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Sandin S, Yip BHK, Yin W, Weiss LA, Dougherty JD, Fass S, Constantino JN, Hailin Z, Turner TN, Marrus N, Gutmann DH, Sanders SJ, Christoffersson B. Examining Sex Differences in Autism Heritability. JAMA Psychiatry 2024; 81:673-680. [PMID: 38630491 PMCID: PMC11024771 DOI: 10.1001/jamapsychiatry.2024.0525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/01/2024] [Indexed: 04/20/2024]
Abstract
Importance Autism spectrum disorder (ASD) is a neurodevelopmental disorder more prevalent in males than in females. The cause of ASD is largely genetic, but the association of genetics with the skewed sex ratio is not yet understood. To our knowledge, no large population-based study has provided estimates of heritability by sex. Objective To estimate the sex-specific heritability of ASD. Design, Setting, and Participants This was a population-based, retrospective analysis using national health registers of nontwin siblings and cousins from Sweden born between January 1, 1985, and December 31, 1998, with follow-up to 19 years of age. Data analysis occurred from August 2022 to November 2023. Main Outcomes and Measures Models were fitted to estimate the relative variance in risk for ASD occurrence owing to sex-specific additive genetics, shared environmental effects, and a common residual term. The residual term conceptually captured other factors that promote individual behavioral variation (eg, maternal effects, de novo variants, rare genetic variants not additively inherited, or gene-environment interactions). Estimates were adjusted for differences in prevalence due to birth year and maternal and paternal age by sex. Results The sample included 1 047 649 individuals in 456 832 families (538 283 males [51.38%]; 509 366 females [48.62%]). Within the entire sample, 12 226 (1.17%) received a diagnosis of ASD, comprising 8128 (1.51%) males and 4098 (0.80%) females. ASD heritability was estimated at 87.0% (95% CI, 81.4%-92.6%) for males and 75.7% (95% CI, 68.4%-83.1%) for females with a difference in heritability estimated at 11.3% (95% CI, 1.0%-21.6%). There was no support for shared environmental contributions. Conclusions and Relevance These findings suggest that the degree of phenotypic variation attributable to genetic differences (heritability) differs between males and females, indicating that some of the underlying causes of the condition may differ between the 2 sexes. The skewed sex ratio in ASD may be partly explained by differences in genetic variance between the sexes.
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Affiliation(s)
- Sven Sandin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
- Seaver Autism Center for Research and Treatment at Mount Sinai, New York, New York
| | - Benjamin H. K. Yip
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR
| | - Weiyao Yin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Lauren A. Weiss
- Institute for Human Genetics, University of California San Francisco
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco
- Weill Institute for Neurosciences, University of California San Francisco
| | - Joseph D. Dougherty
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
- Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St Louis, Missouri
| | - Stuart Fass
- Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri
| | - John N. Constantino
- Pediatric Institute, Emory University School of Medicine, Atlanta, Georgia
- Children’s Healthcare of Atlanta, Atlanta, Georgia
| | - Zhu Hailin
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR
| | - Tychele N. Turner
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St Louis, Missouri
| | - Natasha Marrus
- Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri
| | - David H. Gutmann
- Department of Neurology, Washington University School of Medicine, St Louis, Missouri
- Neurofibromatosis Center, Washington University School of Medicine, St Louis, Missouri
| | - Stephan J. Sanders
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco
| | - Benjamin Christoffersson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Churney ApS, Copenhagen, Denmark
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Kim JH, Koh IG, Lee H, Lee GH, Song DY, Kim SW, Kim Y, Han JH, Bong G, Lee J, Byun H, Son JH, Kim YR, Lee Y, Kim JJ, Park JW, Kim IB, Choi JK, Jang JH, Trost B, Lee J, Kim E, Yoo HJ, An JY. Short tandem repeat expansions in cortical layer-specific genes implicate in phenotypic severity and adaptability of autism spectrum disorder. Psychiatry Clin Neurosci 2024; 78:405-415. [PMID: 38751214 DOI: 10.1111/pcn.13676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/14/2024] [Accepted: 04/15/2024] [Indexed: 07/06/2024]
Abstract
AIM Short tandem repeats (STRs) are repetitive DNA sequences and highly mutable in various human disorders. While the involvement of STRs in various genetic disorders has been extensively studied, their role in autism spectrum disorder (ASD) remains largely unexplored. In this study, we aimed to investigate genetic association of STR expansions with ASD using whole genome sequencing (WGS) and identify risk loci associated with ASD phenotypes. METHODS We analyzed WGS data of 634 ASD families and performed genome-wide evaluation for 12,929 STR loci. We found rare STR expansions that exceeded normal repeat lengths in autism cases compared to unaffected controls. By integrating single cell RNA and ATAC sequencing datasets of human postmortem brains, we prioritized STR loci in genes specifically expressed in cortical development stages. A deep learning method was used to predict functionality of ASD-associated STR loci. RESULTS In ASD cases, rare STR expansions predominantly occurred in early cortical layer-specific genes involved in neurodevelopment, highlighting the cellular specificity of STR-associated genes in ASD risk. Leveraging deep learning prediction models, we demonstrated that these STR expansions disrupted the regulatory activity of enhancers and promoters, suggesting a potential mechanism through which they contribute to ASD pathogenesis. We found that individuals with ASD-associated STR expansions exhibited more severe ASD phenotypes and diminished adaptability compared to non-carriers. CONCLUSION Short tandem repeat expansions in cortical layer-specific genes are associated with ASD and could potentially be a risk genetic factor for ASD. Our study is the first to show evidence of STR expansion associated with ASD in an under-investigated population.
