Jamila Alessandra Perini

The Genomic Ancestry of Individuals from Different Geographical Regions of Brazil Is More Uniform Than Expected

Based on pre-DNA racial/color methodology, clinical and pharmacological trials have traditionally considered the different geographical regions of Brazil as being very heterogeneous. We wished to ascertain how such diversity of regional color categories correlated with ancestry. Using a panel of 40 validated ancestry-informative insertion-deletion DNA polymorphisms we estimated individually the European, African and Amerindian ancestry components of 934 self-categorized White, Brown or Black Brazilians from the four most populous regions of the Country. We unraveled great ancestral diversity between and within the different regions. Especially, color categories in the northern part of Brazil diverged significantly in their ancestry proportions from their counterparts in the southern part of the Country, indicating that diverse regional semantics were being used in the self-classification as White, Brown or Black. To circumvent these regional subjective differences in color perception, we estimated the general ancestry proportions of each of the four regions in a form independent of color considerations. For that, we multiplied the proportions of a given ancestry in a given color category by the official census information about the proportion of that color category in the specific region, to arrive at a “total ancestry” estimate. Once such a calculation was performed, there emerged a much higher level of uniformity than previously expected. In all regions studied, the European ancestry was predominant, with proportions ranging from 60.6% in the Northeast to 77.7% in the South. We propose that the immigration of six million Europeans to Brazil in the 19th and 20th centuries - a phenomenon described and intended as the “whitening of Brazil” - is in large part responsible for dissipating previous ancestry dissimilarities that reflected region-specific population histories. These findings, of both clinical and sociological importance for Brazil, should also be relevant to other countries with ancestrally admixed populations.

Pharmacogenetics of warfarin: development of a dosing algorithm for brazilian patients.

A dosing algorithm including genetic (VKORC1 and CYP2C9 genotypes) and nongenetic factors (age, weight, therapeutic indication, and cotreatment with amiodarone or simvastatin) explained 51% of the variance in stable weekly warfarin doses in 390 patients attending an anticoagulant clinic in a Brazilian public hospital. The VKORC1 3673G>A genotype was the most important predictor of warfarin dose, with a partial R2 value of 23.9%. Replacing the VKORC1 3673G>A genotype with VKORC1 diplotype did not increase the algorithms predictive power. We suggest that three other single‐nucleotide polymorphisms (SNPs) (5808T>G, 6853G>C, and 9041G>A) that are in strong linkage disequilibrium (LD) with 3673G>A would be equally good predictors of the warfarin dose requirement. The algorithms predictive power was similar across the self‐identified “race/color” subsets. “Race/color” was not associated with stable warfarin dose in the multiple regression model, although the required warfarin dose was significantly lower (P = 0.006) in white (29 ± 13 mg/week, n = 196) than in black patients (35 ± 15 mg/week, n = 76).

CYP2C9 genotypes and the pharmacokinetics of tenoxicam in Brazilians

Cytochrome P450 (CYP) 2C9, the product of the polymorphic gene CYP2C9, provides the major catabolic pathway for several anti‐inflammatory drugs, including tenoxicam. Our objectives were (1) to determine the frequency of 2 common CYP2C9 variant alleles (*2 and *3) in the Brazilian population and (2) to evaluate the effects of these polymorphisms on the pharmacokinetics of tenoxicam.

Impact of CYP4F2 rs2108622 on the Stable Warfarin Dose in an Admixed Patient Cohort

There is controversy regarding the association between the CYP4F2 rs2108622 (V33M) polymorphism and warfarin dose requirement in white patients, and there are no data for nonwhite populations. We observed no association in self‐identified white, black, or “intermediate” Brazilian patients (n = 370). The addition of the rs2108622 genotype as a variable has only a marginal effect on the predictive power of a warfarin dosing algorithm derived from this patient cohort. We conclude that prospective CYP4F2 genotyping is not justified in Brazilians who are potential candidates for warfarin therapy.

Global pharmacogenomics: Impact of population diversity on the distribution of polymorphisms in the CYP2C cluster among Brazilians.

