Datasets for rare variant co-occurrence analysis in autism spectrum disorder

The datasets provided here were generated and analyzed in the study “Co-occurrence of rare variants implicates gene pairs in cytoskeletal pathways and is associated with increased severity in autism spectrum disorder (Lee et al.)”. Korean_ASD_sample_list.tsv.gz: List of samples from Korean ASD families included in this study. The table contains three columns: sample (sample identifier), Group (ASD case or control status), and MSSNG_deposited, indicating whether the sample has been deposited in the MSSNG repository. Korean_ASD_DNV_list.tsv.gz: De novo variants identified from whole-genome sequencing of Korean autism spectrum disorder (ASD) families. Korean_SSC_SPARK.EastAsian.rare_het.PTV_dMIS.per_gene_variant_count_matrix.tsv.gz: Sample-by-gene matrix of rare heterozygous damaging variants (AF ≤ 0.1%; PTV and predicted damaging missense) in East Asian samples from Korean ASD families, SSC and SPARK. Each row represents a sample and each column a gene, with values indicating variant counts per gene. The table also includes metadata columns such as Group (case/control status) and is_RareComb_input, indicating whether the sample was used in the RareComb statistical analysis. SSC_SPARK.European.rare_het.PTV_dMIS.per_gene_variant_count_matrix.tsv.gz: Sample-by-gene matrix of rare heterozygous damaging variants (AF ≤ 0.1%; PTV and predicted damaging missense) in European samples from SSC and SPARK. Each row represents a sample and each column a gene, with values indicating variant counts per gene. The table also includes metadata columns such as Group (case/control status) and is_RareComb_input, indicating whether the sample was used in the RareComb statistical analysis. EastAsian_RareComb_variant_combination_statistics.tsv.gz: RareComb statistical results for gene combinations with co-occurring rare damaging variants (AF ≤ 0.1%) in East Asian samples. European_RareComb_variant_combination_statistics.tsv.gz: RareComb statistical results for gene combinations with co-occurring rare damaging variants (AF ≤ 0.1%) in European samples. Scripts used to generate these datasets are available at: https://github.com//Co-occurrence-analysis-in-ASD