1
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Manderstedt E, Lind‐Halldén C, Halldén C, Elf J, Svensson PJ, Engström G, Melander O, Baras A, Lotta LA, Zöller B, Abecasis G, Baras A, Cantor M, Coppola G, Economides A, Lotta LA, Overton JD, Reid JG, Shuldiner A, Beechert C, Forsythe C, Fuller ED, Gu Z, Lattari M, Lopez A, Overton JD, Schleicher TD, Padilla MS, Widom L, Wolf SE, Pradhan M, Manoochehri K, Ulloa RH, Bai X, Balasubramanian S, Blumenfeld A, Boutkov B, Eom G, Habegger L, Hawes A, Khalid S, Krasheninina O, Lanche R, Mansfield AJ, Maxwell EK, Nafde M, O’Keeffe S, Orelus M, Panea R, Polanco T, Rasool A, Reid JG, Salerno W, Staples JC, Jones MB, Mighty J, Mitnaul LJ. Genetic variation of the blood coagulation regulator tissue factor pathway inhibitor and venous thromboembolism among middle‐aged and older adults: A population‐based cohort study. Res Pract Thromb Haemost 2022; 6:e12842. [PMID: 36381289 PMCID: PMC9644338 DOI: 10.1002/rth2.12842] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 09/09/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Background Tissue factor is the main initiator of blood coagulation, and tissue factor pathway inhibitor (TFPI) is the primary inhibitor of the initiation of blood coagulation. The genetic variation of TFPI and the relation to venous thromboembolism (VTE), that is, venous thrombosis and pulmonary embolism, remains to be clarified. This exome sequencing study aimed to determine the molecular epidemiology of the TFPI gene and the relation to VTE in a large population‐based cohort of middle‐aged and older adults. Methods The exomes of TFPI were analyzed for variants in 28,794 subjects without previous VTE (born 1923–1950, 60% women), who participated in the Malmö Diet and Cancer Study (1991–1996). Patients were followed until the first event of VTE, death, or 2018. Qualifying variants were defined as loss‐of‐function or nonbenign (PolyPhen‐2) missense variants with minor allele frequency less than 0.1%. Results No common variant was associated with VTE. Nine rare variants (two loss‐of‐function and seven nonbenign missense) were classified as qualifying and included in collapsing analysis. Prevalence of qualifying variants was 0.09%. Five individuals with VTE compared to 17 individuals without VTE carried one qualifying variant. Cox multivariate regression analysis adjusted for age, sex, body mass index, systolic blood pressure, smoking and alcohol consumption, rs6025, rs1799963, and ancestry showed a hazard ratio of 2.9 (95% CI, 1.2–7.1) for rare qualifying variants. Conclusion Rare qualifying TFPI variants were associated with VTE, suggesting that rare variants in TFPI contribute to the development of VTE. The qualifying TFPI gene variants were very rare, suggesting a constrained gene.
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Affiliation(s)
- Eric Manderstedt
- Department of Environmental Science and Bioscience Kristianstad University Kristianstad Sweden
| | - Christina Lind‐Halldén
- Department of Environmental Science and Bioscience Kristianstad University Kristianstad Sweden
| | - Christer Halldén
- Department of Environmental Science and Bioscience Kristianstad University Kristianstad Sweden
| | - Johan Elf
- Department of Clinical Sciences Lund University, Skåne University Hospital Malmö Sweden
| | - Peter J. Svensson
- Department of Clinical Sciences Lund University, Skåne University Hospital Malmö Sweden
| | - Gunnar Engström
- Department of Clinical Sciences Lund University, Skåne University Hospital Malmö Sweden
| | - Olle Melander
- Department of Clinical Sciences Lund University, Skåne University Hospital Malmö Sweden
| | - Aris Baras
- Regeneron Genetics Center Tarrytown New York USA
| | | | - Bengt Zöller
- Center for Primary Health Care Research Lund University and Region Skåne Malmö Sweden
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2
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Akbari P, Gilani A, Sosina O, Kosmicki JA, Khrimian L, Fang YY, Persaud T, Garcia V, Sun D, Li A, Mbatchou J, Locke AE, Benner C, Verweij N, Lin N, Hossain S, Agostinucci K, Pascale JV, Dirice E, Dunn M, Kraus WE, Shah SH, Chen YDI, Rotter JI, Rader DJ, Melander O, Still CD, Mirshahi T, Carey DJ, Berumen-Campos J, Kuri-Morales P, Alegre-Díaz J, Torres JM, Emberson JR, Collins R, Balasubramanian S, Hawes A, Jones M, Zambrowicz B, Murphy AJ, Paulding C, Coppola G, Overton JD, Reid JG, Shuldiner AR, Cantor M, Kang HM, Abecasis GR, Karalis K, Economides AN, Marchini J, Yancopoulos GD, Sleeman MW, Altarejos J, Della Gatta G, Tapia-Conyer R, Schwartzman ML, Baras A, Ferreira MAR, Lotta LA. Sequencing of 640,000 exomes identifies GPR75 variants associated with protection from obesity. Science 2021; 373:373/6550/eabf8683. [PMID: 34210852 DOI: 10.1126/science.abf8683] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/17/2021] [Indexed: 12/11/2022]
Abstract
Large-scale human exome sequencing can identify rare protein-coding variants with a large impact on complex traits such as body adiposity. We sequenced the exomes of 645,626 individuals from the United Kingdom, the United States, and Mexico and estimated associations of rare coding variants with body mass index (BMI). We identified 16 genes with an exome-wide significant association with BMI, including those encoding five brain-expressed G protein-coupled receptors (CALCR, MC4R, GIPR, GPR151, and GPR75). Protein-truncating variants in GPR75 were observed in ~4/10,000 sequenced individuals and were associated with 1.8 kilograms per square meter lower BMI and 54% lower odds of obesity in the heterozygous state. Knock out of Gpr75 in mice resulted in resistance to weight gain and improved glycemic control in a high-fat diet model. Inhibition of GPR75 may provide a therapeutic strategy for obesity.
