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Solomon O, Huen K, Yousefi P, Küpers LK, González JR, Suderman M, Reese SE, Page CM, Gruzieva O, Rzehak P, Gao L, Bakulski KM, Novoloaca A, Allard C, Pappa I, Llambrich M, Vives M, Jima DD, Kvist T, Baccarelli A, White C, Rezwan FI, Sharp GC, Tindula G, Bergström A, Grote V, Dou JF, Isaevska E, Magnus MC, Corpeleijn E, Perron P, Jaddoe VWV, Nohr EA, Maitre L, Foraster M, Hoyo C, Håberg SE, Lahti J, DeMeo DL, Zhang H, Karmaus W, Kull I, Koletzko B, Feinberg JI, Gagliardi L, Bouchard L, Ramlau-Hansen CH, Tiemeier H, Santorelli G, Maguire RL, Czamara D, Litonjua AA, Langhendries JP, Plusquin M, Lepeule J, Binder EB, Verduci E, Dwyer T, Carracedo Á, Ferre N, Eskenazi B, Kogevinas M, Nawrot TS, Munthe-Kaas MC, Herceg Z, Relton C, Melén E, Gruszfeld D, Breton C, Fallin MD, Ghantous A, Nystad W, Heude B, Snieder H, Hivert MF, Felix JF, Sørensen TIA, Bustamante M, Murphy SK, Raikkönen K, Oken E, Holloway JW, Arshad SH, London SJ, Holland N. Meta-analysis of epigenome-wide association studies in newborns and children show widespread sex differences in blood DNA methylation. Mutat Res Rev Mutat Res 2022; 789:108415. [PMID: 35690418 PMCID: PMC9623595 DOI: 10.1016/j.mrrev.2022.108415] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 02/27/2022] [Accepted: 03/08/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Among children, sex-specific differences in disease prevalence, age of onset, and susceptibility have been observed in health conditions including asthma, immune response, metabolic health, some pediatric and adult cancers, and psychiatric disorders. Epigenetic modifications such as DNA methylation may play a role in the sexual differences observed in diseases and other physiological traits. METHODS We performed a meta-analysis of the association of sex and cord blood DNA methylation at over 450,000 CpG sites in 8438 newborns from 17 cohorts participating in the Pregnancy And Childhood Epigenetics (PACE) Consortium. We also examined associations of child sex with DNA methylation in older children ages 5.5-10 years from 8 cohorts (n = 4268). RESULTS In newborn blood, sex was associated at Bonferroni level significance with differences in DNA methylation at 46,979 autosomal CpG sites (p < 1.3 × 10-7) after adjusting for white blood cell proportions and batch. Most of those sites had lower methylation levels in males than in females. Of the differentially methylated CpG sites identified in newborn blood, 68% (31,727) met look-up level significance (p < 1.1 × 10-6) in older children and had methylation differences in the same direction. CONCLUSIONS This is a large-scale meta-analysis examining sex differences in DNA methylation in newborns and older children. Expanding upon previous studies, we replicated previous findings and identified additional autosomal sites with sex-specific differences in DNA methylation. Differentially methylated sites were enriched in genes involved in cancer, psychiatric disorders, and cardiovascular phenotypes.
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Affiliation(s)
- Olivia Solomon
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Karen Huen
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA.
| | - Paul Yousefi
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK
| | - Leanne K Küpers
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Juan R González
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK
| | - Sarah E Reese
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Center for Occupational and Environmental Medicine, Region Stockholm, Sweden
| | - Peter Rzehak
- Div. Metabolic and Nutritional Medicine, Dept. Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Lu Gao
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Kelly M Bakulski
- School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Catherine Allard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, QC, Canada
| | - Irene Pappa
- Department of Child and Adolescent Psychiatry/ Psychology, Erasmus Medical Center, Sophia Children's Hospital, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands
| | - Maria Llambrich
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Marta Vives
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA; Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606, USA
| | - Tuomas Kvist
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland
| | - Andrea Baccarelli
- Laboratory of Precision Environmental Biosciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Cory White
- Merck Exploratory Science Center, Merck Research Laboratories, Cambridge, MA 02141, USA
| | - Faisal I Rezwan
- Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, SY23 3DB, United Kingdom; Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK
| | - Gwen Tindula
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Center for Occupational and Environmental Medicine, Region Stockholm, Sweden
| | - Veit Grote
- Div. Metabolic and Nutritional Medicine, Dept. Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - John F Dou
- School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elena Isaevska
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Maria C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Eva Corpeleijn
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, QC, Canada; Department of Medicine, Universite de Sherbrooke, QC, Canada
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands
| | - Ellen A Nohr
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark; Centre of Women's, Family and Child Health, University of South-Eastern Norway, Kongsberg, Norway
| | - Lea Maitre
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Maria Foraster
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; PHAGEX Research Group, Blanquerna School of Health Science, Universitat Ramon Llull, Barcelona, Spain
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA; Department of Biological Sciences, North Carolina State University, NC, USA
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Inger Kull
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden; Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Berthold Koletzko
- Div. Metabolic and Nutritional Medicine, Dept. Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Jason I Feinberg
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Luigi Gagliardi
- Department of Woman and Child Health, Ospedale Versilia, Azienda USL Toscana Nord Ovest, Viareggio, Italy
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, QC, Canada; Department of Medical Biology, CIUSSS Saguenay-Lac-Saint-Jean, Chicoutimi Hospital, Saguenay, QC, Canada
| | | | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/ Psychology, Erasmus Medical Center, Sophia Children's Hospital, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands; Department of Social and Behavioral Science, Harvard TH Chan School of Public Health, 677 Huntington Ave, Boston, MA, USA
| | - Gillian Santorelli
- Bradford Institute of Health Research, Bradford Royal Infirmary, Bradford BD9 6RJ, UK
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, NC, USA; Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27701, USA
| | - Darina Czamara
- Dept. Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Augusto A Litonjua
- Division of Pediatric Pulmonology, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | | | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Johanna Lepeule
- Univ. Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, IAB, 38000 Grenoble, France
| | - Elisabeth B Binder
- Dept. Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, USA
| | - Elvira Verduci
- Department of Pediatrics, Ospedale dei Bambini Vittore Buzzi, University of Milan, Milan, Italy; Department of Health Sciences, University of Milan, Milan, Italy
| | - Terence Dwyer
- Clinical Sciences, Heart Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Pediatrics, University of Melbourne, Melbourne, Australia; Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Fundación Pública Galega de Merdicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), SERGAS, Santiago de Compostela, Spain; Centro de Investigación en Red de Enfermedades Raras (CIBERER) y Centro Nacional de Genotipado (CEGEN-PRB3), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Natalia Ferre
- Pediatric Nutrition and Human Development Research Unit, Universitat Rovira i Virgili, IISPV, Reus, Spain
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health, School of Public Health, University of California, Berkeley, CA, USA
| | - Manolis Kogevinas
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; IMIM (Hospital del Mar Medical Research Institute), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium; Department Public Health & Primary care, Leuven University, Belgium