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Affiliation(s)
- Jae Hyun Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - In Gyeong Koh
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Hyeji Lee
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Gang-Hee Lee
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Da-Yea Song
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Soo-Whee Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Yujin Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Jae Hyun Han
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Psychiatry, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Republic of Korea
| | - Guiyoung Bong
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeewon Lee
- Department of Psychiatry, Soonchunhyang University College of Medicine, Asan, Republic of Korea
| | - Heejung Byun
- Department of Neuropsychiatry, Seoul Metropolitan Children's Hospital, Seoul, Republic of Korea
| | - Ji Hyun Son
- Department of Neuropsychiatry, Seoul Metropolitan Children's Hospital, Seoul, Republic of Korea
| | - Ye Rim Kim
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yoojeong Lee
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Justine Jaewon Kim
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jung Woo Park
- Center for Biomedical Computing, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, Republic of Korea
| | - Il Bin Kim
- Department of Psychiatry, Hanyang University Guri Hospital, Guri, Republic of Korea
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Brett Trost
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Junehawk Lee
- Center for Biomedical Computing, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, Republic of Korea
| | - Eunjoon Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Hee Jeong Yoo
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Republic of Korea
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Nóbrega IDS, Teles e Silva AL, Yokota-Moreno BY, Sertié AL. The Importance of Large-Scale Genomic Studies to Unravel Genetic Risk Factors for Autism. Int J Mol Sci 2024; 25:5816. [PMID: 38892002 PMCID: PMC11172008 DOI: 10.3390/ijms25115816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Autism spectrum disorder (ASD) is a common and highly heritable neurodevelopmental disorder. During the last 15 years, advances in genomic technologies and the availability of increasingly large patient cohorts have greatly expanded our knowledge of the genetic architecture of ASD and its neurobiological mechanisms. Over two hundred risk regions and genes carrying rare de novo and transmitted high-impact variants have been identified. Additionally, common variants with small individual effect size are also important, and a number of loci are now being uncovered. At the same time, these new insights have highlighted ongoing challenges. In this perspective article, we summarize developments in ASD genetic research and address the enormous impact of large-scale genomic initiatives on ASD gene discovery.
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Affiliation(s)
| | | | | | - Andréa Laurato Sertié
- Faculdade Israelita de Ciências da Saúde Albert Einstein, Hospital Israelita Albert Einstein, Rua Comendador Elias Jafet, 755. Morumbi, São Paulo 05653-000, Brazil; (I.d.S.N.); (A.L.T.e.S.); (B.Y.Y.-M.)
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Kingdom R, Beaumont RN, Wood AR, Weedon MN, Wright CF. Genetic modifiers of rare variants in monogenic developmental disorder loci. Nat Genet 2024; 56:861-868. [PMID: 38637616 PMCID: PMC11096126 DOI: 10.1038/s41588-024-01710-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/06/2024] [Indexed: 04/20/2024]
Abstract
Rare damaging variants in a large number of genes are known to cause monogenic developmental disorders (DDs) and have also been shown to cause milder subclinical phenotypes in population cohorts. Here, we show that carrying multiple (2-5) rare damaging variants across 599 dominant DD genes has an additive adverse effect on numerous cognitive and socioeconomic traits in UK Biobank, which can be partially counterbalanced by a higher educational attainment polygenic score (EA-PGS). Phenotypic deviators from expected EA-PGS could be partly explained by the enrichment or depletion of rare DD variants. Among carriers of rare DD variants, those with a DD-related clinical diagnosis had a substantially lower EA-PGS and more severe phenotype than those without a clinical diagnosis. Our results suggest that the overall burden of both rare and common variants can modify the expressivity of a phenotype, which may then influence whether an individual reaches the threshold for clinical disease.
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Affiliation(s)
- Rebecca Kingdom
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Robin N Beaumont
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Andrew R Wood
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Michael N Weedon
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Caroline F Wright
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK.
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Chang X, Qu H, Liu Y, Glessner J, Hakonarson H. A Protective Role of Low Polygenic Risk Score in Healthy Individuals Carrying Attention-Deficit/Hyperactivity Disorder-Associated Copy Number Variations. Biol Psychiatry 2024; 95:881-887. [PMID: 37865391 DOI: 10.1016/j.biopsych.2023.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/22/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Previous studies have implicated both rare copy number variations (CNVs) and common variants in liability for attention-deficit/hyperactivity disorder (ADHD). However, how common and rare genetic variants jointly contribute to individual liability requires further investigation in larger cohorts. METHODS This study comprises 9385 participants of European descent and 7810 participants of African American ancestry who were recruited from the greater Philadelphia area by the Children's Hospital of Philadelphia. The polygenic risk score (PRS) of each participant was estimated by linkage disequilibrium pruning and p-value thresholding (P + T) methods using PRSice-2. We investigated whether the risk of ADHD follows a polygenic liability threshold model wherein 1) the risk of ADHD requires less contribution from common variants in the presence of a rare CNV, and 2) control carriers of ADHD-associated CNVs have lower common risk allele burden than noncarriers. RESULTS CNVs previously reported in ADHD cases were significantly associated with ADHD risk in both the European American cohort and the African American cohort. Healthy control participants carrying those same risk CNVs had lower PRSs than those without risk CNVs in the European American cohort. This result was replicated in the African American cohort. However, PRSs were not significantly different in case participants carrying risk CNVs versus those without risk CNVs. CONCLUSIONS These findings provide evidence in support of interactive effects of PRS and ADHD-associated CNVs on disease risk and add novel insights into the genetic basis of ADHD by highlighting a protective role of low PRS in ADHD.
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Affiliation(s)
- Xiao Chang
- College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong, China; Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
| | - Huiqi Qu
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Yichuan Liu
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Joseph Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
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Koko M, Kyle Satterstrom F, Warrier V, Martin H. Contribution of autosomal rare and de novo variants to sex differences in autism. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.13.24305713. [PMID: 38699304 PMCID: PMC11065020 DOI: 10.1101/2024.04.13.24305713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Autism is four times more prevalent in males than females. To study whether this reflects a difference in genetic predisposition attributed to autosomal rare variants, we evaluated the sex differences in effect size of damaging protein-truncating and missense variants on autism predisposition in 47,061 autistic individuals, then compared effect sizes between individuals with and without cognitive impairment or motor delay. Although these variants mediated differential likelihood of autism with versus without motor or cognitive impairment, their effect sizes on the liability scale did not differ significantly by sex exome-wide or in genes sex-differentially expressed in the cortex. Although de novo mutations were enriched in genes with male-biased expression in the fetal cortex, the liability they conferred did not differ significantly from other genes with similar loss-of-function intolerance and sex-averaged cortical expression. In summary, autosomal rare coding variants confer similar liability for autism in females and males.
