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Hickman AR, Selee B, Pauly R, Husain B, Hang Y, Feltus FA. Discovery of eQTL Alleles Associated with Autism Spectrum Disorder: A Case-Control Study. J Autism Dev Disord 2023; 53:3595-3612. [PMID: 35739433 PMCID: PMC10465380 DOI: 10.1007/s10803-022-05631-x] [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] [Accepted: 05/27/2022] [Indexed: 11/27/2022]
Abstract
Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder characterized by challenges in social communication as well as repetitive or restrictive behaviors. Many genetic associations with ASD have been identified, but most associations occur in a fraction of the ASD population. Here, we searched for eQTL-associated DNA variants with significantly different allele distributions between ASD-affected and control. Thirty significant DNA variants associated with 174 tissue-specific eQTLs from ASD individuals in the SPARK project were identified. Several significant variants fell within brain-specific regulatory regions or had been associated with a significant change in gene expression in the brain. These eQTLs are a new class of biomarkers that could control the myriad of brain and non-brain phenotypic traits seen in ASD-affected individuals.
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Affiliation(s)
- Allison R. Hickman
- Genetics and Biochemistry Department, Clemson University, Clemson, SC 29634 USA
| | - Bradley Selee
- Electrical and Computer Engineering Department, Clemson University, Clemson, SC 29634 USA
| | - Rini Pauly
- Biomedical Data Science & Informatics Program, Clemson University, Clemson, SC 29634 USA
| | - Benafsh Husain
- Biomedical Data Science & Informatics Program, Clemson University, Clemson, SC 29634 USA
| | - Yuqing Hang
- Genetics and Biochemistry Department, Clemson University, Clemson, SC 29634 USA
| | - Frank Alex Feltus
- Genetics and Biochemistry Department, Clemson University, Clemson, SC 29634 USA
- Electrical and Computer Engineering Department, Clemson University, Clemson, SC 29634 USA
- Center for Human Genetics, Clemson University, Greenwood, SC 29646 USA
- Biosystems Research Complex, 302C, 105 Collings St, Clemson, SC 29634 USA
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Myers L, Pan P, Remnélius KL, Neufeld J, Marschik PB, Jonsson U, Bölte S. Behavioral and biological divergence in monozygotic twin pairs discordant for autism phenotypes: A systematic review. JCPP ADVANCES 2021. [DOI: 10.1111/jcv2.12017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Lynnea Myers
- Department of Women's and Children's Health Karolinska Institutet Center of Neurodevelopmental Disorders Centre for Psychiatry Research Karolinska Institutet & Stockholm Health Care Services Stockholm Sweden
- Department of Nursing Gustavus Adolphus College St. Peter Minnesota USA
| | - Pei‐Yin Pan
- Department of Women's and Children's Health Karolinska Institutet Center of Neurodevelopmental Disorders Centre for Psychiatry Research Karolinska Institutet & Stockholm Health Care Services Stockholm Sweden
| | - Karl Lundin Remnélius
- Department of Women's and Children's Health Karolinska Institutet Center of Neurodevelopmental Disorders Centre for Psychiatry Research Karolinska Institutet & Stockholm Health Care Services Stockholm Sweden
| | - Janina Neufeld
- Department of Women's and Children's Health Karolinska Institutet Center of Neurodevelopmental Disorders Centre for Psychiatry Research Karolinska Institutet & Stockholm Health Care Services Stockholm Sweden
| | - Peter B. Marschik
- Department of Women's and Children's Health Karolinska Institutet Center of Neurodevelopmental Disorders Centre for Psychiatry Research Karolinska Institutet & Stockholm Health Care Services Stockholm Sweden
- Department of Child and Adolescent Psychiatry and Psychotherapy University Medical Center Göttingen & Leibniz Science Campus Göttingen Germany
- Department of Phoniatrics D –Interdisciplinary Developmental Neuroscience Medical University of Graz Graz Steiermark Austria
| | - Ulf Jonsson
- Department of Women's and Children's Health Karolinska Institutet Center of Neurodevelopmental Disorders Centre for Psychiatry Research Karolinska Institutet & Stockholm Health Care Services Stockholm Sweden
- Department of Neuroscience, Child and Adolescent Psychiatry Uppsala University Uppsala Sweden
| | - Sven Bölte
- Department of Women's and Children's Health Karolinska Institutet Center of Neurodevelopmental Disorders Centre for Psychiatry Research Karolinska Institutet & Stockholm Health Care Services Stockholm Sweden
- Department of Child and Adolescent Psychiatry Stockholm Health Care Services Stockholm Sweden
- Curtin Autism Research Group School of Occupational Therapy, Social Work and Speech Pathology Curtin University Perth Western Australia Australia
