1
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Rockowitz S, LeCompte N, Carmack M, Quitadamo A, Wang L, Park M, Knight D, Sexton E, Smith L, Sheidley B, Field M, Holm IA, Brownstein CA, Agrawal PB, Kornetsky S, Poduri A, Snapper SB, Beggs AH, Yu TW, Williams DA, Sliz P. Children's rare disease cohorts: an integrative research and clinical genomics initiative. NPJ Genom Med 2020; 5:29. [PMID: 32655885 PMCID: PMC7338382 DOI: 10.1038/s41525-020-0137-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [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: 11/23/2019] [Accepted: 06/03/2020] [Indexed: 12/16/2022] Open
Abstract
While genomic data is frequently collected under distinct research protocols and disparate clinical and research regimes, there is a benefit in streamlining sequencing strategies to create harmonized databases, particularly in the area of pediatric rare disease. Research hospitals seeking to implement unified genomics workflows for research and clinical practice face numerous challenges, as they need to address the unique requirements and goals of the distinct environments and many stakeholders, including clinicians, researchers and sequencing providers. Here, we present outcomes of the first phase of the Children’s Rare Disease Cohorts initiative (CRDC) that was completed at Boston Children’s Hospital (BCH). We have developed a broadly sharable database of 2441 exomes from 15 pediatric rare disease cohorts, with major contributions from early onset epilepsy and early onset inflammatory bowel disease. All sequencing data is integrated and combined with phenotypic and research data in a genomics learning system (GLS). Phenotypes were both manually annotated and pulled automatically from patient medical records. Deployment of a genomically-ordered relational database allowed us to provide a modular and robust platform for centralized storage and analysis of research and clinical data, currently totaling 8516 exomes and 112 genomes. The GLS integrates analytical systems, including machine learning algorithms for automated variant classification and prioritization, as well as phenotype extraction via natural language processing (NLP) of clinical notes. This GLS is extensible to additional analytic systems and growing research and clinical collections of genomic and other types of data.
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Affiliation(s)
- Shira Rockowitz
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
| | - Nicholas LeCompte
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
| | - Mary Carmack
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
| | - Andrew Quitadamo
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
| | - Lily Wang
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
| | - Meredith Park
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Devon Knight
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Emma Sexton
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Lacey Smith
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Beth Sheidley
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Michael Field
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA 02115 USA
| | - Ingrid A Holm
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115 USA
| | - Catherine A Brownstein
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115 USA
| | - Pankaj B Agrawal
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115 USA
| | - Susan Kornetsky
- Research Administration, Boston Children's Hospital, Boston, MA 02115 USA
| | - Annapurna Poduri
- Harvard Medical School, Boston, MA 02115 USA.,Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Scott B Snapper
- Harvard Medical School, Boston, MA 02115 USA.,Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA 02115 USA
| | - Alan H Beggs
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115 USA
| | - Timothy W Yu
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115 USA
| | - David A Williams
- Harvard Medical School, Boston, MA 02115 USA.,Division of Hematology/Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115 USA
| | - Piotr Sliz
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
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4
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Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. An integrated map of structural variation in 2,504 human genomes. Nature 2015; 526:75-81. [PMID: 26432246 PMCID: PMC4617611 DOI: 10.1038/nature15394] [Citation(s) in RCA: 1364] [Impact Index Per Article: 151.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 08/20/2015] [Indexed: 12/11/2022]
Abstract
Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.
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Affiliation(s)
- Peter H. Sudmant
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195-5065 Washington USA
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
| | - Eugene J. Gardner
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W Baltimore Street, Baltimore, 21201 Maryland USA
| | - Robert E. Handsaker
- Department of Genetics, Harvard Medical School, 25 Shattuck Street, Boston, Boston, 02115 Massachusetts USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142 Massachusetts USA
| | - Alexej Abyzov
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, 55905 Minnesota USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195-5065 Washington USA
- Howard Hughes Medical Institute, University of Washington, Seattle, 98195 Washington USA
| | - Yan Zhang
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 & 437, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
| | - Kai Ye
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, 63108 Missouri USA
- Department of Genetics, Washington University in St Louis, 4444 Forest Park Avenue, St Louis, 63108 Missouri USA
| | - Goo Jun
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, 48109 Michigan USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler St., Houston, 77030 Texas USA
| | - Markus Hsi-Yang Fritz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
| | - Miriam K. Konkel
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, 70803 Louisiana USA
| | - Ankit Malhotra