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Affiliation(s)
- Mahmoud Koko
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - F. Kyle Satterstrom
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Varun Warrier
- Department of Psychiatry, Autism Research Centre, University of Cambridge, Cambridge, Cambridgeshire, CB2 8AH, UK
| | - Hilary Martin
- Human Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
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Andrews SV, Kukkle PL, Menon R, Geetha TS, Goyal V, Kandadai RM, Kumar H, Borgohain R, Mukherjee A, Wadia PM, Yadav R, Desai S, Kumar N, Joshi D, Murugan S, Biswas A, Pal PK, Oliver M, Nair S, Kayalvizhi A, Samson PL, Deshmukh M, Bassi A, Sandeep C, Mandloi N, Davis OB, Roberts MA, Leto DE, Henry AG, Di Paolo G, Muthane U, Das SK, Peterson AS, Sandmann T, Gupta R, Ramprasad VL. The Genetic Drivers of Juvenile, Young, and Early-Onset Parkinson's Disease in India. Mov Disord 2024; 39:339-349. [PMID: 38014556 DOI: 10.1002/mds.29676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/18/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Recent studies have advanced our understanding of the genetic drivers of Parkinson's disease (PD). Rare variants in more than 20 genes are considered causal for PD, and the latest PD genome-wide association study (GWAS) identified 90 independent risk loci. However, there remains a gap in our understanding of PD genetics outside of the European populations in which the vast majority of these studies were focused. OBJECTIVE The aim was to identify genetic risk factors for PD in a South Asian population. METHODS A total of 674 PD subjects predominantly with age of onset (AoO) ≤50 years (encompassing juvenile, young, or early-onset PD) were recruited from 10 specialty movement disorder centers across India over a 2-year period; 1376 control subjects were selected from the reference population GenomeAsia, Phase 2. We performed various case-only and case-control genetic analyses for PD diagnosis and AoO. RESULTS A genome-wide significant signal for PD diagnosis was identified in the SNCA region, strongly colocalizing with SNCA region signal from European PD GWAS. PD cases with pathogenic mutations in PD genes exhibited, on average, lower PD polygenic risk scores than PD cases lacking any PD gene mutations. Gene burden studies of rare, predicted deleterious variants identified BSN, encoding the presynaptic protein Bassoon that has been previously associated with neurodegenerative disease. CONCLUSIONS This study constitutes the largest genetic investigation of PD in a South Asian population to date. Future work should seek to expand sample numbers in this population to enable improved statistical power to detect PD genes in this understudied group. © 2023 Denali Therapeutics and The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Shan V Andrews
- Denali Therapeutics, South San Francisco, California, USA
| | - Prashanth L Kukkle
- Manipal Hospital, Bangalore, India
- Parkinson's Disease and Movement Disorders Clinic, Bangalore, India
| | | | | | - Vinay Goyal
- All India Institute of Medical Sciences (AIIMS), New Delhi, India
- Medanta Hospital, New Delhi, India
- Medanta, The Medicity, Gurgaon, India
| | - Rukmini Mridula Kandadai
- Nizams Institute of Medical Sciences (NIMS), Hyderabad, India
- Citi Neuro Centre, Hyderabad, India
| | | | - Rupam Borgohain
- Nizams Institute of Medical Sciences (NIMS), Hyderabad, India
- Citi Neuro Centre, Hyderabad, India
| | - Adreesh Mukherjee
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | | | - Ravi Yadav
- National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Soaham Desai
- Department of Neurology, Shree Krishna Hospital and Pramukhaswami Medical College, Bhaikaka University, Anand, India
| | - Niraj Kumar
- All India Institute of Medical Sciences, Rishikesh, India
- All India Institute of Medical Sciences, Bibinagar (Hyderabad Metropolitan Region), Bibinagar, India
| | - Deepika Joshi
- Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | | | - Atanu Biswas
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | - Pramod K Pal
- National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | | | | | | | | | | | | | | | | | - Oliver B Davis
- Denali Therapeutics, South San Francisco, California, USA
| | | | - Dara E Leto
- Denali Therapeutics, South San Francisco, California, USA
| | | | | | - Uday Muthane
- Parkinson and Ageing Research Foundation, Bangalore, India
| | - Shymal K Das
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
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Perini S, Filosi M, Domenici E. Candidate biomarkers from the integration of methylation and gene expression in discordant autistic sibling pairs. Transl Psychiatry 2023; 13:109. [PMID: 37012247 PMCID: PMC10070641 DOI: 10.1038/s41398-023-02407-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
While the genetics of autism spectrum disorders (ASD) has been intensively studied, resulting in the identification of over 100 putative risk genes, the epigenetics of ASD has received less attention, and results have been inconsistent across studies. We aimed to investigate the contribution of DNA methylation (DNAm) to the risk of ASD and identify candidate biomarkers arising from the interaction of epigenetic mechanisms with genotype, gene expression, and cellular proportions. We performed DNAm differential analysis using whole blood samples from 75 discordant sibling pairs of the Italian Autism Network collection and estimated their cellular composition. We studied the correlation between DNAm and gene expression accounting for the potential effects of different genotypes on DNAm. We showed that the proportion of NK cells was significantly reduced in ASD siblings suggesting an imbalance in their immune system. We identified differentially methylated regions (DMRs) involved in neurogenesis and synaptic organization. Among candidate loci for ASD, we detected a DMR mapping to CLEC11A (neighboring SHANK1) where DNAm and gene expression were significantly and negatively correlated, independently from genotype effects. As reported in previous studies, we confirmed the involvement of immune functions in the pathophysiology of ASD. Notwithstanding the complexity of the disorder, suitable biomarkers such as CLEC11A and its neighbor SHANK1 can be discovered using integrative analyses even with peripheral tissues.
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Affiliation(s)
- Samuel Perini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
| | - Michele Filosi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
- EURAC Research, Bolzano, Italy
| | - Enrico Domenici
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy.
- Fondazione The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy.
