Some individuals with autism spectrum disorder (ASD) carry functional mutations rarely observed in the general population. We explored the genes disrupted by these variants from joint analysis of protein-truncating variants (PTVs), missense variants and copy number variants (CNVs) in a cohort of 63,237 individuals. We discovered 72 genes associated with ASD at false discovery rate (FDR) ≤ 0.001 (185 at FDR ≤ 0.05). De novo PTVs, damaging missense variants and CNVs represented 57.5%, 21.1% and 8.44% of association evidence, while CNVs conferred greatest relative risk. Meta-analysis with cohorts ascertained for developmental delay (DD) (n = 91,605) yielded 373 genes associated with ASD/DD at FDR ≤ 0.001 (664 at FDR ≤ 0.05), some of which differed in relative frequency of mutation between ASD and DD cohorts. The DD-associated genes were enriched in transcriptomes of progenitor and immature neuronal cells, whereas genes showing stronger evidence in ASD were more enriched in maturing neurons and overlapped with schizophrenia-associated genes, emphasizing that these neuropsychiatric disorders may share common pathways to risk.

Rare coding variation provides insight into the genetic architecture and phenotypic context of autism / Fu, J. M.; Satterstrom, F. K.; Peng, M.; Brand, H.; Collins, R. L.; Dong, S.; Wamsley, B.; Klei, L.; Wang, L.; Hao, S. P.; Stevens, C. R.; Cusick, C.; Babadi, M.; Banks, E.; Collins, B.; Dodge, S.; Gabriel, S. B.; Gauthier, L.; Lee, S. K.; Liang, L.; Ljungdahl, A.; Mahjani, B.; Sloofman, L.; Smirnov, A. N.; Barbosa, M.; Betancur, C.; Brusco, A.; Chung, B. H. Y.; Cook, E. H.; Cuccaro, M. L.; Domenici, E.; Ferrero, G. B.; Gargus, J. J.; Herman, G. E.; Hertz-Picciotto, I.; Maciel, P.; Manoach, D. S.; Passos-Bueno, M. R.; Persico, A.; Renieri, A.; Sutcliffe, J. S.; Tassone, F.; Trabetti, E.; Campos, G.; Cardaropoli, S.; Carli, D.; Chan, M. C. Y.; Fallerini, C.; Giorgio, E.; Girardi, A. C.; Hansen-Kiss, E.; Lee, S. L.; Lintas, C.; Ludena, Y.; Nguyen, R.; Pavinato, L.; Pericak-Vance, M.; Pessah, I. N.; Schmidt, R. J.; Smith, M.; Costa, C. I. S.; Trajkova, S.; Wang, J. Y. T.; Yu, M. H. C.; Aleksic, B.; Artomov, M.; Benetti, E.; Biscaldi-Schafer, M.; Borglum, A. D.; Carracedo, A.; Chiocchetti, A. G.; Coon, H.; Doan, R. N.; Fernandez-Prieto, M.; Freitag, C. M.; Gerges, S.; Guter, S.; Hougaard, D. M.; Hultman, C. M.; Jacob, S.; Kaartinen, M.; Kolevzon, A.; Kushima, I.; Lehtimaki, T.; Rizzo, C. L.; Maltman, N.; Manara, M.; Meiri, G.; Menashe, I.; Miller, J.; Minshew, N.; Mosconi, M.; Ozaki, N.; Palotie, A.; Parellada, M.; Puura, K.; Reichenberg, A.; Sandin, S.; Scherer, S. W.; Schlitt, S.; Schmitt, L.; Schneider-Momm, K.; Siper, P. M.; Suren, P.; Sweeney, J. A.; Teufel, K.; del Pilar Trelles, M.; Weiss, L. A.; Yuen, R.; Cutler, D. J.; De Rubeis, S.; Buxbaum, J. D.; Daly, M. J.; Devlin, B.; Roeder, K.; Sanders, S. J.; Talkowski, M. E.. - In: NATURE GENETICS. - ISSN 1061-4036. - 54:9(2022), pp. 1320-1331. [10.1038/s41588-022-01104-0]

Rare coding variation provides insight into the genetic architecture and phenotypic context of autism

