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

BACKGROUND: Significant human diseases/phenotypes exist which require both an environmental trigger event and a genetic predisposition before the disease/phenotype emerges, e.g. Carbamazepine with the rare SNP allele of rs3909184 causing Stevens Johnson syndrome, and aminoglycosides with rs267606617 causing sensory neural deafness. The underlying genotypes are fully penetrant only when the correct environmental trigger(s) occur, otherwise they are silent and harmless. Such diseases/phenotypes will not appear to have a Mendelian inheritance pattern, unless the environmental trigger is very common (>50% per lifetime). The known causative genotypes are likely to be protein-altering SNPs with dominant/semi-dominant effect. We questioned whether other diseases and phenotypes could have a similar aetiology. METHODS: We wrote the fSNPd program to analyse multiple exomes from a test cohort simultaneously with the purpose of identifying SNP alleles at a significantly different frequency to that of the general population. fSNPd was tested on trial cohorts, iteratively improved, and modelled for performance against an idealised association study under mutliple parameters. We also assessed the seqeuncing depath of all human exons to determine which were sufficiently well sequenced in an exome to be sued by fSNPd - by assessing forty exomes base by base. RESULTS: We describe a simple methodology for the detection of SNPs capable of causing a phenotype triggered by an environmental event. This uses cohorts of relatively small size (30-100 individuals) with the phenotype being investigated, their exomes, and thence seeks SNP allele frequencies significantly different from expected to identify potentially clinically important, protein altering SNP alleles. The strengths and weaknesses of this approach for discovering significant genetic causes of human disease are comparable to Mendelian disease mutation detection and Association Studies. CONCLUSIONS: The fSNPd methodology is another approach, and has potentially significant advantage over Association studies in needing far fewer individuals, to detect genes involved in the pathogenesis of a diseases/phenotypes. Furthermore, the SNP alleles identified alter amino acids, potentially making it easier to devise functional assays of protein function to determine pathogenicity

Exploring Pain Neurobiology: Molecular Investigation of Genetic Sensory Disorders

[Restricted]Biotechnology and Biological Sciences Research Council (BBSRC) under project reference: 1801406 and grant ID: BB/N504142/1. Research consumable costs also supported by MedImmune Ltd and AstraZeneca plc as part of iCASE studentship under supervision of Dr John Linley

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 individuals’ 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