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Lynham AJ, Knott S, Underwood JFG, Hubbard L, Agha SS, Bisson JI, van den Bree MBM, Chawner SJRA, Craddock N, O'Donovan M, Jones IR, Kirov G, Langley K, Martin J, Rice F, Roberts NP, Thapar A, Anney R, Owen MJ, Hall J, Pardiñas AF, Walters JTR. DRAGON-Data: a platform and protocol for integrating genomic and phenotypic data across large psychiatric cohorts. BJPsych Open 2023; 9:e32. [PMID: 36752340 PMCID: PMC9970169 DOI: 10.1192/bjo.2022.636] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/02/2022] [Accepted: 12/16/2022] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Current psychiatric diagnoses, although heritable, have not been clearly mapped onto distinct underlying pathogenic processes. The same symptoms often occur in multiple disorders, and a substantial proportion of both genetic and environmental risk factors are shared across disorders. However, the relationship between shared symptoms and shared genetic liability is still poorly understood. AIMS Well-characterised, cross-disorder samples are needed to investigate this matter, but few currently exist. Our aim is to develop procedures to purposely curate and aggregate genotypic and phenotypic data in psychiatric research. METHOD As part of the Cardiff MRC Mental Health Data Pathfinder initiative, we have curated and harmonised phenotypic and genetic information from 15 studies to create a new data repository, DRAGON-Data. To date, DRAGON-Data includes over 45 000 individuals: adults and children with neurodevelopmental or psychiatric diagnoses, affected probands within collected families and individuals who carry a known neurodevelopmental risk copy number variant. RESULTS We have processed the available phenotype information to derive core variables that can be reliably analysed across groups. In addition, all data-sets with genotype information have undergone rigorous quality control, imputation, copy number variant calling and polygenic score generation. CONCLUSIONS DRAGON-Data combines genetic and non-genetic information, and is available as a resource for research across traditional psychiatric diagnostic categories. Algorithms and pipelines used for data harmonisation are currently publicly available for the scientific community, and an appropriate data-sharing protocol will be developed as part of ongoing projects (DATAMIND) in partnership with Health Data Research UK.
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Affiliation(s)
- Amy J. Lynham
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Sarah Knott
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Jack F. G. Underwood
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Leon Hubbard
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Sharifah S. Agha
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Jonathan I. Bisson
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Marianne B. M. van den Bree
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Samuel J. R. A. Chawner
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Nicholas Craddock
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Michael O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Ian R. Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Kate Langley
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK; and School of Psychology, Cardiff University, UK
| | - Joanna Martin
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Frances Rice
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Neil P. Roberts
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK; and Directorate of Psychology and Psychological Therapies, Cardiff & Vale University Health Board, UK
| | - Anita Thapar
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Richard Anney
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Michael J. Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Jeremy Hall
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - Antonio F. Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
| | - James T. R. Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, UK
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10
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Bao B, Zahiri J, Gazestani VH, Lopez L, Xiao Y, Kim R, Wen TH, Chiang AWT, Nalabolu S, Pierce K, Robasky K, Wang T, Hoekzema K, Eichler EE, Lewis NE, Courchesne E. A predictive ensemble classifier for the gene expression diagnosis of ASD at ages 1 to 4 years. Mol Psychiatry 2023; 28:822-833. [PMID: 36266569 PMCID: PMC9908553 DOI: 10.1038/s41380-022-01826-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 09/13/2022] [Accepted: 09/27/2022] [Indexed: 11/09/2022]
Abstract
Autism Spectrum Disorder (ASD) diagnosis remains behavior-based and the median age of diagnosis is ~52 months, nearly 5 years after its first-trimester origin. Accurate and clinically-translatable early-age diagnostics do not exist due to ASD genetic and clinical heterogeneity. Here we collected clinical, diagnostic, and leukocyte RNA data from 240 ASD and typically developing (TD) toddlers (175 toddlers for training and 65 for test). To identify gene expression ASD diagnostic classifiers, we developed 42,840 models composed of 3570 gene expression feature selection sets and 12 classification methods. We found that 742 models had AUC-ROC ≥ 0.8 on both Training and Test sets. Weighted Bayesian model averaging of these 742 models yielded an ensemble classifier model with accurate performance in Training and Test gene expression datasets with ASD diagnostic classification AUC-ROC scores of 85-89% and AUC-PR scores of 84-92%. ASD toddlers with ensemble scores above and below the overall ASD ensemble mean of 0.723 (on a scale of 0 to 1) had similar diagnostic and psychometric scores, but those below this ASD ensemble mean had more prenatal risk events than TD toddlers. Ensemble model feature genes were involved in cell cycle, inflammation/immune response, transcriptional gene regulation, cytokine response, and PI3K-AKT, RAS and Wnt signaling pathways. We additionally collected targeted DNA sequencing smMIPs data on a subset of ASD risk genes from 217 of the 240 ASD and TD toddlers. This DNA sequencing found about the same percentage of SFARI Level 1 and 2 ASD risk gene mutations in TD (12 of 105) as in ASD (13 of 112) toddlers, and classification based only on the presence of mutation in these risk genes performed at a chance level of 49%. By contrast, the leukocyte ensemble gene expression classifier correctly diagnostically classified 88% of TD and ASD toddlers with ASD risk gene mutations. Our ensemble ASD gene expression classifier is diagnostically predictive and replicable across different toddler ages, races, and ethnicities; out-performs a risk gene mutation classifier; and has potential for clinical translation.
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Affiliation(s)
- Bokan Bao
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Javad Zahiri
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
| | - Vahid H Gazestani
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Linda Lopez
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
| | - Yaqiong Xiao
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
- Center for Language and Brain, Shenzhen Institute of Neuroscience, Shenzhen, China
| | - Raphael Kim
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Teresa H Wen
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
| | - Austin W T Chiang
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Srinivasa Nalabolu
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
| | - Karen Pierce
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
| | - Kimberly Robasky
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, US
- School of Information and Library Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Carolina Health and Informatics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tianyun Wang
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, 100191, Beijing, China
- Neuroscience Research Institute, Peking University; Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, 100191, Beijing, China
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
| | - Eric Courchesne
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA.
