Supplementary information: Ethnic variations in the Brazilian population
It is widely recognized that population stratification may be a confounding factor in genetic association studies and the impact of stratification in population-based association studies has been discussed extensively (1-3). With respect to the polymorphisms analyzed here, especially PIN3 and PEX4, previous studies demonstrate that allelic and genotypic frequencies are distributed differentially according to ethnic background. For instance, in a case-control study performed by Weston et al. (1997) on the association of TP53 polymorphisms and breast cancer risk in individuals from the ethnically heterogeneous population of New York city, PEX4 and PIN3 allele frequencies were significantly different between Caucasian, Hispanic and African-american individuals (4). These differences were also shown by Marcel et al. (2010) who analyzed 90 Caucasian, Asian and African individuals from the Hapmap dataset (5). Thus, it is be reasonable to consider that population structure interferes with association studies that involve these polymorphisms, in particular in the case of populations reputed as ethnically diverse and heterogeneous such as the population of Brazil.
In the context of the present study, however, both the information available on the population structure in Southern Brazil and our data on phenotypic and genotypic variations among the subjects we have recruited, support that the impact of population structure on allele distributions and associations are, at the most, limited, and do not significantly bias our results. This interpretation is based on the following considerations:
1. Landmark studies conducted with a large number of Brazilian subjects have concluded that the current Brazilians have contributions of different continental ancestries (European, Amerindian and African). However the proportion of the contribution of these parental stocks varies significantly among different Brazilian regions. In one of such recent molecular analyses, Pena and collaborators (2011) demonstrated that European ancestry was predominant in all Brazilian regions, with proportions ranging from around 60% in the Northeast to around 80% in the South (6), corroborating previous studies that show that populations from Southern Brazil have a major European contribution (7-10). Thus, Southern Brazil (including the State of Rio Grande do Sul and the city of Porto Alegre, where the study was conducted), has the largest proportion of European contribution in the country. This has been demonstrated in several studies, where populations from this region have been described as having “transplanted European genomes” (9). Furthermore, even in individuals who self-declare themselves as “Black”, the genomic European contribution is highly significant (6, 7). This first point argues in favor of a less heterogeneous study population with a predominance of European genomes and ancestry, as defined by population-based studies
2. When analyzing self-reported skin color, which in Brazil is commonly used as surrogate to define an equivalent of “race” or ethnic background (6, 11), patients were separated in two groups: “white” (women who defined themselves with Caucasian features) and “non-white” (women that identified themselves with features suggestive of some level of African ancestry, such as “mulato” or “pardo”). No significant difference in the distribution of self-denominated skin color was observed among the four study subgroups. As expected from previous population-based studies in the region of Porto Alegre, Rio Grande do Sul, the majority of individuals in all four groups self-denominated them as “white”, corroborating with the previous assumptions described in argument 1 (see Table S1).
3. When analyzing allele frequencies of TP53 polymorphisms PIN3 and PEX4, no significant differences were observed between any of the 4 subgroups of the present study (IVF, END, Fertile and Unselected) and allele frequencies reported in other studies on European populations (see Table S3).
References
1. Thomas DC, Witte JS. Point: population stratification: a problem for case-control studies of candidate-gene associations? Cancer Epidemiol Biomarkers Prev 2002 Jun; 11(6): 505-512.
2. Wacholder S, Rothman N, Caporaso N. Counterpoint: bias from population stratification is not a major threat to the validity of conclusions from epidemiological studies of common polymorphisms and cancer. Cancer Epidemiol Biomarkers Prev 2002 Jun; 11(6): 513-520.
3. Wang H, Haiman CA, Kolonel LN, Henderson BE, Wilkens LR, Le Marchand L, et al. Self-reported ethnicity, genetic structure and the impact of population stratification in a multiethnic study. Hum Genet 2010 Aug; 128(2): 165-177.
4. Weston A, Pan CF, Ksieski HB, Wallenstein S, Berkowitz GS, Tartter PI, et al. p53 haplotype determination in breast cancer. Cancer Epidemiol Biomarkers Prev 1997 Feb; 6(2): 105-112.
5. Marcel V, Palmero EI, Falagan-Lotsch P, Martel-Planche G, Ashton-Prolla P, Olivier M, et al. TP53 PIN3 and MDM2 SNP309 polymorphisms as genetic modifiers in the Li-Fraumeni syndrome: impact on age at first diagnosis. J Med Genet 2010 Nov; 46(11): 766-772.
6. Pena SD, Di Pietro G, Fuchshuber-Moraes M, Genro JP, Hutz MH, Kehdy Fde S, et al. The genomic ancestry of individuals from different geographical regions of Brazil is more uniform than expected. PLoS One 2011; 6(2): e17063.
7. Salzano FM BM. The Evolution and Genetics of Latin American Populations. Cambridge University Press: Cambridge, 2002, 509 pppp.
8. Parra FC, Amado RC, Lambertucci JR, Rocha J, Antunes CM, Pena SD. Color and genomic ancestry in Brazilians. Proc Natl Acad Sci U S A 2003 Jan 7; 100(1): 177-182.
9. Marrero AR, Das Neves Leite FP, De Almeida Carvalho B, Peres LM, Kommers TC, Da Cruz IM, et al. Heterogeneity of the genome ancestry of individuals classified as White in the state of Rio Grande do Sul, Brazil. Am J Hum Biol 2005 Jul-Aug; 17(4): 496-506.
10. Zembrzuski VM, Callegari-Jacques SM, Hutz MH. Application of an African Ancestry Index as a genomic control approach in a Brazilian population. Ann Hum Genet 2006 Nov; 70(Pt 6): 822-828.
11. Guerreiro-Junior V, Bisso-Machado R, Marrero A, Hunemeier T, Salzano FM, Bortolini MC. Genetic signatures of parental contribution in black and white populations in Brazil. Genet Mol Biol 2009 Jan; 32(1): 1-11.