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Article: Analysis of Shared Haplotypes amongst Palauans Maps Loci for Psychotic Disorders to 4q28 and 5q23-q31.

Bodea, Corneliu A / Middleton, Frank A / Melhem, Nadine M / Klei, Lambertus / Song, Youeun / Tiobech, Josepha / Marumoto, Pearl / Yano, Victor / Faraone, Stephen V / Roeder, Kathryn / Myles-Worsley, Marina / Devlin, Bernie / Byerley, William

Molecular neuropsychiatry

2016 Volume 2, Issue 4, Page(s) 173–184

Abstract: To localize genetic variation affecting risk for psychotic disorders in the population of Palau, we genotyped DNA samples from 203 Palauan individuals diagnosed with psychotic disorders, broadly defined, and 125 control subjects using a genome-wide ... ...

Abstract	To localize genetic variation affecting risk for psychotic disorders in the population of Palau, we genotyped DNA samples from 203 Palauan individuals diagnosed with psychotic disorders, broadly defined, and 125 control subjects using a genome-wide single nucleotide polymorphism array. Palau has unique features advantageous for this study: due to its population history, Palauans are substantially interrelated; affected individuals often, but not always, cluster in families; and we have essentially complete ascertainment of affected individuals. To localize risk variants to genomic regions, we evaluated long-shared haplotypes, ≥10 Mb, identifying clusters of affected individuals who share such haplotypes. This extensive sharing, typically identical by descent, was significantly greater in cases than population controls, even after controlling for relatedness. Several regions of the genome exhibited substantial excess of shared haplotypes for affected individuals, including 3p21, 3p12, 4q28, and 5q23-q31. Two of these regions, 4q28 and 5q23-q31, showed significant linkage by traditional LOD score analysis and could harbor variants of more sizeable risk for psychosis or a multiplicity of risk variants. The pattern of haplotype sharing in 4q28 highlights
Language	English
Publishing date	2016-10-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2806946-8
ISSN	2296-9179 ; 2296-9209
ISSN (online)	2296-9179
ISSN	2296-9209
DOI	10.1159/000450726
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Article: Analysis of Shared Haplotypes amongst Palauans Maps Loci for Psychotic Disorders to 4q28 and 5q23-q31

Bodea, Corneliu A. / Middleton, Frank A. / Melhem, Nadine M. / Klei, Lambertus / Song, Youeun / Tiobech, Josepha / Marumoto, Pearl / Yano, Victor / Faraone, Stephen V. / Roeder, Kathryn / Myles-Worsley, Marina / Devlin, Bernie / Byerley, William

Molecular Neuropsychiatry

2016 Volume 2, Issue 4, Page(s) 173–184

Institution	Department of Statistics, Carnegie Mellon University, Pittsburgh, Pa Department of Psychiatry, SUNY Upstate Medical University, Syracuse, N.Y Department of Psychiatry, University of Pittsburgh School of Medicine, and University of Pittsburgh Medical Center, Pittsburgh, Pa., USA Palau Ministry of Health, Koror, Republic of Palau University of Washington School of Public Health, Seattle, Wash., and Department of Psychiatry, University of California San Francisco, San Francisco, Calif., USA
Abstract	To localize genetic variation affecting risk for psychotic disorders in the population of Palau, we genotyped DNA samples from 203 Palauan individuals diagnosed with psychotic disorders, broadly defined, and 125 control subjects using a genome-wide single nucleotide polymorphism array. Palau has unique features advantageous for this study: due to its population history, Palauans are substantially interrelated; affected individuals often, but not always, cluster in families; and we have essentially complete ascertainment of affected individuals. To localize risk variants to genomic regions, we evaluated long-shared haplotypes, ≥10 Mb, identifying clusters of affected individuals who share such haplotypes. This extensive sharing, typically identical by descent, was significantly greater in cases than population controls, even after controlling for relatedness. Several regions of the genome exhibited substantial excess of shared haplotypes for affected individuals, including 3p21, 3p12, 4q28, and 5q23-q31. Two of these regions, 4q28 and 5q23-q31, showed significant linkage by traditional LOD score analysis and could harbor variants of more sizeable risk for psychosis or a multiplicity of risk variants. The pattern of haplotype sharing in 4q28 highlights PCDH10, encoding a cadherin-related neuronal receptor, as possibly involved in risk.
Keywords	Genetics ; Linkage analysis ; Pedigree ; Penetrance ; Psychosis ; Schizophrenia
Language	English
Publishing date	2016-10-12
Publisher	S. Karger AG
Publishing place	Basel, Switzerland
Document type	Article
Note	Original Paper
ZDB-ID	2806946-8
ISSN	2296-9179 ; 2296-9209 ; 2296-9179
ISSN (online)	2296-9179
ISSN	2296-9209 ; 2296-9179
DOI	10.1159/000450726
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Article ; Online: Modest impact on risk for autism spectrum disorder of rare copy number variants at 15q11.2, specifically breakpoints 1 to 2.

