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Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. Modern Methods for Delineating Metagenomic Complexity. Cell Syst 2015; 1:6-7. [PMID: 27135684 DOI: 10.1016/j.cels.2015.07.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/16/2015] [Accepted: 07/16/2015] [Indexed: 01/31/2023]
Affiliation(s)
- Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA; School of Earth and Environmental Sciences, City University of New York (CUNY) Queens College, Flushing, NY 11367, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Shanin Chowdhury
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA; CUNY Hunter College, New York 10065, NY, USA
| | - Dyala Jaroudi
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Collin Boyer
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Nick Bernstein
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Julia M Maritz
- Center for Genomics, New York University, New York, NY 10065, USA
| | - Darryl Reeves
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY Center for Genomics, USA
| | - Jorge Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sagar Chhangawala
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sofia Ahsanuddin
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA; Department of Biology, CUNY Brooklyn College, Brooklyn, NY 11210, USA
| | - Amber Simmons
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | | | | | | | | | | | - Nell Kirchberger
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Isaac Garcia
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - David Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sean Dhanraj
- Department of Biology, CUNY Brooklyn College, Brooklyn, NY 11210, USA
| | - Tanzina Nawrin
- Department of Biology, CUNY Brooklyn College, Brooklyn, NY 11210, USA
| | - Yogesh Saletore
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY Center for Genomics, USA
| | - Noah Alexander
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Priyanka Vijay
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY Center for Genomics, USA
| | - Elizabeth M Hénaff
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Michael Walsh
- State University of New York, Downstate, Brooklyn, NY 11203, USA
| | - Gregory D O'Mullan
- School of Earth and Environmental Sciences, City University of New York (CUNY) Queens College, Flushing, NY 11367, USA
| | - Scott Tighe
- University of Vermont, Burlington, VT 05405, USA
| | - Joel T Dudley
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
| | - Anya Dunaif
- Rockefeller University, New York, NY 10065, USA
| | - Sean Ennis
- National Children's Research Centre, Our Lady's Children's Hospital, Dublin 12, Ireland; Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College, Dublin 12, Ireland
| | - Eoghan O'Halloran
- National Children's Research Centre, Our Lady's Children's Hospital, Dublin 12, Ireland
| | - Tiago R Magalhaes
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College, Dublin 12, Ireland
| | - Braden Boone
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Angela L Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Theodore R Muth
- Department of Biology, CUNY Brooklyn College, Brooklyn, NY 11210, USA
| | | | | | - Eric E Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029 USA
| | | | - Robert J Prill
- Accelerated Discovery Lab, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Jane M Carlton
- Center for Genomics, New York University, New York, NY 10065, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA; The Feil Family Brain and Mind Research Institute, New York, NY 10065, USA.
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Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. Cell Syst 2015; 1:97-97.e3. [PMID: 27135689 DOI: 10.1016/j.cels.2015.07.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Morrison MA, Magalhaes TR, Ramke J, Smith SE, Ennis S, Simpson CL, Portas L, Murgia F, Ahn J, Dardenne C, Mayne K, Robinson R, Morgan DJ, Brian G, Lee L, Woo SJ, Zacharaki F, Tsironi EE, Miller JW, Kim IK, Park KH, Bailey-Wilson JE, Farrer LA, Stambolian D, DeAngelis MM. Ancestry of the Timorese: age-related macular degeneration associated genotype and allele sharing among human populations from throughout the world. Front Genet 2015. [PMID: 26217379 PMCID: PMC4496576 DOI: 10.3389/fgene.2015.00238] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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] [Indexed: 11/13/2022] Open
Abstract
We observed that the third leading cause of blindness in the world, age-related macular degeneration (AMD), occurs at a very low documented frequency in a population-based cohort from Timor-Leste. Thus, we determined a complete catalog of the ancestry of the Timorese by analysis of whole exome chip data and haplogroup analysis of SNP genotypes determined by sequencing the Hypervariable I and II regions of the mitochondrial genome and 17 genotyped YSTR markers obtained from 535 individuals. We genotyped 20 previously reported AMD-associated SNPs in the Timorese to examine their allele frequencies compared to and between previously documented AMD cohorts of varying ethnicities. For those without AMD (average age > 55 years), genotype and allele frequencies were similar for most SNPs with a few exceptions. The major risk allele of HTRA1 rs11200638 (10q26) was at a significantly higher frequency in the Timorese, as well as 3 of the 5 protective CFH (1q32) SNPs (rs800292, rs2284664, and rs12066959). Additionally, the most commonly associated AMD-risk SNP, CFH rs1061170 (Y402H), was also seen at a much lower frequency in the Korean and Timorese populations than in the assessed Caucasian populations (C ~7 vs. ~40%, respectively). The difference in allele frequencies between the Timorese population and the other genotyped populations, along with the haplogroup analysis, also highlight the genetic diversity of the Timorese. Specifically, the most common ancestry groupings were Oceanic (Melanesian and Papuan) and Eastern Asian (specifically Han Chinese). The low prevalence of AMD in the Timorese population (2 of 535 randomly selected participants) may be due to the enrichment of protective alleles in this population at the 1q32 locus.
