Haploinsufficiency of ITSN1 is associated with a substantial increased risk of Parkinson's disease - summary statistics
Creators: name: Spargo, Thomas
name: Dhindsa, Ryan
Publisher: name: Zenodo
Year: 2025

description: Summary statistics associated with the manuscript 'Haploinsufficiency of ITSN1 is associated with a substantial increased risk of Parkinson’s disease'.

 



Additional File 1. Summary statistics from UK Biobank ExWAS. (AF1_variant_level_sumstats.tsv.gz)




Analysis was performed across 3,702 people with PD and 233,378 non-neurological controls in the UK Biobank European ancestry group. Association results are presented for all genetic models grouped by gene and variant, ordered by p-value from most to least significant with corresponding odds ratios and 95% confidence intervals. Variants are aligned to GRCh38 and indicated in the ‘variantID’ column in the format CHR-POS-REF-ALT (chromosome, position, reference allele, alternate allele). Minor allele frequencies are given overall and for cases and controls individually. The genotype counts for reference allele 'p’ and alternate allele 'q’ are given in the columns ‘caseGenotypes’ and ‘controlGenotypes’, using the format ‘pp/pq/qq’ for autosomal and pseudo-autosomal variants and ‘pp/pq/qq/p/q’ for X-chromosome variants not in the pseudo-autosomal region, representing hemizygous male genotypes separately. The columns ‘Gene_Symbol’, ‘hgnc_id’, and ‘ensembl_gene_id’ label the gene for which each variant is identified as most damaging by SnpEff (v4.3). The columns ‘caseRefCount’, ‘caseAltCount’, ’ctrlRefCount’, ‘ctrlAltCount’ indicate the cell counts for the contingency table analyzed using Fisher’s Exact Test; counts are derived from the genotypes indicated in ‘caseGenotypes’ and ‘controlGenotypes’ and depend upon to the tested genetic model (see Methods). 




 




Additional File 2. Summary statistics from the UKB European-only gene-level collapsing analysis.  (AF2_EUR_gene_level_sumstats.tsv.gz)




Analysis was performed across 3,702 people with PD and 233,378 non-neurological controls. Association results are presented for all collapsing models grouped by gene and ordered by p-value from most to least significant with corresponding odds ratios and 95% confidence intervals. The columns ‘Gene_Symbol’, ‘hgnc_id’, and ‘ensembl_gene_id’ identify the tested gene. The ‘Rank_for_model’ column indicates the rank of each gene compared to other genes under a given collapsing model. The columns ‘NctrlQV’, ‘NctrlNoQV’, ‘NcaseNoQV’, and ‘NcaseQV’ indicate the cell counts for the contingency table analyzed using Fisher’s Exact Test, in accordance with the gene-level test performed for each collapsing model (see Methods). 




 




Additional File 3. Summary statistics for pan-ancestry gene-level analysis in the UK Biobank. (AF3_pan_ancestry_gene_level_sumstats.tsv.gz)




Analysis was performed across 3,809 people with PD and 247,101 non-neurological controls across four superpopulation ancestry groups: AFR (n=4,450 [32 PD cases, 4,418 non-neurological controls]), EAS (n=2,059 [6 cases, 2,053 controls]), EUR (n=237,080 [3,702 cases, 233,378 controls]), SAS (n=7,321 [69 cases, 7,252 controls]). Association results are presented for all collapsing models grouped by gene and ordered by p-value from most to least significant, presented with corresponding odds ratios and 95% confidence intervals. The columns ‘Gene_Symbol’, ‘hgnc_id’, and ‘ensembl_gene_id’ identify the tested gene. The strataInfo column provides a nested summary table to break down the input data for each analysis stratum. The order of subfields is: "Ancestry", "n controls without QV", "n controls with QV", "n cases without QV" and "n cases with QV". Each subfield is delimited by ";" and each stratum is delimited by "|". QV = variant qualifying for collapsing model.