Genetic linkage analysis in familial breast and ovarian cancer: results from 214 families. The Breast Cancer Linkage Consortium.

Breast cancer is known to have an inherited component, consistent in some families with autosomal dominant inheritance; in such families the disease often occurs in association with ovarian cancer. Previous genetic linkage studies have established that in some such families disease occurrence is linked to markers on chromosome 17q. This paper reports the results of a collaborative linkage study involving 214 breast cancer families, including 57 breast-ovarian cancer families; this represents almost all the known families with 17q linkage data. Six markers on 17q, spanning approximately 30 cM, were typed in the families. The aims of the study were to define more precisely the localization of the disease gene, the extent of genetic heterogeneity and the characteristics of linked families and to estimate the penetrance of the 17q gene. Under the assumption of no genetic heterogeneity, the strongest linkage evidence was obtained with D17S588 (maximum LOD score [Zmax] = 21.68 at female recombination fraction [theta f] = .13) and D17S579 (Zmax = 13.02 at theta f = .16). Multipoint linkage analysis allowing for genetic heterogeneity provided evidence that the predisposing gene lies between the markers D17S588 and D17S250, an interval whose genetic length is estimated to be 8.3 cM in males and 18.0 cM in females. This position was supported over other intervals by odds of 66:1. The location of the gene with respect to D17S579 could not be determined unequivocally. Under the genetic model used in the analysis, the best estimate of the proportion of linked breast-ovarian cancer families was 1.0 (lower LOD-1 limit 0.79). In contrast, there was significant evidence of genetic heterogeneity among the families without ovarian cancer, with an estimated 45% being linked. These results suggest that a gene(s) on chromosome 17q accounts for the majority of families in which both early-onset breast cancer and ovarian cancer occur but that other genes predisposing to breast cancer exist. By examining the fit of the linkage data to different penetrance functions, the cumulative risk associated with the 17q gene was estimated to be 59% by age 50 years and 82% by age 70 years. The corresponding estimates for the breast-ovary families were 67% and 76%, and those for the families without ovarian cancer were 49% and 90%; these penetrance functions did not differ significantly from one another.     

Frequent occurrence of BRCA2 linkage in Icelandic breast cancer families and segregation of a common BRCA2 haplotype.

Cloning of a breast cancer-predisposing gene (BRCA2) on chromosome 13Q12-14 has been reported recently. We analyzed seven large Icelandic breast cancer families with markers from the BRCA2 region. Five families showed strong evidence of linkage. The maximum two-point LOD scores for the five BRCA2-linked families ranged from 1.06 to 3.19. Haplotype analyses revealed a region with identical allele sizes between the families, suggesting that they have inherited the mutation from a common ancestor. Cancer types other than breast cancer occur in individuals, segregating the affected haplotype within these families. This suggests that mutations in the gene may also confer some risk of other malignancies in both males and females.     

A low proportion of BRCA2 mutations in Finnish breast cancer families.

One hundred breast cancer families were identified at the Helsinki University Central Hospital in Finland and were screened for germ-line mutations in the coding regions and splice boundaries of the BRCA2 gene. Eight families (8%) were found to carry five different mutations, all of which are predicted to prematurely truncate the protein product. These BRCA2 families have early-onset breast cancer (mean and median age = 49 years), with four of the eight families including ovarian cancer but with no families including male breast cancer. A wide spectrum of other cancers also is seen in these families. Three mutations were identified in more than one family, and haplotype analysis in the families suggested a common founder for each recurrent mutation. One recurrent mutation, 999del5, previously has been noted as a common mutation in Iceland. The relationship between the Icelandic 999del5 mutation and the Finnish 999del5 mutation was explored by comparison of families from both countries. A common haplotype covering a minimal region intragenic to the BRCA2 gene was shared between the Icelandic and the Finnish mutation carriers.     

Estimating the power of linkage analysis in hereditary breast cancer.