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Affiliation(s)
- Margaux A Morrison
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Tiago R Magalhaes
- National Children's Research Centre, Our Lady's Children's Hospital Dublin, Ireland ; Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin Dublin, Ireland
| | | | - Silvia E Smith
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Sean Ennis
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin Dublin, Ireland ; National Centre for Medical Genetics, Our Lady's Children's Hospital Dublin, Ireland
| | - Claire L Simpson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health Baltimore, MD, USA
| | - Laura Portas
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health Baltimore, MD, USA ; Institute of Population Genetics, The National Research Council Sassari, Italy
| | - Federico Murgia
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health Baltimore, MD, USA ; Institute of Population Genetics, The National Research Council Sassari, Italy
| | - Jeeyun Ahn
- Department of Ophthalmology, Seoul National University College of Medicine Seoul, South Korea ; Department of Ophthalmology, Seoul Metropolitan Government Seoul National University Boramae Medical Center Seoul, South Korea
| | - Caitlin Dardenne
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Katie Mayne
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Rosann Robinson
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Denise J Morgan
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Garry Brian
- The Fred Hollows Foundation New Zealand Auckland, New Zealand
| | - Lucy Lee
- The Fred Hollows Foundation New Zealand Auckland, New Zealand ; London School of Hygiene and Tropical Medicine, University of London London, UK
| | - Se J Woo
- Department of Ophthalmology, Seoul National University College of Medicine Seoul, South Korea ; Department of Ophthalmology, Seoul National University Bundang Hospital Seoungnam, South Korea
| | - Fani Zacharaki
- Department of Ophthalmology, University of Thessaly School of Medicine Larissa, Greece
| | - Evangelia E Tsironi
- Department of Ophthalmology, University of Thessaly School of Medicine Larissa, Greece
| | - Joan W Miller
- Retina Service and Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School Boston, MA, USA
| | - Ivana K Kim
- Retina Service and Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School Boston, MA, USA
| | - Kyu H Park
- Department of Ophthalmology, Seoul National University College of Medicine Seoul, South Korea ; Department of Ophthalmology, Seoul National University Bundang Hospital Seoungnam, South Korea
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health Baltimore, MD, USA
| | - Lindsay A Farrer
- Departments of Medicine, Ophthalmology, Neurology, Epidemiology, and Biostatistics, Boston University Schools of Medicine and Public Health Boston, MA, USA
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania Philadelphia, PA, USA
| | - Margaret M DeAngelis
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
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Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. Cell Syst 2015; 1:72-87. [PMID: 26594662 PMCID: PMC4651444 DOI: 10.1016/j.cels.2015.01.001] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [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: 01/08/2023]
Abstract
The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station’s history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.
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Affiliation(s)
- Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; School of Earth and Environmental Sciences, City University of New York (CUNY) Queens College, Flushing, NY 11367, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Shanin Chowdhury
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; CUNY Hunter College, New York, NY 10065, USA
| | - Dyala Jaroudi
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Collin Boyer
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Nick Bernstein
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Julia M Maritz
- Center for Genomics, New York University, New York, NY 10003, USA
| | - Darryl Reeves
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY 10065, USA
| | - Jorge Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sagar Chhangawala
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sofia Ahsanuddin
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA
| | - Amber Simmons
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | | | | | | | | | | | - Nell Kirchberger
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Isaac Garcia
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - David Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Sean Dhanraj
- CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA
| | - Tanzina Nawrin
- CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA
| | - Yogesh Saletore
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY 10065, USA
| | - Noah Alexander
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Priyanka Vijay
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY 10065, USA
| | - Elizabeth M Hénaff
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Michael Walsh
- State University of New York, Downstate, Brooklyn, NY 11203, USA
| | - Gregory D O'Mullan
- School of Earth and Environmental Sciences, City University of New York (CUNY) Queens College, Flushing, NY 11367, USA
| | - Scott Tighe
- University of Vermont, Burlington, VT 05405, USA
| | - Joel T Dudley
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anya Dunaif
- Rockefeller University, New York, NY 10065, USA
| | - Sean Ennis
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin 4, Ireland ; National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland
| | - Eoghan O'Halloran
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin 4, Ireland
| | - Tiago R Magalhaes
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin 4, Ireland ; National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland
| | - Braden Boone
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Angela L Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Theodore R Muth
- CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA
| | | | | | - Eric E Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Robert J Prill
- Accelerated Discovery Lab, IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Jane M Carlton
- Center for Genomics, New York University, New York, NY 10003, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; The Feil Family Brain and Mind Research Institute, New York, NY 10065, USA
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5
