Fig. 1: Sex chromosome aneuploidy identification in the SPARKMC-SCA cohort.

A Log R ratio (LRR) plots are shown for the SPARK Autism Spectrum Disorder (ASD)-positive case cohort and (B) the MyCode ASD-negative control cohort. LRR plots in panels (A and B) are composite images that were created by juxtaposing data across genotype batches and platforms for a cohort-wide visualization. LRR plots for each individual batch are shown in Figures S1 and S2. The x-axis shows the median LRR for the X chromosome and the y-axis shows the median LRR for the Y chromosome. Colors indicate each individual’s sex chromosome complement. Participants with sex chromosome aneuploidies excluded from the analysis: 45, X; 48, XXXX; 48, XXXY; and 48, XXYY are shown in gray. C An example of an X chromosome-wide B allele frequency (BAF) plot for each sex chromosome aneuploidy included in the analysis. The x-axis shows the position along the X chromosome in megabase pairs (Mbp). The y-axis shows the BAF of each genotype and ranges between 0 to 1. The 47, XXY karyotype can occur by inheriting an X chromosome from each parent, called heterodisomy (het) or by inheriting homologous X chromosomes, called uniparental isodisomy (iso). D The table shows the number of ASD-positive cases and ASD-negative controls (outcome) with each sex chromosome complement (exposure) in the SPARKMC-SCA cohort. Source data are provided as a Source Data file.