- The Jackson Laboratory for Genomic Medicine, 10 Discovery 263 Farmington Avenue, Farmington, 06030 Connecticut USA
| | - Adrian M. Stütz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
| | - Xinghua Shi
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, 28223 North Carolina USA
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge UK
| | - Jieming Chen
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 & 437, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, 06520 Connecticut USA
| | - Fereydoun Hormozdiari
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195-5065 Washington USA
| | - Gargi Dayama
- Department of Computational Medicine & Bioinformatics, University of Michigan, 500 S. State Street, Ann Arbor, 48109 Michigan USA
| | - Ken Chen
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, 77030 Texas USA
| | - Maika Malig
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195-5065 Washington USA
| | - Mark J. P. Chaisson
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195-5065 Washington USA
| | - Klaudia Walter
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - Sascha Meiers
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
| | - Seva Kashin
- Department of Genetics, Harvard Medical School, 25 Shattuck Street, Boston, Boston, 02115 Massachusetts USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142 Massachusetts USA
| | - Erik Garrison
- Department of Biology, Boston College, 355 Higgins Hall, 140 Commonwealth Avenue, Chestnut Hill, 02467 Massachusetts USA
| | - Adam Auton
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, 10461 New York USA
| | - Hugo Y. K. Lam
- Bina Technologies, Roche Sequencing, 555 Twin Dolphin Drive, Redwood City, 94065 California USA
| | - Xinmeng Jasmine Mu
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 & 437, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142 Massachusetts USA
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara, 06800 Turkey
| | - Danny Antaki
- University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, 92093 California USA
| | - Taejeong Bae
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, 55905 Minnesota USA
| | - Eliza Cerveira
- The Jackson Laboratory for Genomic Medicine, 10 Discovery 263 Farmington Avenue, Farmington, 06030 Connecticut USA
| | - Peter Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892 Maryland USA
| | - Zechen Chong
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, 77030 Texas USA
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge UK
| | - Elif Dal
- Department of Computer Engineering, Bilkent University, Ankara, 06800 Turkey
| | - Li Ding
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, 63108 Missouri USA
- Department of Genetics, Washington University in St Louis, 4444 Forest Park Avenue, St Louis, 63108 Missouri USA
- Department of Medicine, Washington University in St Louis, 4444 Forest Park Avenue, St Louis, 63108 Missouri USA
- Siteman Cancer Center, 660 South Euclid Avenue, St Louis, 63110 Missouri USA
| | - Sarah Emery
- Department of Human Genetics, University of Michigan, 1241 Catherine Street, Ann Arbor, 48109 Michigan USA
| | - Xian Fan
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, 77030 Texas USA
| | - Madhusudan Gujral
- University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, 92093 California USA
| | - Fatma Kahveci
- Department of Computer Engineering, Bilkent University, Ankara, 06800 Turkey
| | - Jeffrey M. Kidd
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, 48109 Michigan USA
- Department of Human Genetics, University of Michigan, 1241 Catherine Street, Ann Arbor, 48109 Michigan USA
| | - Yu Kong
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, 10461 New York USA
| | - Eric-Wubbo Lameijer
- Molecular Epidemiology, Leiden University Medical Center, Leiden, 2300RA The Netherlands
| | - Shane McCarthy
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge UK
| | - Richard A. Gibbs
- Baylor College of Medicine, 1 Baylor Plaza, Houston, 77030 Texas USA
| | - Gabor Marth
- Department of Biology, Boston College, 355 Higgins Hall, 140 Commonwealth Avenue, Chestnut Hill, 02467 Massachusetts USA
| | - Christopher E. Mason
- The Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, 1305 York Avenue, Weill Cornell Medical College, New York, 10065 New York USA
- The Feil Family Brain and Mind Research Institute, 413 East 69th St, Weill Cornell Medical College, New York, 10065 New York USA
| | - Androniki Menelaou
- University of Oxford, 1 South Parks Road, Oxford, OX3 9DS UK
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, 3584 CG The Netherlands
| | - Donna M. Muzny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York School of Natural Sciences, 1428 Madison Avenue, New York, 10029 New York USA
| | - Bradley J. Nelson
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195-5065 Washington USA
| | - Amina Noor
- University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, 92093 California USA
| | - Nicholas F. Parrish
- Institute for Virus Research, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, 606-8507 Kyoto Japan
| | - Matthew Pendleton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York School of Natural Sciences, 1428 Madison Avenue, New York, 10029 New York USA
| | - Andrew Quitadamo
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, 28223 North Carolina USA
| | - Benjamin Raeder
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York School of Natural Sciences, 1428 Madison Avenue, New York, 10029 New York USA
| | - Mallory Romanovitch
- The Jackson Laboratory for Genomic Medicine, 10 Discovery 263 Farmington Avenue, Farmington, 06030 Connecticut USA
| | - Andreas Schlattl
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York School of Natural Sciences, 1428 Madison Avenue, New York, 10029 New York USA
| | - Andrey A. Shabalin
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Richmond, 23298-0581 Virginia USA
| | - Andreas Untergasser
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
- Zentrum für Molekulare Biologie, University of Heidelberg, Im Neuenheimer Feld 282, Heidelberg, 69120 Germany
| | - Jerilyn A. Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, 70803 Louisiana USA
