High-resolution YAC fragmentation map of 1q21.

Chromosomal band 1q21 contains a number of genes, constituting the Epidermal differentiation complex (EDC), most of which are involved in the process of terminal differentiation of the human epidermis and implicated in several disorders of keratinization and cancer. The physical map of 1q21 has been refined by generating 400 YAC derivatives. These products have allowed us to localize EDC genes and additional ESTs precisely. The transcriptional map of the region has been extended by positioning 20 ESTs reported to map between D1S442 and D1S305. Eight of the ESTs are localized in two distinct clusters, confirmed by isolating PACs and chromosome 1-specific cosmids. Two of the ESTs correspond to the genes for YL1 and selenium-binding protein, both of which have potential tumor suppressor activity. Through the use of fragmented YACs and bacterial clones, the order of markers and ESTs in the region has been established as follows: cen-A002O32-Bda44g03-Cda10d12-Bdab5d06, H60056, A005K39-D1S442-WI5663-WI7969-Cx40-Cda0g e12-Cda0kh05-A002D26- A008S07-Cda0ff08-D1S498-S100A10-WI7815( THH)-WI7217(FLG)-D1S1664-INV-SPRR2A- LOR-A001X21-D1S305-tel

Fine mapping of 39 ESTs on human chromosome 6p23-p25.

Loci conferring susceptibility to schizophrenia, coeliac disease, and orofacial clefting have been assigned to the 6p23-p25 region of human chromosome 6. To facilitate the identification of candidate genes we have sublocalized and ordered 39 ESTs assigned to this interval by radiation hybrid mapping. This was achieved by generating PAC contigs containing the ESTs, genetic markers, and random STSs. For full integration into previously published data a single YAC contig spanning 6p23-p25 was used to unambiguously order the PAC contigs and ESTs along the chromosome. The majority of the ESTs (31/39) were positioned in the 6p23-p24 interval at the proximal half of the map, and of these 8 are located within a single PAC clone. The order of known genes in this region is cen-CD83-ZNF40-EDN1-(GCNT2, CAPZB)-TFAP2-BMP6-DSP-tel

An integrated map of human chromosome 6p23.

The human chromosomal band 6p23 is a Giemsa-negative (light) band that may be expected to be relatively gene rich. The genes for spinocerebellar ataxia type 1 (SCA1), guanosine monophosphate reductase (GMPR), DEK involved in a subtype of acute myeloid leukemia (AML), and the folate-sensitive fragile site FRA6A, have already been mapped to 6p23. Recent linkage data have suggested evidence for a susceptibility locus for schizophrenia in the region. We have constructed a single YAC contig of approximately 100 clones spanning the entire 6p23 band from 6p22.3 to 6p24.1 and covering 7.5-8.5 Mb of DNA. The YAC contig contains 55 markers including genetically mapped STSs, physically mapped STSs, anonymous STSs, anonymous ESTs, and ESTs from the genes mapped to the region. The order of the genetically mapped STSs is consistent with their order in the contig and some of the markers not resolved on the genetic map have been resolved by the YACs. Four of the YACs from 6p23 and covering approximately 3 Mb of DNA have been used to isolate approximately 300 cosmids from a flow-sorted human chromosome 6 cosmid library, which have been organized into pockets. The proposed susceptibility locus for schizophrenia is most closely linked to D6S260, which is located within the YAC contig along with genetic markers < or = 5 cM on either side. Therefore, the presented materials are valuable reagents for characterization of the genomic region implicated in schizophrenia

Evidence of a locus for orofacial clefting on human chromosome 6p24 and STS content map of the region.

Orofacial clefting is genetically complex, no single gene being responsible for all forms. It can, however, result from a single gene defect either as part of a syndrome (e.g. van der Woude syndrome, Treacher-Collins syndrome, velo-cardio-facial syndrome) or as an isolated phenotypic effect (e.g. X-linked cleft palate; non-syndromic, autosomal dominant orofacial clefting). Several studies have suggested that chromosome 6p is a candidate region for a locus involved in orofacial clefting. We have used YAC clones from contigs in 6p25-p23 to investigate three unrelated cases of cleft lip and palate coincident with chromosome 6p abnormalities. Case 1 has bilateral cleft lip and palate and a balanced translocation reported as 46,XY,t(6,7)(p23;q36.1). Case 2 has multiple abnormalities including cleft lip and palate and was reported as 46,XX,del(6)(p23;pter). Case 3 has bilateral cleft lip and palate and carries a balanced translocation reported as 46,XX,t(6;9)(p23;q22.3). We have identified two YAC clones, both of which cross the breakpoint in cases 1 and 3 and are deleted in case 2. These clones map to 6p24.3 and therefore suggest the presence of a locus for orofacial clefting in this region. The HGP22 and AP2 genes, potentially involved in face formation, have been found to flank this region, while F13A maps further telomeric in 6p24.3/25

Remapping the insulin gene/IDDM2 locus in type 1 diabetes.

Type 1 diabetes susceptibility at the IDDM2 locus was previously mapped to a variable number tandem repeat (VNTR) 5' of the insulin gene (INS). However, the observation of associated markers outside a 4.1-kb interval, previously considered to define the limits of IDDM2 association, raised the possibility that the VNTR association might result from linkage disequilibrium (LD) with an unknown polymorphism. We therefore identified a total of 177 polymorphisms and obtained genotypes for 75 of these in up to 434 pedigrees. We found that, whereas disease susceptibility did map to within the 4.1-kb region, there were two equally likely candidates for the causal variant, -23HphI and +1140A/C, in addition to the VNTR. Further analyses in 2,960 pedigrees did not support the difference in association between VNTR lineages that had previously enabled the exclusion of these two polymorphisms. Therefore, we were unable to rule out -23HphI and +1140A/C having an etiological effect. Our mapping results using robust regression methods show how precisely a variant for a common disease can be mapped, even within a region of strong LD, and specifically that IDDM2 maps to one or more of three common variants in a approximately 2-kb region of chromosome 11p15