Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes

Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes

To capture the full spectrum of genetic risk for autism, we performed a two-stage analysis of rare de novo and inherited coding variants in 42,607 autism cases, including 35,130 new cases recruited online by SPARK. We identified 60 genes with exome-wide significance ( P  < 2.5 × 10 −6 ), includin...

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Published in:Nature genetics Vol. 54; no. 9; pp. 1305 - 1319
Main Authors: Zhou, Xueya, Feliciano, Pamela, Shu, Chang, Wang, Tianyun, Astrovskaya, Irina, Hall, Jacob B., Obiajulu, Joseph U., Wright, Jessica R., Murali, Shwetha C., Xu, Simon Xuming, Brueggeman, Leo, Thomas, Taylor R., Marchenko, Olena, Fleisch, Christopher, Barns, Sarah D., Snyder, LeeAnne Green, Han, Bing, Chang, Timothy S., Turner, Tychele N., Harvey, William T., Nishida, Andrew, O’Roak, Brian J., Geschwind, Daniel H., Michaelson, Jacob J., Volfovsky, Natalia, Eichler, Evan E., Shen, Yufeng, Chung, Wendy K.
Format: Journal Article
Language:English
Published: New York Nature Publishing Group US 01-09-2022
Nature Publishing Group
Subjects:
631/208/366/1373
631/208/514
631/378
ADNP protein
Agriculture
Animal Genetics and Genomics
Autism
Autism Spectrum Disorder - genetics
Autistic Disorder - genetics
Biomedical and Life Sciences
Biomedicine
Cancer Research
Cognitive ability
Exome - genetics
Exome Sequencing
Forkhead Transcription Factors - genetics
Foxp1 protein
Gene Function
Genes
Genetic Predisposition to Disease
Genomes
Human Genetics
Humans
Intellectual disabilities
Mutation
Protein-serine/threonine kinase
Repressor Proteins - genetics
Risk
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Abstract To capture the full spectrum of genetic risk for autism, we performed a two-stage analysis of rare de novo and inherited coding variants in 42,607 autism cases, including 35,130 new cases recruited online by SPARK. We identified 60 genes with exome-wide significance ( P  < 2.5 × 10 −6 ), including five new risk genes ( NAV3 , ITSN1 , MARK2 , SCAF1 and HNRNPUL2 ). The association of NAV3 with autism risk is primarily driven by rare inherited loss-of-function (LoF) variants, with an estimated relative risk of 4, consistent with moderate effect. Autistic individuals with LoF variants in the four moderate-risk genes ( NAV3 , ITSN1 , SCAF1 and HNRNPUL2 ; n  = 95) have less cognitive impairment than 129 autistic individuals with LoF variants in highly penetrant genes ( CHD8, SCN2A, ADNP, FOXP1 and SHANK3 ) (59% vs 88%, P  = 1.9 × 10 −6 ). Power calculations suggest that much larger numbers of autism cases are needed to identify additional moderate-risk genes. An integrated analysis of de novo and inherited coding variants in 42,607 individuals with autism spectrum disorder identifies 60 risk genes of which five have not previously been associated with neurodevelopmental disorders.
AbstractList To capture the full spectrum of genetic risk for autism, we performed a two-stage analysis of rare de novo and inherited coding variants in 42,607 autism cases, including 35,130 new cases recruited online by SPARK. We identified 60 genes with exome-wide significance ( P  < 2.5 × 10 −6 ), including five new risk genes ( NAV3 , ITSN1 , MARK2 , SCAF1 and HNRNPUL2 ). The association of NAV3 with autism risk is primarily driven by rare inherited loss-of-function (LoF) variants, with an estimated relative risk of 4, consistent with moderate effect. Autistic individuals with LoF variants in the four moderate-risk genes ( NAV3 , ITSN1 , SCAF1 and HNRNPUL2 ; n  = 95) have less cognitive impairment than 129 autistic individuals with LoF variants in highly penetrant genes ( CHD8, SCN2A, ADNP, FOXP1 and SHANK3 ) (59% vs 88%, P  = 1.9 × 10 −6 ). Power calculations suggest that much larger numbers of autism cases are needed to identify additional moderate-risk genes.
To capture the full spectrum of genetic risk for autism, we performed a two-stage analysis of rare de novo and inherited coding variants in 42,607 autism cases, including 35,130 new cases recruited online by SPARK. We identified 60 genes with exome-wide significance (P < 2.5 × 10-6), including five new risk genes (NAV3, ITSN1, MARK2, SCAF1 and HNRNPUL2). The association of NAV3 with autism risk is primarily driven by rare inherited loss-of-function (LoF) variants, with an estimated relative risk of 4, consistent with moderate effect. Autistic individuals with LoF variants in the four moderate-risk genes (NAV3, ITSN1, SCAF1 and HNRNPUL2; n = 95) have less cognitive impairment than 129 autistic individuals with LoF variants in highly penetrant genes (CHD8, SCN2A, ADNP, FOXP1 and SHANK3) (59% vs 88%, P = 1.9 × 10-6). Power calculations suggest that much larger numbers of autism cases are needed to identify additional moderate-risk genes.