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Affiliation(s)
- Parsa Akbari
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Ankit Gilani
- Department of Pharmacology and Medicine, New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Olukayode Sosina
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Jack A Kosmicki
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Lori Khrimian
- Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Yi-Ya Fang
- Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Trikaldarshi Persaud
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Victor Garcia
- Department of Pharmacology and Medicine, New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Dylan Sun
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Alexander Li
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Joelle Mbatchou
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Adam E Locke
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Christian Benner
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Niek Verweij
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Nan Lin
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Sakib Hossain
- Department of Pharmacology and Medicine, New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Kevin Agostinucci
- Department of Pharmacology and Medicine, New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Jonathan V Pascale
- Department of Pharmacology and Medicine, New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Ercument Dirice
- Department of Pharmacology and Medicine, New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Michael Dunn
- Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | | | | | - William E Kraus
- Division of Cardiology, Duke University Medical Center, Durham, NC 27710, USA.,Duke Center for Living, Duke University Medical Center, Durham, NC 27705, USA
| | - Svati H Shah
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
| | - Yii-Der I Chen
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation, and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation, and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Olle Melander
- Department of Clinical Sciences Malmö, Lund University, 221 00 Malmö, Sweden.,Department of Emergency and Internal Medicine, Skåne University Hospital, 214 28, Malmö, Sweden
| | - Christopher D Still
- Geisinger Obesity Institute, Geisinger Health System, Danville, PA 17882, USA
| | - Tooraj Mirshahi
- Geisinger Obesity Institute, Geisinger Health System, Danville, PA 17882, USA
| | - David J Carey
- Geisinger Obesity Institute, Geisinger Health System, Danville, PA 17882, USA
| | - Jaime Berumen-Campos
- Faculty of Medicine, National Autonomous University of Mexico, Copilco Universidad, Coyoacán, 4360 Ciudad de México, Mexico
| | - Pablo Kuri-Morales
- Faculty of Medicine, National Autonomous University of Mexico, Copilco Universidad, Coyoacán, 4360 Ciudad de México, Mexico
| | - Jesus Alegre-Díaz
- Faculty of Medicine, National Autonomous University of Mexico, Copilco Universidad, Coyoacán, 4360 Ciudad de México, Mexico
| | - Jason M Torres
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, England, UK
| | - Jonathan R Emberson
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, England, UK
| | - Rory Collins
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, England, UK
| | | | - Alicia Hawes
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Marcus Jones
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | | | | | - Charles Paulding
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Giovanni Coppola
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - John D Overton
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Jeffrey G Reid
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Alan R Shuldiner
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Michael Cantor
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Hyun M Kang
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Goncalo R Abecasis
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Katia Karalis
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Aris N Economides
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA.,Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Jonathan Marchini
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | | | - Mark W Sleeman
- Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | | | - Giusy Della Gatta
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Roberto Tapia-Conyer
- Faculty of Medicine, National Autonomous University of Mexico, Copilco Universidad, Coyoacán, 4360 Ciudad de México, Mexico
| | - Michal L Schwartzman
- Department of Pharmacology and Medicine, New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Aris Baras
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA.
| | - Manuel A R Ferreira
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA
| | - Luca A Lotta
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591, USA.
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3
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Backman JD, Li AH, Marcketta A, Sun D, Mbatchou J, Kessler MD, Benner C, Liu D, Locke AE, Balasubramanian S, Yadav A, Banerjee N, Gillies CE, Damask A, Liu S, Bai X, Hawes A, Maxwell E, Gurski L, Watanabe K, Kosmicki JA, Rajagopal V, Mighty J, Jones M, Mitnaul L, Stahl E, Coppola G, Jorgenson E, Habegger L, Salerno WJ, Shuldiner AR, Lotta LA, Overton JD, Cantor MN, Reid JG, Yancopoulos G, Kang HM, Marchini J, Baras A, Abecasis GR, Ferreira MAR. Exome sequencing and analysis of 454,787 UK Biobank participants. Nature 2021; 599:628-634. [PMID: 34662886 PMCID: PMC8596853 DOI: 10.1038/s41586-021-04103-z] [Citation(s) in RCA: 276] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/06/2021] [Indexed: 12/19/2022]
Abstract
A major goal in human genetics is to use natural variation to understand the phenotypic consequences of altering each protein-coding gene in the genome. Here we used exome sequencing1 to explore protein-altering variants and their consequences in 454,787 participants in the UK Biobank study2. We identified 12 million coding variants, including around 1 million loss-of-function and around 1.8 million deleterious missense variants. When these were tested for association with 3,994 health-related traits, we found 564 genes with trait associations at P ≤ 2.18 × 10-11. Rare variant associations were enriched in loci from genome-wide association studies (GWAS), but most (91%) were independent of common variant signals. We discovered several risk-increasing associations with traits related to liver disease, eye disease and cancer, among others, as well as risk-lowering associations for hypertension (SLC9A3R2), diabetes (MAP3K15, FAM234A) and asthma (SLC27A3). Six genes were associated with brain imaging phenotypes, including two involved in neural development (GBE1, PLD1). Of the signals available and powered for replication in an independent cohort, 81% were confirmed; furthermore, association signals were generally consistent across individuals of European, Asian and African ancestry. We illustrate the ability of exome sequencing to identify gene-trait associations, elucidate gene function and pinpoint effector genes that underlie GWAS signals at scale.
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Affiliation(s)
- Joshua D. Backman
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Alexander H. Li
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Anthony Marcketta
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Dylan Sun
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Joelle Mbatchou
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Michael D. Kessler
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Christian Benner
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Daren Liu
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Adam E. Locke
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | | | - Ashish Yadav
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Nilanjana Banerjee
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | | | - Amy Damask
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Simon Liu
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Xiaodong Bai
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Alicia Hawes
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Evan Maxwell
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Lauren Gurski
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Kyoko Watanabe
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Jack A. Kosmicki
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Veera Rajagopal
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Jason Mighty
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | | | | | - Marcus Jones
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Lyndon Mitnaul
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Eli Stahl
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Giovanni Coppola
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Eric Jorgenson
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Lukas Habegger
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - William J. Salerno
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Alan R. Shuldiner
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Luca A. Lotta
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - John D. Overton
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Michael N. Cantor
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Jeffrey G. Reid
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - George Yancopoulos
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Hyun M. Kang
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Jonathan Marchini
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Aris Baras
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
| | - Gonçalo R. Abecasis
- grid.418961.30000 0004 0472 2713Regeneron Genetics Center, Tarrytown, NY USA
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4
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Van Hout CV, Tachmazidou I, Backman JD, Hoffman JD, Liu D, Pandey AK, Gonzaga-Jauregui C, Khalid S, Ye B, Banerjee N, Li AH, O'Dushlaine C, Marcketta A, Staples J, Schurmann C, Hawes A, Maxwell E, Barnard L, Lopez A, Penn J, Habegger L, Blumenfeld AL, Bai X, O'Keeffe S, Yadav A, Praveen K, Jones M, Salerno WJ, Chung WK, Surakka I, Willer CJ, Hveem K, Leader JB, Carey DJ, Ledbetter DH, Cardon L, Yancopoulos GD, Economides A, Coppola G, Shuldiner AR, Balasubramanian S, Cantor M, Nelson MR, Whittaker J, Reid JG, Marchini J, Overton JD, Scott RA, Abecasis GR, Yerges-Armstrong L, Baras A. Exome sequencing and characterization of 49,960 individuals in the UK Biobank. Nature 2020; 586:749-756. [PMID: 33087929 PMCID: PMC7759458 DOI: 10.1038/s41586-020-2853-0] [Citation(s) in RCA: 259] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world1. Here we describe the release of exome-sequence data for the first 49,960 study participants, revealing approximately 4 million coding variants (of which around 98.6% have a frequency of less than 1%). The data include 198,269 autosomal predicted loss-of-function (LOF) variants, a more than 14-fold increase compared to the imputed sequence. Nearly all genes (more than 97%) had at least one carrier with a LOF variant, and most genes (more than 69%) had at least ten carriers with a LOF variant. We illustrate the power of characterizing LOF variants in this population through association analyses across 1,730 phenotypes. In addition to replicating established associations, we found novel LOF variants with large effects on disease traits, including PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on blood cell traits. We further demonstrate the value of exome sequencing by surveying the prevalence of pathogenic variants of clinical importance, and show that 2% of this population has a medically actionable variant. Furthermore, we characterize the penetrance of cancer in carriers of pathogenic BRCA1 and BRCA2 variants. Exome sequences from the first 49,960 participants highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community.