| | - Monica C Munthe-Kaas
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Pediatric Oncology and Hematology, Oslo University Hospital, Norway
| | - Zdenko Herceg
- International Agency for Research on Cancer, Lyon, France
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK
| | - Erik Melén
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden; Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Dariusz Gruszfeld
- Neonatal Department, Children's Memorial Health Institute, Warsaw, Poland
| | - Carrie Breton
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - M D Fallin
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Akram Ghantous
- International Agency for Research on Cancer, Lyon, France
| | - Wenche Nystad
- Department of Chronic Diseases and Ageing, Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Barbara Heude
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, F-75004 Paris, France
| | - Harold Snieder
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Marie-France Hivert
- Department of Medicine, Universite de Sherbrooke, QC, Canada; Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA; Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, P.O. Box 2060, 3000 CB Rotterdam, The Netherlands
| | - Thorkild I A Sørensen
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK; Department of Public Health, Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark; The Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, Faculty of Medical and Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mariona Bustamante
- ISGlobal, Barcelona Institute for Global Health, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27701, USA
| | - Katri Raikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland
| | - Emily Oken
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Nina Holland
- Children's Environmental Health Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
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Bakulski KM, Dou JF, Feinberg JI, Aung MT, Ladd-Acosta C, Volk HE, Newschaffer CJ, Croen LA, Hertz-Picciotto I, Levy SE, Landa R, Feinberg AP, Fallin MD. Autism-Associated DNA Methylation at Birth From Multiple Tissues Is Enriched for Autism Genes in the Early Autism Risk Longitudinal Investigation. Front Mol Neurosci 2021; 14:775390. [PMID: 34899183 PMCID: PMC8655859 DOI: 10.3389/fnmol.2021.775390] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/28/2021] [Indexed: 12/30/2022] Open
Abstract
Background: Pregnancy measures of DNA methylation, an epigenetic mark, may be associated with autism spectrum disorder (ASD) development in children. Few ASD studies have considered prospective designs with DNA methylation measured in multiple tissues and tested overlap with ASD genetic risk loci. Objectives: To estimate associations between DNA methylation in maternal blood, cord blood, and placenta and later diagnosis of ASD, and to evaluate enrichment of ASD-associated DNA methylation for known ASD-associated genes. Methods: In the Early Autism Risk Longitudinal Investigation (EARLI), an ASD-enriched risk birth cohort, genome-scale maternal blood (early n = 140 and late n = 75 pregnancy), infant cord blood (n = 133), and placenta (maternal n = 106 and fetal n = 107 compartments) DNA methylation was assessed on the Illumina 450k HumanMethylation array and compared to ASD diagnosis at 36 months of age. Differences in site-specific and global methylation were tested with ASD, as well as enrichment of single site associations for ASD risk genes (n = 881) from the Simons Foundation Autism Research Initiative (SFARI) database. Results: No individual DNA methylation site was associated with ASD at genome-wide significance, however, individual DNA methylation sites nominally associated with ASD (P < 0.05) in each tissue were highly enriched for SFARI genes (cord blood P = 7.9 × 10-29, maternal blood early pregnancy P = 6.1 × 10-27, maternal blood late pregnancy P = 2.8 × 10-16, maternal placenta P = 5.6 × 10-15, fetal placenta P = 1.3 × 10-20). DNA methylation sites nominally associated with ASD across all five tissues overlapped at 144 (29.5%) SFARI genes. Conclusion: DNA methylation sites nominally associated with later ASD diagnosis in multiple tissues were enriched for ASD risk genes. Our multi-tissue study demonstrates the utility of examining DNA methylation prior to ASD diagnosis.
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Affiliation(s)
- Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - John F Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Jason I Feinberg
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States.,Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Max T Aung
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Christine Ladd-Acosta
- Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States.,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Heather E Volk
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States
| | - Craig J Newschaffer
- College of Health and Human Development, Penn State University, State College, PA, United States
| | - Lisa A Croen
- Kaiser Permanente Division of Research, Oakland, CA, United States
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, School of Medicine, University of California, Davis, Davis, CA, United States.,MIND Institute, University of California, Davis, Davis, CA, United States
| | - Susan E Levy
- Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Rebecca Landa
- Kennedy Krieger Institute Center for Autism and Related Disorders, Baltimore, MD, United States
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States.,Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Margaret D Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Wendy Klag Center for Autism and Developmental Disabilities, Baltimore, MD, United States.,Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, MD, United States
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Terloyeva D, Frey AJ, Park BY, Kauffman EM, Mathew L, Bostwick A, Varner EL, Lee BK, Croen LA, Fallin MD, Hertz-Picciotto I, Newschaffer CJ, Lyall K, Snyder NW. Meconium androgens are correlated with ASD-related phenotypic traits in early childhood in a familial enriched risk cohort. Mol Autism 2020; 11:93. [PMID: 33228808 PMCID: PMC7686740 DOI: 10.1186/s13229-020-00395-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 04/09/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Prenatal exposure to increased androgens has been suggested as a risk factor for autism spectrum disorder (ASD). This hypothesis has been examined by measurement of steroids in amniotic fluid, cord blood, saliva, and blood with mixed results. METHODS To provide an orthogonal measure of fetal exposure, this study used meconium, the first stool of a newborn, to measure prenatal androgen exposure from infants in the Early Autism Risk Longitudinal Investigation (EARLI). EARLI is a familial-enriched risk cohort that enrolled pregnant mothers who already had a child with an ASD diagnosis. In the younger child, we investigated the association between meconium unconjugated (u) and total (t) concentrations of major androgens testosterone (T), dehydroepiandrosterone (DHEA), and androstenedione (A4), and ASD-related traits at 12 and 36 months of age. Traits were measured at 12 months with Autism Observation Scale for Infants (AOSI) and at 36 months with total score on the Social Responsiveness Scale (SRS). One hundred and seventy children had meconium and AOSI, 140 had meconium and SRS, and 137 had meconium and both AOSI and SRS. RESULTS Separate robust linear regressions between each of the log-transformed androgens and log-transformed SRS scores revealed three-way interaction between sex of the child, sex of the proband, and testosterone concentration. In the adjusted analyses, t-T, u-A4, and u-DHEA (P ≤ 0.01) were positively associated with AOSI scores, while u-T (P = 0.004) and u-DHEA (P = 0.007) were positively associated with SRS total score among females with female probands (n = 10). Additionally, higher concentrations of u-T (P = 0.01) and t-T (P = 0.01) predicted higher SRS total score in males with male probands (n = 63). Limitations Since we explored three-way interactions, this resulted in a limited sample size for some analyses. This study was from an enriched-risk cohort which may limit generalizability, and this study used ASD-assessment scales as outcomes instead of diagnostic categories. Additionally, the novel use of meconium in this study limits the ability to compare the results in this cohort to others due to the paucity of research on meconium. CONCLUSIONS This study supports the utility of meconium for studies of endogenous fetal metabolism and suggests the sex of older siblings with autism should be considered as a biological variable in relevant studies.
