A Microdissection Protocol for Proteogenomic Analysis of Histological Sections to Advance Drug Development.

Autor: Shin IJ; Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA., Tangrea M; Department of Biology, Loyola University Maryland, Baltimore, MD, USA., Emmert-Buck M; Avoneaux Medical Institute, Baltimore, MD, USA., Johann DJ Jr; Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA.

Publikováno v: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2024; Vol. 2823, pp. 55-75.

Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples.

Autor: Zhang Y; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA., Blomquist TM; (Formerly) 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., Kusko R; Immuneering Corporation, 245 Main St, Cambridge, MA, 02142, USA., Stetson D; Astrazeneca Pharmaceuticals, 35 Gatehouse Dr, Waltham, MA, 02451, USA., Zhang Z; Research and Development, Burning Rock Biotech, Shanghai, 201114, China., Yin L; (Formerly) Pathology and Laboratory Medicine Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA., Sebra R; Icahn Institute and Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA., Gong B; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA., Lococo JS; Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA., Mittal VK; Thermo Fisher Scientific, 110 Miller Ave, Ann Arbor, MI, 48104, USA., Novoradovskaya N; Agilent Technologies, 11011 N Torrey Pines Rd, La Jolla, CA, 92037, USA., Yeo JY; Department of Pathology, University of Toledo, 3000 Arlington Ave, Toledo, OH, 43614, USA., Dominiak N; Department of Pathology, University of Toledo, 3000 Arlington Ave, Toledo, OH, 43614, USA., Hipp J; Department of Pathology, Strata Oncology, Inc., Ann Arbor, MI, 48103, USA., Raymond A; Astrazeneca Pharmaceuticals, 35 Gatehouse Dr, Waltham, MA, 02451, USA., Qiu F; Research and Development, Burning Rock Biotech, Shanghai, 201114, China., Arib H; Icahn Institute and Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA., Smith ML; Icahn Institute and Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA., Brock JE; Pathology and Laboratory Medicine Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA., Farkas DH; Pathology and Laboratory Medicine Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA., Craig DJ; Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, 43614, USA., Crawford EL; Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, 43614, USA., Li D; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA., Morrison T; Accugenomics, Inc., 1410 Commonwealth Drive, Suite 105, Wilmington, NC, 20403, USA., Tom N; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.; EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands., Xiao W; Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.; Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA., Yang M; Department of Information Science, University of Arkansas at Little Rock, 2801 S. Univ. Ave, Little Rock, AR, 72204, USA., Mason CE; Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA., Richmond TA; Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., 4300 Hacienda Dr, Pleasanton, CA, 94588, USA., Jones W; Q2 Solutions - EA Genomics, 5927 S Miami Blvd, Morrisville, NC, 27560, USA., Johann DJ Jr; Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, USA., Shi L; 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., Tong W; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA., Willey JC; 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. james.willey2@utoledo.edu., Xu J; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA. joshua.xu@fda.hhs.gov.

Publikováno v: Genome biology [Genome Biol] 2022 Jun 29; Vol. 23 (1), pp. 141. Date of Electronic Publication: 2022 Jun 29.

Microdissection Methods Utilizing Single-Cell Subtype Analysis and the Impact on Precision Medicine.

Autor: Johann DJ Jr; Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA., Laun S; Alvin & Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA., Shin IJ; Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA., Weigman R; Alvin & Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA., Stephens O; Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA., Roberge A; Alvin & Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA., Liu M; Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA., Greisman V; Alvin & Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA.; Biology Department, Loyola University Maryland, Baltimore, MD, USA., Steliga M; Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA., Muesse J; Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA., Peterson E; Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA., Emmert-Buck MR; Avoneaux Medical Institute, LifeBridge Health BioIncubator, Baltimore, MD, USA., Tangrea MA; Alvin & Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA. matangrea@loyola.edu.; Biology Department, Loyola University Maryland, Baltimore, MD, USA. matangrea@loyola.edu.

Publikováno v: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2022; Vol. 2394, pp. 93-107.

Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA.

Autor: Willey JC; College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA., Morrison TB; AccuGenomics Inc., The Atrium, Suite 105, 1410 Commonwealth Drive, Wilmington, NC 28403, USA., Austermiller B; AccuGenomics Inc., The Atrium, Suite 105, 1410 Commonwealth Drive, Wilmington, NC 28403, USA., Crawford EL; College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA., Craig DJ; College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA., Blomquist TM; College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA., Jones WD; Q Solutions, EA Genomics, Morrisville, NC 27560, USA., Wali A; Q Solutions, EA Genomics, Morrisville, NC 27560, USA., Lococo JS; Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA., Haseley N; Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA., Richmond TA; Roche Sequencing Solutions Inc., Pleasanton, CA 94588, USA., Novoradovskaya N; Agilent Technologies, La Jolla, CA 92037, USA., Kusko R; Immuneering Corporation, Cambridge, MA 02142, USA., Chen G; University of Texas Southwestern Medical Center, Dallas, TX 75390, USA., Li QZ; University of Texas Southwestern Medical Center, Dallas, TX 75390, USA., Johann DJ Jr; Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W Markham Street, Little Rock, AR 72205, USA., Deveson IW; Garvan Institute of Medical Research, Sydney, NSW 2010, Australia.; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia., Mercer TR; Garvan Institute of Medical Research, Sydney, NSW 2010, Australia.; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia., Wu L; 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.

Publikováno v: Cell reports methods [Cell Rep Methods] 2021 Nov 03; Vol. 1 (7), pp. 100106. Date of Electronic Publication: 2021 Nov 03 (Print Publication: 2021).

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology.