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Imamura A, Morimoto Y, Ono S, Kurotaki N, Kanegae S, Yamamoto N, Kinoshita H, Tsujita T, Okazaki Y, Ozawa H. Genetic and environmental factors of schizophrenia and autism spectrum disorder: insights from twin studies. J Neural Transm (Vienna) 2020; 127:1501-1515. [PMID: 32285255 PMCID: PMC7578126 DOI: 10.1007/s00702-020-02188-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/05/2020] [Indexed: 02/06/2023]
Abstract
Twin studies of psychiatric disorders such as schizophrenia and autism spectrum disorder have employed epidemiological approaches that determine heritability by comparing the concordance rate between monozygotic twins (MZs) and dizygotic twins. The basis for these studies is that MZs share 100% of their genetic information. Recently, biological studies based on molecular methods are now being increasingly applied to examine the differences between MZs discordance for psychiatric disorders to unravel their possible causes. Although recent advances in next-generation sequencing have increased the accuracy of this line of research, there has been greater emphasis placed on epigenetic changes versus DNA sequence changes as the probable cause of discordant psychiatric disorders in MZs. Since the epigenetic status differs in each tissue type, in addition to the DNA from the peripheral blood, studies using DNA from nerve cells induced from postmortem brains or induced pluripotent stem cells are being carried out. Although it was originally thought that epigenetic changes occurred as a result of environmental factors, and thus were not transmittable, it is now known that such changes might possibly be transmitted between generations. Therefore, the potential possible effects of intestinal flora inside the body are currently being investigated as a cause of discordance in MZs. As a result, twin studies of psychiatric disorders are greatly contributing to the elucidation of genetic and environmental factors in the etiology of psychiatric conditions.
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Affiliation(s)
- Akira Imamura
- Child and Adolescent Psychiatry Community Partnership Unit, Nagasaki University Hospital, Nagasaki, Japan.
| | - Yoshiro Morimoto
- Unit of Translation Medicine, Department of Neuropsychiatry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Department of Human Genetics, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shinji Ono
- Department of Human Genetics, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Naohiro Kurotaki
- Department of Clinical Psychiatry, Graduate School of Medicine, Kagawa University, Kita-gun, Japan
| | - Shinji Kanegae
- Child and Adolescent Psychiatry Community Partnership Unit, Nagasaki University Hospital, Nagasaki, Japan
| | - Naoki Yamamoto
- Child and Adolescent Psychiatry Community Partnership Unit, Nagasaki University Hospital, Nagasaki, Japan
- Unit of Translation Medicine, Department of Neuropsychiatry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hirohisa Kinoshita
- Unit of Translation Medicine, Department of Neuropsychiatry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | | | - Yuji Okazaki
- Koseikai Michinoo Hospital, Nagasaki, Japan
- Tokyo Metropolitan Matsuzawa Hospital, Tokyo, Japan
| | - Hiroki Ozawa
- Child and Adolescent Psychiatry Community Partnership Unit, Nagasaki University Hospital, Nagasaki, Japan
- Unit of Translation Medicine, Department of Neuropsychiatry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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Copy Number Variation Analysis of 100 Twin Pairs Enriched for Neurodevelopmental Disorders. Twin Res Hum Genet 2018; 21:1-11. [DOI: 10.1017/thg.2017.69] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hundreds of penetrant risk loci have been identified across different neurodevelopmental disorders (NDDs), and these often involve rare (<1% frequency) copy number variations (CNVs), which can involve one or more genes. Monozygotic (MZ) twin pairs are long thought to share 100% of their genomic information. However, genetic differences in the form of postzygotic somatic variants have been reported recently both in typically developing (TD) and in clinically discordant MZ pairs. We sought to investigate the contribution of rare CNVs in 100 twin pairs enriched for NDD phenotypes with a particular focus on postzygotic CNVs in MZ pairs discordant for autism spectrum disorder (ASD) using the Illumina Infinium PsychArray. In our sample, no postzygotic de novo CNVs were found in 55 MZ twin pairs, including the 13 pairs discordant for ASD. We did detect a higher rate of CNVs overlapping genes involved in disorders of the nervous system, such as a rare deletion affecting HNRNPU, in MZ pairs discordant and concordant for ASD in comparison with TD pairs (p = .02). Our results are in concordance with earlier findings that postzygotic de novo CNV events are typically rare in genomic DNA derived from saliva or blood, and suggests that the discordance of NDDs in our sample of twins is not explained by discordant CNVs. Still, studies investigating postzygotic variation in MZ discordant twins using DNA from different tissues and single cells and higher resolution genomics are needed in the future.
