SNP Filtering Summary.

<p>Variant filtering representation through the number of SNPs remaining after the various filtering steps.</p><p>The Average and Percentage remaining rows represent the average number of variants and percentage of variants remaining per family.</p>a<p>Intronic, intergenic and synonymous variants were discarded. See methods.</p>b<p>Detailed criteria for these filters is reported on the methods section.</p>c<p>Number of variants shared between the two individuals in the family.</p>d<p>Total number of final variants for all the individuals in this study.</p

Final Candidate Variants.

<p>List of final candidate variants passing all filters.</p>a<p>Chromosome in which the variant was mapped.</p>b<p>Position according to the coordinate system (HG18).</p>c<p>Variant consequence: NS = non-synonymous variant UTR3 = 3′ untranslated region variant.</p>d<p>Fisher’s Exact Test P value.</p>e<p>Odds Ratio.</p>f<p>95% confidence interval for the Odds Ratio.</p><p>N/A = not available.</p

INDEL Filtering Summary.

<p>Variant filtering representation through the number of INDELs remaining after the various filtering steps.</p><p>The Average and Percentage remaining rows represent the average number of variants and percentage of variants remaining per family.</p>a<p>Intronic and intergenic variants were discarded. See methods.</p>b<p>Detailed criteria for these filters is reported on the methods section.</p>c<p>Number of variants shared between the two individuals in the family.</p>d<p>Total number of final variants for all the individuals in this study.</p

Summary of the data analysis pipeline followed in the present study.

<p>Raw sequencing data was screened for common artifacts prior to the alignment step in a first quality control phase (QC1). High quality (QC2) genome matches were analyzed for variants, in the form of departures from a consensus reference genome. Subsequently, variants were filtered by keeping those common to both members in each family and then discarding variants present in HapMap controls and dbSNP130. Further filtering by variant consequence, score and gene function (see material and methods for details) resulted in a list of 67 snps and 14 indel candidate variants.</p