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11
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Anna S, Magdalena J. Editorial: Epigenomic contributions to autism spectrum disorders. Front Neurosci 2023; 17:1177378. [PMID: 37144095 PMCID: PMC10151758 DOI: 10.3389/fnins.2023.1177378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Affiliation(s)
- Starnawska Anna
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, CGPM, and Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
- *Correspondence: Starnawska Anna
| | - Janecka Magdalena
- Seaver Autism Center, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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12
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Trost B, Thiruvahindrapuram B, Chan AJS, Engchuan W, Higginbotham EJ, Howe JL, Loureiro LO, Reuter MS, Roshandel D, Whitney J, Zarrei M, Bookman M, Somerville C, Shaath R, Abdi M, Aliyev E, Patel RV, Nalpathamkalam T, Pellecchia G, Hamdan O, Kaur G, Wang Z, MacDonald JR, Wei J, Sung WWL, Lamoureux S, Hoang N, Selvanayagam T, Deflaux N, Geng M, Ghaffari S, Bates J, Young EJ, Ding Q, Shum C, D'Abate L, Bradley CA, Rutherford A, Aguda V, Apresto B, Chen N, Desai S, Du X, Fong MLY, Pullenayegum S, Samler K, Wang T, Ho K, Paton T, Pereira SL, Herbrick JA, Wintle RF, Fuerth J, Noppornpitak J, Ward H, Magee P, Al Baz A, Kajendirarajah U, Kapadia S, Vlasblom J, Valluri M, Green J, Seifer V, Quirbach M, Rennie O, Kelley E, Masjedi N, Lord C, Szego MJ, Zawati MH, Lang M, Strug LJ, Marshall CR, Costain G, Calli K, Iaboni A, Yusuf A, Ambrozewicz P, Gallagher L, Amaral DG, Brian J, Elsabbagh M, Georgiades S, Messinger DS, Ozonoff S, Sebat J, Sjaarda C, Smith IM, Szatmari P, Zwaigenbaum L, Kushki A, Frazier TW, Vorstman JAS, Fakhro KA, Fernandez BA, Lewis MES, Weksberg R, Fiume M, Yuen RKC, Anagnostou E, Sondheimer N, Glazer D, Hartley DM, Scherer SW. Genomic architecture of autism from comprehensive whole-genome sequence annotation. Cell 2022; 185:4409-4427.e18. [PMID: 36368308 PMCID: PMC10726699 DOI: 10.1016/j.cell.2022.10.009] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/30/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022]
Abstract
Fully understanding autism spectrum disorder (ASD) genetics requires whole-genome sequencing (WGS). We present the latest release of the Autism Speaks MSSNG resource, which includes WGS data from 5,100 individuals with ASD and 6,212 non-ASD parents and siblings (total n = 11,312). Examining a wide variety of genetic variants in MSSNG and the Simons Simplex Collection (SSC; n = 9,205), we identified ASD-associated rare variants in 718/5,100 individuals with ASD from MSSNG (14.1%) and 350/2,419 from SSC (14.5%). Considering genomic architecture, 52% were nuclear sequence-level variants, 46% were nuclear structural variants (including copy-number variants, inversions, large insertions, uniparental isodisomies, and tandem repeat expansions), and 2% were mitochondrial variants. Our study provides a guidebook for exploring genotype-phenotype correlations in families who carry ASD-associated rare variants and serves as an entry point to the expanded studies required to dissect the etiology in the ∼85% of the ASD population that remain idiopathic.
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Affiliation(s)
- Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | | | - Ada J S Chan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Edward J Higginbotham
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jennifer L Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Livia O Loureiro
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Miriam S Reuter
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; CGEn, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Delnaz Roshandel
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Joe Whitney
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | | | - Cherith Somerville
- Ted Rogers Centre for Heart Research, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Rulan Shaath
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Mona Abdi
- Department of Human Genetics, Sidra Medicine, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Rohan V Patel
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Omar Hamdan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Gaganjot Kaur
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Zhuozhi Wang
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jeffrey R MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - John Wei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Wilson W L Sung
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sylvia Lamoureux
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ny Hoang
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Thanuja Selvanayagam
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Nicole Deflaux
- Verily Life Sciences, South San Francisco, CA 94080, USA
| | - Melissa Geng
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Siavash Ghaffari
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - John Bates
- Verily Life Sciences, South San Francisco, CA 94080, USA
| | - Edwin J Young
- Genome Diagnostics, Department of Paediatric Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Qiliang Ding
- Ted Rogers Centre for Heart Research, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Carole Shum
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Lia D'Abate
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Clarrisa A Bradley
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Annabel Rutherford
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Vernie Aguda
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Beverly Apresto
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Nan Chen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sachin Desai
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Xiaoyan Du
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Matthew L Y Fong
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sanjeev Pullenayegum
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Kozue Samler
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ting Wang
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Karen Ho
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Tara Paton
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sergio L Pereira
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jo-Anne Herbrick
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Richard F Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | - Olivia Rennie
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Elizabeth Kelley
- Department of Psychology, Queen's University, Kingston, ON K7L 3N6, Canada; Department of Psychiatry, Queen's University, Kingston, ON K7L 7X3, Canada
| | - Nina Masjedi
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Catherine Lord
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Michael J Szego
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Family and Community Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Ma'n H Zawati
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Michael Lang
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Lisa J Strug
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Statistical Sciences, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Christian R Marshall
- Genome Diagnostics, Department of Paediatric Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gregory Costain
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Kristina Calli
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada; BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Alana Iaboni
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada
| | - Afiqah Yusuf
- Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Patricia Ambrozewicz
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Psychology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Louise Gallagher
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 2, Ireland; Department of Psychiatry, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Child, Youth and Family Services, The Centre for Addiction and Mental Health, Toronto, ON M6J 1H4, Canada; Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - David G Amaral
- MIND Institute, University of California, Davis, Sacramento, CA 95817, USA; Department of Psychiatry and Behavioral Sciences, University of California, Davis, Sacramento, CA 95817, USA
| | - Jessica Brian
- Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada; Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada
| | - Mayada Elsabbagh
- Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Stelios Georgiades
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON L8N 3K7, Canada
| | | | - Sally Ozonoff
- MIND Institute, University of California, Davis, Sacramento, CA 95817, USA; Department of Psychiatry and Behavioral Sciences, University of California, Davis, Sacramento, CA 95817, USA
| | - Jonathan Sebat
- Department of Psychiatry and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Calvin Sjaarda
- Department of Psychiatry, Queen's University, Kingston, ON K7L 7X3, Canada; Queen's Genomics Lab at Ongwanada, Queen's University, Kingston, ON K7M 8A6, Canada
| | - Isabel M Smith
- Department of Pediatrics, Dalhousie University, Halifax, NS B3H 4R2, Canada; IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Peter Szatmari
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada; Centre for Addiction and Mental Health, Toronto, ON M6J 1H4, Canada
| | - Lonnie Zwaigenbaum
- Department of Pediatrics, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Azadeh Kushki
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Thomas W Frazier
- Autism Speaks, Princeton, NJ 08540, USA; Department of Psychology, John Carroll University, Cleveland, OH 44118, USA
| | - Jacob A S Vorstman
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar; Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Bridget A Fernandez
- Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90033, USA
| | - M E Suzanne Lewis
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada; BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | | | - Ryan K C Yuen
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Evdokia Anagnostou
- Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada; Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada
| | - Neal Sondheimer
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - David Glazer
- Verily Life Sciences, South San Francisco, CA 94080, USA
| | | | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; McLaughlin Centre, Toronto, ON M5G 0A4, Canada.