Chaste, Pauline / Sanders, Stephan J / Mohan, Kommu N / Klei, Lambertus / Song, Youeun / Murtha, Michael T / Hus, Vanessa / Lowe, Jennifer K / Willsey, A Jeremy / Moreno-De-Luca, Daniel / Yu, Timothy W / Fombonne, Eric / Geschwind, Daniel / Grice, Dorothy E / Ledbetter, David H / Lord, Catherine / Mane, Shrikant M / Martin, Donna M / Morrow, Eric M /

Walsh, Christopher A / Sutcliffe, James S / State, Matthew W / Martin, Christa Lese / Devlin, Bernie / Beaudet, Arthur L / Cook, Edwin H / Kim, Soo-Jeong

Autism research : official journal of the International Society for Autism Research

2014 Volume 7, Issue 3, Page(s) 355–362

Abstract: The proximal region of chromosome 15 is one of the genomic hotspots for copy number variants (CNVs). Among the rearrangements observed in this region, CNVs from the interval between the common breakpoints 1 and 2 (BP1 and BP2) have been reported ... ...

Abstract	The proximal region of chromosome 15 is one of the genomic hotspots for copy number variants (CNVs). Among the rearrangements observed in this region, CNVs from the interval between the common breakpoints 1 and 2 (BP1 and BP2) have been reported cosegregating with autism spectrum disorder (ASD). Although evidence supporting an association between BP1-BP2 CNVs and autism accumulates, the magnitude of the effect of BP1-BP2 CNVs remains elusive, posing a great challenge to recurrence-risk counseling. To gain further insight into their pathogenicity for ASD, we estimated the penetrance of the BP1-BP2 CNVs for ASD as well as their effects on ASD-related phenotypes in a well-characterized ASD sample (n = 2525 families). Transmission disequilibrium test revealed significant preferential transmission only for the duplicated chromosome in probands (20T:9NT). The penetrance of the BP1-BP2 CNVs for ASD was low, conferring additional risks of 0.3% (deletion) and 0.8% (duplication). Stepwise regression analyses suggest a greater effect of the CNVs on ASD-related phenotype in males and when maternally inherited. Taken together, the results are consistent with BP1-BP2 CNVs as risk factors for autism. However, their effect is modest, more akin to that seen for common variants. To be consistent with the current American College of Medical Genetics guidelines for interpretation of postnatal CNV, the BP1-BP2 deletion and duplication CNVs would probably best be classified as variants of uncertain significance (VOUS): they appear to have an impact on risk, but one so modest that these CNVs do not merit pathogenic status.
MeSH term(s)	Adult ; Child ; Child Development Disorders, Pervasive/genetics ; Chromosome Deletion ; Chromosomes, Human, Pair 15/genetics ; DNA Copy Number Variations/genetics ; Female ; Genetic Predisposition to Disease/genetics ; Humans ; Male
Language	English
Publishing date	2014-05-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2481338-2
ISSN	1939-3806 ; 1939-3792
ISSN (online)	1939-3806
ISSN	1939-3792
DOI	10.1002/aur.1378
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Article ; Online: De novo mutations revealed by whole-exome sequencing are strongly associated with autism.