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Affiliation(s)
- Dina Terloyeva
- AJ Drexel Autism Institute, Drexel University, 3020 Market St, Suite 560, Philadelphia, PA, 19104, USA
- Department of Epidemiology and Biostatistics, Drexel University School of Public Health, 3215 Market Street, Philadelphia, PA, 19104, USA
| | - Alexander J Frey
- AJ Drexel Autism Institute, Drexel University, 3020 Market St, Suite 560, Philadelphia, PA, 19104, USA
| | - Bo Y Park
- AJ Drexel Autism Institute, Drexel University, 3020 Market St, Suite 560, Philadelphia, PA, 19104, USA
- Department of Public Health, California State University Fullerton, 800 N. State College Blvd., Fullerton, CA, 92831, USA
| | - Elizabeth M Kauffman
- AJ Drexel Autism Institute, Drexel University, 3020 Market St, Suite 560, Philadelphia, PA, 19104, USA
| | - Leny Mathew
- AJ Drexel Autism Institute, Drexel University, 3020 Market St, Suite 560, Philadelphia, PA, 19104, USA
- Department of Epidemiology and Biostatistics, Drexel University School of Public Health, 3215 Market Street, Philadelphia, PA, 19104, USA
| | - Anna Bostwick
- AJ Drexel Autism Institute, Drexel University, 3020 Market St, Suite 560, Philadelphia, PA, 19104, USA
| | - Erika L Varner
- AJ Drexel Autism Institute, Drexel University, 3020 Market St, Suite 560, Philadelphia, PA, 19104, USA
- Department of Microbiology and Immunology, Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Brian K Lee
- Department of Epidemiology and Biostatistics, Drexel University School of Public Health, 3215 Market Street, Philadelphia, PA, 19104, USA
| | - Lisa A Croen
- Autism Research Program, Kaiser Permanente Division of Research, 2000 Broadway, Oakland, CA, 94612, USA
| | - Margaret D Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, HH 850, Baltimore, MD, 21205, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, School of Medicine, University of California, Davis, Davis, USA
| | - Craig J Newschaffer
- AJ Drexel Autism Institute, Drexel University, 3020 Market St, Suite 560, Philadelphia, PA, 19104, USA
- College of Health and Human Development, Penn State, University Park, PA, 16802, USA
| | - Kristen Lyall
- AJ Drexel Autism Institute, Drexel University, 3020 Market St, Suite 560, Philadelphia, PA, 19104, USA
| | - Nathaniel W Snyder
- AJ Drexel Autism Institute, Drexel University, 3020 Market St, Suite 560, Philadelphia, PA, 19104, USA.
- Department of Microbiology and Immunology, Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA.
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Chan RF, Shabalin AA, Montano C, Hannon E, Hultman CM, Fallin MD, Feinberg AP, Mill J, van den Oord EJCG, Aberg KA. Independent Methylome-Wide Association Studies of Schizophrenia Detect Consistent Case-Control Differences. Schizophr Bull 2020; 46:319-327. [PMID: 31165892 PMCID: PMC7442362 DOI: 10.1093/schbul/sbz056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Methylome-wide association studies (MWASs) are promising complements to sequence variation studies. We used existing sequencing-based methylation data, which assayed the majority of all 28 million CpGs in the human genome, to perform an MWAS for schizophrenia in blood, while controlling for cell-type heterogeneity with a recently generated platform-specific reference panel. Next, we compared the MWAS results with findings from 3 existing large-scale array-based schizophrenia methylation studies in blood that assayed up to ~450 000 CpGs. Our MWAS identified 22 highly significant loci (P < 5 × 10-8) and 852 suggestively significant loci (P < 1 × 10-5). The top finding (P = 5.62 × 10-11, q = 0.001) was located in MFN2, which encodes mitofusin-2 that regulates Ca2+ transfer from the endoplasmic reticulum to mitochondria in cooperation with DISC1. The second-most significant site (P = 1.38 × 10-9, q = 0.013) was located in ALDH1A2, which encodes an enzyme for astrocyte-derived retinoic acid-a key neuronal morphogen with relevance for schizophrenia. Although the most significant MWAS findings were not assayed on the arrays, we observed significant enrichment of overlapping findings with 2 of the 3 array datasets (P = 0.0315, 0.0045, 0.1946). Overrepresentation analysis of Gene Ontology terms for the genes in the significant overlaps suggested high similarity in the biological functions detected by the different datasets. Top terms were related to immune and/or stress responses, cell adhesion and motility, and a broad range of processes essential for neurodevelopment.
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Affiliation(s)
- Robin F Chan
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | - Andrey A Shabalin
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | | | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Margaret D Fallin
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Andrew P Feinberg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
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Leonard AS, Lee J, Schubert D, Croen LA, Fallin MD, Newschaffer CJ, Walker CK, Salafia CM, Morgan SP, Vvedensky DD. Scaling of the surface vasculature on the human placenta. Phys Rev E 2018; 96:040401. [PMID: 29347569 DOI: 10.1103/physreve.96.040401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Indexed: 11/07/2022]
Abstract
The networks of veins and arteries on the chorionic plate of the human placenta are analyzed in terms of Voronoi cells derived from these networks. Two groups of placentas from the United States are studied: a population cohort with no prescreening, and a cohort from newborns with an elevated risk of developing autistic spectrum disorder. Scaled distributions of the Voronoi cell areas in the two cohorts collapse onto a single distribution, indicating common mechanisms for the formation of the complete vasculatures, but which have different levels of activity in the two cohorts.
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Affiliation(s)
- A S Leonard
- The Blackett Laboratory, Imperial College London, London SW7 2AZ, United Kingdom
| | - J Lee
- The Blackett Laboratory, Imperial College London, London SW7 2AZ, United Kingdom
| | - D Schubert
- The Blackett Laboratory, Imperial College London, London SW7 2AZ, United Kingdom
| | - L A Croen
- Division of Research, Kaiser Permanente Northern California, Oakland, California 94612, USA
| | - M D Fallin
- Department of Epidemiology and Department of Biostatistics, Johns Hopkins, Bloomberg School of Public Health, Johns Hopkins University Baltimore, Maryland 21205, USA
| | - C J Newschaffer
- Department of Epidemiology and Biostatistics, Drexel School of Public Health, Drexel University 1505 Race Street, Mail Stop 1033, Philadelphia, Pennsylvania 19102, USA
| | - C K Walker
- Lawrence J. Ellison Ambulatory Care Center, Obstetrics and Gynecology Clinic, University of California-Davis, Sacramento, California 95817, USA
| | - C M Salafia
- Placental Analytics, LLC, 187 Overlook Circle, New Rochelle, New York 10804, USA
| | - S P Morgan
- The Blackett Laboratory, Imperial College London, London SW7 2AZ, United Kingdom
| | - D D Vvedensky
- The Blackett Laboratory, Imperial College London, London SW7 2AZ, United Kingdom
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Park BY, Lee BK, Burstyn I, Tabb LP, Keelan JA, Whitehouse AJO, Croen LA, Fallin MD, Hertz-Picciotto I, Montgomery O, Newschaffer CJ. Umbilical cord blood androgen levels and ASD-related phenotypes at 12 and 36 months in an enriched risk cohort study. Mol Autism 2017; 8:3. [PMID: 28163867 PMCID: PMC5282802 DOI: 10.1186/s13229-017-0118-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 06/03/2016] [Accepted: 01/19/2017] [Indexed: 12/20/2022] Open
Abstract