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13
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Integrative Functional Genomic Analysis in Multiplex Autism Families from Kazakhstan. DISEASE MARKERS 2022; 2022:1509994. [PMID: 36199823 PMCID: PMC9529466 DOI: 10.1155/2022/1509994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/21/2022] [Accepted: 09/06/2022] [Indexed: 12/14/2022]
Abstract
The study of extended pedigrees containing autism spectrum disorder- (ASD-) related broader autism phenotypes (BAP) offers a promising approach to the search for ASD candidate variants. Here, a total of 650,000 genetic markers were tested in four Kazakhstani multiplex families with ASD and BAP to obtain data on de novo mutations (DNMs), common, and rare inherited variants that may contribute to the genetic risk for developing autistic traits. The variants were analyzed in the context of gene networks and pathways. Several previously well-described enriched pathways were identified, including ion channel activity, regulation of synaptic function, and membrane depolarization. Perhaps these pathways are crucial not only for the development of ASD but also for ВАР. The results also point to several additional biological pathways (circadian entrainment, NCAM and BTN family interactions, and interaction between L1 and Ankyrins) and hub genes (CFTR, NOD2, PPP2R2B, and TTR). The obtained results suggest that further exploration of PPI networks combining ASD and BAP risk genes can be used to identify novel or overlooked ASD molecular mechanisms.
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14
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Kuo SS, van der Merwe C, Fu JM, Carey CE, Talkowski ME, Bishop SL, Robinson EB. Developmental Variability in Autism Across 17 000 Autistic Individuals and 4000 Siblings Without an Autism Diagnosis: Comparisons by Cohort, Intellectual Disability, Genetic Etiology, and Age at Diagnosis. JAMA Pediatr 2022; 176:915-923. [PMID: 35849387 PMCID: PMC9295026 DOI: 10.1001/jamapediatrics.2022.2423] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/14/2022] [Indexed: 01/02/2023]
Abstract
Importance Presence of developmental delays in autism is well established, yet few studies have characterized variability in developmental milestone attainment in this population. Objective To characterize variability in the age at which autistic individuals attain key developmental milestones based on co-occurring intellectual disability (ID), presence of a rare disruptive genetic variant associated with neurodevelopmental disorders (NDD), age at autism diagnosis, and research cohort membership. Design The study team harmonized data from 4 cross-sectional autism cohorts: the Autism Genetics Research Exchange (n = 3284; 1997-2015), The Autism Simplex Collection (n = 694; 2008-2011), the Simons Simplex Collection (n = 2753; 2008-2011), and the Simons Foundation Powering Autism Research for Knowledge (n = 10 367; 2016-present). The last sample further included 4145 siblings without an autism diagnosis or ID. Participants Convenience sample of 21 243 autistic individuals or their siblings without an autism diagnosis aged 4 to 17 years. Main Outcomes and Measures Parents reported ages at which participants attained key milestones including smiling, sitting upright, crawling, walking, spoon-feeding self, speaking words, speaking phrases, and acquiring bladder and bowel control. A total of 5295 autistic individuals, and their biological parents, were genetically characterized to identify de novo variants in NDD-associated genes. The study team conducted time-to-event analyses to estimate and compare percentiles in time with milestone attainment across autistic individuals, subgroups of autistic individuals, and the sibling sample. Results Seventeen thousand ninety-eight autistic individuals (mean age, 9.15 years; 80.8% male) compared with 4145 siblings without autism or ID (mean age, 10.2 years; 50.2% female) showed delays in milestone attainment, with median (IQR) delays ranging from 0.7 (0.3-1.6) to 19.7 (11.4-32.2) months. More severe and more variable delays in autism were associated with the presence of co-occurring ID, carrying an NDD-associated rare genetic variant, and being diagnosed with autism by age 5 years. More severe and more variable delays were also associated with membership in earlier study cohorts, consistent with autism's diagnostic and ascertainment expansion over the last 30 years. Conclusions and Relevance As the largest summary to date of developmental milestone attainment in autism, to our knowledge, this study demonstrates substantial developmental variability across different conditions and provides important context for understanding the phenotypic and etiological heterogeneity of autism.
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Affiliation(s)
- Susan S. Kuo
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Celia van der Merwe
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Jack M. Fu
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Caitlin E. Carey
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Michael E. Talkowski
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Somer L. Bishop
- Department of Psychiatry, University of California, San Francisco
| | - Elise B. Robinson
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston
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15
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Gene-based therapeutics for rare genetic neurodevelopmental psychiatric disorders. Mol Ther 2022; 30:2416-2428. [PMID: 35585789 PMCID: PMC9263284 DOI: 10.1016/j.ymthe.2022.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/07/2022] [Accepted: 05/11/2022] [Indexed: 11/23/2022] Open
Abstract
We are in an emerging era of gene-based therapeutics with significant promise for rare genetic disorders. The potential is particularly significant for genetic central nervous system disorders that have begun to achieve Food and Drug Administration approval for select patient populations. This review summarizes the discussions and presentations of the National Institute of Mental Health-sponsored workshop "Gene-Based Therapeutics for Rare Genetic Neurodevelopmental Psychiatric Disorders," which was held in January 2021. Here, we distill the points raised regarding various precision medicine approaches related to neurodevelopmental and psychiatric disorders that may be amenable to gene-based therapies.