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Godar DE, Merrill SJ. Untangling the most probable role for vitamin D 3 in autism. DERMATO-ENDOCRINOLOGY 2017; 9:e1387702. [PMID: 29484101 PMCID: PMC5821151 DOI: 10.1080/19381980.2017.1387702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/02/2017] [Accepted: 09/29/2017] [Indexed: 12/31/2022]
Abstract
Recent studies indicate an important role for vitamin D3 in autism spectrum disorder (ASD), although its mechanism is not completely understood. The most puzzling aspect of ASD is that identical twins, who share identical DNA, do not have 100% concordance rates (∼88% for identical and ∼31% for fraternal twins). These findings provide major clues into the etiology: ASD must involve an environmental factor present in the prenatal milieu that both identical twins are not always exposed to because they do not always share it (i.e., placentas). Combined with the exponential increasing rates of ASD around the world, these observations suggest a contagious disease is probably transferred to the fetus via the placenta becoming infected by a cervical virus. Vitamin D3 boosts immune responses clearing viral infections and increases serotonin and estrogen brain levels. Here we review the different roles and untangle the most probable one vitamin D3 plays in ASD.
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Affiliation(s)
- Dianne E. Godar
- Body of Knowledge, Inc., Division of Human Disease Research Worldwide, Racine, WI, USA
| | - Stephen J. Merrill
- Marquette University, Department of Mathematics, Statistics, and Computer Science, Milwaukee, WI, USA
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Abstract
Monozygotic (MZ) twins are genetically identical at conception, making them informative subjects for studies on somatic mutations. Copy number variants (CNVs) are responsible for a substantial part of genetic variation, have relatively high mutation rates, and are likely to be involved in phenotypic variation. We conducted a genome-wide survey for post-twinning de novo CNVs in 1,097 MZ twin pairs. Comparisons between MZ twins were made by CNVs measured in DNA from blood or buccal epithelium with the Affymetrix 6.0 microarray and two calling algorithms. In addition, CNV concordance rates were compared between the different sources of DNA, and gene-enrichment association analyses were conducted for thought problems (TP) and attention problems (AP) using CNVs concordant within MZ pairs. We found a total of 153 putative post-twinning de novo CNVs >100 kb, of which the majority resided in 15q11.2. Based on the discordance of raw intensity signals a selection was made of 20 de novo CNVs for a qPCR validation experiments. Two out of 20 post-twinning de novo CNVs were validated with qPCR in the same twin pair. The 13-year-old MZ twin pair that showed two discordances in CN in 15q11.2 in their buccal DNA did not show large phenotypic differences. From the remaining 18 putative de novo CNVs, 17 were deletions or duplications that were concordant within MZ twin pairs. Concordance rates within twin pairs of CNV calls with CN ≠ 2 were ~80%. Buccal epithelium-derived DNA showed a slightly but significantly higher concordance rate, and blood-derived DNA showed significantly more concordant CNVs per twin pair. The gene-enrichment analyses on concordant CNVs showed no significant associations between CNVs overlapping with genes involved in neuronal processes and TP or AP after accounting for the source of DNA.
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Association of Copy Number Variations in Autism Spectrum Disorders: A Systematic Review. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/713109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Autism spectrum disorders (ASDs) are characterized by language impairments, social deficits, and repetitive behaviors. The onset of symptoms occurs by the age of 3 and shows a lifelong persistence. Genetics plays a major role in the etiology of ASD. Except genetics, several potential risk factors (environmental factors and epigenetics) may contribute to ASD. Copy number variations (CNVs) are the most widespread structural variations in the human genome. These variations can alter the genome structure either by deletion or by duplication. CNVs can be de novo or inherited. Chromosomal rearrangements have been detected in 5–10% of the patients with ASD and recently copy number changes ranging from a few kilobases (kb) to several megabases (Mb) in size have been reported. Recent data have also revealed that submicroscopic CNVs can have a role in ASD, and de novo CNVs seem to be a more common risk factor in sporadic compared with inherited forms of ASD. CNVs are being implicated as a contributor to the pathophysiology of complex neurodevelopmental disorders and they can affect a wide range of human phenotypes including mental retardation (MR), autism, neuropsychiatric disorders, and susceptibility to other complex traits such as HIV, Crohn’s disease, and psoriasis. This review emphasizes the major CNVs reported to date in ASD.
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