LD based locus assignment and its error sources. At the example of chromosome 8q21.11, LD-based locus assignment is given for 6 exemplary SNPs (blue box). LD information is given by a color scale displaying the LD-measure r2 with red depicting strong LD, blue low LD and white no LD. Example SNPs in LD are connected with black dashed lines. In the gray boxes, the two error sources of automated locus assignment are given. An assignment error I occurs if two variants not in LD, i.e. in two independent LD blocks, are located in the same gene, intergenic region or gene desert and thus are assigned the same locus. Here, this is the case for the variants rs-A/rs-B and rs-E/rs-F, respectively. The consequence of this type of error is a shared association on the locus level not mirrored on the variant level. An assignment error II is introduced if two variants are in LD but diverge in their assigned locus. Here, this is the case for rs-C and rs-D. Due to such abnormalities in the LD data the link between both variants is lost if only the locus level is considered.
Arnold et al. BMC Genomics 2012 13:490 doi:10.1186/1471-2164-13-490