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Affiliation(s)
| | | | | | - Joshua D Hoffman
- GlaxoSmithKline, Collegeville, PA, USA.,Foresite Labs, Cambridge, MA, USA
| | - Daren Liu
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | - Bin Ye
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | - Claudia Schurmann
- Regeneron Genetics Center, Tarrytown, NY, USA.,Digital Health Center, Hasso Plattner Institute, University of Potsdam, Potsdam, Germany.,Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | | | - John Penn
- Regeneron Genetics Center, Tarrytown, NY, USA.,DNANexus, Mountain View, CA, USA
| | | | | | | | | | | | | | | | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | | | | | - Kristian Hveem
- Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | | | | | | | | | | | | | | | | | | | | | - Matthew R Nelson
- GlaxoSmithKline, Collegeville, PA, USA.,Deerfield, New York, NY, USA
| | | | | | | | | | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA.
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5
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Simões EAF, Forleo-Neto E, Geba GP, Kamal M, Yang F, Cicirello H, Houghton MR, Rideman R, Zhao Q, Benvin SL, Hawes A, Fuller ED, Wloga E, Pizarro JMN, Munoz FM, Rush SA, McLellan JS, Lipsich L, Stahl N, Yancopoulos GD, Weinreich DM, Kyratsous CA, Sivapalasingam S. Suptavumab for the Prevention of Medically Attended Respiratory Syncytial Virus Infection in Preterm Infants. Clin Infect Dis 2020; 73:e4400-e4408. [PMID: 32897368 PMCID: PMC8653633 DOI: 10.1093/cid/ciaa951] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/08/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is a major cause of childhood medically attended respiratory infection (MARI). METHODS We conducted a randomized, double-blind, placebo-controlled phase 3 trial in 1154 preterm infants of 1 or 2 doses of suptavumab, a human monoclonal antibody that can bind and block a conserved epitope on RSV A and B subtypes, for the prevention of RSV MARI. The primary endpoint was proportion of subjects with RSV-confirmed hospitalizations or outpatient lower respiratory tract infection (LRTI). RESULTS There were no significant differences between primary endpoint rates (8.1%, placebo; 7.7%, 1-dose; 9.3%, 2-dose). Suptavumab prevented RSV A infections (relative risks, .38; 95% confidence interval [CI], .14-1.05 in the 1-dose group and .39 [95% CI, .14-1.07] in the 2-dose group; nominal significance of combined suptavumab group vs placebo; P = .0499), while increasing the rate of RSV B infections (relative risk 1.36 [95% CI, .73-2.56] in the 1-dose group and 1.69 [95% CI, .92-3.08] in the 2-dose group; nominal significance of combined suptavumab group vs placebo; P = .12). Sequenced RSV isolates demonstrated no suptavumab epitope changes in RSV A isolates, while all RSV B isolates had 2-amino acid substitution in the suptavumab epitope that led to loss of neutralization activity. Treatment emergent adverse events were balanced across treatment groups. CONCLUSIONS Suptavumab did not reduce overall RSV hospitalizations or outpatient LRTI because of a newly circulating mutant strain of RSV B. Genetic variation in circulating RSV strains will continue to challenge prevention efforts. CLINICAL TRIALS REGISTRATION NCT02325791. https://clinicaltrials.gov/ct2/show/NCT02325791.
