Integrated YAC contig map of the Prader-Willi/Angelman region on chromosome 15q11-q13 with average STS spacing of 35 kb

Abstract

Prader-Willi syndrome and Angelman syndrome are associated with parent-of-origin-specific abnormalities of chromosome 15q11-q13, most frequently a deletion of an approximately 4-Mb region. Because of genomic imprinting, paternal deficiency of this region leads to PWS and maternal deficiency to AS. Additionally, this region is frequently involved in other chromosomal rearrangements including duplications, triplications, or supernumerary marker formation. A detailed physical map of this region is important for elucidating the genes and mechanisms involved in genomic imprinting, as well as for understanding the mechanism of recurrent chromosomal rearrangments. An initial YAC contig extended from D15S18 to D15S12 and was comprised of 23 YACs and 21 STSs providing an average resolution of about one STS per 200 kb. To close two gaps in this contig, YAC screening was performed using two STSs that flank the gap between D15S18 and 254B5R and three STSs located distal to the GABRA5-149A9L gap. Additionally, we developed 11 new STSs, including seven polymorphic markers. Although several groups have developed whole-genome genetic and radiation hybrid maps, the depth of coverage for 15q11-q13 has been somewhat limited and discrepancies in marker order exist between the maps. To resolve the inconsistencies and to provide a more detailed map order of STSs in this region, we have constructed an integrated YAC STS-based physical map of chromosome 15q11-q13 containing 118 YACs and 118 STSs, including 38 STRs and 49 genes/ESTs. Using an estimate of 4 Mb for the size of this region, the map provides an average STS spacing of 35 kb. This map provides a valuable resource for identification of disease genes localized to this region as well as a framework for complete DNA sequencing.

Figure 1

Refined YAC STS content map of chromosome 15q11–q13. STSs are listed vertically with STRs italicized and underlined. The region is oriented toward the centromere on the upper left and toward the telomere on the lower right. An asterisk (*) is used to indicate STSs, which also represent either known genes or ESTs. Below the STSs are horizontal lines representing YACs with the YAC name indicated. (•) A positive PCR reaction between the STS and YAC indicated. An X is used to represent a negative PCR reaction. (▪) STSs developed from YAC ends. Above the STSs is a horizontal line indicating the genetic distances between STRs present on the Genethon genetic map. The right end of y254B5, used as a hybridization probe in Mutirangura et al. (1993b), is indicated with a circled R. The brackets indicate STSs that cannot be uniquely ordered.