The impact of biogeographical ancestry, self-reported ‘race/color’ and geographical origin on the frequency distribution of 10 CYP2C functional polymorphisms (CYP2C8*2, *3, *4, CYP2C9*2, *3, *5, *11, CYP2C19*2, *3 and *17) and their haplotypes was assessed in a representative cohort of the Brazilian population (n=1034). TaqMan assays were used for allele discrimination at each CYP2C locus investigated. Individual proportions of European, African and Amerindian biogeographical ancestry were estimated using a panel of insertion-deletion polymorphisms. Multinomial log-linear models were applied to infer the statistical association between the CYP2C alleles and haplotypes (response variables), and biogeographical ancestry, self-reported Color and geographical origin (explanatory variables). The results showed that CYP2C19*3, CYP2C9*5 and CYP2C9*11 were rare alleles (<1%), the frequency of other variants ranged from 3.4% (CYP2C8*4) to 17.3% (CYP2C19*17). Two distinct haplotype blocks were identified: block 1 consists of three single nucleotide polymorphisms (SNPs) (CYP2C19*17, CYP2C19*2 and CYP2C9*2) and block 2 of six SNPs (CYP2C9*11, CYP2C9*3, CYP2C9*5, CYP2C8*2, CYP2C8*4 and CYP2C8*3). Diplotype analysis generated 41 haplotypes, of which eight had frequencies greater than 1% and together accounted for 96.4% of the overall genetic diversity. The distribution of CYP2C8 and CYP2C9 (but not CYP2C19) alleles, and of CYP2C haplotypes was significantly associated with self-reported Color and with the individual proportions of European and African genetic ancestry, irrespective of Color self-identification. The individual odds of having alleles CYP2C8*2, CYP2C8*3, CYP2C9*2 and CYP2C9*3, and haplotypes including these alleles, varied continuously as the proportion of European ancestry increased. Collectively, these data strongly suggest that the intrinsic heterogeneity of the Brazilian population must be acknowledged in the design and interpretation of pharmacogenomic studies of the CYP2C cluster in order to avoid spurious conclusions based on improper matching of study cohorts. This conclusion extends to other polymorphic pharmacogenes among Brazilians, and most likely to other admixed populations of the Americas.

Influence of CYP2C9 genotypes on the pharmacokinetics and pharmacodynamics of piroxicam.

Our objective was to evaluate the influence of cytochrome P450 (CYP) 2C9 polymorphisms on the pharmacokinetics and pharmacodynamics of the nonsteroidal anti‐inflammatory drug piroxicam.

Relative contribution of VKORC1, CYP2C9, and INR response to warfarin stable dose.

To the editor: Li et al reported recently in Blood that much of the information provided by CYP2C9 and VKORC1 genotypes during warfarin initiation therapy in outpatients is captured by early international normalized ratio (INR) responses.[1][1] This confirms and extends previous observations in

Exploring warfarin pharmacogenomics with the extreme-discordant-phenotype methodology: impact of FVII polymorphisms on stable anticoagulation with warfarin

PurposeTo explore the pharmacogenomics of warfarin using the extreme-discordant-phenotype (EDP) methodology.MethodsThe target phenotype was the stable warfarin dose prescribed to 353 patients. Pharmacogenetic polymorphisms assessed were coagulation factor VII (FVII) -401G>T and FVII -402G>A, VKORC1 3673G>A, and CYP2C9*2, *3, *5, and *11 alleles. The EDP analyses contrasted the frequencies of these polymorphisms at different cutoff points (5th through 30th percentiles of the warfarin dose distribution) at opposite ends of the warfarin dose distribution.ResultsSignificant differences existed in FVII -402G>A genotype frequency at the 5th percentile with an over-representation of the wildtype GG genotype at low warfarin doses and in VKORC1 3673G>A and CYP2C9 polymorphisms at all cutoff points where the variant alleles were overrepresented at low warfarin doses.ConclusionThe EDP methodology provides increased statistical power for detection of small contributions of genetic polymorphisms to multiplex drug-response phenotypes, such as warfarin dose requirement for adequate anticoagulation.

