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Whole exome sequencing in dense families suggests genetic pleiotropy amongst Mendelian and complex neuropsychiatric syndromes
Whole Exome Sequencing (WES) studies provide important insights into the genetic architecture of serious mental illness (SMI). Genes that are central to the shared biology of SMIs may be identified by WES in families with multiple affected individuals with diverse SMI (F-SMI). We performed WES in 22...
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Published in: | Scientific reports 2022-12, Vol.12 (1), p.21128-11, Article 21128 |
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creator | Ganesh, Suhas Vemula, Alekhya Bhattacharjee, Samsiddhi Mathew, Kezia Ithal, Dhruva Navin, Karthick Nadella, Ravi Kumar Viswanath, Biju Sullivan, Patrick F. Jain, Sanjeev Purushottam, Meera |
description | Whole Exome Sequencing (WES) studies provide important insights into the genetic architecture of serious mental illness (SMI). Genes that are central to the shared biology of SMIs may be identified by WES in families with multiple affected individuals with diverse SMI (F-SMI). We performed WES in 220 individuals from 75 F-SMI families and 60 unrelated controls. Within pedigree prioritization employed criteria of
rarity, functional consequence,
and
sharing
by ≥ 3 affected members. Across the sample, gene and gene-set-wide case–control association analysis was performed with Sequence Kernel Association Test (SKAT). In 14/16 families with ≥ 3 sequenced affected individuals, we identified a total of 78 rare predicted deleterious variants in 78 unique genes shared by ≥ 3 members with SMI. Twenty (25%) genes were implicated in monogenic CNS syndromes in OMIM (OMIM-CNS), a fraction that is a significant overrepresentation (Fisher’s Exact test OR = 2.47, p = 0.001). In gene-set SKAT, statistically significant association was noted for OMIM-CNS gene-set (SKAT-p = 0.005) but not the synaptic gene-set (SKAT-p = 0.17). In this WES study in F-SMI, we identify private, rare, protein altering variants in genes previously implicated in Mendelian neuropsychiatric syndromes; suggesting pleiotropic influences in neurodevelopment between complex and Mendelian syndromes. |
doi_str_mv | 10.1038/s41598-022-25664-7 |
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rarity, functional consequence,
and
sharing
by ≥ 3 affected members. Across the sample, gene and gene-set-wide case–control association analysis was performed with Sequence Kernel Association Test (SKAT). In 14/16 families with ≥ 3 sequenced affected individuals, we identified a total of 78 rare predicted deleterious variants in 78 unique genes shared by ≥ 3 members with SMI. Twenty (25%) genes were implicated in monogenic CNS syndromes in OMIM (OMIM-CNS), a fraction that is a significant overrepresentation (Fisher’s Exact test OR = 2.47, p = 0.001). In gene-set SKAT, statistically significant association was noted for OMIM-CNS gene-set (SKAT-p = 0.005) but not the synaptic gene-set (SKAT-p = 0.17). In this WES study in F-SMI, we identify private, rare, protein altering variants in genes previously implicated in Mendelian neuropsychiatric syndromes; suggesting pleiotropic influences in neurodevelopment between complex and Mendelian syndromes.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/s41598-022-25664-7</identifier><identifier>PMID: 36476812</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/208 ; 631/208/212 ; 631/208/366 ; 631/208/514 ; 631/378/2583 ; 631/477/2811 ; 631/61/212 ; 631/61/514 ; 692/308 ; Association analysis ; Exome Sequencing ; Genes ; Genetic Pleiotropy ; Humanities and Social Sciences ; Humans ; Medicin och hälsovetenskap ; Mental disorders ; multidisciplinary ; Pleiotropy ; Science ; Science (multidisciplinary) ; Statistical analysis</subject><ispartof>Scientific reports, 2022-12, Vol.12 (1), p.21128-11, Article 21128</ispartof><rights>The Author(s) 2022</rights><rights>2022. The Author(s).</rights><rights>The Author(s) 2022. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c628t-efabee6be9acba2c9526ebd672baa981d791d70681579349d3353011ecdadaac3</citedby><cites>FETCH-LOGICAL-c628t-efabee6be9acba2c9526ebd672baa981d791d70681579349d3353011ecdadaac3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2747549771/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2747549771?