Will the real disease gene please stand up?

Neil Shephard, Sally John, Lon Cardon, Mark I. McCarthy, Eleftheria Zeggini

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


A common dilemma arising in linkage studies of complex genetic diseases is the selection of positive signals, their follow-up with association studies and discrimination between true and false positive results. Several strategies for overcoming these issues have been devised. Using the Genetic Analysis Workshop 14 simulated dataset, we aimed to apply different analytical approaches and evaluate their performance in discerning real associations. We considered a) haplotype analyses, b) different methods adjusting for multiple testing, c) replication in a second dataset, and d) exhaustive genotyping of all markers in a sufficiently powered, large sample group. We found that haplotypebased analyses did not substantially improve over single-point analysis, although this may reflect the low levels of linkage disequilibrium simulated in the datasets provided. Multiple testing correction methods were in general found to be over-conservative. Replication of nominally positive results in a second dataset appears to be less stringent, resulting in the follow-up of false positives. Performing a comprehensive assay of all markers in a large, well-powered dataset appears to be the most effective strategy for complex disease gene identification.

Original languageEnglish
Article numberS66
JournalBMC Genetics
Issue numberSUPPL.1
StatePublished - 30 Dec 2005
Externally publishedYes


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