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Affiliation(s)
- Eric A F Simões
- Department of Pediatrics, University of Colorado School of Medicine, and The Children's Hospital Colorado, Aurora, Colorado, USA
| | | | - Gregory P Geba
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Mohamed Kamal
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Feng Yang
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | | | | | - Ronald Rideman
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Qiong Zhao
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Sarah L Benvin
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Alicia Hawes
- Regeneron Genetics Center, Tarrytown, New York, USA
| | | | - Elzbieta Wloga
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Jose M Novoa Pizarro
- Facultad Medicina Universidad del Desarrollo/CAS, Hospital Padre Hurtado, Santiago, Chile
| | - Flor M Munoz
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Scott A Rush
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Leah Lipsich
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
| | - Neil Stahl
- Regeneron Pharmaceuticals, Inc, Tarrytown, New York, USA
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6
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Linehan WM, Spellman PT, Ricketts CJ, Creighton CJ, Fei SS, Davis C, Wheeler DA, Murray BA, Schmidt L, Vocke CD, Peto M, Al Mamun AAM, Shinbrot E, Sethi A, Brooks S, Rathmell WK, Brooks AN, Hoadley KA, Robertson AG, Brooks D, Bowlby R, Sadeghi S, Shen H, Weisenberger DJ, Bootwalla M, Baylin SB, Laird PW, Cherniack AD, Saksena G, Haake S, Li J, Liang H, Lu Y, Mills GB, Akbani R, Leiserson MD, Raphael BJ, Anur P, Bottaro D, Albiges L, Barnabas N, Choueiri TK, Czerniak B, Godwin AK, Hakimi AA, Ho T, Hsieh J, Ittmann M, Kim WY, Krishnan B, Merino MJ, Mills Shaw KR, Reuter VE, Reznik E, Shelley CS, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Tickoo S, Burnett K, Crain D, Gardner J, Lau K, Mallery D, Morris S, Paulauskis JD, Penny RJ, Shelton C, Shelton WT, Sherman M, Thompson E, Yena P, Avedon MT, Bowen J, Gastier-Foster JM, Gerken M, Leraas KM, Lichtenberg TM, Ramirez NC, Santos T, Wise L, Zmuda E, Demchok JA, Felau I, Hutter CM, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Zhang J(J, Ayala B, Baboud J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Ally A, Balasundaram M, Balu S, Beroukhim R, Bodenheimer T, Buhay C, Butterfield YS, Carlsen R, Carter SL, Chao H, Chuah E, Clarke A, Covington KR, Dahdouli M, Dewal N, Dhalla N, Doddapaneni H, Drummond J, Gabriel SB, Gibbs RA, Guin R, Hale W, Hawes A, Hayes DN, Holt RA, Hoyle AP, Jefferys SR, Jones SJ, Jones CD, Kalra D, Kovar C, Lewis L, Li J, Ma Y, Marra MA, Mayo M, Meng S, Meyerson M, Mieczkowski PA, Moore RA, Morton D, Mose LE, Mungall AJ, Muzny D, Parker JS, Perou CM, Roach J, Schein JE, Schumacher SE, Shi Y, Simons JV, Sipahimalani P, Skelly T, Soloway MG, Sougnez C, Tam A, Tan D, Thiessen N, Veluvolu U, Wang M, Wilkerson MD, Wong T, Wu J, Xi L, Zhou J, Bedford J, Chen F, Fu Y, Gerstein M, Haussler D, Kasaian K, Lai P, Ling S, Radenbaugh A, Van Den Berg D, Weinstein JN, Zhu J, Albert M, Alexopoulou I, Andersen JJ, Auman JT, Bartlett J, Bastacky S, Bergsten J, Blute ML, Boice L, Bollag RJ, Boyd J, Castle E, Chen YB, Cheville JC, Curley E, Davies B, DeVolk A, Dhir R, Dike L, Eckman J, Engel J, Harr J, Hrebinko R, Huang M, Huelsenbeck-Dill L, Iacocca M, Jacobs B, Lobis M, Maranchie JK, McMeekin S, Myers J, Nelson J, Parfitt J, Parwani A, Petrelli N, Rabeno B, Roy S, Salner AL, Slaton J, Stanton M, Thompson RH, Thorne L, Tucker K, Weinberger PM, Winemiller C, Zach LA, Zuna R. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med 2016; 374:135-45. [PMID: 26536169 PMCID: PMC4775252 DOI: 10.1056/nejmoa1505917] [Citation(s) in RCA: 887] [Impact Index Per Article: 110.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist. METHODS We performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis. RESULTS Type 1 and type 2 papillary renal-cell carcinomas were shown to be different types of renal cancer characterized by specific genetic alterations, with type 2 further classified into three individual subgroups on the basis of molecular differences associated with patient survival. Type 1 tumors were associated with MET alterations, whereas type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-antioxidant response element (ARE) pathway. A CpG island methylator phenotype (CIMP) was observed in a distinct subgroup of type 2 papillary renal-cell carcinomas that was characterized by poor survival and mutation of the gene encoding fumarate hydratase (FH). CONCLUSIONS Type 1 and type 2 papillary renal-cell carcinomas were shown to be clinically and biologically distinct. Alterations in the MET pathway were associated with type 1, and activation of the NRF2-ARE pathway was associated with type 2; CDKN2A loss and CIMP in type 2 conveyed a poor prognosis. Furthermore, type 2 papillary renal-cell carcinoma consisted of at least three subtypes based on molecular and phenotypic features. (Funded by the National Institutes of Health.).
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Affiliation(s)
- W. Marston Linehan
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
- Corresponding Author: W. Marston Linehan, M.D., Urologic Oncology Branch, National Cancer Institute, Building 10 CRC Room 1-5940, Bethesda, MD 20892-1107 USA, Tel: 301-496-6353, Fax: 301-402-0922,
| | - Paul T. Spellman
- Oregon Health & Science University, Portland, OR
- Corresponding Author: W. Marston Linehan, M.D., Urologic Oncology Branch, National Cancer Institute, Building 10 CRC Room 1-5940, Bethesda, MD 20892-1107 USA, Tel: 301-496-6353, Fax: 301-402-0922,
| | | | | | | | | | | | - Bradley A. Murray
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Laura Schmidt
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | - Cathy D. Vocke
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | - Myron Peto
- Oregon Health & Science University, Portland, OR
| | | | | | | | - Samira Brooks
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Angela N. Brooks
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | | | - A. Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Denise Brooks
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Sara Sadeghi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Hui Shen
- Van Andel Research Institute, Grand Rapids, MI
| | | | | | | | | | - Andrew D. Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Gordon Saksena
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Scott Haake
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Jun Li
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | - Han Liang
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | - Yiling Lu
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Rehan Akbani
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Pavana Anur
- Oregon Health & Science University, Portland, OR
| | - Donald Bottaro
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | | | | | | | | | | | - A. Ari Hakimi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - James Hsieh
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - William Y. Kim
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Maria J. Merino
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | | | | | - Ed Reznik
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | - Satish Tickoo
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Daniel Crain
- The International Genomics Consortium, Phoenix, AZ
| | | | - Kevin Lau
- The International Genomics Consortium, Phoenix, AZ
| | | | - Scott Morris
- The International Genomics Consortium, Phoenix, AZ
| | | | | | | | | | - Mark Sherman
- The International Genomics Consortium, Phoenix, AZ
| | | | - Peggy Yena
- The International Genomics Consortium, Phoenix, AZ
| | - Melissa T. Avedon
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Jay Bowen
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | | | - Mark Gerken
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Kristen M. Leraas
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | | | - Nilsa C. Ramirez
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Tracie Santos
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Lisa Wise
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Erik Zmuda
- The Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - John A. Demchok
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Ina Felau
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Carolyn M. Hutter
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Margi Sheth
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Heidi J. Sofia
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Roy Tarnuzzer
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Zhining Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Liming Yang
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jean C. Zenklusen
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Brenda Ayala
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Julien Baboud
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Sudha Chudamani
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Rockville MD
| | - Jia Liu
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Rockville MD
| | - Laxmi Lolla
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Rockville MD
| | - Rashi Naresh
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Todd Pihl
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Qiang Sun