Sanders, Stephan J / Murtha, Michael T / Gupta, Abha R / Murdoch, John D / Raubeson, Melanie J / Willsey, A Jeremy / Ercan-Sencicek, A Gulhan / DiLullo, Nicholas M / Parikshak, Neelroop N / Stein, Jason L / Walker, Michael F / Ober, Gordon T / Teran, Nicole A / Song, Youeun / El-Fishawy, Paul / Murtha, Ryan C / Choi, Murim / Overton, John D / Bjornson, Robert D /

Carriero, Nicholas J / Meyer, Kyle A / Bilguvar, Kaya / Mane, Shrikant M / Sestan, Nenad / Lifton, Richard P / Günel, Murat / Roeder, Kathryn / Geschwind, Daniel H / Devlin, Bernie / State, Matthew W

Nature

2012 Volume 485, Issue 7397, Page(s) 237–241

Abstract: Multiple studies have confirmed the contribution of rare de novo copy number variations to the risk for autism spectrum disorders. But whereas de novo single nucleotide variants have been identified in affected individuals, their contribution to risk has ...

Abstract	Multiple studies have confirmed the contribution of rare de novo copy number variations to the risk for autism spectrum disorders. But whereas de novo single nucleotide variants have been identified in affected individuals, their contribution to risk has yet to be clarified. Specifically, the frequency and distribution of these mutations have not been well characterized in matched unaffected controls, and such data are vital to the interpretation of de novo coding mutations observed in probands. Here we show, using whole-exome sequencing of 928 individuals, including 200 phenotypically discordant sibling pairs, that highly disruptive (nonsense and splice-site) de novo mutations in brain-expressed genes are associated with autism spectrum disorders and carry large effects. On the basis of mutation rates in unaffected individuals, we demonstrate that multiple independent de novo single nucleotide variants in the same gene among unrelated probands reliably identifies risk alleles, providing a clear path forward for gene discovery. Among a total of 279 identified de novo coding mutations, there is a single instance in probands, and none in siblings, in which two independent nonsense variants disrupt the same gene, SCN2A (sodium channel, voltage-gated, type II, α subunit), a result that is highly unlikely by chance.
MeSH term(s)	Alleles ; Autistic Disorder/genetics ; Codon, Nonsense/genetics ; Exome/genetics ; Exons/genetics ; Genetic Heterogeneity ; Genetic Predisposition to Disease/genetics ; Humans ; Mutation/genetics ; NAV1.2 Voltage-Gated Sodium Channel ; Nerve Tissue Proteins/genetics ; RNA Splice Sites/genetics ; Siblings ; Sodium Channels/genetics
Chemical Substances	Codon, Nonsense ; NAV1.2 Voltage-Gated Sodium Channel ; Nerve Tissue Proteins ; RNA Splice Sites ; SCN2A protein, human ; Sodium Channels
Language	English
Publishing date	2012-04-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/nature10945
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Article ; Online: Rare copy number variants in tourette syndrome disrupt genes in histaminergic pathways and overlap with autism.

Fernandez, Thomas V / Sanders, Stephan J / Yurkiewicz, Ilana R / Ercan-Sencicek, A Gulhan / Kim, Young-Shin / Fishman, Daniel O / Raubeson, Melanie J / Song, Youeun / Yasuno, Katsuhito / Ho, Winson S C / Bilguvar, Kaya / Glessner, Joseph / Chu, Su Hee / Leckman, James F / King, Robert A / Gilbert, Donald L / Heiman, Gary A / Tischfield, Jay A / Hoekstra, Pieter J /

Devlin, Bernie / Hakonarson, Hakon / Mane, Shrikant M / Günel, Murat / State, Matthew W

Biological psychiatry

2011 Volume 71, Issue 5, Page(s) 392–402

Abstract: Background: Studies of copy number variation (CNV) have characterized loci and molecular pathways in a range of neuropsychiatric conditions. We analyzed rare CNVs in Tourette syndrome (TS) to identify novel risk regions and relevant pathways, to ... ...

