Documentation

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Publication Details

Results for Fu2022:

Summary

Title	Rare coding variation provides insight into the genetic architecture and phenotypic context of autism
Authors	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.M., 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., Autism Sequencing Consortium (ASC), Broad Institute Center for Common Disease Genomics (Broad-CCDG), iPSYCH-BROAD Consortium, Cutler, D.J., De Rubeis, S., Buxbaum, J.D., Daly, M.J., Devlin, B., Roeder, K., Sanders, S.J., Talkowski, M.E.
Technology	Whole exome sequencing
Variant source	Supplementary Table 20: The de novo SNV/indel variants used in TADA association analyses from assembled ASD cohorts
Cohorts	Autism Sequencing Consortium (ASC), Simons Simplex Collection (SSC), Simons Foundation Powering Autism Research for Knowledge (SPARK)
Design	trios
URL	https://dx.doi.org/10.1038/s41588-022-01104-0
Pubmed	35982160
Subject count	11936 The number of subjects for this study could not be determined directly from the variant data; the value given is that reported by the authors in the publication.
Variant event count	26143
Curation notes	View

Breakdown by exonic function

Function	Variant Count
frameshift deletion	653
frameshift insertion	304
nonframeshift deletion	204
nonframeshift insertion	79
nonsynonymous SNV	11202
other	8021
splicing	365
stopgain	824
stoploss	14
synonymous SNV	4371
unknown	107

What am I looking at?

Summary: Information from the literature piece (e.g. Author, Publisher, DOI) and the study experimental design (e.g. sample size, source of probands, sequencing technology.) For a full list of sources of variants, be sure to check out the publications page. Documentation and description of our work can be found on the help page.

Breakdown by exonic function: We annotated the variants with an effect prediction using ANNOVAR. The functions are categories of variants, such as frameshift variants (i.e. frameshift_elongation (SO:0001909)), loss/gain of stop codon, SNVs and non-frameshift variants. See the full list of possible annotations for exonic variants in the documentation.