Background Autism spectrum disorder (ASD) affects more than 1% of children in the USA. The male-to-female prevalence ratio of roughly 4:1 in ASD is a well-recognized but poorly understood phenomenon. An explicit focus on potential etiologic pathways consistent with this sex difference, such as those involving prenatal androgen exposure, may help elucidate causes of ASD. Furthermore, the multi-threshold liability model suggests that the genetic mechanisms in females with ASD may be distinct and may modulate ASD risk in families with female ASD in the pedigree. Methods We examined umbilical cord blood from 137 children in the Early Autism Risk Longitudinal Investigation (EARLI) cohort. EARLI is an ASD-enriched risk cohort with all children having an older sibling already diagnosed with ASD. Fetal testosterone (T), androstenedione (A4), and dehyroepiandrosterone (DHEA) levels were measured in cord blood using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Robust linear regression models were used to determine associations between cord blood androgen levels and 12-month Autism Observation Scales for Infants (AOSI) scores and 36-month Social Responsiveness Scale (SRS) scores adjusting for potential confounders. Results Increasing androgens were not associated with increasing 12-month AOSI score or 36-month total SRS score in either boys or girls. However, the association between T and autistic traits among subjects with a female older affected sibling was greater at 12 months (test of interaction, P = 0.008) and deficits in reciprocal social behavior at 36 months were also greater (test of interaction, P = 0.006) than in subjects whose older affected sibling was male. Conclusions While increased prenatal testosterone levels were not associated with autistic traits at 12 or 36 months, our findings of a positive association in infants whose older ASD-affected siblings were female suggests an androgen-related mechanism that may be dependent on, or related to, genetic liability factors present more often in families containing female ASD cases. However, this initial finding, based on a small subgroup of our sample, should be interpreted with considerable caution. Electronic supplementary material The online version of this article (doi:10.1186/s13229-017-0118-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bo Y Park
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N Broadway HH884, Baltimore, MD 21205 USA
| | - Brian K Lee
- Department of Epidemiology and Biostatistics, Drexel University School of Public Health, 3215 Market Street, Philadelphia, PA 19104 USA.,A.J. Drexel Autism Institute, 3020 Market St. Suite 560, Philadelphia, PA 19104 USA
| | - Igor Burstyn
- Department of Environmental and Occupational Health, Drexel University School of Public Health, 3215 Market Street, Philadelphia, PA 19104 USA.,A.J. Drexel Autism Institute, 3020 Market St. Suite 560, Philadelphia, PA 19104 USA
| | - Loni P Tabb
- Department of Epidemiology and Biostatistics, Drexel University School of Public Health, 3215 Market Street, Philadelphia, PA 19104 USA
| | - Jeff A Keelan
- School of Women's and Infants' Health, University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009 Australia
| | - Andrew J O Whitehouse
- Telethon Kids Institute, University of Western Australia, 100 Roberts Rd, Subiaco, WA 6009 Australia
| | - Lisa A Croen
- Kaiser Permanente Division of Research, 2000 Broadway, Oakland, CA 94612 USA
| | - Margaret D Fallin
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N Broadway HH884, Baltimore, MD 21205 USA
| | - Irva Hertz-Picciotto
- The MIND (Medical Investigations of Neurodevelopmental Disorders) Institute, University of California Davis, One Shields Ave. Med-Sci 1C, Davis, CA 95616 USA
| | - Owen Montgomery
- Department of Obstetrics and Gynecology, Drexel University College of Medicine, 219 N. Broad St, Philadelphia, PA 19107 USA
| | - Craig J Newschaffer
- Department of Epidemiology and Biostatistics, Drexel University School of Public Health, 3215 Market Street, Philadelphia, PA 19104 USA.,A.J. Drexel Autism Institute, 3020 Market St. Suite 560, Philadelphia, PA 19104 USA
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7
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Matteini AM, Li J, Lange EM, Tanaka T, Lange LA, Tracy RP, Wang Y, Biggs ML, Arking DE, Fallin MD, Chakravarti A, Psaty BM, Bandinelli S, Ferrucci L, Reiner AP, Walston JD. Novel gene variants predict serum levels of the cytokines IL-18 and IL-1ra in older adults. Cytokine 2013; 65:10-6. [PMID: 24182552 DOI: 10.1016/j.cyto.2013.10.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 08/23/2013] [Accepted: 10/04/2013] [Indexed: 10/26/2022]
Abstract
Activation of inflammatory pathways measured by serum inflammatory markers such as interleukin-18 (IL-18) and interleukin-1 receptor antagonist (IL-1ra) is strongly associated with the progression of chronic disease states in older adults. Given that these serum cytokine levels are in part a heritable trait, genetic variation may predict increased serum levels. Using the Cardiovascular Health Study and InCHIANTI cohorts, a genome-wide association study was performed to identify genetic variants that influence IL-18 and IL-1ra serum levels among older adults. Multiple linear regression models characterized the association between each SNP and log-transformed cytokine values. Tests for multiple independent signals within statistically significant loci were performed using haplotype analysis and regression models conditional on lead SNP in each region. Multiple SNPs were associated with these cytokines with genome-wide significance, including SNPs in the IL-18-BCO gene region of chromosome 2 for IL-18 (top SNP rs2250417, P=1.9×10(-32)) and in the IL-1 gene family region of chromosome 2 for IL-1ra (rs6743376, P=2.3×10(-26)). Haplotype tests and conditional linear regression models showed evidence of multiple independent signals in these regions. Serum IL-18 levels were also associated with a region on chromosome 2 containing the NLRC4 gene (rs12989936, P=2.7×10(-19)). These data characterize multiple robust genetic signals that influence IL-18 and IL-1ra cytokine production. In particular, the signal for serum IL-18 located on chromosome two is novel and potentially important in inflammasome triggered chronic activation of inflammation in older adults. Replication in independent cohorts is an important next step, as well as molecular studies to better understand the role of NLRC4.
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Affiliation(s)
- A M Matteini
- Division of Geriatric Medicine, Johns Hopkins Medical Institution, Baltimore, MD, USA.
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8
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Reitz C, Tosto G, Vardarajan B, Rogaeva E, Ghani M, Rogers RS, Conrad C, Haines JL, Pericak-Vance MA, Fallin MD, Foroud T, Farrer LA, Schellenberg GD, George-Hyslop PS, Mayeux R. Independent and epistatic effects of variants in VPS10-d receptors on Alzheimer disease risk and processing of the amyloid precursor protein (APP). Transl Psychiatry 2013; 3:e256. [PMID: 23673467 PMCID: PMC3669917 DOI: 10.1038/tp.2013.13] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Genetic variants in the sortilin-related receptor (SORL1) and the sortilin-related vacuolar protein sorting 10 (VPS10) domain-containing receptor 1 (SORCS1) are associated with increased risk of Alzheimer's disease (AD), declining cognitive function and altered amyloid precursor protein (APP) processing. We explored whether other members of the (VPS10) domain-containing receptor protein family (the sortilin-related VPS10 domain-containing receptors 2 and 3 (SORCS2 and SORCS3) and sortilin (SORT1)) would have similar effects either independently or together. We conducted the analyses in a large Caucasian case control data set (n=11,840 cases, 10,931 controls) to determine the associations between single nucleotide polymorphisms (SNPs) in all the five homologous genes and AD risk. Evidence for interactions between SNPs in the five VPS10 domain receptor family genes was determined in epistatic statistical models. We also compared expression levels of SORCS2, SORCS3 and SORT1 in AD and control brains using microarray gene expression analyses and assessed the effects of these genes on γ-secretase processing of APP. Several SNPs in SORL1, SORCS1, SORCS2 and SORCS3 were associated with AD. In addition, four specific linkage disequilibrium blocks in SORCS1, SORCS2 and SORCS3 showed additive epistatic effects on the risk of AD (P≤0.0006). SORCS3, but not SORCS2 or SORT1, showed reduced expression in AD compared with control brains, but knockdown of all the three genes using short hairpin RNAs in HEK293 cells caused a significant threefold increase in APP processing (from P<0.001 to P<0.05). These findings indicate that in addition to SORL1 and SORCS1, variants in other members of the VPS10 domain receptor family (that is, SORCS1, SORCS2, SORCS3) are associated with AD risk and alter APP processing. More importantly, the results indicate that variants within these genes have epistatic effects on AD risk.