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16
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Campbell C, Leu C, Feng YCA, Wolking S, Moreau C, Ellis C, Ganesan S, Martins H, Oliver K, Boothman I, Benson K, Molloy A, Brody L, Michaud JL, Hamdan FF, Minassian BA, Lerche H, Scheffer IE, Sisodiya S, Girard S, Cosette P, Delanty N, Lal D, Cavalleri GL. The role of common genetic variation in presumed monogenic epilepsies. EBioMedicine 2022; 81:104098. [PMID: 35679801 PMCID: PMC9188960 DOI: 10.1016/j.ebiom.2022.104098] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/11/2022] [Accepted: 05/20/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The developmental and epileptic encephalopathies (DEEs) are the most severe group of epilepsies which co-present with developmental delay and intellectual disability (ID). DEEs usually occur in people without a family history of epilepsy and have emerged as primarily monogenic, with damaging rare mutations found in 50% of patients. Little is known about the genetic architecture of patients with DEEs in whom no pathogenic variant is identified. Polygenic risk scoring (PRS) is a method that measures a person's common genetic burden for a trait or condition. Here, we used PRS to test whether genetic burden for epilepsy is relevant in individuals with DEEs, and other forms of epilepsy with ID. METHODS Genetic data on 2,759 cases with DEEs, or epilepsy with ID presumed to have a monogenic basis, and 447,760 population-matched controls were analysed. We compared PRS for 'all epilepsy', 'focal epilepsy', and 'genetic generalised epilepsy' (GGE) between cases and controls. We performed pairwise comparisons between cases stratified for identifiable rare deleterious genetic variants and controls. FINDINGS Cases of presumed monogenic severe epilepsy had an increased PRS for 'all epilepsy' (p<0.0001), 'focal epilepsy' (p<0.0001), and 'GGE' (p=0.0002) relative to controls, which explain between 0.08% and 3.3% of phenotypic variance. PRS was increased in cases both with and without an identified deleterious variant of major effect, and there was no significant difference in PRS between the two groups. INTERPRETATION We provide evidence that common genetic variation contributes to the aetiology of DEEs and other forms of epilepsy with ID, even when there is a known pathogenic variant of major effect. These results provide insight into the genetic underpinnings of the severe epilepsies and warrant a shift in our understanding of the aetiology of the DEEs as complex, rather than monogenic, disorders. FUNDING Science foundation Ireland, Human Genome Research Institute; National Heart, Lung, and Blood Institute; German Research Foundation.
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Affiliation(s)
- Ciarán Campbell
- The SFI FutureNeuro Research Centre, RCSI Dublin, Republic of Ireland; The School of Pharmacy and Biomolecular Sciences, RCSI Dublin, Republic of Ireland
| | - Costin Leu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America; UCL Queen Square Institute of Neurology, London WC1N 3BG and Chalfont Centre for Epilepsy, Bucks, United Kingdom; Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, United States of America
| | - Yen-Chen Anne Feng
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, United States of America; Division of Biostatistics, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Stefan Wolking
- Department of Neurology & Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; Department of Epileptology and Neurology, University of Aachen, Aachen, Germany; Axe Neurosciences, Centre de recherche de l'Université de Montréal, Université de Montréal, Montréal, Canada
| | - Claudia Moreau
- Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, Canada
| | - Colin Ellis
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shiva Ganesan
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Helena Martins
- UCL Queen Square Institute of Neurology, London WC1N 3BG and Chalfont Centre for Epilepsy, Bucks, United Kingdom
| | - Karen Oliver
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Melbourne, Victoria, Australia
| | - Isabelle Boothman
- The SFI FutureNeuro Research Centre, RCSI Dublin, Republic of Ireland; The School of Pharmacy and Biomolecular Sciences, RCSI Dublin, Republic of Ireland
| | - Katherine Benson
- The SFI FutureNeuro Research Centre, RCSI Dublin, Republic of Ireland; The School of Pharmacy and Biomolecular Sciences, RCSI Dublin, Republic of Ireland
| | - Anne Molloy
- Department of Medical Gerontology, School of Medicine, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Lawrence Brody
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Fadi F Hamdan
- CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Berge A Minassian
- Department of Pediatrics, Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Holger Lerche
- Department of Neurology & Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Ingrid E Scheffer
- University of Melbourne, Austin and Royal Children's Hospitals, Melbourne, Australia; Florey Institute and Murdoch Children's Research Institute, Melbourne, Australia
| | - Sanjay Sisodiya
- UCL Queen Square Institute of Neurology, London WC1N 3BG and Chalfont Centre for Epilepsy, Bucks, United Kingdom
| | - Simon Girard
- Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, Canada
| | - Patrick Cosette
- Department of Medicine, Neurology Division, Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Norman Delanty
- The School of Pharmacy and Biomolecular Sciences, RCSI Dublin, Republic of Ireland; Department of Neurology, Beaumont Hospital, Dublin, Republic of Ireland
| | - Dennis Lal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America; Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, United States of America; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA; Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Gianpiero L Cavalleri
- The SFI FutureNeuro Research Centre, RCSI Dublin, Republic of Ireland; The School of Pharmacy and Biomolecular Sciences, RCSI Dublin, Republic of Ireland.
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17
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Thomas TR, Koomar T, Casten LG, Tener AJ, Bahl E, Michaelson JJ. Clinical autism subscales have common genetic liabilities that are heritable, pleiotropic, and generalizable to the general population. Transl Psychiatry 2022; 12:247. [PMID: 35697691 PMCID: PMC9192633 DOI: 10.1038/s41398-022-01982-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 04/26/2022] [Accepted: 05/20/2022] [Indexed: 12/31/2022] Open
Abstract
The complexity of autism's phenotypic spectra is well-known, yet most genetic research uses case-control status as the target trait. It is undetermined if autistic symptom domain severity underlying this heterogeneity is heritable and pleiotropic with other psychiatric and behavior traits in the same manner as autism case-control status. In N = 6064 autistic children in the SPARK cohort, we investigated the common genetic properties of twelve subscales from three clinical autism instruments measuring autistic traits: the Social Communication Questionnaire (SCQ), the Repetitive Behavior Scale-Revised (RBS-R), and the Developmental Coordination Disorder Questionnaire (DCDQ). Educational attainment polygenic scores (PGS) were significantly negatively correlated with eleven subscales, while ADHD and major depression PGS were positively correlated with ten and eight of the autism subscales, respectively. Loneliness and neuroticism PGS were also positively correlated with many subscales. Significant PGS by sex interactions were found-surprisingly, the autism case-control PGS was negatively correlated in females and had no strong correlation in males. SNP-heritability of the DCDQ subscales ranged from 0.04 to 0.08, RBS-R subscales ranged from 0.09 to 0.24, and SCQ subscales ranged from 0 to 0.12. GWAS in SPARK followed by estimation of polygenic scores (PGS) in the typically-developing ABCD cohort (N = 5285), revealed significant associations of RBS-R subscale PGS with autism-related behavioral traits, with several subscale PGS more strongly correlated than the autism case-control PGS. Overall, our analyses suggest that the clinical autism subscale traits show variability in SNP-heritability, PGS associations, and significant PGS by sex interactions, underscoring the heterogeneity in autistic traits at a genetic level. Furthermore, of the three instruments investigated, the RBS-R shows the greatest evidence of genetic signal in both (1) autistic samples (greater heritability) and (2) general population samples (strongest PGS associations).