To capture the full spectrum of genetic risk for autism, we performed a two-stage analysis of rare de novo and inherited coding variants in 42,607 autism cases, including 35,130 new cases recruited online by SPARK. We identified 60 genes with exome-wide significance (P < 2.5 × 10 ), including five new risk genes (NAV3, ITSN1, MARK2, SCAF1 and HNRNPUL2). The association of NAV3 with autism risk is primarily driven by rare inherited loss-of-function (LoF) variants, with an estimated relative risk of 4, consistent with moderate effect. Autistic individuals with LoF variants in the four moderate-risk genes (NAV3, ITSN1, SCAF1 and HNRNPUL2; n = 95) have less cognitive impairment than 129 autistic individuals with LoF variants in highly penetrant genes (CHD8, SCN2A, ADNP, FOXP1 and SHANK3) (59% vs 88%, P = 1.9 × 10 ). Power calculations suggest that much larger numbers of autism cases are needed to identify additional moderate-risk genes.
To capture the full spectrum of genetic risk for autism, we performed a two-stage analysis of rare de novo and inherited coding variants in 42,607 autism cases, including 35,130 new cases recruited online by SPARK. We identified 60 genes with exome-wide significance ( P  < 2.5 × 10 −6 ), including five new risk genes ( NAV3 , ITSN1 , MARK2 , SCAF1 and HNRNPUL2 ). The association of NAV3 with autism risk is primarily driven by rare inherited loss-of-function (LoF) variants, with an estimated relative risk of 4, consistent with moderate effect. Autistic individuals with LoF variants in the four moderate-risk genes ( NAV3 , ITSN1 , SCAF1 and HNRNPUL2 ; n  = 95) have less cognitive impairment than 129 autistic individuals with LoF variants in highly penetrant genes ( CHD8, SCN2A, ADNP, FOXP1 and SHANK3 ) (59% vs 88%, P  = 1.9 × 10 −6 ). Power calculations suggest that much larger numbers of autism cases are needed to identify additional moderate-risk genes. An integrated analysis of de novo and inherited coding variants in 42,607 individuals with autism spectrum disorder identifies 60 risk genes of which five have not previously been associated with neurodevelopmental disorders.
Author Michaelson, Jacob J.
Obiajulu, Joseph U.
Geschwind, Daniel H.
Astrovskaya, Irina
Zhou, Xueya
Brueggeman, Leo
Feliciano, Pamela
Wang, Tianyun
Marchenko, Olena
Snyder, LeeAnne Green
Fleisch, Christopher
Chung, Wendy K.
Xu, Simon Xuming
Barns, Sarah D.
Hall, Jacob B.
Turner, Tychele N.
Harvey, William T.
Shen, Yufeng
Nishida, Andrew
Volfovsky, Natalia
Chang, Timothy S.
Eichler, Evan E.
Wright, Jessica R.
O’Roak, Brian J.
Shu, Chang
Thomas, Taylor R.
Murali, Shwetha C.
Han, Bing
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/35982159$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
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2022. The Author(s).
Copyright Nature Publishing Group Sep 2022
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License 2022. The Author(s).
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  publication-title: Nature
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  publication-title: Nat. Genet.
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Snippet To capture the full spectrum of genetic risk for autism, we performed a two-stage analysis of rare de novo and inherited coding variants in 42,607 autism...
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SubjectTerms 631/208/366/1373
631/208/514
631/378
ADNP protein
Agriculture
Animal Genetics and Genomics
Autism
Autism Spectrum Disorder - genetics
Autistic Disorder - genetics
Biomedical and Life Sciences
Biomedicine
Cancer Research
Cognitive ability
Exome - genetics
Exome Sequencing
Forkhead Transcription Factors - genetics
Foxp1 protein
Gene Function
Genes
Genetic Predisposition to Disease
Genomes
Human Genetics
Humans
Intellectual disabilities
Mutation
Protein-serine/threonine kinase
Repressor Proteins - genetics
Risk
Title Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes
URI https://link.springer.com/article/10.1038/s41588-022-01148-2
https://www.ncbi.nlm.nih.gov/pubmed/35982159
https://www.proquest.com/docview/2714944805
https://search.proquest.com/docview/2704868476
https://pubmed.ncbi.nlm.nih.gov/PMC9470534
Volume 54
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