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Affiliation(s)
- C Reitz
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA,Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - G Tosto
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - B Vardarajan
- Department of Biostatistics, Boston University Schools of Medicine and Public Health, Boston, MA, USA
| | - E Rogaeva
- Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada
| | - M Ghani
- Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada
| | - R S Rogers
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - C Conrad
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - J L Haines
- Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M A Pericak-Vance
- Miami Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - M D Fallin
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - T Foroud
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN, USA
| | - L A Farrer
- Department of Biostatistics, Boston University Schools of Medicine and Public Health, Boston, MA, USA,Department of Medicine (Biomedical Genetics), Boston University Schools of Medicine and Public Health, Boston, MA, USA,Department of Neurology, Boston University Schools of Medicine and Public Health, Boston, MA, USA,Department of Ophthalmology, Boston University Schools of Medicine and Public Health, Boston, MA, USA,Department of Genetics and Genomics, Boston University Schools of Medicine and Public Health, Boston, MA, USA,Department of Epidemiology, Boston University Schools of Medicine and Public Health, Boston, MA, USA
| | - G D Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - P S George-Hyslop
- Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada,Department of Medicine, University Health Network, Toronto, Ontario, Canada,Department of Clinical Neurosciences, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - R Mayeux
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA,Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA,Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York, NY, USA,Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA,Department of Epidemiology, School of Public Health, Columbia University, New York, NY, USA,Gertrude H. Sergievsky Center, Columbia University, 630 West 168th Street, New York, NY 10032, USA. E-mail:
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Benke KS, Carlson MC, Doan BQ, Walston JD, Xue QL, Reiner AP, Fried LP, Arking DE, Chakravarti A, Fallin MD. The association of genetic variants in interleukin-1 genes with cognition: findings from the cardiovascular health study. Exp Gerontol 2011; 46:1010-9. [PMID: 21968104 DOI: 10.1016/j.exger.2011.09.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 09/14/2011] [Accepted: 09/16/2011] [Indexed: 10/17/2022]
Abstract
The inflammatory cytokine interleukin-1 (IL1) potentially plays a role in cognitive deterioration through pathology due to a dementing disorder or due to an aging process. Study of genetic variants in the IL1 genes has been mostly limited to diseases such as Alzheimer's, however, there may be benefit to studying a continuous measure of cognition. Using data from the Cardiovascular Health Study, we evaluate genetic variation in the genes encoding inflammatory agonists IL1A and IL1B, and the antagonist IL1RN, with repeated measures of global cognition (3MS) and processing speed (DSST), using mixed effects models. We found statistically significant minor allele SNP associations with baseline performance on the 3MS in the IL1RN gene for Caucasians (rs17042917: beta=0.47, 95%CI=0.09, 0.85, p=0.016; rs4251961: beta=-0.36, 95%CI=-0.13,-0.60, p=0.0027; rs931471: beta=0.39, 95%CI=0.13, 0.65, p=0.0032), and the IL1B gene for African Americans (rs1143627: beta=1.6, 95%CI=0.48, 2.8; p=0.006 and rs1143634: beta=2.09, 95%CI=0.39, 3.8; p=0.016). Associations appear to be weaker in a subgroup with higher education level. Upon removing those diagnosed with dementia, effect sizes and statistical significance attenuated. These results provide supporting evidence that genetic variants in IL1 genes may be involved in inflammatory-related lowered cognition, that higher education may modify genetic predisposition, and that these associations may be driven by a dementia process.
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Affiliation(s)
- K S Benke
- Johns Hopkins Medical Institutions, Baltimore, MD, USA.
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10
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Matteini AM, Walston JD, Bandeen-Roche K, Arking DE, Allen RH, Fried LP, Chakravarti A, Stabler SP, Fallin MD. Transcobalamin-II variants, decreased vitamin B12 availability and increased risk of frailty. J Nutr Health Aging 2010; 14:73-7. [PMID: 20082058 PMCID: PMC3042247 DOI: 10.1007/s12603-010-0013-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVE This project was designed to follow-up prior evidence that demonstrated a significant association between vitamin B12 transport and metabolism and the frailty syndrome in community-dwelling older women. The cross-sectional relationship between genetic variants within six candidate genes along this pathway with serum methylmalonic acid (MMA) levels and frailty was evaluated in this same population of older women. METHODS Baseline measures were collected prior to folate fortification from 326 women in the Women's Health and Aging Studies I and II. Odds ratios and statistical tests were estimated for single SNP and haplotype via linear regression models for serum MMA, a marker for available vitamin B12, and in logistic regression models for frailty. RESULTS Fifty-six SNPs from CBS, MTHFR, MTR, MTRR, TCN1 and TCN2 genes were genotyped. Several SNPs in MTHFR, MTR and MTRR demonstrated a modest association to elevated MMA, while SNPs in TCN2 showed significant association to the frailty syndrome. TCN2 polymorphisms, particularly one SNP reported to be in perfect LD with functional variant Pro259Arg, were significantly associated with increased odds of frailty, after adjustment for age, presence of cardiovascular disease and elevated MMA (OR = 2.25, p-value = 0.009). CONCLUSIONS Using MMA as a marker for vitamin B12, these results suggest that TCN2 gene variants may lead to decreased vitamin B12 availability, leading to reduced energy metabolism, ultimately contributing to frailty pathology. Further studies to determine the biological role of functional TCN2 polymorphisms in frailty are needed.
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Affiliation(s)
- A M Matteini
- Johns Hopkins University, Baltimore, MD 21205, USA.
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Barnes KC, Grant AV, Baltadzhieva D, Zhang S, Berg T, Shao L, Zambelli-Weiner A, Anderson W, Nelsen A, Pillai S, Yarnall DP, Dienger K, Ingersoll RG, Scott AF, Fallin MD, Mathias RA, Beaty TH, Garcia JGN, Wills-Karp M. Variants in the gene encoding C3 are associated with asthma and related phenotypes among African Caribbean families. Genes Immun 2009; 7:27-35. [PMID: 16355111 DOI: 10.1038/sj.gene.6364267] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Proinflammatory and immunoregulatory products from C3 play a major role in phagocytosis, respiratory burst, and airways inflammation. C3 is critical in adaptive immunity; studies in mice deficient in C3 demonstrate that features of asthma are significantly attenuated in the absence of C3. To test the hypothesis that the C3 gene on chromosome 19p13.3-p13.2 contains variants associated with asthma and related phenotypes, we genotyped 25 single nucleotide polymorphism (SNP) markers distributed at intervals of approximately 1.9 kb within the C3 gene in 852 African Caribbean subjects from 125 nuclear and extended pedigrees. We used the multiallelic test in the family-based association test program to examine sliding windows comprised of 2-6 SNPs. A five-SNP window between markers rs10402876 and rs366510 provided strongest evidence for linkage in the presence of linkage disequilibrium for asthma, high log[total IgE], and high log[IL-13]/[log[IFN-gamma] in terms of global P-values (P = 0.00027, 0.00013, and 0.003, respectively). A three-SNP haplotype GGC for the first three of these markers showed best overall significance for the three phenotypes (P = 0.003, 0.007, 0.018, respectively) considering haplotype-specific tests. Taken together, these results implicate the C3 gene as a priority candidate controlling risk for asthma and allergic disease in this population of African descent.