Because evidence from several sources suggests the existence of a major genetic factor contributing to the risk for breast cancer, there is current interest in searching for genetic linkage between the putative cancer susceptibility gene(s) and polymorphic DNA markers. However, because of high population rates of the nongenetic form of the condition, and because of the possibility of underlying genetic heterogeneity, it is expected that the number of informative families required for detection of linkage will be greater for breast cancer than for other conditions with major genetic components. Computer simulation approaches may be useful in estimating the power of proposed linkage studies. Here we have simulated multiple genotypes for a medium-sized breast-cancer family and have analyzed the generated pedigrees with a linkage program. The effects of possible phenocopies and of genetic heterogeneity were measured by comparing the results obtained when the parameters were varied in the models. When population-based rates for sporadic cases of breast cancer were incorporated, the number of families required to detect linkage was approximately twice that expected in the absence of phenocopies. Incorrect specification of the probability of phenocopies in the analytic model did not materially alter the power of the proposed study, although significant effects on the estimated recombination fractions were noted.     

A cohort study of breast cancer risk in breast reduction patients.

Surgical reduction of the female breast (reduction mammaplasty) is very common in plastic surgery. The purpose of this study was to determine whether women who have undergone breast reduction surgery are at the same, greater, or lesser risk of developing breast cancer than women who have not undergone breast reduction surgery. This study incorporates a population-based, non-concurrent cohort linkage methodology. The Canadian Institute for Health Information hospital records were used to identify all Ontario women who had undergone breast reduction surgery in Ontario between 1979 and 1992. Three computerized probabilistic record linkages were performed. The first linkage was between a file of the 28,042 Ontario women who had undergone bilateral breast reduction surgery between April 1, 1979, and December 31, 1992, and a file of incident cancer cases among Ontario women for the calendar period 1979 to 1993. Follow-up of the cohort was undertaken starting from the date of breast reduction surgery, and vital status was ascertained as of December 31, 1993, by record linkage with the Ontario Mortality Database maintained at the Ontario Cancer Registry. The incidence of cancer in the Ontario breast reduction cohort was compared with the cancer incidence of the general Ontario population after appropriate adjustments for age and calendar time period. The expected number of cancers was calculated using the "PERSON YEARS" computer program. Within the cohort, followed for an average of 6.5 years after bilateral breast reduction surgery, 101 breast cancers were observed and 165.8 were expected, for a standardized incidence ratio of 0.61 (0.50 to 0.74, 95 percent confidence interval). This effect was independent of patient age at breast reduction. This study demonstrates that there is no increased risk of breast cancer after bilateral breast reduction surgery and, in fact, a significant decreased risk existed in women followed for an average of 6.5 years.     

A study of genetic linkage heterogeneity in 35 adult-onset polycystic kidney disease families

A genetic heterogeneity analysis of 35 kindreds with adult-onset polycystic kidney disease (ADPKD) was carried out using the D16S85, D16S84, D16S125 and D16S94 loci that are closely linked to the PKD1 locus on chromosome 16. The results show that the likelihood of two ADPKD loci is 2,514.9 times greater than for a single locus (P < 0.0001). The maximum likelihood lod score is 27.38 under heterogeneity with PKD1 lying 4.9 cM proximal to D16S85 (in males). At least 3% of kindreds are unlinked to PKD1, since the 95% confidence limits of alpha, the proportion of families linked to PKD1, are 0.54–0.97. Only 2 out of 35 kindreds (5.7%) show statistically significant evidence of non-linkage to PKD1, with conditional probabilities of 0.987 and 0.993 that the disease locus is unlinked. This confirms the existence of a small subgroup of ADPKD kindreds that are unlinked to PKD1 and provides a firm basis for genetic counselling of this population on the basis of DNA probes.     