Abstract	Background: Studies of copy number variation (CNV) have characterized loci and molecular pathways in a range of neuropsychiatric conditions. We analyzed rare CNVs in Tourette syndrome (TS) to identify novel risk regions and relevant pathways, to evaluate burden of structural variation in cases versus controls, and to assess overlap of identified variations with those in other neuropsychiatric syndromes. Methods: We conducted a case-control study of 460 individuals with TS, including 148 parent-child trios and 1131 controls. CNV analysis was undertaken using 370 K to 1 M probe arrays, and genotyping data were used to match cases and controls for ancestry. CNVs present in < 1% of the population were evaluated. Results: While there was no significant increase in the number of de novo or transmitted rare CNVs in cases versus controls, pathway analysis using multiple algorithms showed enrichment of genes within histamine receptor (subtypes 1 and 2) signaling pathways (p = 5.8 × 10(-4) - 1.6 × 10(-2)), as well as axon guidance, cell adhesion, nervous system development, and synaptic structure and function processes. Genes mapping within rare CNVs in TS showed significant overlap with those previously identified in autism spectrum disorders but not intellectual disability or schizophrenia. Three large, likely pathogenic, de novo events were identified, including one disrupting multiple gamma-aminobutyric acid receptor genes. Conclusions: We identify further evidence supporting recent findings regarding the involvement of histaminergic and gamma-aminobutyric acidergic mechanisms in the etiology of TS and show an overlap of rare CNVs in TS and autism spectrum disorders.
MeSH term(s)	Adult ; Autistic Disorder/genetics ; Case-Control Studies ; Child ; DNA Copy Number Variations/genetics ; Genetic Predisposition to Disease/genetics ; Genome-Wide Association Study/methods ; Genotype ; Humans ; Intellectual Disability ; Receptors, GABA/genetics ; Receptors, Histamine H1/genetics ; Receptors, Histamine H2/genetics ; Schizophrenia/genetics ; Signal Transduction/physiology ; Tourette Syndrome/genetics
Chemical Substances	Receptors, GABA ; Receptors, Histamine H1 ; Receptors, Histamine H2
Language	English
Publishing date	2011-12-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209434-4
ISSN	1873-2402 ; 0006-3223
ISSN (online)	1873-2402
ISSN	0006-3223
DOI	10.1016/j.biopsych.2011.09.034
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Article ; Online: Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.

Sanders, Stephan J / Ercan-Sencicek, A Gulhan / Hus, Vanessa / Luo, Rui / Murtha, Michael T / Moreno-De-Luca, Daniel / Chu, Su H / Moreau, Michael P / Gupta, Abha R / Thomson, Susanne A / Mason, Christopher E / Bilguvar, Kaya / Celestino-Soper, Patricia B S / Choi, Murim / Crawford, Emily L / Davis, Lea / Wright, Nicole R Davis / Dhodapkar, Rahul M / DiCola, Michael /

DiLullo, Nicholas M / Fernandez, Thomas V / Fielding-Singh, Vikram / Fishman, Daniel O / Frahm, Stephanie / Garagaloyan, Rouben / Goh, Gerald S / Kammela, Sindhuja / Klei, Lambertus / Lowe, Jennifer K / Lund, Sabata C / McGrew, Anna D / Meyer, Kyle A / Moffat, William J / Murdoch, John D / O'Roak, Brian J / Ober, Gordon T / Pottenger, Rebecca S / Raubeson, Melanie J / Song, Youeun / Wang, Qi / Yaspan, Brian L / Yu, Timothy W / Yurkiewicz, Ilana R / Beaudet, Arthur L / Cantor, Rita M / Curland, Martin / Grice, Dorothy E / Günel, Murat / Lifton, Richard P / Mane, Shrikant M / Martin, Donna M / Shaw, Chad A / Sheldon, Michael / Tischfield, Jay A / Walsh, Christopher A / Morrow, Eric M / Ledbetter, David H / Fombonne, Eric / Lord, Catherine / Martin, Christa Lese / Brooks, Andrew I / Sutcliffe, James S / Cook, Edwin H / Geschwind, Daniel / Roeder, Kathryn / Devlin, Bernie / State, Matthew W