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Yunhu Wan
- SRA International, Inc., 4300 Fair Lakes Court, Fairfax, VA
| | - Ye Wu
- Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Rockville MD
| | - Adrian Ally
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Miruna Balasundaram
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Saianand Balu
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Rameen Beroukhim
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Tom Bodenheimer
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Rebecca Carlsen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Scott L. Carter
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Hsu Chao
- Baylor College of Medicine, Houston, TX
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Amanda Clarke
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | | | | | - Noreen Dhalla
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | | | - Stacey B. Gabriel
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | | | - Ranabir Guin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | | | - D. Neil Hayes
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Robert A. Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Alan P. Hoyle
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Steven J.M. Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Corbin D. Jones
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | - Jie Li
- Baylor College of Medicine, Houston, TX
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Marco A. Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Michael Mayo
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Shaowu Meng
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Matthew Meyerson
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | | | - Richard A. Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | - Lisle E. Mose
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Andrew J. Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | - Joel S. Parker
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Jeffrey Roach
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Steven E. Schumacher
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Yan Shi
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Janae V. Simons
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Payal Sipahimalani
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Tara Skelly
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Carrie Sougnez
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, MA
| | - Angela Tam
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Donghui Tan
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Nina Thiessen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | | | - Min Wang
- Baylor College of Medicine, Houston, TX
| | | | - Tina Wong
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Junyuan Wu
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Liu Xi
- Baylor College of Medicine, Houston, TX
| | - Jane Zhou
- Baylor College of Medicine, Houston, TX
| | | | | | - Yao Fu
- Yale University, New Haven, CT
| | | | - David Haussler
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA
| | - Katayoon Kasaian
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Phillip Lai
- University of Southern California, Los Angeles, CA
| | - Shiyun Ling
- Univ. of Texas MD Anderson Cancer Center, Houston, TX
| | - Amie Radenbaugh
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA
| | | | | | - Jingchun Zhu
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA
| | - Monique Albert
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | | | - J. Todd Auman
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - John Bartlett
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sheldon Bastacky
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Julie Bergsten
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | | | - Lori Boice
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Jeff Boyd
- Fox Chase Cancer Center, Philadelphia, PA
| | | | - Ying-Bei Chen
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Erin Curley
- The International Genomics Consortium, Phoenix, AZ
| | - Benjamin Davies
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - April DeVolk
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | - Rajiv Dhir
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | | | - John Eckman
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | - Jay Engel
- Kingston General Hospital, Kingston, Ontario, Canada
| | - Jodi Harr
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | - Ronald Hrebinko
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Mei Huang
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Mary Iacocca
- Helen F Graham Cancer Center at Christiana Care Health Systems, Newark, DE
| | - Bruce Jacobs
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Michael Lobis
- Helen F Graham Cancer Center at Christiana Care Health Systems, Newark, DE
| | - Jodi K. Maranchie
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Scott McMeekin
- University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Jerome Myers
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | - Joel Nelson
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | | | - Anil Parwani
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | - Nicholas Petrelli
- Helen F Graham Cancer Center at Christiana Care Health Systems, Newark, DE
| | - Brenda Rabeno
- Helen F Graham Cancer Center at Christiana Care Health Systems, Newark, DE
| | - Somak Roy
- University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA
| | | | - Joel Slaton
- University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | | | | | - Leigh Thorne
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kelinda Tucker
- Penrose-St. Francis Health Services, Colorado Springs, CO
| | | | | | | | - Rosemary Zuna
- University of Oklahoma Health Sciences Center, Oklahoma City, OK
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Yang Y, Muzny DM, Xia F, Niu Z, Person R, Ding Y, Ward P, Braxton A, Wang M, Buhay C, Veeraraghavan N, Hawes A, Chiang T, Leduc M, Beuten J, Zhang J, He W, Scull J, Willis A, Landsverk M, Craigen WJ, Bekheirnia MR, Stray-Pedersen A, Liu P, Wen S, Alcaraz W, Cui H, Walkiewicz M, Reid J, Bainbridge M, Patel A, Boerwinkle E, Beaudet AL, Lupski JR, Plon SE, Gibbs RA, Eng CM. Molecular findings among patients referred for clinical whole-exome sequencing. JAMA 2014; 312:1870-9. [PMID: 25326635 PMCID: PMC4326249 DOI: 10.1001/jama.2014.14601] [Citation(s) in RCA: 991] [Impact Index Per Article: 99.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE Clinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders. OBJECTIVE To perform clinical whole-exome sequencing and report (1) the rate of molecular diagnosis among phenotypic groups, (2) the spectrum of genetic alterations contributing to disease, and (3) the prevalence of medically actionable incidental findings such as FBN1 mutations causing Marfan syndrome. DESIGN, SETTING, AND PATIENTS Observational study of 2000 consecutive patients with clinical whole-exome sequencing analyzed between June 2012 and August 2014. Whole-exome sequencing tests were performed at a clinical genetics laboratory in the United States. Results were reported by clinical molecular geneticists certified by the American Board of Medical Genetics and Genomics. Tests were ordered by the patient's physician. The patients were primarily pediatric (1756 [88%]; mean age, 6 years; 888 females [44%], 1101 males [55%], and 11 fetuses [1% gender unknown]), demonstrating diverse clinical manifestations most often including nervous system dysfunction such as developmental delay. MAIN OUTCOMES AND MEASURES Whole-exome sequencing diagnosis rate overall and by phenotypic category, mode of inheritance, spectrum of genetic events, and reporting of incidental findings. RESULTS A molecular diagnosis was reported for 504 patients (25.2%) with 58% of the diagnostic mutations not previously reported. Molecular diagnosis rates for each phenotypic category were 143/526 (27.2%; 95% CI, 23.5%-31.2%) for the neurological group, 282/1147 (24.6%; 95% CI, 22.1%-27.2%) for the neurological plus other organ systems group, 30/83 (36.1%; 95% CI, 26.1%-47.5%) for the specific neurological group, and 49/244 (20.1%; 95% CI, 15.6%-25.8%) for the nonneurological group. The Mendelian disease patterns of the 527 molecular diagnoses included 280 (53.1%) autosomal dominant, 181 (34.3%) autosomal recessive (including 5 with uniparental disomy), 65 (12.3%) X-linked, and 1 (0.2%) mitochondrial. Of 504 patients with a molecular diagnosis, 23 (4.6%) had blended phenotypes resulting from 2 single gene defects. About 30% of the positive cases harbored mutations in disease genes reported since 2011. There were 95 medically actionable incidental findings in genes unrelated to the phenotype but with immediate implications for management in 92 patients (4.6%), including 59 patients (3%) with mutations in genes recommended for reporting by the American College of Medical Genetics and Genomics. CONCLUSIONS AND RELEVANCE Whole-exome sequencing provided a potential molecular diagnosis for 25% of a large cohort of patients referred for evaluation of suspected genetic conditions, including detection of rare genetic events and new mutations contributing to disease. The yield of whole-exome sequencing may offer advantages over traditional molecular diagnostic approaches in certain patients.
