Clinical sensitivity of BRCA1/2 testing for common founder mutations

mutations

As mentioned previously, founder effects in certain populations result in an elevated frequency of one or more specific variants in BRCA1/2 among descendants of a common group of ancestors. It is important to distinguish founder mutations from mutations that are recurrent because they arise at genetic “hot spots” but do not occur in families with a common ancestor or common haplotypes [Evans et al., 2004a].

We calculated estimates of clinical sensitivity for the testing of specific BRCA1/2 mutations from studies providing the distribution of common and non-common mutations known to confer risk in different populations with founder effects. A similar computational method as above was applied to derive minimal and maximal values. Results and key features of the original study samples are presented in Table 21, while details and calculations can be found in Appendix G.

Ashkenazi Jewish

Research in the Ashkenazi Jewish (AJ)

population has shown that one individual in 40 (~2.5%) carries one of three common point mutations: BRCA1 185delAG, BRCA1 5382insC or BRCA2 6174delT [Iau et al., 2001; Culver et al., 2000]. In contrast to the large spectrum of BRCA1/2 mutations found in heterogeneous populations, only about 30 other mutations have been found in the AJ population according to Phelan et al. [2002]. We estimated the clinical sensitivity of testing for the three common AJ BRCA1/2 mutations from the distribution of founder and non-founder mutations within AJ HBOC families. The values were 47.1 and 88.9% for Schubert et al. [1997] and 38.3 and 90% for Frank et al. [1998]. Phelan and

colleagues [2002] did not screen for non-founder mutations in the BRCA2 gene, likely

underestimating the overall proportion of non-founder mutations [Phelan et al., 2002].

In several review articles on BRCA1/2 genetic testing (published between January 2001 and June 2002), we found statements that the three common mutations account for about 90% of all BRCA mutations in the AJ population (for example, Srivastava et al. [2001]; Taylor [2001]), but no references were given for this figure. We believe that this proportion denotes the prevalence of the three mutations in high risk AJ families as reported by Tonin and colleagues [1996]. In this study of 28 families with at least two cases of breast cancer and at least two cases of ovarian cancer, 25 families carried one of the three common mutations (25/28 ≈ 90%) [Tonin et al., 1996]. However, no screening for other types of BRCA1/2 mutations was carried out among the three families who tested negative for the common mutations. Although this figure of 90% is very similar to our maximum value derived from the studies by Schubert et al.

[1997] and Frank et al. [1998], it is based on the opposite assumption, i.e., that the remaining three families are true negatives for common mutations.

Dutch

A high proportion of large rearrangements in BRCA1, including two founder mutations, was first reported in the Dutch population. According to the original study by Petrij-Bosch et al.

[1997], the clinical sensitivity for three large BRCA1 deletions in Dutch HBOC families can be estimated as 8.2 to 38.2%. Papelard and colleagues [2000] report that screening for 35 BRCA1 mutations using the DSDI (Detection of Small Deletions and Insertions) test allows for the detection of 75% of the Dutch and Belgian mutations, according to a mutation database (given as http://ruly70.medfac.leidenuniv.nl, not accessible). Among these 35 mutations, three are the large-size deletions found by Petrij-Bosch et al. [1997] and 10 are small insertions or

deletions that recur in HBOC families of Dutch and Belgian origin [Peelen et al., 1997]. It is possible that some of these mutations are recurrent rather than founder mutations.

Papelard et al. [2000] also report on the distribution of BRCA1 mutations in 370 carrier families identified in eight genetics clinics in the Netherlands. Unfortunately these data are presented according to the number of unique mutations rather than for the total number of mutations identified. The authors point out that the mutation spectrum for BRCA1 is not

complete since genetic screening in the different centers did not provide full coverage of the coding regions of the gene. In 2003, Hogervorst et al. reported on a large sample of breast and/or ovarian cancer families, in whom the estimated proportion of large BRCA1 rearrangements varied from 4.3 to 27.3%. The two founder mutations described by Petrij-Bosch et al.

[1997] were identified in 28 families out of the 33 carrying large rearrangements.

Finnish

We estimated the clinical sensitivity of testing for common BRCA1/2 mutations using two studies of Finnish families at high risk for breast or ovarian cancer (Table 21). Huusko et al.

[1998] studied families from the Oulu region (in the north of Finland) among whom five different mutations were identified; four of these were considered common and yielded clinical

sensitivity estimates of 11.4 to 91% (this particularly wide difference is due to the low proportion of mutation carriers). Vehmanen et al. [1997a, b] analysed BRCA1/2 mutations in families from other regions of Finland (Helsinki region and the southern part of the country).

Eight mutations were considered common among the 16 different mutations identified. We calculated several values for the clinical

sensitivity of testing for common mutations in these families: (1) figures of 14 to 61.9% for the eight common mutations, and (2) figures of 6.5 to 28.6% for the four common mutations which were reported in the study by Huusko et al.

[1998]. It is clear that specific testing for the four founder mutations considered by both studies is likely to be more sensitive in Oulu than in Helsinki and more southern regions.

It appears that the frequency of large BRCA1/2 genomic rearrangements in the Finnish

population is much lower than in American, French and Dutch populations, based on our point estimates. In fact, no large rearrangements in the BRCA1/2 genes were detected among 82 families from a sample of 149 families testing negative after EX/SP screening [Lahti-Domenici et al., 2001]. The authors of this study did not describe how the 82 families were selected so we cannot assess their representativeness.