Trends in incidence of breast cancer among women under 40 in seven European countries: A GRELL cooperative study

Young women are not usually screened for breast cancer (BC). The trends in incidence in this population may better reflect changes in risk factors. However, studies on this subject are scarce and heterogeneous. The aim of this study was to describe the trends in incidence of BC in women under 40 from 1990 to 2008, using pooled European data. Thirty-seven European population-based cancer registries from Belgium, Bulgaria, France, Italy, Portugal, Spain and Switzerland participated in this study. World age-standardized incidence rates were first analyzed graphically and then using a Poisson regression model, in order to estimate average annual percent changes (AAPCs). The overall incidence rate of BC in the area covered increased linearly during the study period by 1.19% (0.93; 1.46) on average per year. This increase varied between countries from 0.20% (?0.53; 0.64) in Bulgaria to 2.68% (1.97; 3.40) in Portugal. In Italy, after a significant rise of 2.33% (1.14; 3.54) per year, BC incidence began decreasing in 2002 by ?2.30% (?4.07; ?0.50) yearly. The rise in incidence was greater for women under 35 and for ductal carcinomas. This increase can be due to a rise in risk factors and/or changes in diagnosis and surveillance practices, but we could not clearly distinguish between these two non-exclusive explanations.     

Tests for linkage and association in nuclear families.

The transmission/disequilibrium test (TDT) originally was introduced to test for linkage between a genetic marker and a disease-susceptibility locus, in the presence of association. Recently, the TDT has been used to test for association in the presence of linkage. The motivation for this is that linkage analysis typically identifies large candidate regions, and further refinement is necessary before a search for the disease gene is begun, on the molecular level. Evidence of association and linkage may indicate which markers in the region are closest to a disease locus. As a test of linkage, transmissions from heterozygous parents to all of their affected children can be included in the TDT; however, the TDT is a valid chi2 test of association only if transmissions to unrelated affected children are used in the analysis. If the sample contains independent nuclear families with multiple affected children, then one procedure that has been used to test for association is to select randomly a single affected child from each sibship and to apply the TDT to those data. As an alternative, we propose two statistics that use data from all of the affected children. The statistics give valid chi2 tests of the null hypothesis of no association or no linkage and generally are more powerful than the TDT with a single, randomly chosen, affected child from each family.     

Chromosome 17q linkage studies of 18 Utah breast cancer kindreds.

In this paper we present linkage results from the analysis of 18 Utah breast cancer kindreds, for three 17q markers. Four kindreds had LOD scores greater than 1.0 for at least one of the marker loci. One of these kindreds has a LOD score of 6.07 with D17S579, and we believe it to be the most informative 17q family reported to date. Among the kindreds which appear unlinked to 17q were an early-onset breast cancer family, a large breast-ovarian family, and a kindred with mixed age at onset. Analysis of individual recombinants in the linked families localizes the BRCA1 gene between THRA1 and D17S579 (Mfd188). A comparison of the Cancer and Steroid Hormone Study (CASH) model and a model which assumes a rare dominant susceptibility locus with low penetrance and no phenocopies stresses the difficulties in assessing linkage if the assumptions of the CASH model in terms of age at onset of breast cancer are not appropriate for the BRCA1 locus. A hypothetical breast cancer pedigree is used to calculate gene carrier probabilities under the CASH model, thereby illustrating some of our concerns regarding the use of this model to detect and exclude 17q linkage in breast cancer families.     

Genetic linkage analysis of hemoglobin variants in 175 families.

Linkage analysis using the LIPED program developed by Ott for the analysis of whole family data was performed on 175 families with variants of the hemoglobin beta- or gamma-chain. Comparison of our results with those in the literature indicate that there is little evidence for linkage with any of the currently used markers, although there is considerable heterogeneity in lod scores between sexes for the Duffy and MNS blood groups. It is suggested that the most successful approach in the future will be to analyze markers known to be localized on chromosomes which have been indicated as likely sites of the beta-chain locus from hybridization studies.     

Linkage disequilibrium and linkage information from one-child families.

