FA 5 Progress Report WV-INBRE - Joan C. Edwards School of ...

Program Director/Principal Investigator (Last, First, Middle): Rankin, Gary O 66Family Affected/normal members115001 8 affected + 1 normal115021 3 affected + 1 normal115027 9 affected + 1 normal115028 4 affected + 2 normal116003 5 affected + 2 normal117005 4 affected + 1 normalTable 2. Numbers of individuals for whom exomes have been sequenced. *Some normals arerelatives and others are married in.To date, we have performed discrete filtering on family 115027. We focused our efforts on thisfamily because of the large numbers of affected members. Our filtering process considered totalSNPs and indels and contained the following stages:(1) Inclusion of all variants present in an exome but absent from the reference human genome(hg19)(2) Inclusion of all variants present in all affected members and exclusion of all variants present inone normal relative and one unrelated normal.(3) Exclusion of all variants with allele frequencies greater than 5% or 15%. (Given an autosomaldominant mode of inheritance, an affected genotype frequency of 5% (AA and Aa) and HardyWeinberg equilibrium, the mutant allele frequency would be ~2.5%.)In the filration process, we assumed that (1) the trait was transmitted as an autosomal dominantwith complete penetrance, (2) all affected members have carry the mutation, and (3) the hg19reference genome does not have the FCH mutation. After stage (1), we found an average of231,213 SNPs and 12,273 indels per family member. Retention of SNPs present in all affectedmembers and removal of SNPs present in the two normals reduced the number of SNPs to 624and indels to 47 (stage 2). When we eliminate SNPs whose allele frequency is less than 5% or15%, total SNPS are reduced to 29 or 70 SNPS, respectively (stage 3). (Indel allele frequencieshave been obtained at this time. Table 3 shows the number of shared variants after each stageVariants per stage Filter SNPS IndelsStage 1 Total (mean per subject) 231,213 12,273Stage 2 Filtered by affected-normal 624 47Stage 3 Filtered by MAF = 15% 70 NATable 3. Variants present after each filtration stage.In order to identify pathogenic SNPs, we categorized the variants as shown in Table 4. Many of thevariants were located in intronic regions or unknown (uncharacterized) loci. At the 15% minor allelefrequency cutoff, two missense variants mapped to uncharacterized open reading frames onchromosomes 1 and 17.Variant Type Minor Allele Frequency5% 15%synonymous coding SNPs 1 4intronic 8 30 (1 in ACLY in splice site)missense 0 2 (uncharacterized ORFs)Near 3’ end of gene 1 2Near 5’ end of gene 1 1Unknown (1 on Y chromosome)11 133’ untranslated region 2 13PHS 2590 (Rev. 06/09)Continuation Format Page