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Yap CX, Henders AK, Alvares GA, Wood DLA, Krause L, Tyson GW, Restuadi R, Wallace L, McLaren T, Hansell NK, Cleary D, Grove R, Hafekost C, Harun A, Holdsworth H, Jellett R, Khan F, Lawson LP, Leslie J, Frenk ML, Masi A, Mathew NE, Muniandy M, Nothard M, Miller JL, Nunn L, Holtmann G, Strike LT, de Zubicaray GI, Thompson PM, McMahon KL, Wright MJ, Visscher PM, Dawson PA, Dissanayake C, Eapen V, Heussler HS, McRae AF, Whitehouse AJO, Wray NR, Gratten J. Autism-related dietary preferences mediate autism-gut microbiome associations. Cell 2024; 187:495-510. [PMID: 38242089 DOI: 10.1016/j.cell.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
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Yap CX, Henders AK, Alvares GA, Giles C, Huynh K, Nguyen A, Wallace L, McLaren T, Yang Y, Hernandez LM, Gandal MJ, Hansell NK, Cleary D, Grove R, Hafekost C, Harun A, Holdsworth H, Jellett R, Khan F, Lawson LP, Leslie J, Levis Frenk M, Masi A, Mathew NE, Muniandy M, Nothard M, Miller JL, Nunn L, Strike LT, Cadby G, Moses EK, de Zubicaray GI, Thompson PM, McMahon KL, Wright MJ, Visscher PM, Dawson PA, Dissanayake C, Eapen V, Heussler HS, Whitehouse AJO, Meikle PJ, Wray NR, Gratten J. Interactions between the lipidome and genetic and environmental factors in autism. Nat Med 2023; 29:936-949. [PMID: 37076741 PMCID: PMC10115648 DOI: 10.1038/s41591-023-02271-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 02/22/2023] [Indexed: 04/21/2023]
Abstract
Autism omics research has historically been reductionist and diagnosis centric, with little attention paid to common co-occurring conditions (for example, sleep and feeding disorders) and the complex interplay between molecular profiles and neurodevelopment, genetics, environmental factors and health. Here we explored the plasma lipidome (783 lipid species) in 765 children (485 diagnosed with autism spectrum disorder (ASD)) within the Australian Autism Biobank. We identified lipids associated with ASD diagnosis (n = 8), sleep disturbances (n = 20) and cognitive function (n = 8) and found that long-chain polyunsaturated fatty acids may causally contribute to sleep disturbances mediated by the FADS gene cluster. We explored the interplay of environmental factors with neurodevelopment and the lipidome, finding that sleep disturbances and unhealthy diet have a convergent lipidome profile (with potential mediation by the microbiome) that is also independently associated with poorer adaptive function. In contrast, ASD lipidome differences were accounted for by dietary differences and sleep disturbances. We identified a large chr19p13.2 copy number variant genetic deletion spanning the LDLR gene and two high-confidence ASD genes (ELAVL3 and SMARCA4) in one child with an ASD diagnosis and widespread low-density lipoprotein-related lipidome derangements. Lipidomics captures the complexity of neurodevelopment, as well as the biological effects of conditions that commonly affect quality of life among autistic people.
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Affiliation(s)
- Chloe X Yap
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia.
| | - Anjali K Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
| | - Gail A Alvares
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Corey Giles
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kevin Huynh
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anh Nguyen
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
| | - Tiana McLaren
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
| | - Yuanhao Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
| | - Leanna M Hernandez
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Lifespan Brain Institute at Penn Medicine and The Children's Hospital of Philadelphia, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Narelle K Hansell
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Dominique Cleary
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Rachel Grove
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Faculty of Health, University of Technology Sydney, Sydney, New South Wales, Australia
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Claire Hafekost
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Alexis Harun
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Helen Holdsworth
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Rachel Jellett
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, Victoria, Australia
| | - Feroza Khan
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Lauren P Lawson
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Department of Psychology, Counselling and Therapy, La Trobe University, Melbourne, Victoria, Australia
| | - Jodie Leslie
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Mira Levis Frenk
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Anne Masi
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Nisha E Mathew
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Melanie Muniandy
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, Victoria, Australia
| | - Michaela Nothard
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, Victoria, Australia
| | - Jessica L Miller
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Lorelle Nunn
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Lachlan T Strike
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Gemma Cadby
- School of Population and Global Health, The University of Western Australia, Perth, Western Australia, Australia
| | - Eric K Moses
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Greig I de Zubicaray
- School of Psychology and Counselling, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Katie L McMahon
- School of Clinical Sciences, Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Margaret J Wright
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Queensland, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Paul A Dawson
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
| | - Cheryl Dissanayake
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, Victoria, Australia
| | - Valsamma Eapen
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Academic Unit of Child Psychiatry South West Sydney, Ingham Institute for Applied Medical Research, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Helen S Heussler
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- Child Development Program, Children's Health Queensland, Brisbane, Queensland, Australia
| | - Andrew J O Whitehouse
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Jacob Gratten
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia.
