Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing.

Autor: Gong B; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Li D; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Łabaj PP; Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.; Bioinformatics Research, Institute of Molecular Biotechnology, Boku University Vienna, Vienna, Austria., Pan B; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Novoradovskaya N; Agilent Technologies, Inc., 11011 N Torrey Pines Rd., La Jolla, CA, 92037, USA., Thierry-Mieg D; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA., Thierry-Mieg J; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA., Chen G; Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, 5323 Harry Hine Blvd., Dallas, TX, 75390, USA., Bergstrom Lucas A; Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, CA, 95051, USA., LoCoco JS; Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA., Richmond TA; Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., 4300 Hacienda Dr., Pleasanton, CA, 94588, USA., Tseng E; PacBio, San Francisco, USA., Kusko R; Cellino Bio, 750 Main Street, Cambridge, MA, 02143, USA., Happe S; Agilent Technologies, Inc., 1834 State Hwy 71 West, Cedar Creek, TX, 78612, USA., Mercer TR; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia., Pabón-Peña C; Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, CA, 95051, USA., Salmans M; Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA., Tilgner HU; Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.; Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA., Xiao W; Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA.; Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA., Johann DJ Jr; Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301W Markham St., Little Rock, AR, 72205, USA., Jones W; Q squared Solutions Genomics, 2400 Elis Road, Durham, NC, 27703, USA., Tong W; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Mason CE; Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA. chm2042@med.cornell.edu.; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu.; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu., Kreil DP; Bioinformatics Research, Institute of Molecular Biotechnology, Boku University Vienna, Vienna, Austria. David.Kreil@boku.ac.at., Xu J; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA. Joshua.Xu@fda.hhs.gov.

Publikováno v: Scientific data [Sci Data] 2024 Aug 16; Vol. 11 (1), pp. 892. Date of Electronic Publication: 2024 Aug 16.

Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA.

Autor: Gong B; Division of Bioinformatics and Biostatistics, Office of Research, National Center for Toxicological Research, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA., Lababidi S; Health Informatics Staff, 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., Kusko R; Cellino Biotech, 750 Main Street, Cambridge, MA, 02143, USA., Bouri K; Office of Regulatory Science and Innovation, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA., Prezek S; Booz Allen Hamilton, McLean, VA, 22102, USA., Thovarai V; Booz Allen Hamilton, McLean, VA, 22102, USA., Prasanna A; Booz Allen Hamilton, McLean, VA, 22102, USA., Maier EJ; Booz Allen Hamilton, McLean, VA, 22102, USA., Golkaram M; Illumina, Inc., San Diego, CA, 92122, USA., Sun X; Genetalks, Changsha, Hunan, China., Kyriakidis K; UC Santa Cruz Genomics Institute, Santa Cruz, CA, 95060, USA., Kitajima JP; Mendelics, Av. Braz Leme, 1631-Santana, São Paulo, SP, 02511-000, Brazil., Ebrahim Sahraeian SM; Roche Sequencing Solutions, Santa Clara, CA, 95050, USA., Guo Y; Roche Sequencing Solutions, Santa Clara, CA, 95050, USA., Johanson E; Health Informatics Staff, 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., Jones W; Q squared Solutions Genomics, 2400 Elis Road, Durham, NC, 27703, USA., Tong W; Division of Bioinformatics and Biostatistics, Office of Research, National Center for Toxicological Research, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA., Xu J; Division of Bioinformatics and Biostatistics, Office of Research, National Center for Toxicological Research, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA. Joshua.Xu@fda.hhs.gov.

Publikováno v: Scientific reports [Sci Rep] 2024 Apr 08; Vol. 14 (1), pp. 8165. Date of Electronic Publication: 2024 Apr 08.

Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies.

Autor: Talsania K; Sequencing Facility Bioinformatics Group, Advanced Biomedical and Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.; Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA., Shen TW; Sequencing Facility Bioinformatics Group, Advanced Biomedical and Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.; Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA., Chen X; Sequencing Facility Bioinformatics Group, Advanced Biomedical and Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.; Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA., Jaeger E; Illumina Inc, Foster City, CA, USA., Li Z; Sentieon Inc, Mountain View, CA, USA., Chen Z; Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA., Chen W; Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA., Tran B; Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA., Kusko R; Immuneering Corp, Cambridge, MA, USA., Wang L; Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA., Pang AWC; Bionano Genomics, San Diego, CA92121, USA., Yang Z; 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., Choudhari S; Sequencing Facility Bioinformatics Group, Advanced Biomedical and Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.; Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA., Colgan M; Center for Drug Evaluation and Research, FDA, Silver Spring, MD, USA., Fang LT; Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc, 1301 Shoreway Road, Belmont, CA, 94002, USA., Carroll A; DNAnexus, Mountain View, CA, USA., Shetty J; Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA., Kriga Y; Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA., German O; Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA., Smirnova T; Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA., Liu T; Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA., Li J; 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., Kellman B; Bionano Genomics, San Diego, CA92121, USA., Hong K; Bionano Genomics, San Diego, CA92121, USA., Hastie AR; Bionano Genomics, San Diego, CA92121, USA., Natarajan A; Illumina Inc, Foster City, CA, USA., Moshrefi A; Illumina Inc, Foster City, CA, USA., Granat A; Illumina Inc, Foster City, CA, USA., Truong T; Illumina Inc, Foster City, CA, USA., Bombardi R; Illumina Inc, Foster City, CA, USA., Mankinen V; Dovetail Genomics, Scotts Valley, CA, USA., Meerzaman D; Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD, USA., Mason CE; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA., Collins J; Sequencing Facility Bioinformatics Group, Advanced Biomedical and Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.; Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA., Stahlberg E; Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA., Xiao C; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA., Wang C; Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA. chwang@llu.edu., Xiao W; Center for Drug Evaluation and Research, FDA, Silver Spring, MD, USA. Wenming.Xiao@fda.hhs.gov., Zhao Y; Sequencing Facility Bioinformatics Group, Advanced Biomedical and Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA. Yongmei.Zhao@nih.gov.; Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA. Yongmei.Zhao@nih.gov.

