee J, Szankasi P, Tan H, Tang LY, Tao Y, Thakkar S, Thierry-Mieg D, Thierry-Mieg J, Thodima VJ, Thomas D, Tichý B, Tom N, Garcia EV, Verma S, Walker K, Wang C, Wang J, Wang Y, Wen Z, Wirta V, Wu L, Xiao C, Xiao W, Xu S, Yang M, Ying J, Yip SH, Zhang G, Zhang S, Zhao M, Zheng Y, Zhou X, Mason CE, Mercer T, Tong W, Shi L, Jones W, Xu J. Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. Genome Biol 2021; 22:109. [PMID: 33863344 PMCID: PMC8051090 DOI: 10.1186/s13059-021-02315-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/18/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Targeted 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. RESULTS All 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. CONCLUSION This 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.
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Affiliation(s)
- 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
| | | | - Yifan Zhang
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
- Department of Information Science, University of Arkansas at Little Rock, 2801 S. Univ. Ave, Little Rock, AR, 72204, USA
| | - Shangzi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China
| | - Carlos Pabón-Peña
- Agilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, CA, 95051, USA
| | - Zhihong Zhang
- Research and Development, Burning Rock Biotech, Shanghai, 201114, China
| | - Kevin Lai
- Bioinformatics, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Wanshi Cai
- iGeneTech, 8 Shengmingyuan Rd., Zhongguancun Life Science Park, Changping District, Beijing, 100080, China
| | | | - Eric Lader
- Research and Development, QIAGEN Sciences Inc., Frederick, MD, 21703, USA
| | - Todd A Richmond
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., 4300 Hacienda Dr, Pleasanton, CA, 94588, USA
| | - Vinay K Mittal
- Thermo Fisher Scientific, 110 Miller Ave, Ann Arbor, MI, 48104, USA
| | - Liang-Chun Liu
- Clinical Diagnostic Division, Thermo Fisher Scientific, 46500 Kato Rd, Fremont, CA, 94538, USA
| | - Donald J Johann
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, USA
| | - James C Willey
- 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
| | - Pierre R Bushel
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China
| | - Chang Xu
- Research and Development, QIAGEN Sciences Inc., Frederick, MD, 21703, USA
| | - Guangchun Chen
- Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, 5323 Harry Hine Blvd, Dallas, TX, 75390, USA
| | - Daniel Burgess
- Research and Development, Roche Sequencing Solutions Inc., 500 South Rosa Rd, Madison, WI, 53719, USA
| | - Simon Cawley
- Clinical Sequencing Division, Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA, 94080, USA
| | - Kristina Giorda
- Marketing, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Nathan Haseley
- Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Fujun Qiu
- Research and Development, Burning Rock Biotech, Shanghai, 201114, China
| | - Katherine Wilkins
- Agilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, CA, 95051, USA
| | - Hanane Arib
- Icahn Institute and Dept. of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA
| | | | - Kevin Babson
- Greenwood Genetic Center, 106 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Longlong Bao
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Institute of Pathology, Fudan University, Shanghai, 200032, China
| | - Wenjun Bao
- JMP Life Sciences, SAS Institute Inc., Cary, NC, 27519, USA
| | | | - Hunter Best
- Departments of Pathology and Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT, 84108, USA
| | | | - Halil Bisgin
- Department of Computer Science, Engineering and Physics, University of Michigan-Flint, Flint, MI, 48502, USA
| | - James Blackburn
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2010, Australia
| | - Thomas M Blomquist
- Department of Pathology, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, 43614, USA
- Lucas County Coroner's Office, 2595 Arlington Ave., Toledo, OH, 43614, USA
| | - Lisa Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Blake Burgher
- OmniSeq, Inc. 700 Ellicott St, Buffalo, NY, 14203, USA
| | - Daniel J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
| | - Chia-Jung Chang
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA
| | - Alka Chaubey
- Greenwood Genetic Center, 106 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Tao Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | | | - Christopher R Chin
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
| | - Devin Close
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT, 84108, USA
| | | | | | - Daniel J Craig
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, 43614, USA
| | - Erin Crawford