Autor: Deveson IW; 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., Gong B; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA., Lai K; Bioinformatics, Integrated DNA Technologies, Inc., Coralville, IA, USA., LoCoco JS; Illumina, Inc., San Diego, CA, USA., Richmond TA; Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA., Schageman J; Clinical Sequencing Division, Thermo Fisher Scientific, Austin, TX, USA., Zhang Z; Research and Development, Burning Rock Biotech, Shanghai, China., Novoradovskaya N; Agilent Technologies, La Jolla, CA, USA., Willey JC; Departments of Medicine, Pathology, and Cancer Biology, College of Medicine and Life Sciences, University of Toledo Health Sciences Campus, Toledo, OH, USA., Jones W; Q2 Solutions - EA Genomics, Morrisville, NC, USA., Kusko R; Immuneering Corporation, Cambridge, MA, USA., Chen G; Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA., Madala BS; Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia., Blackburn J; Cancer Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia.; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia., Stevanovski I; Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia., Bhandari A; ResearchDx, Inc., Irvine, CA, USA., Close D; R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA., Conroy J; OmniSeq, Inc., Buffalo, NY, USA., Hubank M; NIHR Biomedical Research Centre, Royal Marsden Hospital, Sutton, Surrey, UK., Marella N; Cancer Genetics, Inc., Rutherford, NJ, USA., Mieczkowski PA; Department of Genetics, University of North Carolina, Chapel Hill, NC, USA., Qiu F; Research and Development, Burning Rock Biotech, Shanghai, China., Sebra R; Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA., Stetson D; Astrazeneca Pharmaceuticals, Waltham, MA, USA., Sun L; Elim Biopharmaceuticals, Inc., Hayward, CA, USA., Szankasi P; R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA., Tan H; Primbio Genes Biotechnology, East Lake High-tech Development Zone, Wuhan, Hubei, China., Tang LY; Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA., Arib H; Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA., Best H; 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., Burgher B; OmniSeq, Inc., Buffalo, NY, USA., Bushel PR; National Institute of Environmental Health Sciences, Research Triangle Park, Morrisville, NC, USA., Casey F; Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA., Cawley S; Clinical Sequencing Division, Thermo Fisher Scientific, South San Francisco, CA, USA., Chang CJ; Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA., Choi J; Roche Sequencing Solutions, Inc., Pleasanton, CA, USA., Dinis J; Roche Sequencing Solutions, Inc., Pleasanton, CA, USA., Duncan D; Cancer Genetics, Inc., Rutherford, NJ, USA., Eterovic AK; Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA., Feng L; Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA., Ghosal A; ResearchDx, Inc., Irvine, CA, USA., Giorda K; Marketing, Integrated DNA Technologies, Inc., Coralville, IA, USA., Glenn S; OmniSeq, Inc., Buffalo, NY, USA., Happe S; Agilent Technologies, Cedar Creek, TX, USA., Haseley N; Illumina, Inc., San Diego, CA, USA., Horvath K; ResearchDx, Inc., Irvine, CA, USA., Hung LY; Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Jarosz M; NGS Products and Services, Integrated DNA Technologies, Inc., Coralville, IA, USA., Kushwaha G; Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA., Li D; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA., Li QZ; Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA., Li Z; Intramural Research Program, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA., Liu LC; Clinical Diagnostic Division, Thermo Fisher Scientific, Fremont, CA, USA., Liu Z; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA., Ma C; Cancer Genetics, Inc., Rutherford, NJ, USA., Mason CE; Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, USA., Megherbi DB; CMINDS Research Center, Department of Electrical and Computer Engineering, College of Engineering, University of Massachusetts Lowell, Lowell, MA, USA., Morrison T; Accugenomics, Inc., Wilmington, NC, USA., Pabón-Peña C; Agilent Technologies, Santa Clara, CA, USA., Pirooznia M; Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA., Proszek PZ; NIHR Biomedical Research Centre, Royal Marsden Hospital, Sutton, Surrey, UK., Raymond A; Astrazeneca Pharmaceuticals, Waltham, MA, USA., Rindler P; R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA., Ringler R; ResearchDx, Inc., Irvine, CA, USA., Scherer A; 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., Shaknovich R; Cancer Genetics, Inc., Rutherford, NJ, USA., Shi T; Center for Bioinformatics and Computational Biology and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China., Smith M; Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA., Song P; Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA., Strahl M; Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA., Thodima VJ; Cancer Genetics, Inc., Rutherford, NJ, USA., Tom N; EATRIS ERIC- European Infrastructure for Translational Medicine, Amsterdam, The Netherlands.; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic., Verma S; ResearchDx, Inc., Irvine, CA, USA., Wang J; Research and Development, Integrated DNA Technologies, Inc., Coralville, IA, USA., Wu L; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA., Xiao W; Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.; Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Xu C; Research and Development, QIAGEN Sciences, Inc., Frederick, MD, USA., Yang M; Department of Information Science, University of Arkansas at Little Rock, Little Rock, AR, USA., Zhang G; Clinical Laboratory, Burning Rock Biotech, Guangzhou, China., Zhang S; Clinical Laboratory, Burning Rock Biotech, Guangzhou, China., Zhang Y; Elim Biopharmaceuticals, Inc., Hayward, CA, USA., Shi L; 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., Tong W; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA., Johann DJ Jr; Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA. djjohann@uams.edu., Mercer TR; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia. t.mercer@garvan.org.au.; Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia. t.mercer@garvan.org.au.; Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Queensland, QLD, Australia. t.mercer@garvan.org.au., Xu J; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA. joshua.xu@fda.hhs.gov.

Publikováno v: Nature biotechnology [Nat Biotechnol] 2021 Sep; Vol. 39 (9), pp. 1115-1128. Date of Electronic Publication: 2021 Apr 12.