Following the convention introduced in (4), the ‘Gene’ node has a score of 1 for all genes and its contribution to the overall score takes into account SNP/gene functional properties using a mechanism called the ‘link index’. In general, the link index is used to describe the strength or the manner in which a connection is made to a node. Missense mutations, for example, have a default link index of 2 and so the contribution of the ‘Gene’ node becomes 2*1 = 2. The overall score is the sum of the contributions S =∑ LiSi over the link indices Li and scores Si of the nodes. The link index of the gene node is completely determined by the user for SNP/gene transcript functional properties. These include nonsense, frameshift, missense and 5′and 3′-UTR designations. The SNP/gene transcript functional properties we used are from dbSNP build 130 (8). The 5′- and 3′-UTR specifications imply only that SNPs are located in these ends of the transcribed region; there is currently no additional information on putative promoters, transcription factor binding sites or other regulatory data.