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Affiliation(s)
- Taylor R Thomas
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Tanner Koomar
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Lucas G Casten
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Ashton J Tener
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Ethan Bahl
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Jacob J Michaelson
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA.
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, USA.
- Hawkeye Intellectual and Developmental Disabilities Research Center (Hawk-IDDRC), University of Iowa, Iowa City, IA, USA.
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18
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Gunter C, Harris RA, Kovacs-Balint Z, Raveendran M, Michopoulos V, Bachevalier J, Raper J, Sanchez MM, Rogers J. Heritability of social behavioral phenotypes and preliminary associations with autism spectrum disorder risk genes in rhesus macaques: A whole exome sequencing study. Autism Res 2022; 15:447-463. [PMID: 35092647 PMCID: PMC8930433 DOI: 10.1002/aur.2675] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 11/15/2021] [Accepted: 01/11/2022] [Indexed: 12/14/2022]
Abstract
Nonhuman primates and especially rhesus macaques (Macaca mulatta) have been indispensable animal models for studies of various aspects of neurobiology, developmental psychology, and other aspects of neuroscience. While remarkable progress has been made in our understanding of influences on atypical human social behavior, such as that observed in autism spectrum disorders (ASD), many significant questions remain. Improved understanding of the relationships among variation in specific genes and variation in expressed social behavior in a nonhuman primate would benefit efforts to investigate risk factors, developmental mechanisms, and potential therapies for behavioral disorders including ASD. To study genetic influences on key aspects of social behavior and interactions-individual competence and/or motivation for specific aspects of social behavior-we quantified individual variation in social interactions among juvenile rhesus macaques using both a standard macaque ethogram and a macaque-relevant modification of the human Social Responsiveness Scale. Our analyses demonstrate that various aspects of juvenile social behavior exhibit significant genetic heritability, with estimated quantitative genetic effects similar to that described for ASD in human children. We also performed exome sequencing and analyzed variants in 143 genes previously suggested to influence risk for human ASD. We find preliminary evidence for genetic association between specific variants and both individual behaviors and multi-behavioral factor scores. To our knowledge, this is the first demonstration that spontaneous social behaviors performed by free-ranging juvenile rhesus macaques display significant genetic heritability and then to use exome sequencing data to examine potential macaque genetic associations in genes associated with human ASD.
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Affiliation(s)
- Chris Gunter
- Marcus Autism Center, Children’s Healthcare of Atlanta, Atlanta, GA, USA,Departments of Pediatrics Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Vasiliki Michopoulos
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA,Department of Psychiatry & Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Jocelyne Bachevalier
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA,Department of Psychology, Emory University, Atlanta, GA, USA
| | - Jessica Raper
- Departments of Pediatrics Human Genetics, Emory University School of Medicine, Atlanta, GA, USA,Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Mar M. Sanchez
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA,Department of Psychiatry & Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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19
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Mahjani B, Klei L, Mattheisen M, Halvorsen MW, Reichenberg A, Roeder K, Pedersen NL, Boberg J, de Schipper E, Bulik CM, Landén M, Fundín B, Mataix-Cols D, Sandin S, Hultman CM, Crowley JJ, Buxbaum JD, Rück C, Devlin B, Grice DE. The Genetic Architecture of Obsessive-Compulsive Disorder: Contribution of Liability to OCD From Alleles Across the Frequency Spectrum. Am J Psychiatry 2022; 179:216-225. [PMID: 34789012 PMCID: PMC8897260 DOI: 10.1176/appi.ajp.2021.21010101] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
OBJECTIVE Obsessive-compulsive disorder (OCD) is known to be substantially heritable; however, the contribution of genetic variation across the allele frequency spectrum to this heritability remains uncertain. The authors used two new homogeneous cohorts to estimate the heritability of OCD from inherited genetic variation and contrasted the results with those of previous studies. METHODS The sample consisted of 2,090 Swedish-born individuals diagnosed with OCD and 4,567 control subjects, all genotyped for common genetic variants, specifically >400,000 single-nucleotide polymorphisms (SNPs) with minor allele frequency (MAF) ≥0.01. Using genotypes of these SNPs to estimate distant familial relationships among individuals, the authors estimated the heritability of OCD, both overall and partitioned according to MAF bins. RESULTS Narrow-sense heritability of OCD was estimated at 29% (SE=4%). The estimate was robust, varying only modestly under different models. Contrary to an earlier study, however, SNPs with MAF between 0.01 and 0.05 accounted for 10% of heritability, and estimated heritability per MAF bin roughly followed expectations based on a simple model for SNP-based heritability. CONCLUSIONS These results indicate that common inherited risk variation (MAF ≥0.01) accounts for most of the heritable variation in OCD. SNPs with low MAF contribute meaningfully to the heritability of OCD, and the results are consistent with expectation under the "infinitesimal model" (also referred to as the "polygenic model"), where risk is influenced by a large number of loci across the genome and across MAF bins.
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Affiliation(s)
- Behrang Mahjani
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Division of Tics, Obsessive-Compulsive Disorder (OCD) and Related Disorders, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Manuel Mattheisen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Matthew W. Halvorsen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Genetics, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Abraham Reichenberg
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kathryn Roeder
- Department of Statistics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.,Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Nancy L. Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Julia Boberg
- Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Elles de Schipper
- Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Cynthia M. Bulik
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mikael Landén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Bengt Fundín
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - David Mataix-Cols
- Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Sven Sandin
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Christina M. Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - James J. Crowley
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Genetics, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Joseph D. Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christian Rück
- Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.,Health Care Services, Region Stockholm, Stockholm, Sweden
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Dorothy E. Grice
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Division of Tics, Obsessive-Compulsive Disorder (OCD) and Related Disorders, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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