| | - Min Wang
- Baylor College of Medicine, 1 Baylor Plaza, Houston, 77030 Texas USA
| | - Fuli Yu
- Baylor College of Medicine, 1 Baylor Plaza, Houston, 77030 Texas USA
| | - Chengsheng Zhang
- The Jackson Laboratory for Genomic Medicine, 10 Discovery 263 Farmington Avenue, Farmington, 06030 Connecticut USA
| | - Jing Zhang
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 & 437, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
| | - Xiangqun Zheng-Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge UK
| | - Wanding Zhou
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, 77030 Texas USA
| | - Thomas Zichner
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
| | - Jonathan Sebat
- University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, 92093 California USA
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, 70803 Louisiana USA
| | - Steven A. McCarroll
- Department of Genetics, Harvard Medical School, 25 Shattuck Street, Boston, Boston, 02115 Massachusetts USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142 Massachusetts USA
| | - The 1000 Genomes Project Consortium
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195-5065 Washington USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W Baltimore Street, Baltimore, 21201 Maryland USA
- Department of Genetics, Harvard Medical School, 25 Shattuck Street, Boston, Boston, 02115 Massachusetts USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142 Massachusetts USA
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, 55905 Minnesota USA
- Howard Hughes Medical Institute, University of Washington, Seattle, 98195 Washington USA
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 & 437, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, 63108 Missouri USA
- Department of Genetics, Washington University in St Louis, 4444 Forest Park Avenue, St Louis, 63108 Missouri USA
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, 48109 Michigan USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler St., Houston, 77030 Texas USA
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, 70803 Louisiana USA
- The Jackson Laboratory for Genomic Medicine, 10 Discovery 263 Farmington Avenue, Farmington, 06030 Connecticut USA
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, 28223 North Carolina USA
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge UK
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, 06520 Connecticut USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, 500 S. State Street, Ann Arbor, 48109 Michigan USA
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, 77030 Texas USA
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
- Department of Biology, Boston College, 355 Higgins Hall, 140 Commonwealth Avenue, Chestnut Hill, 02467 Massachusetts USA
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, 10461 New York USA
- Bina Technologies, Roche Sequencing, 555 Twin Dolphin Drive, Redwood City, 94065 California USA
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142 Massachusetts USA
- Department of Computer Engineering, Bilkent University, Ankara, 06800 Turkey
- University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, 92093 California USA
- National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892 Maryland USA
- Department of Medicine, Washington University in St Louis, 4444 Forest Park Avenue, St Louis, 63108 Missouri USA
- Siteman Cancer Center, 660 South Euclid Avenue, St Louis, 63110 Missouri USA
- Department of Human Genetics, University of Michigan, 1241 Catherine Street, Ann Arbor, 48109 Michigan USA
- Molecular Epidemiology, Leiden University Medical Center, Leiden, 2300RA The Netherlands
- Baylor College of Medicine, 1 Baylor Plaza, Houston, 77030 Texas USA
- The Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, 1305 York Avenue, Weill Cornell Medical College, New York, 10065 New York USA
- The Feil Family Brain and Mind Research Institute, 413 East 69th St, Weill Cornell Medical College, New York, 10065 New York USA
- University of Oxford, 1 South Parks Road, Oxford, OX3 9DS UK
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, 3584 CG The Netherlands
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York School of Natural Sciences, 1428 Madison Avenue, New York, 10029 New York USA
- Institute for Virus Research, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, 606-8507 Kyoto Japan
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Richmond, 23298-0581 Virginia USA
- Zentrum für Molekulare Biologie, University of Heidelberg, Im Neuenheimer Feld 282, Heidelberg, 69120 Germany
- Department of Computer Science, Yale University, 51 Prospect Street, New Haven, 06511 Connecticut USA
- Department of Graduate Studies – Life Sciences, Ewha Womans University, Ewhayeodae-gil, Seodaemun-gu, 120-750 Seoul South Korea
| | - Ryan E. Mills
- Department of Computational Medicine & Bioinformatics, University of Michigan, 500 S. State Street, Ann Arbor, 48109 Michigan USA
- Department of Human Genetics, University of Michigan, 1241 Catherine Street, Ann Arbor, 48109 Michigan USA
| | - Mark B. Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 & 437, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
- Department of Computer Science, Yale University, 51 Prospect Street, New Haven, 06511 Connecticut USA
| | - Ali Bashir
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York School of Natural Sciences, 1428 Madison Avenue, New York, 10029 New York USA
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge UK
| | - Scott E. Devine
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W Baltimore Street, Baltimore, 21201 Maryland USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, 10 Discovery 263 Farmington Avenue, Farmington, 06030 Connecticut USA
- Department of Graduate Studies – Life Sciences, Ewha Womans University, Ewhayeodae-gil, Seodaemun-gu, 120-750 Seoul South Korea
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195-5065 Washington USA
- Howard Hughes Medical Institute, University of Washington, Seattle, 98195 Washington USA
| | - Jan O. Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge UK
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