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, 43614, USA
| | - Angela Del Pozo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, CIBERER Instituto de Salud Carlos III, 28046, Madrid, Spain
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Daniel Duncan
- Cancer Genetics Inc, 201 Route 17 N, Meadows Office Building, Rutherford, NJ, 07070, USA
| | - Agda Karina Eterovic
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, 6565 MD Anderson Blvd, Houston, TX, 77030, USA
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
| | | | | | - Sean Glenn
- OmniSeq, Inc. 700 Ellicott St, Buffalo, NY, 14203, USA
| | - Meijian Guan
- JMP Life Sciences, SAS Institute Inc., Cary, NC, 27519, USA
| | - Christine Haag
- Molecular Laboratory, Prof. F. Raue, Im Weiher 12, Heidelberg, Germany
| | - Xinyi Hang
- iGeneTech, 8 Shengmingyuan Rd., Zhongguancun Life Science Park, Changping District, Beijing, 100080, China
| | - Scott Happe
- Agilent Technologies, 1834 State Hwy 71 West, Cedar Creek, TX, 78612, USA
| | - Brittany Hennigan
- Greenwood Genetic Center, 106 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Jennifer Hipp
- Department of Pathology, Strata Oncology, Inc., Ann Arbor, MI, 48103, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Kyle Horvath
- ResearchDx, Inc., 5 Mason, Irvine, CA, 92618, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Li-Yuan Hung
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Mirna Jarosz
- NGS Products and Services, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, 800 Commissioners Rd E, London, Ontario, N6A5W9, Canada
| | - Benjamin Kipp
- Division of Anatomic Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - David Philip Kreil
- Bioinformatics Research, Institute of Molecular Biotechnology, Boku University Vienna, Vienna, Austria
| | - Paweł Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Department of Biotechnology, Boku University, Vienna, Austria
| | - Pablo Lapunzina
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPaz, CIBERER Instituto de Salud Carlos III, 28046, Madrid, Spain
- ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, European Commission, Lille, France
| | - Peng Li
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Quan-Zhen Li
- Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, 5323 Harry Hine Blvd, Dallas, TX, 75390, USA
| | - Weihua Li
- Department 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 Li
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Yu Liang
- Geneis, 5 Guangshun North St., Chaoyang District, Beijing, 100102, China
| | - Shaoqing Liu
- GeneSmile Ltd Co., Jiangsu Cancer Hospital, 42 Baiziting St., Xuanwu District, Nanjing, 210009, Jiangsu, China
| | - Zhichao Liu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Charles Ma
- Cancer Genetics Inc, 201 Route 17 N, Meadows Office Building, Rutherford, NJ, 07070, USA
| | - Narasimha Marella
- Cancer Genetics Inc, 201 Route 17 N, Meadows Office Building, Rutherford, NJ, 07070, USA
| | - Rubén Martín-Arenas
- Genycell Biotech España, Calle Garrido Atienza, 18320 Santa Fe, Granada, Spain
| | - Dalila B Megherbi
- CMINDS Research Center, Department of Electrical and Computer Engineering, College of Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Piotr A Mieczkowski
- Department of Genetics, University of North Carolina, 250 Bell Tower Drive, Chapel Hill, NC, 27599, USA
| | - Tom Morrison
- Accugenomics, Inc., 1410 Commonwealth Drive, Suite 105, Wilmington, NC, 20403, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Baitang Ning
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Barbara L Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Cloud P Paweletz
- Translational Research Laboratory, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, 360 Longwood Ave, Boston, MA, 02215, USA
| | - Mehdi Pirooznia
- Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Wubin Qu
- iGeneTech, 8 Shengmingyuan Rd., Zhongguancun Life Science Park, Changping District, Beijing, 100080, China
| | - Amelia Raymond
- Astrazeneca Pharmaceuticals, 35 Gatehouse Dr, Waltham, MA, 02451, USA
| | - Paul Rindler
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT, 84108, USA
| | | | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, 800 Commissioners Rd E, London, Ontario, N6A5W9, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, N6A3K7, Canada
| | - Andreas Scherer
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands
- Institute for Molecular Medicine Finland (FIMM), Nordic EMBL Partnership for Molecular Medicine, HiLIFE Unit, Biomedicum Helsinki 2U (D302b), P.O. Box 20, (Tukholmankatu 8), FI-00014 University of Helsinki, Helsinki, Finland
| | - Egbert Schulze