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Yap CX, Henders AK, Alvares GA, Wood DLA, Krause L, Tyson GW, Restuadi R, Wallace L, McLaren T, Hansell NK, Cleary D, Grove R, Hafekost C, Harun A, Holdsworth H, Jellett R, Khan F, Lawson LP, Leslie J, Frenk ML, Masi A, Mathew NE, Muniandy M, Nothard M, Miller JL, Nunn L, Holtmann G, Strike LT, de Zubicaray GI, Thompson PM, McMahon KL, Wright MJ, Visscher PM, Dawson PA, Dissanayake C, Eapen V, Heussler HS, McRae AF, Whitehouse AJO, Wray NR, Gratten J. Autism-related dietary preferences mediate autism-gut microbiome associations. Cell 2021; 184:5916-5931.e17. [PMID: 34767757 DOI: 10.1016/j.cell.2021.10.015] [Citation(s) in RCA: 134] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 06/14/2021] [Accepted: 10/13/2021] [Indexed: 12/24/2022]
Abstract
There is increasing interest in the potential contribution of the gut microbiome to autism spectrum disorder (ASD). However, previous studies have been underpowered and have not been designed to address potential confounding factors in a comprehensive way. We performed a large autism stool metagenomics study (n = 247) based on participants from the Australian Autism Biobank and the Queensland Twin Adolescent Brain project. We found negligible direct associations between ASD diagnosis and the gut microbiome. Instead, our data support a model whereby ASD-related restricted interests are associated with less-diverse diet, and in turn reduced microbial taxonomic diversity and looser stool consistency. In contrast to ASD diagnosis, our dataset was well powered to detect microbiome associations with traits such as age, dietary intake, and stool consistency. Overall, microbiome differences in ASD may reflect dietary preferences that relate to diagnostic features, and we caution against claims that the microbiome has a driving role in ASD.
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Affiliation(s)
- Chloe X Yap
- Mater Research Institute, The University of Queensland, Woolloongabba, Queensland 4102, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Anjali K Henders
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Gail A Alvares
- Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia 6009, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - David L A Wood
- Microba Life Sciences, Brisbane, Queensland 4000, Australia
| | - Lutz Krause
- Microba Life Sciences, Brisbane, Queensland 4000, Australia
| | - Gene W Tyson
- Microba Life Sciences, Brisbane, Queensland 4000, Australia; Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, Queensland 4102, Australia
| | - Restuadi Restuadi
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Tiana McLaren
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Narelle K Hansell
- Queensland Brain Institute, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Dominique Cleary
- Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia 6009, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Rachel Grove
- Faculty of Health, University of Technology Sydney, Sydney, New South Wales 2007, Australia; School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2052, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Claire Hafekost
- Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia 6009, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Alexis Harun
- Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia 6009, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Helen Holdsworth
- Mater Research Institute, The University of Queensland, Woolloongabba, Queensland 4102, Australia; Child Health Research Centre, The University of Queensland, South Brisbane, Queensland 4101, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Rachel Jellett
- Olga Tennison Autism Research Centre, La Trobe University, Bundoora, Victoria 3086, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Feroza Khan
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2052, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Lauren P Lawson
- Olga Tennison Autism Research Centre, La Trobe University, Bundoora, Victoria 3086, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Jodie Leslie
- Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia 6009, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Mira Levis Frenk
- Mater Research Institute, The University of Queensland, Woolloongabba, Queensland 4102, Australia; Child Health Research Centre, The University of Queensland, South Brisbane, Queensland 4101, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Anne Masi
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2052, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Nisha E Mathew
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2052, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Melanie Muniandy
- Olga Tennison Autism Research Centre, La Trobe University, Bundoora, Victoria 3086, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Michaela Nothard
- Mater Research Institute, The University of Queensland, Woolloongabba, Queensland 4102, Australia; Child Health Research Centre, The University of Queensland, South Brisbane, Queensland 4101, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Jessica L Miller
- Queensland Brain Institute, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lorelle Nunn
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Gerald Holtmann
- Faculty of Medicine and Faculty of Health and Behavioural Science, University of Queensland, St Lucia, Queensland 4072, Australia; Department of Gastroenterology & Hepatology, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Lachlan T Strike