Persico A.;
2022

Abstract

Some individuals with autism spectrum disorder (ASD) carry functional mutations rarely observed in the general population. We explored the genes disrupted by these variants from joint analysis of protein-truncating variants (PTVs), missense variants and copy number variants (CNVs) in a cohort of 63,237 individuals. We discovered 72 genes associated with ASD at false discovery rate (FDR) ≤ 0.001 (185 at FDR ≤ 0.05). De novo PTVs, damaging missense variants and CNVs represented 57.5%, 21.1% and 8.44% of association evidence, while CNVs conferred greatest relative risk. Meta-analysis with cohorts ascertained for developmental delay (DD) (n = 91,605) yielded 373 genes associated with ASD/DD at FDR ≤ 0.001 (664 at FDR ≤ 0.05), some of which differed in relative frequency of mutation between ASD and DD cohorts. The DD-associated genes were enriched in transcriptomes of progenitor and immature neuronal cells, whereas genes showing stronger evidence in ASD were more enriched in maturing neurons and overlapped with schizophrenia-associated genes, emphasizing that these neuropsychiatric disorders may share common pathways to risk.
2022
NATURE GENETICS
54
9
1320
1331
WOS:000842689300001
2-s2.0-85136292014
35982160
Rare coding variation provides insight into the genetic architecture and phenotypic context of autism / Fu, J. M.; Satterstrom, F. K.; Peng, M.; Brand, H.; Collins, R. L.; Dong, S.; Wamsley, B.; Klei, L.; Wang, L.; Hao, S. P.; Stevens, C. R.; Cusick, C.; Babadi, M.; Banks, E.; Collins, B.; Dodge, S.; Gabriel, S. B.; Gauthier, L.; Lee, S. K.; Liang, L.; Ljungdahl, A.; Mahjani, B.; Sloofman, L.; Smirnov, A. N.; Barbosa, M.; Betancur, C.; Brusco, A.; Chung, B. H. Y.; Cook, E. H.; Cuccaro, M. L.; Domenici, E.; Ferrero, G. B.; Gargus, J. J.; Herman, G. E.; Hertz-Picciotto, I.; Maciel, P.; Manoach, D. S.; Passos-Bueno, M. R.; Persico, A.; Renieri, A.; Sutcliffe, J. S.; Tassone, F.; Trabetti, E.; Campos, G.; Cardaropoli, S.; Carli, D.; Chan, M. C. Y.; Fallerini, C.; Giorgio, E.; Girardi, A. C.; Hansen-Kiss, E.; Lee, S. L.; Lintas, C.; Ludena, Y.; Nguyen, R.; Pavinato, L.; Pericak-Vance, M.; Pessah, I. N.; Schmidt, R. J.; Smith, M.; Costa, C. I. S.; Trajkova, S.; Wang, J. Y. T.; Yu, M. H. C.; Aleksic, B.; Artomov, M.; Benetti, E.; Biscaldi-Schafer, M.; Borglum, A. D.; Carracedo, A.; Chiocchetti, A. G.; Coon, H.; Doan, R. N.; Fernandez-Prieto, M.; Freitag, C. M.; Gerges, S.; Guter, S.; Hougaard, D. M.; Hultman, C. M.; Jacob, S.; Kaartinen, M.; Kolevzon, A.; Kushima, I.; Lehtimaki, T.; Rizzo, C. L.; Maltman, N.; Manara, M.; Meiri, G.; Menashe, I.; Miller, J.; Minshew, N.; Mosconi, M.; Ozaki, N.; Palotie, A.; Parellada, M.; Puura, K.; Reichenberg, A.; Sandin, S.; Scherer, S. W.; Schlitt, S.; Schmitt, L.; Schneider-Momm, K.; Siper, P. M.; Suren, P.; Sweeney, J. A.; Teufel, K.; del Pilar Trelles, M.; Weiss, L. A.; Yuen, R.; Cutler, D. J.; De Rubeis, S.; Buxbaum, J. D.; Daly, M. J.; Devlin, B.; Roeder, K.; Sanders, S. J.; Talkowski, M. E.. - In: NATURE GENETICS. - ISSN 1061-4036. - 54:9(2022), pp. 1320-1331. [10.1038/s41588-022-01104-0]
Fu, J. M.; Satterstrom, F. K.; Peng, M.; Brand, H.; Collins, R. L.; Dong, S.; Wamsley, B.; Klei, L.; Wang, L.; Hao, S. P.; Stevens, C. R.; Cusick, C.; Babadi, M.; Banks, E.; Collins, B.; Dodge, S.; Gabriel, S. B.; Gauthier, L.; Lee, S. K.; Liang, L.; Ljungdahl, A.; Mahjani, B.; Sloofman, L.; Smirnov, A. N.; Barbosa, M.; Betancur, C.; Brusco, A.; Chung, B. H. Y.; Cook, E. H.; Cuccaro, M. L.; Domenici, E.; Ferrero, G. B.; Gargus, J. J.; Herman, G. E.; Hertz-Picciotto, I.; Maciel, P.; Manoach, D. S.; Passos-Bueno, M. R.; Persico, A.; Renieri, A.; Sutcliffe, J. S.; Tassone, F.; Trabetti, E.; Campos, G.; Cardaropoli, S.; Carli, D.; Chan, M. C. Y.; Fallerini, C.; Giorgio, E.; Girardi, A. C.; Hansen-Kiss, E.; Lee, S. L.; Lintas, C.; Ludena, Y.; Nguyen, R.; Pavinato, L.; Pericak-Vance, M.; Pessah, I. N.; Schmidt, R. J.; Smith, M.; Costa, C. I. S.; Trajkova, S.; Wang, J. Y. T.; Yu, M. H. C.; Aleksic, B.; Artomov, M.; Benetti, E.; Biscaldi-Schafer, M.; Borglum, A. D.; Carracedo, A.; Chiocchetti, A. G.; Coon, H.; Doan, R. N.; Fernandez-Prieto, M.; Freitag, C. M.; Gerges, S.; Guter, S.; Hougaard, D. M.; Hultman, C. M.; Jacob, S.; Kaartinen, M.; Kolevzon, A.; Kushima, I.; Lehtimaki, T.; Rizzo, C. L.; Maltman, N.; Manara, M.; Meiri, G.; Menashe, I.; Miller, J.; Minshew, N.; Mosconi, M.; Ozaki, N.; Palotie, A.; Parellada, M.; Puura, K.; Reichenberg, A.; Sandin, S.; Scherer, S. W.; Schlitt, S.; Schmitt, L.; Schneider-Momm, K.; Siper, P. M.; Suren, P.; Sweeney, J. A.; Teufel, K.; del Pilar Trelles, M.; Weiss, L. A.; Yuen, R.; Cutler, D. J.; De Rubeis, S.; Buxbaum, J. D.; Daly, M. J.; Devlin, B.; Roeder, K.; Sanders, S. J.; Talkowski, M. E.
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