In linkage analysis a single-child family is usually considered to be completely uninformative. This article shows that such a family can provide information on linkage disequilibrium, even if it provides no information on linkage equilibrium. A transition matrix consisting of the recombination fraction and the phase proportion is proposed to study the genetic transmission from a pair of parents to their single child. The information about linkage for a single-child family is shown to be confounded by the phase proportion. This explains why such a family used to be considered uninformative under the assumption of linkage equilibrium. By reparametrizing the recombination fraction and the phase proportion into one parameter, it is demonstrated that extracting information on linkage disequilibrium is feasible. The study of power of the testing method proposed here is carried out by simulation.     

Genetic linkage analysis of prostate cancer families to Xq27-28

OBJECTIVES: A recent linkage analysis of 360 families at high risk for prostate cancer identified the q27-28 region on chromosome X as the potential location of a gene involved in prostate cancer susceptibility. Here we report on linkage analysis at this putative HPCX locus in an independent set of 186 prostate cancer families participating in the Prostate Cancer Genetic Research Study (PROGRESS). METHODS: DNA samples from these families were genotyped at 8 polymorphic markers spanning 14.3 cM of the HPCX region. RESULTS: Two-point parametric analysis of the total data set resulted in positive lod scores at only two markers, DXS984 and DXS1193, with scores of 0.628 at a recombination fraction (theta) of 0.36 and 0.012 at theta = 0.48, respectively. The stratification of pedigrees according to the assumed mode of transmission increased the evidence of linkage at DXS984 in 81 families with no evidence of male-to-male transmission (lod = 1.062 at theta = 0.28). CONCLUSIONS: Although this analysis did not show statistically significant evidence for the linkage of prostate cancer susceptibility to Xq27-28, the results are consistent with a small percentage of families being linked to this region. The analysis further highlights difficulties in replicating linkage results in an etiologically heterogeneous, complexly inherited disease.     

HLA-GLO linkage analysis in 57 informative families

The HLA-GLO linkage relationship was investigated among 37 single backcross families with 97 children and 20 double intercross families with 51 children. For the total number of families the value Zmas = 14.600 for theta = 0.060 was found. A total of 11 cross-overs between HLA and GLO were found leading to a recombination fraction of 0.067. 221 unrelated haplotypes were examined for linkage disequilibrium between HLA and GLO, and no disequilibrium was found.     

Linkage analysis with markers on 17q in 29 Swedish breast cancer families.

Recently, a putative breast cancer gene was localized to the long arm of chromosome 17. A collaboration study was undertaken to confirm linkage, to further map the gene, and to determine to what extent breast cancer families are linked to this locus. The Swedish material consisted of 29 breast cancer families in which 68 affected members were studied. Linkage analysis of breast cancer susceptibility was performed with a number of markers on 17q. In this material a weakly positive LOD score in favor of linkage was observed in a subgroup of families with early onset, while no such linkage was observed in a subgroup of families with late onset.     

Detection of eight BRCA1 mutations in 10 breast/ovarian cancer families, including 1 family with male breast cancer.

Genetic epidemiological evidence suggests that mutations in BRCA1 may be responsible for approximately one half of early onset familial breast cancer and the majority of familial breast/ovarian cancer. The recent cloning of BRCA1 allows for the direct detection of mutations, but the feasibility of presymptomatic screening for cancer susceptibility is unknown. We analyzed genomic DNA from one affected individual from each of 24 families with at least three cases of ovarian or breast cancer, using SSCP assays. Variant SSCP bands were subcloned and sequenced. Allele-specific oligonucleotide hybridization was used to verify sequence changes and to screen DNA from control individuals. Six frameshift and two missense mutations were detected in 10 different families. A frameshift mutation was detected in a male proband affected with both breast and prostate cancer. A 40-bp deletion was detected in a patient who developed intra-abdominal carcinomatosis 1 year after prophylactic oophorectomy. Mutations were detected throughout the gene, and only one was detected in more than a single family. These results provide further evidence that inherited breast and ovarian cancer can occur as a consequence of a wide array of BRCA1 mutations. These results suggests that development of a screening test for BRCA1 mutations will be technically challenging. The finding of a mutation in a family with male breast cancer, not previously thought to be related to BRCA1, also illustrates the potential difficulties of genetic counseling for individuals known to carry mutations.