VKORC1 polymorphisms in Amerindian populations of Brazil

Noncoding polymorphisms in the VKORC1 gene associate with variation of interindividual dosing requirements of warfarin and other coumarin anticoagulants. The frequency of VKORC1 polymorphisms displays distinct interpopulation differences. Here, we report the distribution of the VKORC1 3673G>A, 5808T>G, 6853G>C and 9041G>A SNPs in three endogamous Amerindian (Native American) populations, namely, Guarani-Kaiowá, Guarani-Nandeva and Kaingang. Individual DNA from 180 healthy adults was genotyped for the VKORC1 polymorphisms using TaqMan Detection System assays. The ARLEQUIN 3.1 software package was used to estimate haplotype frequency and linkage disequilibrium. The VKORC1 3673G>A, 5808T>G, 6853G>C and 9041G>A polymorphisms were in Hardy-Weinberg equilibrium in each population. The 5808G allele was absent or rare (<3%), whereas 3673A, 6853C and 9041A were frequent (34-63%) in the three Amerindian populations. No difference was detected in allele or genotype frequency bewteen the two Guarani populations, whereas significant differences were observed between Kaingang and Guarani. Polymorphisms 3673G>A, 6853G>C and 9041G>A were in significant linkage disequilibrium in both Guarani and Kaingang (pairwise r2 values: 0.77-1.0). Haplotypes ATCG and GTGA accounted for more than 94% of the haplotypes in both populations, ATCG being the most common in Guarani (49.5%) and GTGA in Kaingang (54%). These data disclose the uniqueness of the frequency distribution of the VKORC1 SNPs in the Amerindians, compared with Asian, African and European populations. In view of the vast interpopulational diversity among Amerindians, the present data should not be interpreted as representative of other extant Amerindian peoples. Our estimates that 40% of Kaingang and 60% of Guarani have haplotypes including the variant 3673A allele suggest that these two Amerindian populations comprise high proportions of individuals requiring reduced warfarin doses.

Detection of CYP2C9*5 in a White Brazilian Subject

o the Editor: The polymorphic CYP2C9 gene encodes the cytochrome 450 (CYP) enzyme CYP2C9, responsible for the inactivaion of a wide range of clinically important drugs. In this ournal we recently reported the frequency of CYP2C9*2 C430T) and CYP2C9*3 (A1075C) alleles in Brazilians, who ere classified as white, black, and intermediate (pardo in ortuguese) according to the Brazilian Census. During subequent deoxyribonucleic acid (DNA) sequencing analysis, e detected the C1080G transversion in exon 7, which denes the CYP2C9*5 allele, in a self-identified white individal. This result at first seems inconsistent with reports that YP2C9*5 is absent in Europeans and their descendants; ndeed, this allele has been previously detected only in Afrian Americans and Sub-Saharan Africans. This apparent iscordance, in addition to the awareness of extensive admixure in the Brazilian population, prompted a genealogic tudy of the proband and DNA sequencing of the subject’s arents and 2 brothers for the CYP2C9*5 polymorphism. The se of ancestry-informative markers developed for the trihyrid Brazilian population revealed that the relative contribuions of European, African, and Amerindian roots to the roband’s genetic pool were 92.0%, 7.5%, and 0.5%, respecively (Fig 1). Significantly, the mitochondrial DNA markers or matrilineal inheritance of the proband indicated the presnce of haplotype L3d, characteristic of Western African opulations. The G1080C transversion occurred also in the other and one brother (both self-identified as intermediate) ut not in the father and the other brother (both self-declared s white). Thus the CYP2C9*5 allele in the proband and one rother were inherited from the matrilineal, African ancestry. These results highlight the dilemma of global extrapolation f pharmacogenomic data, an issue that is all the more perinent because interethnic crosses are increasingly common in any, if not most, populations. Although differences in the revalence of pharmacologically relevant genetic polymorhisms across populations are well documented, rarely, if ver, is a given polymorphism present or absent exclusively n 1 of the 3 major continental populations (African, Asian, nd European) that have been more extensively investigated. his notion is consistent with the current observation of the YP2C9*5 allele in a white Brazilian. This case emphasizes he hazards (previously stressed by us) of equating color or race” with geographic ancestry and of interchangeably using (