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Affiliation(s)
- K C Barnes
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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12
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Matteini AM, Walston JD, Fallin MD, Bandeen-Roche K, Kao WHL, Semba RD, Allen RH, Guralnik J, Fried LP, Stabler SP. Markers of B-vitamin deficiency and frailty in older women. J Nutr Health Aging 2008; 12:303-8. [PMID: 18443711 PMCID: PMC2739594 DOI: 10.1007/bf02982659] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To evaluate the association between markers of vitamins B12, B6 and folate deficiency and the geriatric syndrome of frailty. DESIGN Cross-sectional study of baseline measures from the combined Women's Health and Aging Studies. SETTING Baltimore, Maryland. PARTICIPANTS Seven hundred three community-dwelling women, aged 70-79. MEASUREMENTS Frailty was defined by five-component screening criteria that include weight, grip strength, endurance, physical activity and walking speed measurements and modeled as binary and 3-level polytomous outcomes. Independent variables serum vitamin B6, vitamin B12, methylmalonic acid, total homocysteine, cystathionine and folate were modeled continuously and as abnormal versus normal. RESULTS Serum biomarker levels varied significantly by race. All analyses were race-stratified and results are reported only for Caucasian women due to small African American sample size. In polytomous logistic regression models of 3-level frailty, Caucasian women with increasing MMA, defined either continuously or using a predefined threshold, had 40-60% greater odds of being prefrail (p-values < 0.07) and 1.66-2.33 times greater odds of being frail (p-values < 0.02) compared to nonfrails after adjustment for age, education, low serum carotenoids, alcohol intake, cardiovascular disease and renal impairment. Both binary and polytomous frailty models evaluating vitamin B12 as the main exposure estimated odds ratios that were similar in trend yet slightly less significant than the MMA results. CONCLUSIONS These results suggest that vitamin B12 deficiency may contribute to the frailty syndrome in community-dwelling older women. Future studies are needed to explore these relationships longitudinally.
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Roy-Gagnon MH, Mathias RA, Fallin MD, Jee SH, Broman KW, Wilson AF. An extension of the regression of offspring on mid-parent to test for association and estimate locus-specific heritability: the revised ROMP method. Ann Hum Genet 2007; 72:115-25. [PMID: 18042270 DOI: 10.1111/j.1469-1809.2007.00401.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Regression of Offspring on Mid-Parent (ROMP) method is a test of association between a quantitative trait and a candidate locus. ROMP estimates the trait heritability and the heritability attributable to a locus and requires genotyping the offspring only. In this study, the theory underlying ROMP was revised (ROMP(rev)) and extended. Computer simulations were used to determine the type I error and power of the test of association, and the accuracy of the locus-specific heritability estimate. The ROMP(rev) test had good power at the 5% significance level with properly controlled type I error. Locus-specific heritability estimates were, on average, close to simulated values. For non-zero locus-specific heritability, the proposed standard error was downwardly biased, yielding reduced coverage of 95% confidence intervals. A bootstrap approach with proper coverage is suggested as a second step for loci of interest. ROMP(rev) was applied to a study of cardiovascular-related traits to illustrate its use. An association between polymorphisms within the fibrinogen gene cluster and plasma fibrinogen was detected (p < 0.005) that accounted for 29% of the estimated fibrinogen heritability. The ROMP(rev) method provides a computationally fast and simple way of testing for association and obtaining accurate estimates of locus-specific heritability while minimizing the genotyping required.
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Affiliation(s)
- M-H Roy-Gagnon
- Genometrics Section, Inherited Disease Research Branch, National Human Genome Research Institute, NIH, Baltimore, MD 21224, USA
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Bray PF, Mathias RA, Faraday N, Yanek LR, Fallin MD, Herrera-Galeano JE, Wilson AF, Becker LC, Becker DM. Heritability of platelet function in families with premature coronary artery disease. J Thromb Haemost 2007; 5:1617-23. [PMID: 17663734 DOI: 10.1111/j.1538-7836.2007.02618.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Variations in platelet function among individuals may be related to differences in platelet-related genes. The major goal of our study was to estimate the contribution of inheritance to the variability in platelet function in unaffected individuals from white and African American families with premature coronary artery disease. METHODS Platelet reactivity, in the absence of antiplatelet agents, was assessed by in vitro aggregation and the platelet function analyzer closure time. Heritability was estimated using a variance components model. RESULTS Both white (n = 687) and African American (n = 321) subjects exhibited moderate to strong heritability (h(2)) for epinephrine- and adenosine diphosphate-induced aggregation (0.36-0.42 for white and >0.71 for African American subjects), but heritability for collagen-induced platelet aggregation in platelet-rich plasma was prominent only in African American subjects. Platelet lag phase after collagen stimulation was heritable in both groups (0.47-0.50). A limited genotype analysis demonstrated that the C825T polymorphism of GNB3 was associated with the platelet aggregation response to 2 muM epinephrine, but the effect differed by race. CONCLUSIONS Considering the few and modest genetic effects reported to affect platelet function, our findings suggest the likely existence of undiscovered important genes that modify platelet reactivity, some of which affect multiple aspects of platelet biology.
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Affiliation(s)
- P F Bray
- Jefferson College of Medicine, Philadelphia, PA, USA.
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15
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Mulle JG, Fallin MD, Lasseter VK, McGrath JA, Wolyniec PS, Pulver AE. Dense SNP association study for bipolar I disorder on chromosome 18p11 suggests two loci with excess paternal transmission. Mol Psychiatry 2007; 12:367-75. [PMID: 17389904 DOI: 10.1038/sj.mp.4001916] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Parent-of-origin effects have been implicated as mediators of genetic susceptibility for a number of complex disease phenotypes, including bipolar disorder. Specifically, evidence for linkage on chromosome 18 is modified when allelic parent-of-origin is accommodated in the analysis. Our goal was to characterize the susceptibility locus for bipolar I disorder on chromosome 18p11 and investigate this parent-of-origin hypothesis in an association context. This was achieved by genotyping single nucleotide polymorphisms (SNPs) at a high density (1 SNP/5 kb) along 13.6 megabases of the linkage region. To increase our ability to detect a susceptibility locus, we restricted the phenotype definition to include only bipolar I probands. We also restricted our study population to Ashkenazi Jewish individuals; this population has characteristics of a genetic isolate and may therefore facilitate detection of variants for complex disease. Three hundred and forty-four pedigrees (363 parent/child trios) where probands were affected with bipolar 1 disorder were genotyped. Transmission disequilibrium test analysis revealed no statistically significant association to SNPs or haplotypes within this region in this sample. However, when parent-of-origin of transmitted SNPs was taken into account, suggestive association was revealed for two separate loci.
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Affiliation(s)
- J G Mulle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA
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16
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Cheslack-Postava K, Fallin MD, Avramopoulos D, Connors SL, Zimmerman AW, Eberhart CG, Newschaffer CJ. beta2-Adrenergic receptor gene variants and risk for autism in the AGRE cohort. Mol Psychiatry 2007; 12:283-91. [PMID: 17199132 DOI: 10.1038/sj.mp.4001940] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The beta2-adrenergic receptor is part of the catecholamine system, and variants at two polymorphic sites in the gene coding for the receptor (ADRB2) confer increased activity. Overstimulation of this receptor may alter brain development, and has been linked to autism in non-identical twins. The objective of this study was to determine whether alleles in ADRB2 are associated with diagnosis of autism in the Autism Genetic Resource Exchange (AGRE) population. Three hundred and thirty-one independent autism case-parent trios were included in the analysis. Subjects were genotyped at activity-related polymorphisms rs1042713 (codon 16) and rs1042714 (codon 27). Association between autism and genotypes at each polymorphic site was tested using genotype-based transmission disequilibrium tests, and effect modification by family and pregnancy characteristics was evaluated. Sensitivity to designation of the proband in each family was assessed by performing 1000 repeats of the analysis selecting affected children randomly. A statistically significant OR of 1.66 for the Glu27 homozygous genotype was observed. Increased associations with this genotype were observed among a subset of Autism Diagnostic Observation Schedule confirmed cases and a subset reporting experience of pregnancy-related stressors. In conclusion, the Glu27 allele of the ADRB2 gene may confer increased risk of autism and shows increased strength with exposure to pregnancy related stress.