Publikováno v: Genome biology [Genome Biol] 2022 Dec 13; Vol. 23 (1), pp. 255. Date of Electronic Publication: 2022 Dec 13.

Ultra-deep multi-oncopanel sequencing of benchmarking samples with a wide range of variant allele frequencies.

Autor: Gong B; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Kusko R; Immuneering Corporation, One Broadway, 14th Floor, Cambridge, MA, 02142, USA., Jones W; Q2 Solutions - EA Genomics, 5927 S Miami Blvd., Morrisville, NC, 27560, USA., Tong W; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Xu J; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA. Joshua.Xu@fda.hhs.gov.

Publikováno v: Scientific data [Sci Data] 2022 Jun 09; Vol. 9 (1), pp. 288. Date of Electronic Publication: 2022 Jun 09.

Assessing reproducibility of inherited variants detected with short-read whole genome sequencing.

Autor: Pan B; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Ren L; State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.; Human Phenome Institute, Fudan University, Shanghai, 200438, China., Onuchic V; Illumina Inc., San Diego, CA, 92122, USA., Guan M; SAS Institute Inc., Cary, NC, 27513, USA., Kusko R; Immuneering Corporation, Cambridge, MA, 02142, USA., Bruinsma S; Illumina Inc., San Diego, CA, 92122, USA., Trigg L; Real Time Genomics, Hamilton, New Zealand., Scherer A; Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.; EATRIS ERIC- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands., Ning B; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Zhang C; School of Computing Sciences and Computer Engineering, University of Southern Mississippi, Hattiesburg, MS, 39406, USA., Glidewell-Kenney C; Illumina Inc., San Diego, CA, 92122, USA., Xiao C; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA., Donaldson E; Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA., Sedlazeck FJ; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA., Schroth G; Illumina Inc., San Diego, CA, 92122, USA., Yavas G; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Grunenwald H; Illumina Inc., San Diego, CA, 92122, USA., Chen H; Sentieon Inc., San Jose, CA, 95134, USA., Meinholz H; Illumina Inc., San Diego, CA, 92122, USA., Meehan J; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Wang J; Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China., Yang J; State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.; Human Phenome Institute, Fudan University, Shanghai, 200438, China., Foox J; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA., Shang J; State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.; Human Phenome Institute, Fudan University, Shanghai, 200438, China., Miclaus K; SAS Institute Inc., Cary, NC, 27513, USA., Dong L; Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China., Shi L; State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.; Human Phenome Institute, Fudan University, Shanghai, 200438, China., Mohiyuddin M; Roche Sequencing Solutions, Santa Clara, CA, 95050, USA., Pirooznia M; Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA., Gong P; Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, 39180, USA., Golshani R; Illumina Inc., San Diego, CA, 92122, USA., Wolfinger R; SAS Institute Inc., Cary, NC, 27513, USA., Lababidi S; Office of Health Informatics, Office of the Commissioner, US Food and Drug Administration, Silver Spring, MD, 20993, USA., Sahraeian SME; Roche Sequencing Solutions, Santa Clara, CA, 95050, USA., Sherry S; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA., Han T; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Chen T; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Shi T; The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China., Hou W; State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.; Human Phenome Institute, Fudan University, Shanghai, 200438, China., Ge W; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Zou W; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Guo W; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Bao W; SAS Institute Inc., Cary, NC, 27513, USA., Xiao W; Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA, 94305, USA., Fan X; Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China., Gondo Y; Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, 259-1193, Japan., Yu Y; State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.; Human Phenome Institute, Fudan University, Shanghai, 200438, China., Zhao Y; CCR-SF Bioinformatics Group, Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA., Su Z; Takeda Pharmaceuticals, Cambridge, MA, 02139, USA., Liu Z; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Tong W; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA., Xiao W; Division of Molecular Genetics and Pathology, Center for Device and Radiological Health, US Food and Drug Administration, Silver Spring, MD, 20993, USA., Zook JM; Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA. justin.zook@nist.gov., Zheng Y; State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China. zhengyuanting@fudan.edu.cn.; Human Phenome Institute, Fudan University, Shanghai, 200438, China. zhengyuanting@fudan.edu.cn., Hong H; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA. huixiao.hong@fda.hhs.gov.

Publikováno v: Genome biology [Genome Biol] 2022 Jan 03; Vol. 23 (1), pp. 2. Date of Electronic Publication: 2022 Jan 03.