Hungarian

In HBOC families of Hungarian origin, three BRCA1 mutations (185delAG, 5382insC and 300TÆG) have an important founder effect and are reported to account for as much as 80% of all BRCA1 mutations identified [van der Looij et al., 2000]. As shown in Table 21, we identified one study with which we could estimate the clinical sensitivity of screening for common mutations among high risk Hungarian families, based on the distribution of BRCA1 mutations [Ramus et al., 1997]. The figures of 21.4 to 85.7% apply only to the detection of two common mutations (BRCA1 185delAG and 5382insC).

French Canadian

Seven common BRCA mutations were initially identified in the French Canadian population [Tonin et al., 1998]. More recently two groups have presented or published data that allow for the calculation of clinical sensitivity estimates.

Simard and colleagues¹⁰⁵ performed a systematic analysis of EX/SP regions in high-risk French Canadian families and identified 4 recurrent mutations and 11 unique mutations [Simard et al., 2004] (J. Simard¹⁰⁶). The two most frequent mutations, BRCA1 C4446T and BRCA2

8765delAG, are founder mutations in this population. We calculated clinical sensitivity in a subset of 191/256 families wherein testing was performed on a member affected with cancer or an obligate carrier. For the two founder

mutations BRCA1 C4446T and BRCA2 8765delAG, the estimated clinical sensitivity values were 22 and 75% and for the four recurrent mutations, they were 24.1 and 82.1%

(Table 21). False negative results are unlikely in this study because quite a systematic and extensive EX/SP mutation analysis was performed. No genomic rearrangements were detected by MLPA analysis for the BRCA1 gene in the 135 families negative after the EX/SP screen, nor for the BRCA2 gene in 133 of these families (no MLPA analysis in BRCA2 was done for two families). Southern blot analysis

likewise revealed no large rearrangements in a sub-sample of 61 of the families negative after the EX/SP screen (in which 63 individuals were tested). These analyses suggest there are no recurrent BRCA1/2 genomic rearrangements in the French Canadian population.

The second group, Oros and colleagues [2004], screened for a panel of 20 BRCA1/2

105. Data have been extracted from an oral presentation and a poster presentation, and completed with personal communication with J. Simard (January 28, 2005).

106. 1. Oral presentation “Familial breast/ovarian cancer in the French Canadian founder population”, Oncogenetics:

Achievements and challenges. Les 17ièmes Entretiens du Centre Jacques Cartier, Oct 7-8, 2004, Montréal, Québec, Oct 7-8, 2004.

2. J. Simard, personal communication, January 28, 2005.

mutations¹⁰⁷ in a cohort of high-risk French-Canadian families. Amongst BRCA1/2 positive families, 15 distinct mutations were identified: 7 mutations were recurrent and 8 mutations were unique. Haplotype analyses suggested a founder effect for 5 mutations (BRCA1 4446C→T and 2953del3insC, BRCA2 6085G→T, 8765delAG and 3398delAAAAG). Subsequent molecular analyses of the BRCA1/2 genes were done in some negative families but these did not reveal any new variants. However, the techniques used to detect the BRCA1/2 mutations were not the same in all families (see Table 21). We calculated two sets of values of clinical sensitivity from these data: one set for the 5 founder BRCA1/2 mutations, which varied from 36.7 to 83.8%; and one set for the 7 recurrent mutations, which was only slightly higher (39 and 89.2%).

The profile of founder mutations differs somewhat in the research by Simard et al.

[2004] and Oros et al. [2004] although the two most frequent mutations are the same

(BRCA1 4446C→T and BRCA2 8765delAG ).

The clinical sensitivity estimates for

BRCA1 4446C→T and BRCA2 8765delAG were about 25 to 57% in the study by Oros and colleagues and were 22 to 75% in the study by Simard and colleagues. Of the 3 remaining founder mutations identified by Oros et al., only one mutation, BRCA1 2953del3insC, was identified by Simard et al. These differences could be due to regional founder effects, but other explanations cannot be excluded at

present. The protocols used to analyse mutations and the selection criteria differed between these studies.

Polish

In order to establish the relative contribution of founder and non-founder mutations, Gorski et al. [2004a] determined, by EX/SP sequencing, the spectrum of BRCA1/2 mutations in 200 high

107. The 20 mutations had already been identified in the French-Canadian population: BRCA1 360C→T, 1081G→A,

1623delTTAAA, 2072insG, 2953delGTAinsC, 3768insA, 3875delGTCT, 4160delAG, 4184delTCAA, 4446C→T, 5221delTG; BRCA2 2558insA, 2816insA, 3034delAAAC, 3398delAAAAG, 3773delTT, 6085G→T, 6503delTT, 7235G→A, 8765delAG.

risk families: 100 families with three or more cases of breast cancer but no ovarian cancer, and 100 families with cases of both breast and ovarian cancer. Based on this study, the clinical sensitivity of testing for three founder mutations in BRCA1, 5382insC, C16G, and 4153delA, varied from 55.5 to 86.0% in the Polish population (Table 21). Screening for a larger panel including the six most common mutations would increase the maximal estimate of clinical sensitivity from 86 to 92%.

Greek

The BRCA1 5382insC mutation seems to be the most frequent in the Greek population. On the basis of one study on 85 high risk breast and ovarian cancer families, the clinical sensitivity of the common 5382insC mutation was estimated as 8.2 to 50% [Ladopoulou et al., 2002].

8.3.3 Clinical sensitivity of the protein