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The Identification of Admixture Patterns Could Refine Pharmacogenetic Counseling: Analysis of a Population-Based Sample in Mexico.

ABSTRACT: Pharmacogenetic analysis has generated translational data that could be applied to guide treatments according to individual genetic variations. However, pharmacogenetic counseling in some mestizo (admixed) populations may require tailoring to different patterns of admixture. The identification and clustering of individuals with related admixture patterns in such populations could help to refine the practice of pharmacogenetic counseling. This study identifies related groups in a highly admixed population-based sample from Mexico, and analyzes the differential distribution of actionable pharmacogenetic variants. A subsample of 1728 individuals from the Mexican Genomic Database for Addiction Research (MxGDAR/Encodat) was analyzed. Genotyping was performed with the commercial PsychArray BeadChip, genome-wide ancestry was estimated using EIGENSOFT, and model-based clustering was applied to defined admixture groups. Actionable pharmacogenetic variants were identified with a query to the Pharmacogenomics Knowledge Base (PharmGKB) database, and functional prediction using the Variant Effect Predictor (VEP). Allele frequencies were compared with chi-square tests and differentiation was estimated by FST. Seven admixture groups were identified in Mexico. Some, like Group 1, Group 4, and Group 5, were found exclusively in certain geographic areas. More than 90% of the individuals, in some groups (Group 1, Group 4 and Group 5) were found in the Central-East and Southeast region of the country. MTRR p.I49M, ABCG2 p.Q141K, CHRNA5 p.D398N, SLCO2B1 rs2851069 show a low degree of differentiation between admixture groups. ANKK1 p.G318R and p.H90R, had the lowest allele frequency of Group 1. The reduction in these alleles reduces the risk of toxicity from anticancer and antihypercholesterolemic drugs. Our analysis identified different admixture patterns and described how they could be used to refine the practice of pharmacogenetic counseling for this admixed population.

SUBMITTER: Martinez-Magana JJ

PROVIDER: S-EPMC7188951 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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The Identification of Admixture Patterns Could Refine Pharmacogenetic Counseling: Analysis of a Population-Based Sample in Mexico.

Martínez-Magaña José Jaime JJ Genis-Mendoza Alma Delia AD Villatoro Velázquez Jorge Ameth JA Camarena Beatriz B Martín Del Campo Sanchez Raul R Fleiz Bautista Clara C Bustos Gamiño Marycarmen M Reséndiz Esbehidy E Aguilar Alejandro A Medina-Mora María Elena ME Nicolini Humberto H

Frontiers in pharmacology 20200422

Pharmacogenetic analysis has generated translational data that could be applied to guide treatments according to individual genetic variations. However, pharmacogenetic counseling in some <i>mestizo</i> (admixed) populations may require tailoring to different patterns of admixture. The identification and clustering of individuals with related admixture patterns in such populations could help to refine the practice of pharmacogenetic counseling. This study identifies related groups in a highly ad ...[more]

PMID: 32390825

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Project description:BackgroundBreastfeeding rates in Mexico are far from World Health Organization (WHO) recommendations with 28.8% of Exclusive Breastfeeding (EBF) under 6 months of age, according to the 2018 National Health and Nutrition Survey. Formative research has shown that culturally appropriate counseling is an effective breastfeeding intervention. The objective of the current study was to evaluate the effect of interpersonal counseling on EBF in a primary healthcare center in Tijuana, México.MethodsThis was a randomized controlled trial pilot with a sample of mothers with infants under 4 months of age from a primary care center. Participants were randomized into two groups: 1) Control group, received counseling on immunizations and standard infant feeding information, and 2) Intervention group, receiving breastfeeding counseling using a socio-ecological framework. Changes in breastfeeding attitudes, self-efficacy and EBF were evaluated at 2 months post-intervention.ResultsA total of 80 mothers completed the 2 month follow up assessment (40 in each group). The mean age at baseline was 26.4 years for mothers and 1.4 months for infants. There was a 30% increase in EBF at 2 months follow up in the intervention group and 15% decrease in the control group post-intervention. We observed a significant improvement in breastfeeding attitudes (P = 0.0001), self-efficacy (P = 0.046) and EBF (P = 0.0001) in the intervention group. Reported obstacles were discomfort of breastfeeding in public (23%), infant dissatisfaction (23%), pain (19%), insufficient milk supply (15%) and returning to work (8%).ConclusionsBreastfeeding counseling based on previous formative research improved breastfeeding attitudes, self-efficacy and practices in this population. These findings suggest that the promotion of breastfeeding utilizing a socio-ecological framework may improve breastfeeding rates by addressing the needs of women within their varying sociocultural contexts.Trial registrationACTRN: ACTRN12621000915853 . Retrospectively registered.

Project description:BACKGROUND:The Afrikaner population of South Africa is the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the Coloured populations of South Africa. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct and characteristic admixture patterns in the Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records previously estimated the contribution of non-Europeans into the Afrikaners to be between 5.5 and 7.2%. RESULTS:To investigate the genetic ancestry of the Afrikaner population today (11-13 generations after initial colonization), we genotyped approximately five million genome-wide markers in 77 Afrikaner individuals and compared their genotypes to populations across the world to determine parental source populations and admixture proportions. We found that the majority of Afrikaner ancestry (average 95.3%) came from European populations (specifically northwestern European populations), but that almost all Afrikaners had admixture from non-Europeans. The non-European admixture originated mostly from people who were brought to South Africa as slaves and, to a lesser extent, from local Khoe-San groups. Furthermore, despite a potentially small founding population, there is no sign of a recent bottleneck in the Afrikaner compared to other European populations. Admixture amongst diverse groups from Europe and elsewhere during early colonial times might have counterbalanced the effects of a small founding population. CONCLUSIONS:While Afrikaners have an ancestry predominantly from northwestern Europe, non-European admixture signals are ubiquitous in the Afrikaner population. Interesting patterns and similarities could be observed between genealogical predictions and our genetic inferences. Afrikaners today have comparable inbreeding levels to current-day European populations.

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The Identification of Admixture Patterns Could Refine Pharmacogenetic Counseling: Analysis of a Population-Based Sample in Mexico.

Publications

The Identification of Admixture Patterns Could Refine Pharmacogenetic Counseling: Analysis of a Population-Based Sample in Mexico.

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