Dynamic Molecular Combing: Stretching the Whole Human Genome for High-Resolution StudiesDNA in amounts representative of hundreds of eukaryotic genomes was extended on silanized surfaces by dynamic molecular combing. The precise measurement of hybridized DNA probes was achieved directly without requiring normalization. This approach was validated with the high-resolution mapping of cosmid contigs on a yeast artificial chromosome (YAC) within yeast genomic DNA. It was extended to human genomic DNA for precise measurements ranging from 7 to 150 kilobases, of gaps within a contig, and of microdeletions in the tuberous sclerosis 2 gene on patients' DNA. The simplicity, reproducibility, and precision of this approach makes it a powerful tool for a variety of genomic studies.
Allelic loss is frequent in tuberous sclerosis kidney lesions but rare in brain lesions.Tuberous sclerosis (TSC) is an autosomal dominant disorder characterized by seizures, mental retardation, and hamartomatous lesions. Although hamartomas can occur in almost any organ, they are most common in the brain, kidney, heart, and skin. Allelic loss or loss of heterozygosity (LOH) in TSC lesions has previously been reported on chromosomes 16p13 and 9q34, the locations of the TSC2 and TSC1 genes, respectively, suggesting that the TSC genes act as tumor-suppressor genes. In our study, 87 lesions from 47 TSC patients were analyzed for LOH in the TSC1 and TSC2 chromosomal regions. Three findings resulted from this analysis. First, we confirmed that the TSC1 critical region is distal to D9S149. Second, we found LOH more frequently on chromosome 16p13 than on 9q34. Of the 28 patients with angiomyolipomas or rhabdomyomas, 16p13 LOH was detected in lesions from 12 (57%) of 21 informative patients, while 9q34 LOH was detected in lesions from only 1 patient (4%). This could indicate that TSC2 tumors are more likely than TSC1 tumors to require surgical resection or that TSC2 is more common than TSC1 in our patient population. It is also possible that small regions of 9q34 LOH were missed. Lastly, LOH was found in 56% of renal angiomyolipomas and cardiac rhabdomyormas but in only 4% of TSC brain lesions. This suggests that brain lesions can result from different pathogenic mechanisms than kidney and heart lesions.
Genetic and Epigenetic Analysis of von Hippel-Lindau ( <i>VHL</i> ) Gene Alterations and Relationship with Clinical Variables in Sporadic Renal CancerGenetic and epigenetic changes in the von Hippel-Lindau (VHL) tumor suppressor gene are common in sporadic conventional renal cell carcinoma (cRCC). Further insight into the clinical significance of these changes may lead to increased biological understanding and identification of subgroups of patients differing prognostically or who may benefit from specific targeted treatments. We have comprehensively examined the VHL status in tissue samples from 115 patients undergoing nephrectomy, including 96 with sporadic cRCC. In patients with cRCC, loss of heterozygosity was found in 78.4%, mutation in 71%, and promoter methylation in 20.4% of samples. Multiplex ligation-dependent probe amplification identified intragenic copy number changes in several samples including two which were otherwise thought to be VHL-noninvolved. Overall, evidence of biallelic inactivation was found in 74.2% of patients with cRCC. Many of the mutations were novel and approximately two-thirds were potentially truncating. Examination of these and other published findings confirmed mutation hotspots affecting codons 117 and 164, and revealed a common region of mutation in codons 60 to 78. Gender-specific differences in methylation and mutation were seen, although not quite achieving statistical significance (P = 0.068 and 0.11), and a possible association between methylation and polymorphism was identified. No significant differences were seen between VHL subgroups with regard to clinicopathologic features including stage, grade, tumor size, cancer-free and overall survival, with the exception of a significant association between loss of heterozygosity and grade, although a possible trend for survival differences based on mutation location was apparent.
Mutation of the 9q34 gene TSC1 in sporadic bladder cancerThe genetics of tasting in mice VII. Glycine revisited, and the chromosomal location of<i>Sac</i>and<i>Soa</i>Previous work which appeared to show that some strains of mice taste glycine solutions as bitter has been found to be in error. The bitterness came from copper glycinate which formed in the brass drinking spouts. Taste testing with copper glycinate shows that the genetical data identifying the gene Glb are still valid. The close linkage of Glb and Rua has been confirmed. Most strains of mice prefer glycine solution to water, presumably because the glycine tastes sweet. The degree of preference for glycine is correlated with the degree of preference for other sweet substances such as saccharin or acesulfame. The gene dpa appears not to be involved. The sweetness tasting gene Sac has been mapped to chromosome 4 at 8.1 +/- 3.4 cM distal to Nppa (formerly Pnd). The bitterness tasting gene Soa is very closely linked to Prp on chromosome 6 (no recombinants among 67 backcross progeny). It is suggested that the sweetness and bitterness tasting genes have descended from a common ancestral tasting gene which existed before the tetraploidization of the genome which took place in early vertebrate evolution.