A preliminary gene map for the Van der Woude syndrome critical region derived from 900 kb of genomic sequence at 1q32-q41

Abstract

Van der Woude syndrome (VWS) is a common form of syndromic cleft lip and palate and accounts for approximately 2% of all cleft lip and palate cases. Distinguishing characteristics include cleft lip with or without cleft palate, isolated cleft palate, bilateral lip pits, hypodontia, normal intelligence, and an autosomal-dominant mode of transmission with a high degree of penetrance. Previously, the VWS locus was mapped to a 1.6-cM region in 1q32-q41 between D1S491 and D1S205, and a 4.4-Mb contig of YAC clones of this region was constructed. In the current investigation, gene-based and anonymous STSs were developed from the existing physical map and were then used to construct a contig of sequence-ready bacterial clones across the entire VWS critical region. All STSs and BAC clones were shared with the Sanger Centre, which developed a contig of PAC clones over the same region. A subset of 11 clones from both contigs was selected for high-throughput sequence analysis across the approximately 1.1-Mb region; all but two of these clones have been sequenced completely. Over 900 kb of genomic sequence, including the 350-kb VWS critical region, were analyzed and revealed novel polymorphisms, including an 8-kb deletion/insertion, and revealed 4 known genes, 11 novel genes, 9 putative genes, and 3 psuedogenes. The positional candidates LAMB3, G0S2, HIRF6, and HSD11 were excluded as the VWS gene by mutation analysis. A preliminary gene map for the VWS critical region is as follows: [see text] 41-TEL. The data provided here will help lead to the identification of the VWS gene, and this study provides a model for how laboratories that have a regional interest in the human genome can contribute to the sequencing efforts of the entire human genome.

Figure 1

Physical and gene map of the VWS critical region. The VWS critical region is defined by genetic recombinants at D1S491 and D1S205 (open box at top). The CEPH YAC clone 785B2 contains both flanking markers in the original YAC contig (Schutte et al. 1996). STS content for this YAC and each of the BAC clones is indicated by long vertical lines. Restriction sites are indicated by short vertical bars and include BssHII (B), MluI (M), NotI (N), and NruI (Nr). Parentheses indicate restriction sites that were absent on the indicated clone. The specific address for each BAC and PAC clone is shown. Sequencing of these clones is complete (thick line), partial (thick, shaded line), or only at their ends (thin lines). The sequence at the T7 (□) and Sp6 (●) ends for each BAC clone was determined. The presence and location of the 8-kb deletion/insertion polymorphism is indicated by an open rectangle. The order and orientation of genes, putative genes, and psuedogenes are indicated with arrowheads. For the putative genes VWS26, VWS37, VWS38, and VWS42, the direction of transcripton could not be deduced (flat bar). See text for definitions of genes, putative genes, and psuedogenes.

Figure 2

Comparison of gene recognition programs. Genomic sequences containing the indicated genes were analyzed for exon content with the suite of programs contained in Genotator. Exons for each gene are numbered. Those that contain part of the translated ORFs are shaded. All other shaded boxes indicate a hit with the indicated analysis program.

Figure 3

Mouse synteny map for human chromosome 1q32–q41. Ideogram (left) and genetic map (middle) for the distal end of mouse chromosome 1 are shown. Vertical rectangles at right represent syntenic region at the indicated human chromosome band.