- Laboratory for Molecular Genetics, Endocrine Practice, Im Weiher 12, 69121, Heidelberg, Germany
| | - Robert Sebra
- Icahn Institute and Dept. of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA
| | - Rita Shaknovich
- Cancer Genetics Inc, 201 Route 17 N, Meadows Office Building, Rutherford, NJ, 07070, USA
| | - Qiang Shi
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Tieliu Shi
- 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
| | | | - Melissa Smith
- Icahn 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 López
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, CIBERER Instituto de Salud Carlos III, 28046, Madrid, Spain
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands
| | - Ping Song
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, 6565 MD Anderson Blvd, Houston, TX, 77030, USA
| | - Daniel Stetson
- Astrazeneca Pharmaceuticals, 35 Gatehouse Dr, Waltham, MA, 02451, USA
| | - Maya Strahl
- Icahn Institute and Dept. of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, 800 Commissioners Rd E, London, Ontario, N6A5W9, Canada
| | - Julianna Supplee
- Translational Research Laboratory, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, 360 Longwood Ave, Boston, MA, 02215, USA
| | - Philippe Szankasi
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT, 84108, USA
| | - Haowen Tan
- Primbio Genes Biotechnology, Building C6-501, Biolake, No.666 Gaoxin Ave., East Lake High-tech Development Zone, Wuhan, 430074, Hubei, China
| | - Lin-Ya Tang
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, 6565 MD Anderson Blvd, Houston, TX, 77030, USA
| | - Yonghui Tao
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Institute of Pathology, Fudan University, Shanghai, 200032, China
| | - Shraddha Thakkar
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Venkat J Thodima
- Cancer Genetics Inc, 201 Route 17 N, Meadows Office Building, Rutherford, NJ, 07070, USA
| | - David Thomas
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2010, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Boris Tichý
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Nikola Tom
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Elena Vallespin Garcia
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, CIBERER Instituto de Salud Carlos III, 28046, Madrid, Spain
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands
| | - Suman Verma
- ResearchDx, Inc., 5 Mason, Irvine, CA, 92618, USA
| | - Kimbley Walker
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
- Division of Microbiology & Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Junwen Wang
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, 85259, USA
- Department of Health Sciences, Mayo Clinic, Scottsdale, AZ, 85259, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, AZ, 85259, USA
| | - Yexun Wang
- Research and Development, QIAGEN Sciences Inc., Frederick, MD, 21703, USA
| | - Zhining Wen
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China
| | - Valtteri Wirta
- Science for Life Laboratory, Karolinska Institutet, Tomtebodavägen 23B, 171 65, Solna, Sweden
| | - Leihong Wu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Chunlin Xiao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD, 20894, USA
| | - Wenzhong Xiao
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Shibei Xu
- Department of Biostatistics, Columbia Mailman School of Public Health, 722 West 168th St., New York, NY, 10032, USA
| | - Mary Yang
- Department of Information Science, University of Arkansas at Little Rock, 2801 S. Univ. Ave, Little Rock, AR, 72204, USA
| | - Jianming Ying
- Department 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 Yip
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, 85259, USA
- Center for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Guangliang Zhang
- Clinical Laboratory, Burning Rock Biotech, Guangzhou, 510300, Guangdong, China
| | - Sa Zhang
- Clinical Laboratory, Burning Rock Biotech, Guangzhou, 510300, Guangdong, China
| | - Meiru Zhao
- Geneplus, PKUCare Industrial Park, Changping District, Beijing, 102206, China
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Institute of Pathology, Fudan University, Shanghai, 200032, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
| | - Timothy Mercer
- Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China.
- Human Phenome Institute, Fudan University, Shanghai, 201203, China.
- Fudan-Gospel Joint Research Center for Precision Medicine, Fudan University, Shanghai, 200438, China.
| | - Wendell Jones
- Q2 Solutions - EA Genomics, 5927 S Miami Blvd, Morrisville, NC, 27560, USA.
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
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