2 SEQUENCE-READY CONTIGS SPANNING THE 2 COPIES OF A 200-KB DUPLICATION ON HUMAN 21Q - PARTIAL SEQUENCE AND POLYMORPHISMS

Physical mapping across a duplication can be a tour de force if the re gion is larger than the size of a bacterial clone. This was the case o f the 170- to 275-kb duplication present on the long arm of chromosome 21 in normal human at 21q11.1 (proximal region) and at 21q22.1 (dista l region), which we described previously, We have constructed sequence -ready contigs of the two copies of the duplication of which all the c lones are genuine representatives of one copy or the other. This requi red the identification of four duplicon polymorphisms that are copy-sp ecific and nonallelic variations in the sequence of the STSs. Thirteen STSs were mapped inside the duplicated region and 5 outside but close to the boundaries. Among these STSs 10 were end clones from YACs, PAC s, or cosmids, and the average interval between two markers in the dup licated region was 16 kb, Eight PACs and cosmids showing minimal overl aps were selected in both copies of the duplication, Comparative seque nce analysis along the duplication showed three single-basepair change s between the two copies over 659 bp sequenced (4 STSs), suggesting th at the duplication is recent (less than 4 mya), Two CpG islands were l ocated in the duplication, but no genes were identified after a 36-kb cosmid from the proximal copy of the duplication was sequenced. The ho mology of this chromosome 21 duplicated region with the pericentromeri c regions of chromosomes 13, 2, and 18 suggests that the mechanism inv olved is probably similar to pericentromeric-directed mechanisms descr ibed in interchromosomal duplications. (C) 1998 Academic Press