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Pinto D, Delaby E, Merico D, Barbosa M, Merikangas A, Klei L, Thiruvahindrapuram B, Xu X, Ziman R, Wang Z, Vorstman JAS, Thompson A, Regan R, Pilorge M, Pellecchia G, Pagnamenta AT, Oliveira B, Marshall CR, Magalhaes TR, Lowe JK, Howe JL, Griswold AJ, Gilbert J, Duketis E, Dombroski BA, De Jonge MV, Cuccaro M, Crawford EL, Correia CT, Conroy J, Conceição IC, Chiocchetti AG, Casey JP, Cai G, Cabrol C, Bolshakova N, Bacchelli E, Anney R, Gallinger S, Cotterchio M, Casey G, Zwaigenbaum L, Wittemeyer K, Wing K, Wallace S, van Engeland H, Tryfon A, Thomson S, Soorya L, Rogé B, Roberts W, Poustka F, Mouga S, Minshew N, McInnes LA, McGrew SG, Lord C, Leboyer M, Le Couteur AS, Kolevzon A, Jiménez González P, Jacob S, Holt R, Guter S, Green J, Green A, Gillberg C, Fernandez BA, Duque F, Delorme R, Dawson G, Chaste P, Café C, Brennan S, Bourgeron T, Bolton PF, Bölte S, Bernier R, Baird G, Bailey AJ, Anagnostou E, Almeida J, Wijsman EM, Vieland VJ, Vicente AM, Schellenberg GD, Pericak-Vance M, Paterson AD, Parr JR, Oliveira G, Nurnberger JI, Monaco AP, Maestrini E, Klauck SM, Hakonarson H, Haines JL, Geschwind DH, Freitag CM, Folstein SE, Ennis S, Coon H, Battaglia A, Szatmari P, Sutcliffe JS, Hallmayer J, Gill M, Cook EH, Buxbaum JD, Devlin B, Gallagher L, Betancur C, Scherer SW. Convergence of genes and cellular pathways dysregulated in autism spectrum disorders. Am J Hum Genet 2014; 94:677-94. [PMID: 24768552 PMCID: PMC4067558 DOI: 10.1016/j.ajhg.2014.03.018] [Citation(s) in RCA: 659] [Impact Index Per Article: 65.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 03/25/2014] [Indexed: 12/15/2022] Open
Abstract
Rare copy-number variation (CNV) is an important source of risk for autism spectrum disorders (ASDs). We analyzed 2,446 ASD-affected families and confirmed an excess of genic deletions and duplications in affected versus control groups (1.41-fold, p = 1.0 × 10−5) and an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated with dominant or X-linked ASD and intellectual disability (odds ratio = 12.62, p = 2.7 × 10−15, ∼3% of ASD subjects). Pathogenic CNVs, often showing variable expressivity, included rare de novo and inherited events at 36 loci, implicating ASD-associated genes (CHD2, HDAC4, and GDI1) previously linked to other neurodevelopmental disorders, as well as other genes such as SETD5, MIR137, and HDAC9. Consistent with hypothesized gender-specific modulators, females with ASD were more likely to have highly penetrant CNVs (p = 0.017) and were also overrepresented among subjects with fragile X syndrome protein targets (p = 0.02). Genes affected by de novo CNVs and/or loss-of-function single-nucleotide variants converged on networks related to neuronal signaling and development, synapse function, and chromatin regulation.
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Affiliation(s)
- Dalila Pinto
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elsa Delaby
- Institut National de la Santé et de la Recherche Médicale U1130, 75005 Paris, France; Centre National de la Recherche Scientifique UMR 8246, 75005 Paris, France; Neuroscience Paris Seine, Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, 75005 Paris, France
| | - Daniele Merico
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Mafalda Barbosa
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alison Merikangas
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Bhooma Thiruvahindrapuram
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Xiao Xu
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert Ziman
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Zhuozhi Wang
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Jacob A S Vorstman
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Ann Thompson
- Department of Psychiatry and Behavioural Neurosciences, Offord Centre for Child Studies, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Regina Regan
- National Children's Research Centre, Our Lady's Children's Hospital, Dublin 12, Ireland; Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
| | - Marion Pilorge
- Institut National de la Santé et de la Recherche Médicale U1130, 75005 Paris, France; Centre National de la Recherche Scientifique UMR 8246, 75005 Paris, France; Neuroscience Paris Seine, Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, 75005 Paris, France
| | - Giovanna Pellecchia
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | | | - Bárbara Oliveira
- Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; Center for Biodiversity, Functional, & Integrative Genomics, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal
| | - Christian R Marshall
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; McLaughlin Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Tiago R Magalhaes
- National Children's Research Centre, Our Lady's Children's Hospital, Dublin 12, Ireland; Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
| | - Jennifer K Lowe
- Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jennifer L Howe
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - John Gilbert
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Eftichia Duketis
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Goethe University, 60528 Frankfurt am Main, Germany
| | - Beth A Dombroski
- Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maretha V De Jonge
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Michael Cuccaro
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Emily L Crawford
- Vanderbilt Brain Institute, Center for Human Genetics Research, and Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Catarina T Correia
- Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; Center for Biodiversity, Functional, & Integrative Genomics, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal
| | - Judith Conroy
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland; Children's University Hospital Temple Street, Dublin 1, Ireland
| | - Inês C Conceição
- Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; Center for Biodiversity, Functional, & Integrative Genomics, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal
| | - Andreas G Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Goethe University, 60528 Frankfurt am Main, Germany
| | - Jillian P Casey
- National Children's Research Centre, Our Lady's Children's Hospital, Dublin 12, Ireland; Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
| | - Guiqing Cai
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christelle Cabrol
- Institut National de la Santé et de la Recherche Médicale U1130, 75005 Paris, France; Centre National de la Recherche Scientifique UMR 8246, 75005 Paris, France; Neuroscience Paris Seine, Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, 75005 Paris, France
| | - Nadia Bolshakova
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Elena Bacchelli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Richard Anney
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Steven Gallinger
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | | | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Lonnie Zwaigenbaum
- Department of Pediatrics, University of Alberta, Edmonton, AB T6B 2H3, Canada
| | | | - Kirsty Wing
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Simon Wallace
- Department of Psychiatry, University of Oxford and Warneford Hospital, Oxford OX3 7JX, UK
| | - Herman van Engeland
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584CX Utrecht, the Netherlands
| | - Ana Tryfon
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Susanne Thomson
- Vanderbilt Brain Institute, Center for Human Genetics Research, and Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Latha Soorya
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bernadette Rogé
- Unité de Recherche Interdisciplinaire Octogone, Centre d'Etudes et de Recherches en Psychopathologie, Toulouse 2 University, 31058 Toulouse, France
| | - Wendy Roberts
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Fritz Poustka
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Goethe University, 60528 Frankfurt am Main, Germany
| | - Susana Mouga