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Affiliation(s)
- Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Zhiyv Niu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Richard Person
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yan Ding
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Patricia Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Alicia Braxton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Min Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Christian Buhay
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | | | - Alicia Hawes
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Magalie Leduc
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Joke Beuten
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Jing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Weimin He
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Jennifer Scull
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Alecia Willis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Megan Landsverk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - William J Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas3Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Mir Reza Bekheirnia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shu Wen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Wendy Alcaraz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Hong Cui
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Jeffrey Reid
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Matthew Bainbridge
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas4Human Genetics Center, University of Texas Health Science Center, Houston
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas2Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas3Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Sharon E Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas3Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas2Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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8
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Butte NF, Voruganti VS, Cole SA, Haack K, Comuzzie AG, Muzny DM, Wheeler DA, Chang K, Hawes A, Gibbs RA. Resequencing of IRS2 reveals rare variants for obesity but not fasting glucose homeostasis in Hispanic children. Physiol Genomics 2011; 43:1029-37. [PMID: 21771880 DOI: 10.1152/physiolgenomics.00019.2011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Our objective was to resequence insulin receptor substrate 2 (IRS2) to identify variants associated with obesity- and diabetes-related traits in Hispanic children. Exonic and intronic segments, 5' and 3' flanking regions of IRS2 (∼14.5 kb), were bidirectionally sequenced for single nucleotide polymorphism (SNP) discovery in 934 Hispanic children using 3730XL DNA Sequencers. Additionally, 15 SNPs derived from Illumina HumanOmni1-Quad BeadChips were analyzed. Measured genotype analysis tested associations between SNPs and obesity and diabetes-related traits. Bayesian quantitative trait nucleotide analysis was used to statistically infer the most likely functional polymorphisms. A total of 140 SNPs were identified with minor allele frequencies (MAF) ranging from 0.001 to 0.47. Forty-two of the 70 coding SNPs result in nonsynonymous amino acid substitutions relative to the consensus sequence; 28 SNPs were detected in the promoter, 12 in introns, 28 in the 3'-UTR, and 2 in the 5'-UTR. Two insertion/deletions (indels) were detected. Ten independent rare SNPs (MAF = 0.001-0.009) were associated with obesity-related traits (P = 0.01-0.00002). SNP 10510452_139 in the promoter region was shown to have a high posterior probability (P = 0.77-0.86) of influencing BMI, fat mass, and waist circumference in Hispanic children. SNP 10510452_139 contributed between 2 and 4% of the population variance in body weight and composition. None of the SNPs or indels were associated with diabetes-related traits or accounted for a previously identified quantitative trait locus on chromosome 13 for fasting serum glucose. Rare but not common IRS2 variants may play a role in the regulation of body weight but not an essential role in fasting glucose homeostasis in Hispanic children.
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Affiliation(s)
- Nancy F Butte
- Department of Pediatrics, Baylor College of Medicine, US Department of Agriculture/Agricultural Research Service Children's Nutrition Research Center, Houston, TX, USA.
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9
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Schaaf CP, Sabo A, Sakai Y, Crosby J, Muzny D, Hawes A, Lewis L, Akbar H, Varghese R, Boerwinkle E, Gibbs RA, Zoghbi HY. Oligogenic heterozygosity in individuals with high-functioning autism spectrum disorders. Hum Mol Genet 2011; 20:3366-75. [PMID: 21624971 PMCID: PMC3153303 DOI: 10.1093/hmg/ddr243] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Autism spectrum disorders (ASDs) are a heterogeneous group of neuro-developmental disorders. While significant progress has been made in the identification of genes and copy number variants associated with syndromic autism, little is known to date about the etiology of idiopathic non-syndromic autism. Sanger sequencing of 21 known autism susceptibility genes in 339 individuals with high-functioning, idiopathic ASD revealed de novo mutations in at least one of these genes in 6 of 339 probands (1.8%). Additionally, multiple events of oligogenic heterozygosity were seen, affecting 23 of 339 probands (6.8%). Screening of a control population for novel coding variants in CACNA1C, CDKL5, HOXA1, SHANK3, TSC1, TSC2 and UBE3A by the same sequencing technology revealed that controls were carriers of oligogenic heterozygous events at significantly (P < 0.01) lower rate, suggesting oligogenic heterozygosity as a new potential mechanism in the pathogenesis of ASDs.
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Affiliation(s)
- Christian P Schaaf
- Department of Molecular and Human Genetics, Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
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10
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Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Peltonen L, Dermitzakis E, Bonnen PE, Altshuler DM, Gibbs RA, de Bakker PIW, Deloukas P, Gabriel SB, Gwilliam R, Hunt S, Inouye M, Jia X, Palotie A, Parkin M, Whittaker P, Yu F, Chang K, Hawes A, Lewis LR, Ren Y, Wheeler D, Gibbs RA, Muzny DM, Barnes C, Darvishi K, Hurles M, Korn JM, Kristiansson K, Lee C, McCarrol SA, Nemesh J, Dermitzakis E, Keinan A, Montgomery SB, Pollack S, Price AL, Soranzo N, Bonnen PE, Gibbs RA, Gonzaga-Jauregui C, Keinan A, Price AL, Yu F, Anttila V, Brodeur W, Daly MJ, Leslie S, McVean G, Moutsianas L, Nguyen H, Schaffner SF, Zhang Q, Ghori MJR, McGinnis R, McLaren W, Pollack S, Price AL, Schaffner SF, Takeuchi F, Grossman SR, Shlyakhter I, Hostetter EB, Sabeti PC, Adebamowo CA, Foster MW, Gordon DR, Licinio J, Manca MC, Marshall PA, Matsuda I, Ngare D, Wang VO, Reddy D, Rotimi CN, Royal CD, Sharp RR, Zeng C, Brooks LD, McEwen JE. Integrating common and rare genetic variation in diverse human populations. Nature 2010; 467:52-8. [PMID: 20811451 DOI: 10.1038/nature09298] [Citation(s) in RCA: 2019] [Impact Index Per Article: 144.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 06/21/2010] [Indexed: 12/24/2022]
Abstract
Despite great progress in identifying genetic variants that influence human disease, most inherited risk remains unexplained. A more complete understanding requires genome-wide studies that fully examine less common alleles in populations with a wide range of ancestry. To inform the design and interpretation of such studies, we genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations, and sequenced ten 100-kilobase regions in 692 of these individuals. This integrated data set of common and rare alleles, called 'HapMap 3', includes both SNPs and copy number polymorphisms (CNPs). We characterized population-specific differences among low-frequency variants, measured the improvement in imputation accuracy afforded by the larger reference panel, especially in imputing SNPs with a minor allele frequency of <or=5%, and demonstrated the feasibility of imputing newly discovered CNPs and SNPs. This expanded public resource of genome variants in global populations supports deeper interrogation of genomic variation and its role in human disease, and serves as a step towards a high-resolution map of the landscape of human genetic variation.