- Queensland Brain Institute, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Greig I de Zubicaray
- School of Psychology and Counselling, Faculty of Health, Queensland University of Technology, Kelvin Grove, Queensland 4059, Australia
| | - Paul M Thompson
- Imaging Genetics Center, Mark & Mary Stevens Institute for Neuroimaging & Informatics, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Katie L McMahon
- School of Clinical Sciences, Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Margaret J Wright
- Queensland Brain Institute, The University of Queensland, St Lucia, Queensland 4072, Australia; Centre for Advanced Imaging, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Paul A Dawson
- Mater Research Institute, The University of Queensland, Woolloongabba, Queensland 4102, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Cheryl Dissanayake
- Olga Tennison Autism Research Centre, La Trobe University, Bundoora, Victoria 3086, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Valsamma Eapen
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2052, Australia; Academic Unit of Child Psychiatry South West Sydney, Ingham Institute, Liverpool Hospital, Sydney, New South Wales, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Helen S Heussler
- Child Health Research Centre, The University of Queensland, South Brisbane, Queensland 4101, Australia; Child Development Program, Children's Health Queensland, South Brisbane, Queensland 4101, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Andrew J O Whitehouse
- Telethon Kids Institute, The University of Western Australia, Nedlands, Western Australia 6009, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia; Queensland Brain Institute, The University of Queensland, St Lucia, Queensland 4072, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia
| | - Jacob Gratten
- Mater Research Institute, The University of Queensland, Woolloongabba, Queensland 4102, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia; Cooperative Research Centre for Living with Autism (Autism CRC), Long Pocket, Queensland 4068, Australia.
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Yap CX, Alvares GA, Henders AK, Lin T, Wallace L, Farrelly A, McLaren T, Berry J, Vinkhuyzen AAE, Trzaskowski M, Zeng J, Yang Y, Cleary D, Grove R, Hafekost C, Harun A, Holdsworth H, Jellett R, Khan F, Lawson L, Leslie J, Levis Frenk M, Masi A, Mathew NE, Muniandy M, Nothard M, Visscher PM, Dawson PA, Dissanayake C, Eapen V, Heussler HS, Whitehouse AJO, Wray NR, Gratten J. Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank. Mol Autism 2021; 12:12. [PMID: 33568206 PMCID: PMC7874616 DOI: 10.1186/s13229-020-00407-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/17/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a complex neurodevelopmental condition whose biological basis is yet to be elucidated. The Australian Autism Biobank (AAB) is an initiative of the Cooperative Research Centre for Living with Autism (Autism CRC) to establish an Australian resource of biospecimens, phenotypes and genomic data for research on autism. METHODS Genome-wide single-nucleotide polymorphism genotypes were available for 2,477 individuals (after quality control) from 546 families (436 complete), including 886 participants aged 2 to 17 years with diagnosed (n = 871) or suspected (n = 15) ASD, 218 siblings without ASD, 1,256 parents, and 117 unrelated children without an ASD diagnosis. The genetic data were used to confirm familial relationships and assign ancestry, which was majority European (n = 1,964 European individuals). We generated polygenic scores (PGS) for ASD, IQ, chronotype and height in the subset of Europeans, and in 3,490 unrelated ancestry-matched participants from the UK Biobank. We tested for group differences for each PGS, and performed prediction analyses for related phenotypes in the AAB. We called copy-number variants (CNVs) in all participants, and intersected these with high-confidence ASD- and intellectual disability (ID)-associated CNVs and genes from the public domain. RESULTS The ASD (p = 6.1e-13), sibling (p = 4.9e-3) and unrelated (p = 3.0e-3) groups had significantly higher ASD PGS than UK Biobank controls, whereas this was not the case for height-a control trait. The IQ PGS was a significant predictor of measured IQ in undiagnosed children (r = 0.24, p = 2.1e-3) and parents (r = 0.17, p = 8.0e-7; 4.0% of variance), but not the ASD group. Chronotype PGS predicted sleep disturbances within the ASD group (r = 0.13, p = 1.9e-3; 1.3% of variance). In the CNV analysis, we identified 13 individuals with CNVs overlapping ASD/ID-associated CNVs, and 12 with CNVs overlapping ASD/ID/developmental delay-associated genes identified on the basis of de novo variants. LIMITATIONS This dataset is modest in size, and the publicly-available genome-wide-association-study (GWAS) summary statistics used to calculate PGS for ASD and other traits are relatively underpowered. CONCLUSIONS We report on common genetic variation and rare CNVs within the AAB. Prediction analyses using currently available GWAS summary statistics are largely consistent with expected relationships based on published studies. As the size of publicly-available GWAS summary statistics grows, the phenotypic depth of the AAB dataset will provide many opportunities for analyses of autism profiles and co-occurring conditions, including when integrated with other omics datasets generated from AAB biospecimens (blood, urine, stool, hair).