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clinica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal; University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Nancy Minshew
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - L Alison McInnes
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Susan G McGrew
- Department of Pediatrics, Vanderbilt University, Nashville, TN 37232, USA
| | - Catherine Lord
- NewYork-Presbyterian/Weill Cornell Medical Center, New York, NY 10065, USA
| | - Marion Leboyer
- FondaMental Foundation, 94010 Créteil, France; Institut National de la Santé et de la Recherche U955, Psychiatrie Génétique, 94010 Créteil, France; Faculté de Médecine, Université Paris Est, 94010 Créteil, France; Department of Psychiatry, Henri Mondor-Albert Chenevier Hospital, Assistance Publique - Hôpitaux de Paris, 94010 Créteil, France
| | - Ann S Le Couteur
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne NE1 4LP, UK
| | - Alexander Kolevzon
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patricia Jiménez González
- Child Developmental and Behavioral Unit, Hospital Nacional de Niños Dr. Sáenz Herrera, Caja Costarricense de Seguro Social, San José, Costa Rica
| | - Suma Jacob
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA; Institute of Translational Neuroscience and Department of Psychiatry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Richard Holt
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Stephen Guter
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA
| | - Jonathan Green
- Institute of Brain, Behaviour, and Mental Health, University of Manchester, Manchester M13 9PL, UK; Manchester Academic Health Sciences Centre, Manchester M13 9NT, UK
| | - Andrew Green
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland; National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland
| | - Christopher Gillberg
- Gillberg Neuropsychiatry Centre, University of Gothenburg, 41119 Gothenburg, Sweden
| | - Bridget A Fernandez
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada
| | - Frederico Duque
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clinica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal; University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Richard Delorme
- FondaMental Foundation, 94010 Créteil, France; Human Genetics and Cognitive Functions Unit, Institut Pasteur, 75015 Paris, France; Centre National de la Recherche Scientifique URA 2182 (Genes, Synapses, and Cognition), Institut Pasteur, 75015 Paris, France; Department of Child and Adolescent Psychiatry, Robert Debré Hospital, Assistance Publique - Hôpitaux de Paris, 75019 Paris, France
| | - Geraldine Dawson
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Pauline Chaste
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; FondaMental Foundation, 94010 Créteil, France
| | - Cátia Café
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clinica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal
| | - Sean Brennan
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Thomas Bourgeron
- FondaMental Foundation, 94010 Créteil, France; Human Genetics and Cognitive Functions Unit, Institut Pasteur, 75015 Paris, France; Centre National de la Recherche Scientifique URA 2182 (Genes, Synapses, and Cognition), Institut Pasteur, 75015 Paris, France; University Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Patrick F Bolton
- Institute of Psychiatry, King's College London, London SE5 8AF, UK; South London & Maudsley Biomedical Research Centre for Mental Health, London SE5 8AF, UK
| | - Sven Bölte
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University of Frankfurt, 60528 Frankfurt, Germany
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Gillian Baird
- Paediatric Neurodisability, King's Health Partners, King's College London, London WC2R 2LS, UK
| | - Anthony J Bailey
- Department of Psychiatry, University of Oxford and Warneford Hospital, Oxford OX3 7JX, UK
| | - Evdokia Anagnostou
- Bloorview Research Institute, University of Toronto, Toronto, ON M4G 1R8, Canada
| | - Joana Almeida
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clinica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal
| | - Ellen M Wijsman
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Veronica J Vieland
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Astrid M Vicente
- Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal; Center for Biodiversity, Functional, & Integrative Genomics, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal
| | - Gerard D Schellenberg
- Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Margaret Pericak-Vance
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Andrew D Paterson
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; Dalla Lana School of Public Health, Toronto, ON M5T 3M7, Canada
| | - Jeremy R Parr
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Guiomar Oliveira
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clinica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal; University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - John I Nurnberger
- Institute of Psychiatric Research, Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Medical and Molecular Genetics and Program in Medical Neuroscience, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Anthony P Monaco
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Office of the President, Tufts University, Medford, MA 02155, USA
| | - Elena Maestrini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Sabine M Klauck
- Division of Molecular Genome Analysis, German Cancer Research Center (Deutsches Krebsforschungszentrum), 69120 Heidelberg, Germany
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan L Haines
- Vanderbilt Brain Institute, Center for Human Genetics Research, and Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Daniel H Geschwind
- Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Goethe University, 60528 Frankfurt am Main, Germany
| | - Susan E Folstein
- Division of Child and Adolescent Psychiatry, Department of Psychiatry, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Sean Ennis
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland; National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland
| | - Hilary Coon
- Utah Autism Research Program, Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Agatino Battaglia
- Stella Maris Clinical Research Institute for Child and Adolescent Neuropsychiatry, 56128 Calambrone, Pisa, Italy
| | - Peter Szatmari
- Department of Psychiatry and Behavioural Neurosciences, Offord Centre for Child Studies, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - James S Sutcliffe
- Vanderbilt Brain Institute, Center for Human Genetics Research, and Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Joachim Hallmayer
- Department of Psychiatry, Stanford University Medical School, Stanford, CA 94305, USA
| | - Michael Gill
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Edwin H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60608, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Louise Gallagher
- Discipline of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Catalina Betancur
- Institut National de la Santé et de la Recherche Médicale U1130, 75005 Paris, France; Centre National de la Recherche Scientifique UMR 8246, 75005 Paris, France; Neuroscience Paris Seine, Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, 75005 Paris, France.
