Additional file 1: of Functional SNP allele discovery (fSNPd): an approach to find highly penetrant, environmental-triggered genotypes underlying complex human phenotypes

Use of fSNPd and the Supplementary Figure. This firstly documents the instructions for the installation of fSNPd, and its use. Secondly, it contains the Supplemental Figure entitled: Average read depth per base of genes in a test cohort of 40 individualsâ exomes - data derived from Supplemental Table S1. This shows a graph of calculate the average read coverage by all genes, and the legend details the methodology used. References used are given after the legend. Read number statistics of average depth of sequence reads for each exon of each gene included in the exomes of forty individuals. This is a large spreadsheet giving the detailed analysis of read depth achieved. Results and statistics are given for each gene and exon of each gene. Thus, the coverage of an exome of any desired exon can be determined. Simulations of the performance of fSNPd compared to an Association study approach in a variety of scenarios. Simulations were performed assuming that a rare SNP allele was fully penetrant when present (unless otherwise stated). For each Simulation SNP-1 is a common SNP (such as are used in Association studies) with allele A frequency = allele B frequency = 0.5 and SNP-2 (analysed in fSNPd) has the rare allele A frequency = .01 and the common allele B frequency = .99. The SNP-2 allele A is disease associated and always on a SNP-1 allele A background. Simulation are of: the number of SNPs causing a phenotype; different SNP-2 rare allele frequencies; if half of cases are non-genetic or rare SNPs allele penetrance 50%; and of using a cohort size of 3000, rather than 100 as used for all other simulations. (ZIP 8041 kb)