Somatic deletions in hereditary breast cancers implicate 13q21 as a putative novel breast cancer susceptibility locus

Abstract

A significant proportion of familial breast cancers cannot be explained by mutations in the BRCA1 or BRCA2 genes. We applied a strategy to identify predisposition loci for breast cancer by using mathematical models to identify early somatic genetic deletions in tumor tissues followed by targeted linkage analysis. Comparative genomic hybridization was used to study 61 breast tumors from 37 breast cancer families with no identified BRCA1 or BRCA2 mutations. Branching and phylogenetic tree models predicted that loss of 13q was one of the earliest genetic events in hereditary cancers. In a Swedish family with five breast cancer cases, all analyzed tumors showed distinct 13q deletions, with the minimal region of loss at 13q21-q22. Genotyping revealed segregation of a shared 13q21 germ-line haplotype in the family. Targeted linkage analysis was carried out in a set of 77 Finnish, Icelandic, and Swedish breast cancer families with no detected BRCA1 and BRCA2 mutations. A maximum parametric two-point logarithm of odds score of 2.76 was obtained for a marker at 13q21 (D13S1308, theta = 0.10). The multipoint logarithm of odds score under heterogeneity was 3.46. The results were further evaluated by simulation to assess the probability of obtaining significant evidence in favor of linkage by chance as well as to take into account the possible influence of the BRCA2 locus, located at a recombination fraction of 0.25 from the new locus. The simulation substantiated the evidence of linkage at D13S1308 (P < 0.0017). The results warrant studies of this putative breast cancer predisposition locus in other populations.

Figure 1

A schematic representation of results from the tree analysis of nonrandom genomic alterations of BRCAX breast carcinomas. The root represents a normal diploid mammary cell, whereas only events above the 95th percentile of the distribution are shown (see text for details). (A) Shown is how the observed probabilities of events and observed joint probabilities of pairs could be used to assign a weight to each possible “edge” between pairs and events. The edge represents a putative cause-and-effect relationship between events, whereas clusters of events may define a genetic subclass of tumors. (B) The result obtained from the best fitting distance matrix, weighted Fitch tree (see text for details). Both independent probabilistic approaches thus led to the following finding: The loss of chromosome 13 seems to be an early event in the pathogenesis of BRCAX breast cancers, and it is not strongly associated with other early or late events.

Figure 2

Pedigree Lund 5 shown with the CGH profiles of chromosome 13, demonstrating loss of 13q21-q22 in all five tumors from the four affected individuals. The haplotypes with markers from 13q are shown next to the CGH profiles (the marker map is located on the left). Markers located near BRCA2 were not shared between the affected individuals (D13S260 and D13S267). At 13q21-q22, however, all five affected women shared a 7 cM haplotype (red box). Below the CGH profile of a bilateral breast cancer is the original CGH image (FITC hybridization with tumor DNA). The interstitial 13q21-q22 loss can be observed as an absence of FITC signal (green color) in the middle of the chromosome (a). Hybridization with a Texas red-labeled yeast artificial chromosome probe for marker D13S1257 demonstrates that the region of the shared haplotype coincided with the region of deletion by CGH (b).