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; McLaughlin Centre, University of Toronto, Toronto, ON M5S 1A1, Canada.
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6
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Anney R, Klei L, Pinto D, Almeida J, Bacchelli E, Baird G, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Casey J, Conroy J, Correia C, Corsello C, Crawford EL, de Jonge M, Delorme R, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Gilbert J, Gillberg C, Glessner JT, Green A, Green J, Guter SJ, Heron EA, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Jacob S, Kenny GP, Kim C, Kolevzon A, Kustanovich V, Lajonchere CM, Lamb JA, Law-Smith M, Leboyer M, Le Couteur A, Leventhal BL, Liu XQ, Lombard F, Lord C, Lotspeich L, Lund SC, Magalhaes TR, Mantoulan C, McDougle CJ, Melhem NM, Merikangas A, Minshew NJ, Mirza GK, Munson J, Noakes C, Nygren G, Papanikolaou K, Pagnamenta AT, Parrini B, Paton T, Pickles A, Posey DJ, Poustka F, Ragoussis J, Regan R, Roberts W, Roeder K, Roge B, Rutter ML, Schlitt S, Shah N, Sheffield VC, Soorya L, Sousa I, Stoppioni V, Sykes N, Tancredi R, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Vorstman JAS, Wallace S, Wing K, Wittemeyer K, Wood S, Zurawiecki D, Zwaigenbaum L, Bailey AJ, Battaglia A, Cantor RM, Coon H, Cuccaro ML, Dawson G, Ennis S, Freitag CM, Geschwind DH, Haines JL, Klauck SM, McMahon WM, Maestrini E, Miller J, Monaco AP, Nelson SF, Nurnberger JI, Oliveira G, Parr JR, Pericak-Vance MA, Piven J, Schellenberg GD, Scherer SW, Vicente AM, Wassink TH, Wijsman EM, Betancur C, Buxbaum JD, Cook EH, Gallagher L, Gill M, Hallmayer J, Paterson AD, Sutcliffe JS, Szatmari P, Vieland VJ, Hakonarson H, Devlin B. Individual common variants exert weak effects on the risk for autism spectrum disorders. Hum Mol Genet 2012; 21:4781-92. [PMID: 22843504 PMCID: PMC3471395 DOI: 10.1093/hmg/dds301] [Citation(s) in RCA: 254] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 07/13/2012] [Accepted: 07/19/2012] [Indexed: 11/13/2022] Open
Abstract
While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASDs), the contribution of common variation to the risk of developing ASD is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating the association of individual single nucleotide polymorphisms (SNPs), we also sought evidence that common variants, en masse, might affect the risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest P-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. In contrast, allele scores derived from the transmission of common alleles to Stage 1 cases significantly predict case status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm< 1%). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele score results, it is reasonable to conclude that common variants affect the risk for ASD but their individual effects are modest.