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Affiliation(s)
- K Cheslack-Postava
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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17
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Ding J, Nicklas BJ, Fallin MD, de Rekeneire N, Kritchevsky SB, Pahor M, Rodondi N, Li R, Zmuda JM, Harris TB. Plasminogen activator inhibitor type 1 gene polymorphisms and haplotypes are associated with plasma plasminogen activator inhibitor type 1 levels but not with myocardial infarction or stroke. Am Heart J 2006; 152:1109-15. [PMID: 17161063 DOI: 10.1016/j.ahj.2006.06.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Accepted: 06/07/2006] [Indexed: 11/29/2022]
Abstract
BACKGROUND The 4G allele in the promoter region of the plasminogen activator inhibitor type 1 (PAI-1) gene is associated with higher plasma PAI-1 levels and activity, but its association with cardiovascular diseases is unclear. We investigated the association of polymorphisms and common haplotypes of the PAI-1 gene with plasma PAI-1 levels, as well as the risk of myocardial infarction and stroke. METHODS AND RESULTS This study is a prospective analysis of 2995 community-based participants (41% blacks and 51% women) aged 70 to 79 years old in the Health, Aging, and Body Composition Study. From 1997/1998 to 2001, 177 myocardial infarction events and 101 stroke events were identified. In addition to the 4G/5G polymorphism, 2 potential functional variants and other 4 haplotype-tagging variants were genotyped. In general linear models, the 4G allele was associated with higher PAI-1 levels after adjusting for age, sex, race, and site (26, 29, and 32 ng/mL for 5G/5G, 4G/5G, and 4G/4G, respectively; P for trend < .0001), but none of the other 6 polymorphisms was associated with PAI-1 levels. Haplotype analysis produced similar results. However, in Cox proportional hazard models, neither the polymorphisms nor the common haplotypes of the PAI-1 gene was associated with the risk of either myocardial infarction or stroke. CONCLUSIONS The 4G allele is associated with higher PAI-1 levels, but this study does not support an association of the PAI gene polymorphisms with the risk of either myocardial infarction or stroke.
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Affiliation(s)
- Jingzhong Ding
- Department of Internal Medicine/Geriatrics, Wake Forest University Baptist Medical Center, Winston-Salem, NC 27157, USA.
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18
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Beaty TH, Hetmanski JB, Fallin MD, Park JW, Sull JW, McIntosh I, Liang KY, Vanderkolk CA, Redett RJ, Boyadjiev SA, Jabs EW, Chong SS, Cheah FSH, Wu-Chou YH, Chen PK, Chiu YF, Yeow V, Ng ISL, Cheng J, Huang S, Ye X, Wang H, Ingersoll R, Scott AF. Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations. Hum Genet 2006; 120:501-18. [PMID: 16953426 DOI: 10.1007/s00439-006-0235-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Revised: 07/13/2006] [Accepted: 07/17/2006] [Indexed: 02/07/2023]
Abstract
Isolated oral clefts, including cleft lip with/without cleft palate (CL/P) and cleft palate (CP), have a complex and heterogeneous etiology. Case-parent trios from three populations were used to study genes spanning chromosome 2, where single nucleotide polymorphic (SNP) markers were analyzed individually and as haplotypes. Case-parent trios from three populations (74 from Maryland, 64 from Singapore and 95 from Taiwan) were genotyped for 962 SNPs in 104 genes on chromosome 2, including two well-recognized candidate genes: TGFA and SATB2. Individual SNPs and haplotypes (in sliding windows of 2-5 SNPs) were used to test for linkage and disequilibrium separately in CL/P and CP trios. A novel candidate gene (ZNF533) showed consistent evidence of linkage and disequilibrium in all three populations for both CL/P and CP. SNPs in key regions of ZNF533 showed considerable variability in estimated genotypic odds ratios and their significance, suggesting allelic heterogeneity. Haplotype frequencies for regions of ZNF533 were estimated and used to partition genetic variance into among-and within-population components. Wright's fixation index, a measure of genetic diversity, showed little difference between Singapore and Taiwan compared with Maryland. The tensin-1 gene (TNS1) also showed evidence of linkage and disequilibrium among both CL/P and CP trios in all three populations, albeit at a lower level of significance. Additional genes (VAX2, GLI2, ZHFX1B on 2p; WNT6-WNT10A and COL4A3-COL4A4 on 2q) showed consistent evidence of linkage and disequilibrium only among CL/P trios in all three populations, and TGFA showed significant evidence in two of three populations.
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Affiliation(s)
- T H Beaty
- Johns Hopkins University, Baltimore, MD, USA.
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19
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Park JW, Hetmanski JB, Jabs EW, VanderKolk C, Wu-Chou Y, Chen KT, Chong SS, Jee SH, Mcintosh I, Fallin MD, Ingersoll R, Scott AF, Beaty TH. Association Between IRF6 and Nonsyndromic Oral Clefts In 4 Populations. Am J Epidemiol 2006. [DOI: 10.1093/aje/163.suppl_11.s127-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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20
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Liu Y, Berthier-Schaad Y, Fallin MD, Fink NE, Tracy RP, Klag MJ, Smith MW, Coresh J. IL-6 haplotypes, inflammation, and risk for cardiovascular disease in a multiethnic dialysis cohort. J Am Soc Nephrol 2006; 17:863-70. [PMID: 16467451 DOI: 10.1681/asn.2005050465] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
It is unknown whether IL-6, a central regulator of inflammation, is a cause of or just a marker of atherosclerosis. Studies of genetic susceptibility to inflammation, however, avoid the potential for reverse causality. Variation in IL6 gene was studied as a predictor of cardiovascular disease (CVD) risk in a cohort of 775 incident dialysis patients, in whom IL-6 levels are elevated. On the basis of published resequencing data on the IL6 gene, a phylogenetic tree with three main branches (clades 1 to 3) was constructed. Two "clade tag" polymorphisms, -174G/C and 1888G/T, and two missense variants, Pro32Ser and Asp162Val, were genotyped. Circulating IL-6 and albumin were measured a median of 5 mo after the start of dialysis. CVD events were ascertained from medical records. During a median follow-up of 2.5 yr, 294 CVD events occurred. The two coding variants, Pro32Ser (present only in black patients, 10% Ser allele) and Asp162Val (present only in white patients, 1% Val), were associated with lower levels of IL-6 and higher levels of albumin. The common variant in the promoter region, -174G/C, was strongly associated with higher CVD risk and weakly with IL-6 levels. Clade 3 (-174C carriers in the absence of 162 Val allele) was associated with higher IL-6 levels (P=0.03) and higher CVD risk (hazard ratio 1.44, P=0.006) after adjustment for covariates. The IL6 gene has functional variants that affect inflammation and risk for CVD among dialysis patients, supporting a causal role for IL6 in CVD.
