The spectrum of BRCA1 and BRCA2 alleles in Latin America and the Caribbean: a clinical perspective

In recent years, increasing accessibility of next-generation sequencing (NGS) has resulted in its increased use in clinical genetic testing [25]. NGS approaches allows the cost-effective interrogation of multiple targets and has driven the expansion from BRCA1 and BRCA2 testing to the so-called ‘panel testing,’ in which a number of additional high- and moderate-penetrance hereditary cancer genes (demonstrated and suspected) are included [26]. Despite these advances, the cost of comprehensive BRCA1 and BRCA2 analysis is still prohibitive for low income individuals in these countries. Importantly, although the technical sensitivity of these assays is very high and virtually all variants can be accurately detected, our ability to clinically annotate these variants has lagged.

As a solution, amplicon-based single-site panels of recurrent Latin American BRCA pathogenic variants that would constitute the first line of screening of at-risk individuals prior to performing comprehensive BRCA analysis have been developed. Such model of tiered testing has been widely successful in the Ashkenazi Jewish population in which three common pathogenic variants explain 78.4 % of the cases [27]. The development of a clinically useful panel in Latin America will require knowledge of the pathogenic variant spectrum in each region or country and depend on the presence of recurrent variants explaining a majority of the hereditary breast and ovarian cancer cases.

To provide a comprehensive picture we have conducted a literature review of the BRCA1 and BRCA2 variants identified in Latin America (Supplementary Fig. 1). Between 1994 and August 2015, 33 publications reported BRCA variants in populations from 13 countries of Central and South America, the Caribbean, and Hispanic/Latino populations from the US. Taken together, these studies have screened a total of 4835 individuals and identified 167 different pathogenic variants (Supplementary Table 1). Table 1 summarizes the characteristics of the cohorts, the prevalence of the BRCA variants reported, and screening methods for each of the study reviewed.

The size of the cohorts ranged from 19 to 815 individuals, the majority identified through hospital or clinic-based recruitment strategies (Table 1). Several methodological factors preclude a systematic comparison across studies. There was significant variation in the inclusion criteria from unselected cases to cases selected for family history and/or personal history criteria such as age of onset and tumor molecular profile. Indirect mutation detection methods or approaches that restrict the search to panels of known mutations are expected to detect only a fraction of the variants present in the sample screened. For instance, the sensitivity of single-stranded conformation polymorphism (SSCP) ranges from 50 to 96 %, while conformation-sensitive gel electrophoresis (CSGE) and for the protein truncation test (PTT) are estimated to detect only 75 and 76 % of the BRCA1 and BRCA2 variants, respectively [28].

Early BRCA testing focused on the detection of single nucleotide variants (point mutations) and small insertions or deletions rather than large genomic rearrangements. The prevalence of such rearrangement variants has been shown to vary significantly in different populations [29]. Large genomic rearrangements may account for up to 21.4 % of the BRCA inactivating variants in high-risk patients from Latin America and the Caribbean [30]. In Hispanics from the Northern California Breast Cancer Family Registry, the BRCA1 deletion of exon 9–12 represented over 10 % of the BRCA1 pathogenic variants identified [31]. In Puerto Rico, the BRCA2 exon 1–2 deletion is one of the three most frequent pathogenic variants, accounting for 18 % of the BRCA cases [32]. Less than half of the studies reviewed reported screening for large scale rearrangements and only four reported performing comprehensive screening through Multiplex Ligation-dependent Probe Amplification (MLPA) (Table 1). As a result of these factors, the prevalence and the diversity of the BRCA pathogenic variants may be underestimated in several of the published studies.

Despite those limitations, some observations stand out. In unselected breast cancer cases from Brazil [33], Colombia [34, 35], Cuba [36], Mexico [37, 38], and Peru [39], the prevalence ranged between 1.2 and 4.9 %, which is similar to what has been reported for US non-Hispanic White populations [40]. One exception is in the Bahamas, where it is estimated that 27.1 % of breast cancer cases were carriers of a BRCA pathogenic variant, regardless of age of onset or family history of cancers [41, 42].

Currently, recommendations to offer genetic testing for hereditary cancers are based on family history and/or personal history suggestive of Hereditary Breast and Ovarian Cancer. Recently, this practice has been challenged and screening every woman as part of the routine medical examination has been proposed [43]. The high prevalence in the Bahamas provides an argument in favor of a more aggressive BRCA screening approach in such populations.