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Affiliation(s)
- Richard Anney
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15232, USA
| | - Dalila Pinto
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Toronto, ON, CanadaM5G 1L7
| | - Joana Almeida
- Hospital Pediátrico de Coimbra, 3000–076 Coimbra, Portugal
| | - Elena Bacchelli
- Department of Biology, University of Bologna, 40126 Bologna, Italy
| | - Gillian Baird
- Guy's and St Thomas' NHS Trust & King's College, London SE1 9RT, UK
| | - Nadia Bolshakova
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Sven Bölte
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, 60528 Frankfurt, Germany
| | | | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur and
- University Paris Diderot-Paris 7, CNRS URA 2182, Fondation FondaMental, 75015 Paris, France
| | - Sean Brennan
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Jessica Brian
- Autism Research Unit, The Hospital for Sick Children and Bloorview Kids Rehabilitation, University of Toronto, Toronto, ON, CanadaM5G 1Z8
| | - Jillian Casey
- School of Medicine, Medical Science University College, Dublin 4, Ireland
| | - Judith Conroy
- School of Medicine, Medical Science University College, Dublin 4, Ireland
| | - Catarina Correia
- Instituto Nacional de Saude Dr Ricardo Jorge and Instituto Gulbenkian de Cîencia, 1649-016 Lisbon, Portugal
- BioFIG—Center for Biodiversity, Functional and Integrative Genomics, Campus da FCUL, C2.2.12, Campo Grande, 1749-016 Lisboa, Portugal
| | - Christina Corsello
- Department of Psychology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emily L. Crawford
- Department of Molecular Physiology and Biophysics, Vanderbilt Kennedy Center, and Centers for Human Genetics Research and Molecular Neuroscience and
| | - Maretha de Jonge
- Department of Child Psychiatry, University Medical Center, Utrecht, 3508 GA, The Netherlands
| | - Richard Delorme
- Child and Adolescent Psychiatry, APHP, Hôpital Robert Debré, 75019 Paris, France
| | - Eftichia Duketis
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, 60528 Frankfurt, Germany
| | | | | | - Penny Farrar
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Bridget A. Fernandez
- Disciplines of Genetics and Medicine, Memorial University of Newfoundland,St John's, NL, CanadaA1B 3V6
| | - Susan E. Folstein
- Department of Psychiatry, University of Miami School of Medicine, Miami, FL 33136, USA
| | - Eric Fombonne
- Division of Psychiatry, McGill University, Montreal, QC, CanadaH3A 1A1
| | - John Gilbert
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33101, USA
| | - Christopher Gillberg
- Gillberg Neuropsychiatry Centre, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Joseph T. Glessner
- The Center for Applied Genomics, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Andrew Green
- School of Medicine, Medical Science University College, Dublin 4, Ireland
| | - Jonathan Green
- Academic Department of Child Psychiatry, University of Manchester, Manchester M9 7AA, UK
| | - Stephen J. Guter
- Department of Psychiatry, Institute for Juvenile Research, University of Illinois at Chicago, Chicago, IL 60608, USA
| | - Elizabeth A. Heron
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Richard Holt
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Jennifer L. Howe
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Toronto, ON, CanadaM5G 1L7
| | - Gillian Hughes
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Vanessa Hus
- Department of Psychology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Roberta Igliozzi
- BioFIG—Center for Biodiversity, Functional and Integrative Genomics, Campus da FCUL, C2.2.12, Campo Grande, 1749-016 Lisboa, Portugal
| | - Suma Jacob
- Department of Psychiatry, Institute for Juvenile Research, University of Illinois at Chicago, Chicago, IL 60608, USA
| | - Graham P. Kenny
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Cecilia Kim
- The Center for Applied Genomics, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexander Kolevzon
- The Seaver Autism Center for Research and Treatment, Department of Psychiatry, The Friedman Brain Institute, Mount Sinai School of Medicine, New York NY 10029, USA
| | - Vlad Kustanovich
- Autism Genetic Resource Exchange, Autism Speaks, Los Angeles, CA 90036-4234, USA
| | - Clara M. Lajonchere
- Autism Genetic Resource Exchange, Autism Speaks, Los Angeles, CA 90036-4234, USA
| | | | - Miriam Law-Smith
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Marion Leboyer
- Department of Psychiatry, Groupe hospitalier Henri Mondor-Albert Chenevier, INSERM U995, AP-HP; University Paris 12, Fondation FondaMental, Créteil 94000, France
| | - Ann Le Couteur
- Institutes of Neuroscience and Health and Society, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Bennett L. Leventhal
- Nathan Kline Institute for Psychiatric Research (NKI), 140 Old Orangeburg Road, Orangeburg, NY 10962, USA
- Department of Child and Adolescent Psychiatry, New York University, NYU Child Study Center, New York, NY 10016, USA
| | - Xiao-Qing Liu
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Frances Lombard
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Catherine Lord
- Center for Autism and the Developing Brain, Weill Cornell Medical College, White Plains, NY, USA
| | - Linda Lotspeich
- Department of Psychiatry, Division of Child and Adolescent Psychiatry and Child Development, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sabata C. Lund
- Department of Molecular Physiology and Biophysics, Vanderbilt Kennedy Center, and Centers for Human Genetics Research and Molecular Neuroscience and
| | - Tiago R. Magalhaes
- Instituto Nacional de Saude Dr Ricardo Jorge and Instituto Gulbenkian de Cîencia, 1649-016 Lisbon, Portugal
- BioFIG—Center for Biodiversity, Functional and Integrative Genomics, Campus da FCUL, C2.2.12, Campo Grande, 1749-016 Lisboa, Portugal
| | - Carine Mantoulan
- Centre d'Eudes et de Recherches en Psychopathologie, University de Toulouse Le Mirail, Toulouse 31200, France
| | - Christopher J. McDougle
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Nadine M. Melhem
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15232, USA
| | - Alison Merikangas
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Nancy J. Minshew