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Affiliation(s)
- Yongmei Liu
- Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
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21
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Park JW, Cai J, McIntosh I, Jabs EW, Fallin MD, Ingersoll R, Hetmanski JB, Vekemans M, Attie-Bitach T, Lovett M, Scott AF, Beaty TH. High throughput SNP and expression analyses of candidate genes for non-syndromic oral clefts. J Med Genet 2006; 43:598-608. [PMID: 16415175 PMCID: PMC2564555 DOI: 10.1136/jmg.2005.040162] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Recent work suggests that multiple genes and several environmental risk factors influence risk for non-syndromic oral clefts, one of the most common birth defects in humans. Advances in high-throughput genotyping technology now make it possible to test multiple markers in many candidate genes simultaneously. METHODS We present findings from family based association tests of single nucleotide polymorphism (SNP) markers in 64 candidate genes genotyped using the BeadArray approach in 58 case-parent trios from Maryland (USA) to illustrate how multiple markers in multiple genes can be analysed. To assess whether these genes were expressed in human craniofacial structures relevant to palate and lip development, we also analysed data from the Craniofacial and Oral Gene Expression Network (COGENE) consortium, and searched public databases for expression profiles of these genes. RESULTS Thirteen candidate genes showed significant evidence of linkage in the presence of disequilibrium, and ten of these were found to be expressed in relevant embryonic tissues: SP100, MLPH, HDAC4, LEF1, C6orf105, CD44, ALX4, ZNF202, CRHR1, and MAPT. Three other genes showing statistical evidence (ADH1C, SCN3B, and IMP5) were not expressed in the embryonic tissues examined here. CONCLUSIONS This approach demonstrates how statistical evidence on large numbers of SNP markers typed in case-parent trios can be combined with expression data to identify candidate genes for complex disorders. Many of the genes reported here have not been previously studied as candidates for oral clefts and warrant further investigation.
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Affiliation(s)
- J W Park
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
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22
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Bjornsson HT, Cui H, Gius D, Fallin MD, Feinberg AP. The new field of epigenomics: implications for cancer and other common disease research. Cold Spring Harb Symp Quant Biol 2005; 69:447-56. [PMID: 16117680 PMCID: PMC5434869 DOI: 10.1101/sqb.2004.69.447] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- H T Bjornsson
- Predoctoral Program in Human Genetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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23
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Liu Y, Berthier-Schaad Y, Fink NE, Fallin MD, Tracy RP, Klag MJ, Smith MW, Coresh J. Beta-fibrinogen haplotypes and the risk for cardiovascular disease in a dialysis cohort. Am J Kidney Dis 2005; 46:78-85. [PMID: 15983960 DOI: 10.1053/j.ajkd.2005.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Elevated plasma fibrinogen levels are common in dialysis patients and may be related to an elevated risk for cardiovascular disease (CVD). We tested the hypothesis that genetic variation in the beta-fibrinogen ( FGB ) gene, shown to explain 1% to 5% of fibrinogen level variation in the general population, has an important role in elevated fibrinogen levels and excess CVD risk in dialysis patients. METHODS Plasma fibrinogen was measured in 735 dialysis patients a median of 3 months from the start of dialysis therapy by using an automated clot-rate assay. Seven polymorphisms of the FGB gene were determined. Haplotype analysis was conducted using the Phase program to estimate haplotypes, with stratification for race. CVD events were ascertained from medical records. RESULTS During a median follow-up of 2.1 years, 279 CVD events occurred. Genotype frequencies were in Hardy-Weinberg equilibrium. Four common haplotypes identified were not associated with fibrinogen levels or CVD risk in the entire cohort or after stratification by race. The -455A allele, known to increase gene expression in vitro, was marginally associated with fibrinogen levels only in patients without diabetes (regression coefficient [beta], 20 mg/dL [for +1 copy of the A allele; P = 0.06]), adjusted for age, sex, race, smoking, baseline dialysis modality, comorbidity, and history of diabetes and CVD. Post hoc analysis showed that -249C-->T (defining haplotype 3) was associated with greater fibrinogen levels and CVD risk among patients without diabetes and current smokers. CONCLUSION The FGB gene likely does not have an important role in determining the variation in elevated plasma fibrinogen levels or excess CVD risk in dialysis patients.
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Affiliation(s)
- Yongmei Liu
- Wake Forest University School of Medicine, Winston-Salem, NC, USA.
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24
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Daugherty SE, Platz EA, Fallin MD, Welch R, Reding D, Huang WY, Chatterjee N, Hayes RB. L3: Alpha-Methylacyl-Coa Racemase (AMACR) Variants and Prostate Cancer in PLCO. Am J Epidemiol 2005. [DOI: 10.1093/aje/161.supplement_1.s150c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - E A Platz
- Division of Cancer Epidemiology and Genetics, NCI
| | - M D Fallin
- Division of Cancer Epidemiology and Genetics, NCI
| | - R Welch
- Division of Cancer Epidemiology and Genetics, NCI
| | - D Reding
- Division of Cancer Epidemiology and Genetics, NCI
| | - W-Y Huang
- Division of Cancer Epidemiology and Genetics, NCI
| | - N Chatterjee
- Division of Cancer Epidemiology and Genetics, NCI
| | - R B Hayes
- Division of Cancer Epidemiology and Genetics, NCI
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Beaty TH, Fallin MD, Hetmanski JB, McIntosh I, Chong SS, Ingersoll R, Sheng X, Chakraborty R, Scott AF. Haplotype diversity in 11 candidate genes across four populations. Genetics 2005; 171:259-67. [PMID: 15965248 PMCID: PMC1456517 DOI: 10.1534/genetics.105.043075] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Analysis of haplotypes based on multiple single-nucleotide polymorphisms (SNP) is becoming common for both candidate gene and fine-mapping studies. Before embarking on studies of haplotypes from genetically distinct populations, however, it is important to consider variation both in linkage disequilibrium (LD) and in haplotype frequencies within and across populations, as both vary. Such diversity will influence the choice of "tagging" SNPs for candidate gene or whole-genome association studies because some markers will not be polymorphic in all samples and some haplotypes will be poorly represented or completely absent. Here we analyze 11 genes, originally chosen as candidate genes for oral clefts, where multiple markers were genotyped on individuals from four populations. Estimated haplotype frequencies, measures of pairwise LD, and genetic diversity were computed for 135 European-Americans, 57 Chinese-Singaporeans, 45 Malay-Singaporeans, and 46 Indian-Singaporeans. Patterns of pairwise LD were compared across these four populations and haplotype frequencies were used to assess genetic variation. Although these populations are fairly similar in allele frequencies and overall patterns of LD, both haplotype frequencies and genetic diversity varied significantly across populations. Such haplotype diversity has implications for designing studies of association involving samples from genetically distinct populations.
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Affiliation(s)
- T H Beaty
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland 21205, USA
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26
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Swift-Scanlan T, Lan TH, Fallin MD, Coughlin JM, Potash JB, DePaulo JR, McInnis MG. Genetic analysis of the (CTG)n NOTCH4 polymorphism in 65 multiplex bipolar pedigrees. Psychiatr Genet 2002; 12:43-7. [PMID: 11901359 DOI: 10.1097/00041444-200203000-00006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A strong genetic association between the NOTCH4 locus on chromosome 6 and schizophrenia was recently reported. Based on the data suggesting overlapping susceptibility for schizophrenia and bipolar disorder, we genotyped the polymorphic (CTG)n encoding polyleucine repeat in exon 1 of NOTCH4 in 65 pedigrees ascertained for a genetic linkage study of bipolar disorder. In addition, we analyzed a subset of our pedigrees with psychotic features at this locus. We failed to find any association between the (CTG)n NOTCH4 polymorphism and either the bipolar or the psychotic bipolar phenotype in our 65 pedigrees.
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Affiliation(s)
- T Swift-Scanlan
- George Browne Genetics Laboratory, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Public Health, Baltimore, Maryland, USA
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