Genome-wide Rare Variant Score Associates With Morphological Subtypes of Autism Spectrum Disorder

Defining different genetic subtypes of Autism Spectrum Disorder (ASD) can help predict developmental outcomes. Based on minor physical and major congenital anomalies, we categorized 325 Canadian children with ASD into dysmorphic and non-dysmorphic subgroupings. We developed a method to calculate a genome-wide rare variant score (GRVS) from whole-genome sequencing (WGS) data for each ASD proband. GRVS is a sum of the number of variants in morphology-associated coding and non-coding regions, weighted by their effect sizes. Probands with dysmorphic ASD had a significantly higher GRVS compared to those with non-dysmorphic ASD (P= 0.027). Using the polygenic transmission disequilibrium test, we observed an over-transmission of ASD-associated common variants in non-dysmorphic ASD probands (P= 2.9×10-3). We replicated our findings using 442 ASD probands that had accompanying morphology data in the Simons Simplex Collection. Our findings provide support for an alternative genomic classification of ASD subgroups using morphology data, which may inform intervention protocols.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

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Dataset ID	Description	Technology	Samples
EGAD00001008452	We extracted DNA from whole blood or lymphoblast-derived cell lines and assessed the DNA quality with PicoGreenTM and gel electrophoresis. Whole genome sequencing was performed (Illumina HiSeq2000 and Illumina HiSeq X). WGS reads were mapped to the human reference genome assembly hg19 (GRCh37) using Burrows-Wheeler Aligner v.0.7.12 (TCAG) or Isaac v.2.0.13 (Macrogen). For each genome, we performed local realignment and quality recalibration and detected SNVs and small indels using GATK Haplotype Caller v.3.4.6 without genotype refinement. We detected CNVs using ERDS (estimation by read depth with single nucleotide variants) and CNVnator. We detected structural variants using Manta v.0.29.6. When available by the variant caller (i.e. GATK and Manta), trio-based joint variant calling was conducted for each family.	HiSeq X Five Illumina HiSeq 2000	112

Publications	Citations
Genome-wide rare variant score associates with morphological subtypes of autism spectrum disorder. Chan AJS, Engchuan W, Reuter MS, Wang Z, Thiruvahindrapuram B, Trost B, Nalpathamkalam T, Negrijn C, Lamoureux S, Pellecchia G, Patel RV, Sung WWL, MacDonald JR, Howe JL, Vorstman J, Sondheimer N, Takahashi N, Miles JH, Anagnostou E, Tammimies K, Zarrei M, Merico D, Stavropoulos DJ, Yuen RKC, Fernandez BA, Scherer SW. Nat Commun 13: 2022 6463	4

Publications

Citations

Genome-wide rare variant score associates with morphological subtypes of autism spectrum disorder.
Chan AJS, Engchuan W, Reuter MS, Wang Z, Thiruvahindrapuram B, Trost B, Nalpathamkalam T, Negrijn C, Lamoureux S, Pellecchia G, Patel RV, Sung WWL, MacDonald JR, Howe JL, Vorstman J, Sondheimer N, Takahashi N, Miles JH, Anagnostou E, Tammimies K, Zarrei M, Merico D, Stavropoulos DJ, Yuen RKC, Fernandez BA, Scherer SW. Nat Commun 13: 2022 6463