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15232, USA
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ghazala K. Mirza
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Jeff Munson
- Department of Psychiatry and Behavioral Sciences
| | - Carolyn Noakes
- Autism Research Unit, The Hospital for Sick Children and Bloorview Kids Rehabilitation, University of Toronto, Toronto, ON, CanadaM5G 1Z8
| | - Gudrun Nygren
- Gillberg Neuropsychiatry Centre, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Katerina Papanikolaou
- University Department of Child Psychiatry, Athens University, Medical School, Agia Sophia Children's Hospital, 115 27 Athens, Greece
| | | | - Barbara Parrini
- Stella Maris Institute for Child and Adolescent Neuropsychiatry, 56128 Calambrone (Pisa), Italy
| | - Tara Paton
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Toronto, ON, CanadaM5G 1L7
| | - Andrew Pickles
- Department of Medicine, School of Epidemiology and Health Science, University of Manchester, Manchester M13 9PT, UK
| | - David J. Posey
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Fritz Poustka
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, 60528 Frankfurt, Germany
| | - Jiannis Ragoussis
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Regina Regan
- School of Medicine, Medical Science University College, Dublin 4, Ireland
| | - Wendy Roberts
- Autism Research Unit, The Hospital for Sick Children and Bloorview Kids Rehabilitation, University of Toronto, Toronto, ON, CanadaM5G 1Z8
| | - Kathryn Roeder
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Bernadette Roge
- Centre d'Eudes et de Recherches en Psychopathologie, University de Toulouse Le Mirail, Toulouse 31200, France
| | - Michael L. Rutter
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College, London SE5 8AF, UK
| | - Sabine Schlitt
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, 60528 Frankfurt, Germany
| | - Naisha Shah
- School of Medicine, Medical Science University College, Dublin 4, Ireland
| | - Val C. Sheffield
- Department of Pediatrics and Howard Hughes Medical Institute Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Latha Soorya
- The Seaver Autism Center for Research and Treatment, Department of Psychiatry, The Friedman Brain Institute, Mount Sinai School of Medicine, New York NY 10029, USA
| | - Inês Sousa
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Vera Stoppioni
- Neuropsichiatria Infantile, Ospedale Santa Croce, 61032 Fano, Italy
| | - Nuala Sykes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Raffaella Tancredi
- Stella Maris Institute for Child and Adolescent Neuropsychiatry, 56128 Calambrone (Pisa), Italy
| | - Ann P. Thompson
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, CanadaL8N 3Z5
| | - Susanne Thomson
- Department of Molecular Physiology and Biophysics, Vanderbilt Kennedy Center, and Centers for Human Genetics Research and Molecular Neuroscience and
| | - Ana Tryfon
- The Seaver Autism Center for Research and Treatment, Department of Psychiatry, The Friedman Brain Institute, Mount Sinai School of Medicine, New York NY 10029, USA
| | - John Tsiantis
- University Department of Child Psychiatry, Athens University, Medical School, Agia Sophia Children's Hospital, 115 27 Athens, Greece
| | - Herman Van Engeland
- Department of Child Psychiatry, University Medical Center, Utrecht, 3508 GA, The Netherlands
| | - John B. Vincent
- Centre for Addiction and Mental Health, Clarke Institute and Department of Psychiatry, University of Toronto, Toronto, ON, CanadaM5G 1X8
| | - Fred Volkmar
- Child Study Centre, Yale University, New Haven, CT 06520, USA
| | - JAS Vorstman
- Department of Psychiatry, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Simon Wallace
- Department of Psychiatry, University of Oxford, Warneford Hospital, Headington, Oxford, OX3 7JX, UK
| | - Kirsty Wing
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kerstin Wittemeyer
- Department of Psychiatry, University of Oxford, Warneford Hospital, Headington, Oxford, OX3 7JX, UK
| | - Shawn Wood
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15232, USA
| | - Danielle Zurawiecki
- The Seaver Autism Center for Research and Treatment, Department of Psychiatry, The Friedman Brain Institute, Mount Sinai School of Medicine, New York NY 10029, USA
| | - Lonnie Zwaigenbaum
- Department of Pediatrics, University of Alberta, Edmonton, AB, CanadaT6G 2J3
| | - Anthony J. Bailey
- BC Mental Health and Addictions Research Unit, University of British Columbia, Vancouver, BC, CanadaV5Z4H4
| | - Agatino Battaglia
- Stella Maris Institute for Child and Adolescent Neuropsychiatry, 56128 Calambrone (Pisa), Italy
| | | | - Hilary Coon
- Psychiatry Department, University of Utah Medical School, Salt Lake City, UT 84108, USA
| | - Michael L. Cuccaro
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33101, USA
| | | | - Sean Ennis
- School of Medicine, Medical Science University College, Dublin 4, Ireland
| | - Christine M. Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, 60528 Frankfurt, Germany
| | - Daniel H. Geschwind
- Department of Neurology, Los Angeles School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Jonathan L. Haines
- Center for Human Genetics Research, Vanderbilt University Medical Centre, Nashville, TN 37232, USA
| | - Sabine M. Klauck
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - William M. McMahon
- Psychiatry Department, University of Utah Medical School, Salt Lake City, UT 84108, USA
| | - Elena Maestrini
- Department of Biology, University of Bologna, 40126 Bologna, Italy
| | - Judith Miller
- Psychiatry Department, University of Utah Medical School, Salt Lake City, UT 84108, USA
| | - Anthony P. Monaco
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Office of the President, Tufts University, Boston, MA, USA
| | | | - John I. Nurnberger
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Jeremy R. Parr
- Institutes of Neuroscience and Health and Society, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | | | - Joseph Piven
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3366, USA
| | - Gerard D. Schellenberg
- Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Toronto, ON, CanadaM5G 1L7
| | - Astrid M. Vicente
- Instituto Nacional de Saude Dr Ricardo Jorge and Instituto Gulbenkian de Cîencia, 1649-016 Lisbon, Portugal
