Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank

Abstract
Background

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition whose biological basis is yet to be elucidated. The Australian Autism Biobank (AAB) is an initiative of the Cooperative Research Centre for Living with Autism (Autism CRC) to establish an Australian resource of biospecimens, phenotypes and genomic data for research on autism.

Methods

Genome-wide single-nucleotide polymorphism genotypes were available for 2,477 individuals (after quality control) from 546 families (436 complete), including 886 participants aged 2 to 17 years with diagnosed (n = 871) or suspected (n = 15) ASD, 218 siblings without ASD, 1,256 parents, and 117 unrelated children without an ASD diagnosis. The genetic data were used to confirm familial relationships and assign ancestry, which was majority European (n = 1,964 European individuals). We generated polygenic scores (PGS) for ASD, IQ, chronotype and height in the subset of Europeans, and in 3,490 unrelated ancestry-matched participants from the UK Biobank. We tested for group differences for each PGS, and performed prediction analyses for related phenotypes in the AAB. We called copy-number variants (CNVs) in all participants, and intersected these with high-confidence ASD- and intellectual disability (ID)-associated CNVs and genes from the public domain.

Results

The ASD (p = 6.1e−13), sibling (p = 4.9e−3) and unrelated (p = 3.0e−3) groups had significantly higher ASD PGS than UK Biobank controls, whereas this was not the case for height—a control trait. The IQ PGS was a significant predictor of measured IQ in undiagnosed children (r = 0.24, p = 2.1e−3) and parents (r = 0.17, p = 8.0e−7; 4.0% of variance), but not the ASD group. Chronotype PGS predicted sleep disturbances within the ASD group (r = 0.13, p = 1.9e−3; 1.3% of variance). In the CNV analysis, we identified 13 individuals with CNVs overlapping ASD/ID-associated CNVs, and 12 with CNVs overlapping ASD/ID/developmental delay-associated genes identified on the basis of de novo variants.

Citation
Yap, C.X., Alvares, G.A., Henders, A.K., Lin, T., Wallace, L., Farrelly, A., McLaren, T., Berry, J., Vinkhuyzen, A.A.E., Trzaskowski, M., Zeng, J., Yang, Y., Cleary, D., Grove, R., Hafekost, C., Harun, A., Holdsworth, H., Jellett, R., Khan, F., Lawson, L.P., Leslie, J., Frenk, M.L., Masi, A., Mathew, N.E., Muniandy, M., Nothard, M., Visscher, P.M., Dawson, P.A., Dissanayake, C., Eapen, V., Heussler, H.S., Whitehouse, A.J.O., Wray, N.R. & Gratten, J. (2021). Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank. Molecular Autism, 12(12). doi: 10.1186/s13229-020-004

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