Allelic association discriminates draft orders.

Abstract

A year ago there was hope that a finished sequence of the human genome would soon be publicly available and would give a more reliable locus order than an unconstrained radiation hybrid or genetic map. Alas, there are now different draft orders for each region, none of which may be correct because of gaps, uncertain polarity of contigs, and errors in assembly. Shortly before these drafts became available, we analysed allelic association (also called linkage disequilibrium, LD) in the FRAX region in a large sample of haplotypes (Ennis et al. 2000). We demonstrate here that this material discriminates among alternative draft orders. To express support for discrimination between two values of ?2 = ?2 ln L we use the Akaike criterion AIC = df[?2/min ?2?1]. Excluding premutations and full mutations at FMR1, all maps have 715 degrees of freedom (df) among 717 pairs of alleles after accepting L = 0 and estimating M, in the Malecot equation E(?) = Me d, where ? is the association between a pair of alleles at distance d. An AIC in excess of 2 provides evidence against a map with the larger ?2.