An integrated physical and genetic map of a 35 Mb region on chromosome Xp22.3–Xp21.3

Abstract

We have constructed a detailed physical map of the 35 Mb region spanning human chromosome Xp22.3-Xp21.3. The backbone of the map is represented by a single oriented contiguous stretch of 585 overlapping yeast artificial chromosome (YAC) clones covering the entire region. The map is formatted with 615 map objects that include 324 YACs, 185 sequence tagged sites, 28 genes, 85 chromosomal breakpoints and 37 highly polymorphic markers. Physical mapping was both guided and confirmed using 183 bins defined by chromosomal breakpoints and by overlapping regions of YAC clones. The localization of polymorphic markers in the physical map permits the integration of physical and genetic data across the region. These data establish chromosome Xp22.3-Xp21.3 as one of the best characterized large regions in the human genome. The map should greatly facilitate finer scale mapping and sequencing as well as the identification of disease genes from this portion of the human genome.

A very high density microsatellite map (1 STR / 41 kb) of 1.7 Mb on Xp22 spanning the microphthalmia with linear skin defects (MLS) syndrome critical region

“…13 Ten of these 13 loci mapped to the cosmids with a relative physical order that was consistent with previous YAC data, 13 with the exception of DXS410 which was mapped distal instead of proximal to CLCN4. Locus DXS6836, was localised between DXF22S5 and AMG, two to three bin positions away from its originally reported location.…”

“…Locus DXS6836, was localised between DXF22S5 and AMG, two to three bin positions away from its originally reported location. 13 Four other loci investigated (DXS8051, DXS7103, DXS1313 and DXS1380) did not map within the current cosmid contig boundaries. Of note, an additional STS (HUMUT280; Genbank accession #L31676) has been fortuitously localised adjacent to DXS6848 in cosmid U188H7 ( Figure 1) by homology searches from initial sequencing efforts (unpublished data).…”

“…Over 40 new polymorphic repeat markers have been developed and these, together with all relevant anchor STS markers from the larger linkage and YAC-based physical maps. 12,13 have been precisely positioned on the cosmids to unequivocally correlate genetic and physical distances. The microsatellites have been used to analyse breakpoint positions in three MLS patients with Xp22 cytogenetic abnormalities and to search for submicroscopic deletions in two exceptional karyotypically normal cases with features of MLS.…”

Opitz G/BBB syndrome, a defect of midline development, is due to mutations in a new RING finger gene on Xp22

“…To localize the Xp22 inversion breakpoint, we performed fluorescence in situ hybridization (FISH) on chro mosome spreads from individuals carrying the inverted X chro mosome and a normal control, using as probes YAC clones known to map to Xp22 (ref. 20). The overlapping YACs 184F6 and 61B3 (ref.…”

Generation of a transcription map of a 1 Mbase region containing the HFE gene (6p22)

“…• 899G1-1, ALUG7, ALUG12, 792G12-3 are four anonymous probes obtained by Alu-PCR from YAC 899G1, 790G7 and 792G12 using a mix 1:4 of ALUJ/ALUS primers 5 and PCR conditions of: annealing 58°C for 1', and extension 72°C for 2' for 35 cycles. Aliquots of the PCR products or specific ALU bands were isolated from low-melting agarose gel and used as probes.…”