Genetic testing for mutations in the breast cancer susceptibility genes BRCA1 and BRCA2 was underway by the mid-1990 s and is now commonly performed. Important decisions regarding the clinical ...management of individuals from high-risk families are often made based on whether the proband carries a pathogenic variant or not. However, test results are often confounding. In addition to sequence variants that are highly likely to cause disease (for example, protein-truncating mutations that result from a number of different kinds of underlying sequence alterations), clinical mutation screening often reveals missense substitutions, potential splicing variants, and/or small in-frame insertion–deletion variants (indels) that are initially classified as variants of uncertain clinical significance (variously referred to as unclassified clinical variants, UCVs; variants of uncertain significance, VUSs; and unclassified variants
There is a clear genetic component to prostate cancer susceptibility. Regions reported to be linked to prostate cancer include 1q24–25 (
HPC-1), 1q42.2–43, and Xq27–28. There is limited genetic ...information on familial prostate tumors. We used the Utah Population Database to identify familial prostate cancer cases and selected 35 cases from high-risk families. Tissue blocks containing discernable tumor were available from 19 cases; 13 of these yielded adequate specimens for analysis. Six cases came from families with linkage to HPC-1, 3 were known to have linkage to Xq27–28, and 4 had no linkage to a known locus; 7 cases were analyzed from patients who showed no known linkage (sporadic tumors) as controls. These paraffin-embedded tumors were laser microdissected, degenerate oligonucleotide (DOP)-amplified, and labeled for fluorescence detection by comparative genomic hybridization (CGH). Loss of 7q, 10q, and 16q and gain of 8q were common abnormalities present in both familial and sporadic tumors. Distinctive abnormalities included loss of 3p12–3p22 in 3 of 6
HPC-1-linked cases and in 2 of 3 X-linked cases and gain of 6q11–6q21 in 2 each of
HPC-1 and X-linked tumors. In conclusion, laser microdissection, DOP-PCR, and CGH is a feasible method for analysis of paraffin-embedded prostate tumors. This study provides preliminary data suggesting that familial prostate cancer harbors some unique genetic changes when compared with sporadic prostate tumors.
The VH1-related human protein (VHR) gene was localized to human chromosome 17q21 in a region thought to contain the BRCA1 locus, a locus that confers susceptibility to breast and ovarian cancer. VHR ...encodes a phosphatase with dual specificity for tyrosine and serine residues. Thus it is a plausible candidate for a tumor suppressor gene such as BRCA1. To test this possibility, the VHR coding sequence was screened in individuals with familial breast cancer and in sporadic breast tumor and breast cancer cell lines. No mutations were detected, suggesting that the VHR gene is not BRCA1.
An integrated approach involving physical mapping, identification of transcribed sequences, and computational analysis of genomic sequence was used to generate a detailed transcription map of the ...1.0-Mb region containing the breast cancer susceptibility locusBRCA2on chromosome 13q12–q13. This region is included in the genetic interval bounded byD13S1444andD13S310.Retrieved sequences from exon amplification or hybrid selection procedures were grouped into physical intervals and subsequently grouped into transcription units by clone overlap. Overlap was established by direct hybridization, cDNA library screening, PCR cDNA linking (island hopping), and/or sequence alignment. Extensive genomic sequencing was performed in an effort to understand transcription unit organization. In total, approximately 500 kb of genomic sequence was completed. The transcription units were further characterized by hybridization to RNA from a series of human tissues. Evidence for seven genes, two putative pseudogenes, and nine additional putative transcription units was obtained. One of the transcription units was recently identified as BRCA2 but all others are novel genes of unknown function as only limited alignment to sequences in public databases was observed. One large gene with a transcript size of 10.7 kb showed significant similarity to a gene predicted by theCaenorhabditis elegansgenome and theSaccharomyces cerevisiaegenome sequencing efforts, while another contained a motif sequence similar to the human 2′, 3′ cyclic nucleotide 3′ phosphodiesterase gene. Several retrieved transcribed sequences were not aligned into transcription units because no corresponding cDNAs were obtained when screening libraries or because of a lack of definitive evidence for splicing signals or putative coding sequence based on computational analysis. However, the presence of additional genes in the BRCA2 interval is suggested as groups of putative exons and hybrid selected clones that were transcribed in consistent orientations could be localized to common physical intervals.
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