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Affiliation(s)
- Chloe X Yap
- Mater Research Institute, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
| | - Gail A Alvares
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Anjali K Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Alaina Farrelly
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Tiana McLaren
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Jolene Berry
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Anna A E Vinkhuyzen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Maciej Trzaskowski
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Max Kelsen, Fortitude Valley, QLD, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Yuanhao Yang
- Mater Research Institute, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Dominique Cleary
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Rachel Grove
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - Claire Hafekost
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Alexis Harun
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Helen Holdsworth
- Mater Research Institute, The University of Queensland, Brisbane, QLD, Australia
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Rachel Jellett
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, VIC, Australia
| | - Feroza Khan
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - Lauren Lawson
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, VIC, Australia
| | - Jodie Leslie
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Mira Levis Frenk
- Mater Research Institute, The University of Queensland, Brisbane, QLD, Australia
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Anne Masi
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - Nisha E Mathew
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - Melanie Muniandy
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, VIC, Australia
| | - Michaela Nothard
- Mater Research Institute, The University of Queensland, Brisbane, QLD, Australia
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Paul A Dawson
- Mater Research Institute, The University of Queensland, Brisbane, QLD, Australia
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
| | - Cheryl Dissanayake
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, VIC, Australia
| | - Valsamma Eapen
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
- Academic Unit of Child Psychiatry South West Sydney, Ingham Institute, Liverpool Hospital, Sydney, NSW, Australia
| | - Helen S Heussler
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Child Development Program, Children's Health Queensland, Brisbane, QLD, Australia
| | - Andrew J O Whitehouse
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Jacob Gratten
- Mater Research Institute, The University of Queensland, Brisbane, QLD, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
- Cooperative Research Centre for Living With Autism (Autism CRC), Long Pocket, Brisbane, QLD, Australia.
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Mallan KM, Nothard M, Thorpe K, Nicholson JM, Wilson A, Scuffham PA, Daniels LA. The role of fathers in child feeding: perceived responsibility and predictors of participation. Child Care Health Dev 2014; 40:715-22. [PMID: 23902382 DOI: 10.1111/cch.12088] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/10/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND The role of fathers in shaping their child's eating behaviour and weight status through their involvement in child feeding has rarely been studied. This study aims to describe fathers' perceived responsibility for child feeding, and to identify predictors of how frequently fathers eat meals with their child. METHODS Four hundred and thirty-six Australian fathers (M age = 37 years, SD = 6 years; 34% university educated) of a 2-5-year-old child (M age = 3.5 years, SD = 0.9 years; 53% boys) were recruited via contact with mothers enrolled in existing research projects or a university staff and student email list. Data were collected from fathers via a self-report questionnaire. Descriptive and hierarchical linear regression analyses were conducted. RESULTS The majority of fathers reported that the family often/mostly ate meals together (79%). Many fathers perceived that they were responsible at least half of the time for feeding their child in terms of organizing meals (42%); amount offered (50%) and deciding if their child eats the 'right kind of foods' (60%). Time spent in paid employment was inversely associated with how frequently fathers ate meals with their child (β = -0.23, P < 0.001); however, both higher perceived responsibility for child feeding (β = 0.16, P < 0.004) and a more involved and positive attitude toward their role as a father (β = 0.20, P < 0.001) were positively related to how often they ate meals with their child, adjusting for a range of paternal and child covariates, including time spent in paid employment. CONCLUSIONS Fathers from a broad range of educational backgrounds appear willing to participate in research studies on child feeding. Most fathers were engaged and involved in family meals and child feeding. This suggests that fathers, like mothers, should be viewed as potential agents for the implementation of positive feeding practices within the family.
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Affiliation(s)
- K M Mallan
- Institute of Health and Biomedical Innovation and School of Exercise and Nutrition Sciences, Queensland University of Technology, Brisbane, Qld, Australia
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Mallan KM, Daniels LA, Nothard M, Nicholson JM, Wilson A, Cameron CM, Scuffham PA, Thorpe K. Dads at the dinner table. A cross-sectional study of Australian fathers’ child feeding perceptions and practices. Appetite 2014; 73:40-4. [DOI: 10.1016/j.appet.2013.10.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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