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Affiliation(s)
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- Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02138, USA.
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11
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Gioia J, Yerrapragada S, Qin X, Jiang H, Igboeli OC, Muzny D, Dugan-Rocha S, Ding Y, Hawes A, Liu W, Perez L, Kovar C, Dinh H, Lee S, Nazareth L, Blyth P, Holder M, Buhay C, Tirumalai MR, Liu Y, Dasgupta I, Bokhetache L, Fujita M, Karouia F, Eswara Moorthy P, Siefert J, Uzman A, Buzumbo P, Verma A, Zwiya H, McWilliams BD, Olowu A, Clinkenbeard KD, Newcombe D, Golebiewski L, Petrosino JF, Nicholson WL, Fox GE, Venkateswaran K, Highlander SK, Weinstock GM. Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032. PLoS One 2007; 2:e928. [PMID: 17895969 PMCID: PMC1976550 DOI: 10.1371/journal.pone.0000928] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Accepted: 08/31/2007] [Indexed: 11/25/2022] Open
Abstract
Background Bacillus spores are notoriously resistant to unfavorable conditions such as UV radiation, γ-radiation, H2O2, desiccation, chemical disinfection, or starvation. Bacillus pumilus SAFR-032 survives standard decontamination procedures of the Jet Propulsion Lab spacecraft assembly facility, and both spores and vegetative cells of this strain exhibit elevated resistance to UV radiation and H2O2 compared to other Bacillus species. Principal Findings The genome of B. pumilus SAFR-032 was sequenced and annotated. Lists of genes relevant to DNA repair and the oxidative stress response were generated and compared to B. subtilis and B. licheniformis. Differences in conservation of genes, gene order, and protein sequences are highlighted because they potentially explain the extreme resistance phenotype of B. pumilus. The B. pumilus genome includes genes not found in B. subtilis or B. licheniformis and conserved genes with sequence divergence, but paradoxically lacks several genes that function in UV or H2O2 resistance in other Bacillus species. Significance This study identifies several candidate genes for further research into UV and H2O2 resistance. These findings will help explain the resistance of B. pumilus and are applicable to understanding sterilization survival strategies of microbes.
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Affiliation(s)
- Jason Gioia
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shailaja Yerrapragada
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Huaiyang Jiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Okezie C. Igboeli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shannon Dugan-Rocha
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Yan Ding
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alicia Hawes
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wen Liu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lesette Perez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Christie Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Huyen Dinh
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sandra Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lynne Nazareth
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Peter Blyth
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael Holder
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Christian Buhay
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Yamei Liu
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Indrani Dasgupta
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Lina Bokhetache
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Fathi Karouia
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Prahathees Eswara Moorthy
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Johnathan Siefert
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Akif Uzman
- Department of Natural Sciences, University of Houston‐Downtown, Houston, Texas, United States of America
| | - Prince Buzumbo
- Department of Natural Sciences, University of Houston‐Downtown, Houston, Texas, United States of America
| | - Avani Verma
- Department of Natural Sciences, University of Houston‐Downtown, Houston, Texas, United States of America
| | - Hiba Zwiya
- Department of Natural Sciences, University of Houston‐Downtown, Houston, Texas, United States of America
| | - Brian D. McWilliams
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Adeola Olowu
- University of St. Thomas, Houston Texas, United States of America
| | - Kenneth D. Clinkenbeard
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - David Newcombe
- University of Idaho Coeur d'Alene, Coeur d'Alene, Idaho, United States of America
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, United States of America
| | - Lisa Golebiewski
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wayne L. Nicholson
- Department of Microbiology and Cell Science, University of Florida Space Life Sciences Laboratory, Kennedy Space Center, Florida, United States of America
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, United States of America
| | - Sarah K. Highlander
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - George M. Weinstock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- * To whom correspondence should be addressed. E-mail:
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12
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Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K, Muzny D, Platzer M, Howell GR, Burrows C, Bird CP, Frankish A, Lovell FL, Howe KL, Ashurst JL, Fulton RS, Sudbrak R, Wen G, Jones MC, Hurles ME, Andrews TD, Scott CE, Searle S, Ramser J, Whittaker A, Deadman R, Carter NP, Hunt SE, Chen R, Cree A, Gunaratne P, Havlak P, Hodgson A, Metzker ML, Richards S, Scott G, Steffen D, Sodergren E, Wheeler DA, Worley KC, Ainscough R, Ambrose KD, Ansari-Lari MA, Aradhya S, Ashwell RIS, Babbage AK, Bagguley CL, Ballabio A, Banerjee R, Barker GE, Barlow KF, Barrett IP, Bates KN, Beare DM, Beasley H, Beasley O, Beck A, Bethel G, Blechschmidt K, Brady N, Bray-Allen S, Bridgeman AM, Brown AJ, Brown MJ, Bonnin D, Bruford EA, Buhay C, Burch P, Burford D, Burgess J, Burrill W, Burton J, Bye JM, Carder C, Carrel L, Chako J, Chapman JC, Chavez D, Chen E, Chen G, Chen Y, Chen Z, Chinault C, Ciccodicola A, Clark SY, Clarke G, Clee CM, Clegg S, Clerc-Blankenburg K, Clifford K, Cobley V, Cole CG, Conquer JS, Corby N, Connor RE, David R, Davies J, Davis C, Davis J, Delgado O, Deshazo D, Dhami P, Ding Y, Dinh H, Dodsworth S, Draper H, Dugan-Rocha S, Dunham A, Dunn M, Durbin