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,37013,44590,53791,53793,75126</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36476812$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttp://kipublications.ki.se/Default.aspx?queryparsed=id:151521512$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>Ganesh, Suhas</creatorcontrib><creatorcontrib>Vemula, Alekhya</creatorcontrib><creatorcontrib>Bhattacharjee, Samsiddhi</creatorcontrib><creatorcontrib>Mathew, Kezia</creatorcontrib><creatorcontrib>Ithal, Dhruva</creatorcontrib><creatorcontrib>Navin, Karthick</creatorcontrib><creatorcontrib>Nadella, Ravi Kumar</creatorcontrib><creatorcontrib>Viswanath, Biju</creatorcontrib><creatorcontrib>Sullivan, Patrick F.</creatorcontrib><creatorcontrib>Jain, Sanjeev</creatorcontrib><creatorcontrib>Purushottam, Meera</creatorcontrib><creatorcontrib>ADBS Consortium</creatorcontrib><creatorcontrib>The ADBS Consortium</creatorcontrib><title>Whole exome sequencing in dense families suggests genetic pleiotropy amongst Mendelian and complex neuropsychiatric syndromes</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Whole Exome Sequencing (WES) studies provide important insights into the genetic architecture of serious mental illness (SMI). Genes that are central to the shared biology of SMIs may be identified by WES in families with multiple affected individuals with diverse SMI (F-SMI). We performed WES in 220 individuals from 75 F-SMI families and 60 unrelated controls. Within pedigree prioritization employed criteria of
rarity, functional consequence,
and
sharing
by ≥ 3 affected members. Across the sample, gene and gene-set-wide case–control association analysis was performed with Sequence Kernel Association Test (SKAT). In 14/16 families with ≥ 3 sequenced affected individuals, we identified a total of 78 rare predicted deleterious variants in 78 unique genes shared by ≥ 3 members with SMI. Twenty (25%) genes were implicated in monogenic CNS syndromes in OMIM (OMIM-CNS), a fraction that is a significant overrepresentation (Fisher’s Exact test OR = 2.47, p = 0.001). In gene-set SKAT, statistically significant association was noted for OMIM-CNS gene-set (SKAT-p = 0.005) but not the synaptic gene-set (SKAT-p = 0.17). 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ADBS Consortium</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Whole exome sequencing in dense families suggests genetic pleiotropy amongst Mendelian and complex neuropsychiatric syndromes</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2022-12-07</date><risdate>2022</risdate><volume>12</volume><issue>1</issue><spage>21128</spage><epage>11</epage><pages>21128-11</pages><artnum>21128</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Whole Exome Sequencing (WES) studies provide important insights into the genetic architecture of serious mental illness (SMI). Genes that are central to the shared biology of SMIs may be identified by WES in families with multiple affected individuals with diverse SMI (F-SMI). We performed WES in 220 individuals from 75 F-SMI families and 60 unrelated controls. Within pedigree prioritization employed criteria of
rarity, functional consequence,
and
sharing
by ≥ 3 affected members. Across the sample, gene and gene-set-wide case–control association analysis was performed with Sequence Kernel Association Test (SKAT). In 14/16 families with ≥ 3 sequenced affected individuals, we identified a total of 78 rare predicted deleterious variants in 78 unique genes shared by ≥ 3 members with SMI. Twenty (25%) genes were implicated in monogenic CNS syndromes in OMIM (OMIM-CNS), a fraction that is a significant overrepresentation (Fisher’s Exact test OR = 2.47, p = 0.001). In gene-set SKAT, statistically significant association was noted for OMIM-CNS gene-set (SKAT-p = 0.005) but not the synaptic gene-set (SKAT-p = 0.17). In this WES study in F-SMI, we identify private, rare, protein altering variants in genes previously implicated in Mendelian neuropsychiatric syndromes; suggesting pleiotropic influences in neurodevelopment between complex and Mendelian syndromes.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>36476812</pmid><doi>10.1038/s41598-022-25664-7</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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subjects | 631/208 631/208/212 631/208/366 631/208/514 631/378/2583 631/477/2811 631/61/212 631/61/514 692/308 Association analysis Exome Sequencing Genes Genetic Pleiotropy Humanities and Social Sciences Humans Medicin och hälsovetenskap Mental disorders multidisciplinary Pleiotropy Science Science (multidisciplinary) Statistical analysis |
title | Whole exome sequencing in dense families suggests genetic pleiotropy amongst Mendelian and complex neuropsychiatric syndromes |
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