It is expected that countries for which smaller cohorts were screened show less diversity in the BRCA variants identified, not because they are less genetically diverse but rather as a consequence of the limitations associated with sample size in characterizing rare variants. This is exemplified by Brazil [33, 44‐48], Mexico [37, 38, 49‐52], and in US Hispanics [31, 53‐57] where the number of different pathogenic variants detected ranged from 37 to 45 as a result of over 1300 individuals screened (Table 2). Variants such as 185delAG, 5382insC, and R1443X are among the 20 most frequent BRCA1 variants reported by the Breast Cancer Information Core (BIC) database (http://​research.​nhgri.​nih.​gov/​bic/​), and it is therefore not surprising that they are recurrent in several countries of Latin America as well. In contrast, BRCA1 A1708E was among the 10 most frequent pathogenic variants in Latin America, observed in four different countries, but is not one of the most frequent BRCA1 variants overall. This represents an example of a recurrent pathogenic variant specific to these populations. Interestingly, the ratio of BRCA1 to BRCA2 carriers also shows significant variations across Latin America. In most populations, BRCA1 variants are more frequent than BRCA2, and this holds true for most countries of Latin America. However, in Costa Rica [58], Cuba [36], Puerto Rico [32], and Uruguay [59], over 80 % of the carriers had a pathogenic variant in BRCA2. This observation has important clinical implications as the characteristics of the cancer spectrum, and tumor pathology is expected to differ according to the gene mutated [60]. For instance, BRCA1 and BRCA2 carriers show differences in both overall risk of developing breast and ovarian cancer and age distribution of risk [13]. Cancers associated with BRCA1 germline mutations are more frequently medullary of high mitotic counts, while BRCA2-associated cancers have higher score for tubule formation with lower mitotic counts [61]. Compared to sporadic breast tumors, basal subtype markers are more common in tumors arising in BRCA1 carriers [62] but not in BRCA2 carriers [63]. In contrast, BRCA2-associated tumors are more likely to be of the luminal subtype and estrogen receptor positive when compared to controls [64].

In some countries, a few recurrent variants explain the majority of cases linked to BRCA-inactivation. As a result, a PCR-based MassARRAY (Sequenom) panel of recurrent mutations, the HISPANEL, was developed in the US and validated among US Hispanic and Mexican populations. Compared with direct sequencing, this approach was estimated to have a sensitivity of 68 % but for a fraction of the cost, which is an important factor to consider in countries where resources are limited. Such an approach could be considered for Colombia where despite having identified 63 carriers in 1195 individuals screened, three recurrent variants explained over 88 % of the cases [34, 35, 65, 66]. On the other hand, this strategy may not be adequate for countries such Argentina [67], Uruguay [59], and Venezuela [68] where most recurrent pathogenic variants are not frequent. (Table 2).

In addition, the question remains whether this panel could be transferable from one country to another. The E1308X variant is the most frequent in Puerto Rico and has been observed in the US but has not been observed in any other countries of Latin America. Within Latin America, only 8.02 % (n = 13) of the pathogenic variants reported were present in two or more countries. Caution should also be taken in studying US Hispanic to make inferences about the populations of origin of these immigrants. The BRCA2 6174delT variant was one of the most frequently observed in Latin America (except for Mexico) but has still not been reported in US Hispanics. Many of the recurrent variants found in Chile [69, 70] have not been observed in US Hispanics. Overall, of the 167 BRCA pathogenic variants identified in this literature review, only 10.4 % (n = 17) were shared between US Hispanics and Latin America. While these observations may be the result of the limited sample sizes available for some of the countries, it suggests that the Latin America immigrants established in the US might not represent the genetics of their populations of origin in their complexity. It is also a reflection of the demographics of the US Hispanic populations, where countries like Mexico and Puerto Rico are overrepresented. As illustrated by the network of interaction of recurrent BRCA variants between the Latin America countries (Fig. 1), it can be observed that the most frequent variants are more likely to be shared across countries, but a significant number of recurrent variants are found in one country only. Therefore, the available data, even though limited, suggest that the development of a low-cost Latin American screening panel that would be widely offered is unlikely as a result of the limited overlap in the spectrum of reported BRCA1 and BRCA2 variants in Latin America and US Hispanics.

The genetic makeup of modern populations in Latin America is a combination of pre-Colombian and colonial heritage, both in the diversity of the gene pools imported in the Americas and their subsequent admixture. Accordingly, heterogeneity in admixture patterns has been shown to vary significantly across and within the continent [71‐76]. From the 15th century, the European colonial migration to the New World nearly decimated the Native American populations [77]. European founders were mainly of Spanish and Portuguese origin but also reflected the diversity of the Iberian peninsula [71]. During the Atlantic trade between 1451 and 1870, an estimated nine million slaves were brought to the Americas from the West Coast of Africa [78]. In the context of testing for hereditary cancer predisposition variants, data from the 1000 Genomes Consortium demonstrated that rare variants are more likely to be specific to a continent or country than common variants [79], suggesting that one should account for the diversity of the populations inhabiting Latin America when designing screening and prevention strategies.

Some recurrent pathogenic variants in the populations from Latin America can be associated with documented migration events. The origin of the Jewish pathogenic variant BRCA1 185delAG can be traced back to 1492 when, coinciding with the start of the colonization of the Americas, Jews were forced to convert or be expelled from the Iberian Peninsula. In the view of the long-lasting genetic admixture of Sephardic and Ashkenazi Jews, and following migration of Jews into the countries of South and North America, it is not surprising that typical founder Jewish mutations are commonly found in the modern Argentina, Peru, Brazil, Chile, and US Hispanics. In some cases, haplotype analysis has confirmed that the origin of the 185delAG in populations from Latin America was in fact the same as the Jewish founder mutation [57].