KJ, Dutta I, Eades T, Ellwood M, Emery-Cohen A, Errington H, Evans KL, Faulkner L, Francis F, Frankland J, Fraser AE, Galgoczy P, Gilbert J, Gill R, Glöckner G, Gregory SG, Gribble S, Griffiths C, Grocock R, Gu Y, Gwilliam R, Hamilton C, Hart EA, Hawes A, Heath PD, Heitmann K, Hennig S, Hernandez J, Hinzmann B, Ho S, Hoffs M, Howden PJ, Huckle EJ, Hume J, Hunt PJ, Hunt AR, Isherwood J, Jacob L, Johnson D, Jones S, de Jong PJ, Joseph SS, Keenan S, Kelly S, Kershaw JK, Khan Z, Kioschis P, Klages S, Knights AJ, Kosiura A, Kovar-Smith C, Laird GK, Langford C, Lawlor S, Leversha M, Lewis L, Liu W, Lloyd C, Lloyd DM, Loulseged H, Loveland JE, Lovell JD, Lozado R, Lu J, Lyne R, Ma J, Maheshwari M, Matthews LH, McDowall J, McLaren S, McMurray A, Meidl P, Meitinger T, Milne S, Miner G, Mistry SL, Morgan M, Morris S, Müller I, Mullikin JC, Nguyen N, Nordsiek G, Nyakatura G, O'Dell CN, Okwuonu G, Palmer S, Pandian R, Parker D, Parrish J, Pasternak S, Patel D, Pearce AV, Pearson DM, Pelan SE, Perez L, Porter KM, Ramsey Y, Reichwald K, Rhodes S, Ridler KA, Schlessinger D, Schueler MG, Sehra HK, Shaw-Smith C, Shen H, Sheridan EM, Shownkeen R, Skuce CD, Smith ML, Sotheran EC, Steingruber HE, Steward CA, Storey R, Swann RM, Swarbreck D, Tabor PE, Taudien S, Taylor T, Teague B, Thomas K, Thorpe A, Timms K, Tracey A, Trevanion S, Tromans AC, d'Urso M, Verduzco D, Villasana D, Waldron L, Wall M, Wang Q, Warren J, Warry GL, Wei X, West A, Whitehead SL, Whiteley MN, Wilkinson JE, Willey DL, Williams G, Williams L, Williamson A, Williamson H, Wilming L, Woodmansey RL, Wray PW, Yen J, Zhang J, Zhou J, Zoghbi H, Zorilla S, Buck D, Reinhardt R, Poustka A, Rosenthal A, Lehrach H, Meindl A, Minx PJ, Hillier LW, Willard HF, Wilson RK, Waterston RH, Rice CM, Vaudin M, Coulson A, Nelson DL, Weinstock G, Sulston JE, Durbin R, Hubbard T, Gibbs RA, Beck S, Rogers J, Bentley DR. The DNA sequence of the human X chromosome. Nature 2005; 434:325-37. [PMID: 15772651 PMCID: PMC2665286 DOI: 10.1038/nature03440] [Citation(s) in RCA: 738] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2005] [Accepted: 02/07/2005] [Indexed: 01/19/2023]
Abstract
The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.
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MESH Headings
- Animals
- Antigens, Neoplasm/genetics
- Centromere/genetics
- Chromosomes, Human, X/genetics
- Chromosomes, Human, Y/genetics
- Contig Mapping
- Crossing Over, Genetic/genetics
- Dosage Compensation, Genetic
- Evolution, Molecular
- Female
- Genetic Linkage/genetics
- Genetics, Medical
- Genomics
- Humans
- Male
- Polymorphism, Single Nucleotide/genetics
- RNA/genetics
- Repetitive Sequences, Nucleic Acid/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Testis/metabolism
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Affiliation(s)
- Mark T Ross
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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13
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Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Simons R, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 2004; 428:493-521. [PMID: 15057822 DOI: 10.1038/nature02426] [Citation(s) in RCA: 1512] [Impact Index Per Article: 75.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2003] [Accepted: 02/20/2004] [Indexed: 01/16/2023]
Abstract
The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
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Affiliation(s)
- Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu
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Williams JK, Wood RJ, Hawes A, Mansour KA. The use of the pectoralis myocutaneous flap for repair of a retrosternal esophagocolonic anastomotic leak. Plast Reconstr Surg 1998; 101:802-5. [PMID: 9500399 DOI: 10.1097/00006534-199803000-00032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- J K Williams
- Division of Plastic and Reconstructive Surgery, Emory University School of Medicine, Atlanta, Ga, USA
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Staiano-Coico L, Krueger JG, Rubin JS, D'limi S, Vallat VP, Valentino L, Fahey T, Hawes A, Kingston G, Madden MR. Human keratinocyte growth factor effects in a porcine model of epidermal wound healing. J Exp Med 1993; 178:865-78. [PMID: 8350059 PMCID: PMC2191158 DOI: 10.1084/jem.178.3.865] [Citation(s) in RCA: 167] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Keratinocyte growth factor (KGF) is a member of the fibroblast growth factor (FGF) family (hence the alternative designation FGF-7). It is produced by stromal cells, but acts as a mitogen for epithelial cells. We examined the effects of topically applied KGF on healing of wounds in a porcine model. In partial-thickness wounds, KGF stimulated the rate of reepithelialization (p < 0.0002), associated with a thickening of the epidermis (p < 0.0001). Epidermis from KGF-treated full-thickness wound sites was significantly thicker (0.31 +/- 0.22 mm) compared with mirror image control sites (0.18 +/- 0.12 mm) (p < 0.0001). Moreover, the majority (77%) of KGF-treated wounds exhibited epidermis with a deep rete ridge pattern as compared with control sites. These effects were observed as early as 14 d and persisted for at least 4 wk. KGF treatment also increased the number of serrated basal cells associated with increased deposition of collagen fibers in the superficial dermis adjacent to the acanthotic epidermis. Electron microscopy revealed better developed hemidesmosomes associated with thicker bundles of tonofilaments in the serrated cells. The pattern of epidermal thickening observed in KGF-treated wounds resembled psoriasis. Psoriasis is a disease associated with epidermal thickening, parakeratosis as well as hyperproliferation that extends beyond the basal layer. In striking contrast to psoriasis, KGF-treated wounds exhibited normal orthokeratotic maturation, and proliferation was localized to the basal cells. Our present findings have significant implications concerning the role of KGF as a paracrine modulator of epidermal proliferation and differentiation.
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Affiliation(s)
- L Staiano-Coico
- Department of Surgery, Cornell University Medical College, New York 10021
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16
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Van Horn G, Hawes A. Global aphasia without hemiparesis: a sign of embolic encephalopathy. Neurology 1982; 32:403-6. [PMID: 7199663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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