- BioFIG—Center for Biodiversity, Functional and Integrative Genomics, Campus da FCUL, C2.2.12, Campo Grande, 1749-016 Lisboa, Portugal
| | - Thomas H. Wassink
- Department of Psychiatry, Carver College of Medicine, Iowa City, IA 52242, USA
| | - Ellen M. Wijsman
- Department of Biostatistics and
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Catalina Betancur
- INSERM U952
- CNRS UMR 7224 and
- UPMC Univ Paris 06, Paris 75005, France and
| | - Joseph D. Buxbaum
- The Seaver Autism Center for Research and Treatment, Department of Psychiatry, The Friedman Brain Institute, Mount Sinai School of Medicine, New York NY 10029, USA
| | - Edwin H. Cook
- Department of Psychiatry, Institute for Juvenile Research, University of Illinois at Chicago, Chicago, IL 60608, USA
| | - Louise Gallagher
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Michael Gill
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Joachim Hallmayer
- Department of Psychiatry, Division of Child and Adolescent Psychiatry and Child Development, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Andrew D. Paterson
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Toronto, ON, CanadaM5G 1L7
| | - James S. Sutcliffe
- Department of Molecular Physiology and Biophysics, Vanderbilt Kennedy Center, and Centers for Human Genetics Research and Molecular Neuroscience and
| | - Peter Szatmari
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, CanadaL8N 3Z5
| | - Veronica J. Vieland
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital and The Ohio State University, Columbus, OH 43205, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15232, USA
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7
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Anney R, Klei L, Pinto D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Sykes N, Pagnamenta AT, Almeida J, Bacchelli E, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Carson AR, Casallo G, Casey J, Chu SH, Cochrane L, Corsello C, Crawford EL, Crossett A, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Melhem NM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Piven J, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Wing K, Wittemeyer K, Wood S, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Betancur C, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Gallagher L, Geschwind DH, Gill M, Haines JL, Miller J, Monaco AP, Nurnberger JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Scherer SW, Sutcliffe JS, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Devlin B, Ennis S, Hallmayer J. A genome-wide scan for common alleles affecting risk for autism. Hum Mol Genet 2010; 19:4072-82. [PMID: 20663923 PMCID: PMC2947401 DOI: 10.1093/hmg/ddq307] [Citation(s) in RCA: 432] [Impact Index Per Article: 30.9] [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: 01/20/2023] Open
Abstract
Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10−8. When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10−8 threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.
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Affiliation(s)
- Richard Anney
- Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
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8
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Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, Bader GD, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Bryson SE, Carson AR, Casallo G, Casey J, Chung BHY, Cochrane L, Corsello C, Crawford EL, Crossett A, Cytrynbaum C, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green A, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Pilorge M, Piven J, Ponting CP, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Sequeira AF, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stein O, Sykes N, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Webber C, Weksberg R, Wing K, Wittemeyer K, Wood S, Wu J, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Devlin B, Ennis S, Gallagher L, Geschwind DH, Gill M, Haines JL, Hallmayer J, Miller J, Monaco AP, Nurnberger JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Scherer SW, Sutcliffe JS, Betancur C. Functional impact of global rare copy number variation in autism spectrum disorders. Nature 2010; 466:368-72. [PMID: 20531469 DOI: 10.1038/nature09146] [Citation(s) in RCA: 1442] [Impact Index Per Article: 103.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 05/07/2010] [Indexed: 12/18/2022]
Abstract
The autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in reciprocal social interaction and communication, and the presence of restricted and repetitive behaviours. Individuals with an ASD vary greatly in cognitive development, which can range from above average to intellectual disability. Although ASDs are known to be highly heritable ( approximately 90%), the underlying genetic determinants are still largely unknown. Here we analysed the genome-wide characteristics of rare (<1% frequency) copy number variation in ASD using dense genotyping arrays. When comparing 996 ASD individuals of European ancestry to 1,287 matched controls, cases were found to carry a higher global burden of rare, genic copy number variants (CNVs) (1.19 fold, P = 0.012), especially so for loci previously implicated in either ASD and/or intellectual disability (1.69 fold, P = 3.4 x 10(-4)). Among the CNVs there were numerous de novo and inherited events, sometimes in combination in a given family, implicating many novel ASD genes such as SHANK2, SYNGAP1, DLGAP2 and the X-linked DDX53-PTCHD1 locus. We also discovered an enrichment of CNVs disrupting functional gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signalling. Our results reveal many new genetic and functional targets in ASD that may lead to final connected pathways.
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Affiliation(s)
- Dalila Pinto
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
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Rutowitsch MS, Magalhaes TR. An orthodontic-retentive approach during prosthodontic rehabilitation in cleft lip and palate patients: a case report. Cleft Palate J 1976; 13:284-90. [PMID: 780005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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