In trans variant calling reveals enrichment for compound heterozygous variants in genes involved in neuronal development and growth.

Allison J Cox; Fillan Grady; Gabriel Velez; Vinit B Mahajan; Polly J Ferguson; Andrew Kitchen; Benjamin W Darbro; Alexander G Bassuk

Using R statistical software, a Fisher's exact test was used to detect transcripts with significant differences in the proportion of individuals with homozygous or compound heterozygous variants between the Epi4k dataset and the 1000 genomes dataset. Odds ratios and p-values were calculated using the number of individuals with and without qualifying mutations in each superpopulation. Analyses were performed using all ancestries, and for only individuals of European ancestry. Both Bonferroni and Benjamini-Hochberg adjustments were used to determine significance thresholds after correction for multiple testing. The number of tests was based on the number of transcripts with at least one individual in either the Epi4k or 1000 genomes dataset with in trans coding variants with minor allele frequencies below the set threshold.