Fewer recurrent variants are traced back to the African continent, despite a significant contribution of African ancestry to the genetic pool of some of the populations of Latin America. Among the factors proposed to explain, this observation is the exceptional genetic diversity both within Africa and in the numerous ethnic groups that were brought to the Americas during the Atlantic slave trade. One exception is the BRCA1 943ins10 mutation, which is the most frequently pathogenic variant reported in African-Americans by Myriad Genetics Laboratories, representing 10 % of the 279 African-American BRCA pathogenic variants [80]. The presence of a single haplotype in families from the Ivory Coast, Florida, Southeastern US, and the Bahamas is consistent with a founder effect originating in West Africa [81].

Taken together, these examples indicate that the mutation spectrum of each Latin American population is expected to be strongly linked to their migration history. Hence, one could extrapolate that the extent of the overlap in the frequent BRCA mutations observed between countries will be, at least in part, determined by the shared events and interchanges that characterize the migration history of each geographical region. The BRCA1 deletion of exons 9–12 is a recurrent pathogenic variant observed in unrelated families of Mexican origin, which are geographically dispersed in the US [31, 82]. Haplotype analysis pointed to a founder effect of a variant that would have originated in Amerindian or Mestizo populations [82]. Other examples include a BRCA1 3450del4 identified in multiple breast and ovarian cancer patients from Brazil [45, 47], Chile [70], and Colombia [34, 35, 65, 66], which is also common in breast cancer populations from Spain [83] and Portugal [84]. In contrast, the BRCA1 5382insC founder pathogenic variant is most frequently reported in Brazil by several independent studies [33, 44, 45, 48] but has not been observed elsewhere in South America with the exception of an Ashkenazi community in Argentina [67]. This indicates that the genetic background of the Latin American populations is also shaped by events leading to unique population structures within and between countries.

Caution should be taken when making inferences about the origin of BRCA variants based solely on the co-occurrence in two populations. In the absence of haplotype analysis, one cannot distinguish whether a variant has migrated from one historically linked geographic area to another or is the result of independent mutational events. Therefore, not all carriers of the recurrent pathogenic variants or well-known founder mutations are expected to share a common ancestor. For example, BRCA2 3034del4 is a recurrent variant, which was also observed as a de novo germline mutation in a case of early onset breast cancer with no strong family history of cancer [85]. In families of Northern Europe Caucasian ancestry, this same mutation was observed in seven different countries and showed considerable haplotype diversity [86]. Haplotype analyses have identified multiple origins for several other recurrent mutations, including BRCA1 185delAG [87]. This suggests that some regions of the BRCA1 and BRCA2 genes might be prone to mutations. It is also noteworthy in light of the small proportion of studies who conduct mutation screening in the context of haplotype analysis. Finally, de novo variants may also be underreported as the majority of individuals undergoing BRCA testing are selected for having strong family history of cancer.

While hereditary clinical testing of Latin American and US Hispanic populations could greatly benefit from a better understanding of the mutation spectrum in the BRCA genes, social-economic aspects of genetic testing will also need to be addressed to improve access. In its policy statement on genetic and genomic testing, ASCO emphasizes the role of the informed consent process and recommends that cancer genetic susceptibility testing be conducted in the context of pre- and post-testing genetic counseling [88]. Positive outcomes associated with testing may be limited in the absence of genetic counseling and integrated clinical management structure ensuring that carriers are engaged in appropriate screening and prevention programs. Given that Hispanics in the US are 1.8 times more likely to receive an inconclusive result (variant of uncertain significance) [80], the participation of genetics professionals pre- and post-testing becomes especially important to provide support to the patients and physicians. Finally, a negative test results in the absence of a known mutation in the family may provide a false reassurance, especially when testing is not conducted in the context of extended panels of genes [89].

Studies reporting on awareness and access to genetic testing in Latin America are sparse, but the situation in the US has been more documented. In a cross-sectional analysis of 46,276 women who underwent BRCA genetic testing between 1996 and 2006, only 4.2 % were of Latin American ethnicity [80]. In a US sample of 1414 women diagnosed with breast cancer at or before 40 years of age between 2004 and 2007, Hispanic women were significantly less likely to be tested for BRCA1 and BRCA2 mutations [90]. This disparity in access to cancer genetic testing is especially alarming knowing that the Hispanic population accounts for approximately 16.3 % of the US population [21]. Genetic testing awareness has been shown to be significantly lower in Hispanics of the US when compared to non-Hispanic whites [91]. Acculturation, especially the use of the English language, strongly correlated with awareness of genetic testing for cancer in the US [92]. Once informed, participants held favorable attitudes toward risk assessment and counseling [93, 94]. In some parts of Latin America, limited resources both monetary and in the availability of trained genetic professional may impede accessibility to cancer genetic testing. Recently, BRCA1/2 telephone counseling was shown to be as effective in providing psychological support and guiding informed decisions [95]. This might contribute to improve access to genetic counseling in Latin American, especially in rural setting.