Neuron

2011 Volume 70, Issue 5, Page(s) 863–885

Abstract: We have undertaken a genome-wide analysis of rare copy-number variation (CNV) in 1124 autism spectrum disorder (ASD) families, each comprised of a single proband, unaffected parents, and, in most kindreds, an unaffected sibling. We find significant ... ...

Abstract	We have undertaken a genome-wide analysis of rare copy-number variation (CNV) in 1124 autism spectrum disorder (ASD) families, each comprised of a single proband, unaffected parents, and, in most kindreds, an unaffected sibling. We find significant association of ASD with de novo duplications of 7q11.23, where the reciprocal deletion causes Williams-Beuren syndrome, characterized by a highly social personality. We identify rare recurrent de novo CNVs at five additional regions, including 16p13.2 (encompassing genes USP7 and C16orf72) and Cadherin 13, and implement a rigorous approach to evaluating the statistical significance of these observations. Overall, large de novo CNVs, particularly those encompassing multiple genes, confer substantial risks (OR = 5.6; CI = 2.6-12.0, p = 2.4 × 10(-7)). We estimate there are 130-234 ASD-related CNV regions in the human genome and present compelling evidence, based on cumulative data, for association of rare de novo events at 7q11.23, 15q11.2-13.1, 16p11.2, and Neurexin 1.
MeSH term(s)	Adolescent ; Cadherins/genetics ; Calcium-Binding Proteins ; Cell Adhesion Molecules, Neuronal/genetics ; Child ; Child Development Disorders, Pervasive/genetics ; Child, Preschool ; Chromosomes, Human, Pair 16/genetics ; Chromosomes, Human, Pair 7/genetics ; Chromosomes, Human, X/genetics ; DNA Copy Number Variations/genetics ; Family Health ; Female ; Gene Duplication/genetics ; Gene Expression Profiling ; Genome-Wide Association Study ; Genotype ; Humans ; Male ; Nerve Tissue Proteins/genetics ; Neural Cell Adhesion Molecules ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Proteins/genetics ; Siblings ; Ubiquitin Thiolesterase/genetics ; Ubiquitin-Specific Peptidase 7 ; Williams Syndrome/genetics
Chemical Substances	CEP20 protein, human ; Cadherins ; Calcium-Binding Proteins ; Cell Adhesion Molecules, Neuronal ; H-cadherin ; NRXN1 protein, human ; Nerve Tissue Proteins ; Neural Cell Adhesion Molecules ; Proteins ; USP7 protein, human (EC 3.4.19.12) ; Ubiquitin Thiolesterase (EC 3.4.19.12) ; Ubiquitin-Specific Peptidase 7 (EC 3.4.19.12)
Language	English
Publishing date	2011-03-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	808167-0
ISSN	1097-4199 ; 0896-6273
ISSN (online)	1097-4199
ISSN	0896-6273
DOI	10.1016/j.neuron.2011.05.002
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Article: Analysis of Shared Haplotypes amongst Palauans Maps Loci for Psychotic Disorders to 4q28 and 5q23-q31.

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Article: Analysis of Shared Haplotypes amongst Palauans Maps Loci for Psychotic Disorders to 4q28 and 5q23-q31

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Article ; Online: Modest impact on risk for autism spectrum disorder of rare copy number variants at 15q11.2, specifically breakpoints 1 to 2.

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Article ; Online: De novo mutations revealed by whole-exome sequencing are strongly associated with autism.

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Article ; Online: Rare copy number variants in tourette syndrome disrupt genes in histaminergic pathways and overlap with autism.

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Article ; Online: Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism.

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