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Genomic Regions 10q22.2, 17q21.31, and 2p23.1 Can Contribute to a Lower Lung Function in African Descent Populations.

ABSTRACT: Accumulated evidence supports the contribution of genetic factors in modulating airway function, especially ancestry. We investigated whether genetic polymorphisms can affect lung function in a mixed Brazilian child population using the admixture mapping strategy through RFMix software version 1.5.4 (Stanford University, Stanford, CA, USA), followed by fine mapping, to identify regions whereby local African or European ancestry is associated with lung function measured by the forced expiratory volume in the first second (FEV1)/forced vital capacity (FVC) ratio, an indicator of airway obstruction. The research cohort included 958 individuals aged 4 to 11 years enrolled in the SCAALA (Social Change, Asthma, Allergy in Latin America) Program. We identified that African ancestry at 17q21.31, 10q22.2, and 2p23.1 regions was associated with lower lung function measured by FEV1/FVC p < 1.9 × 10-4. In contrast, European ancestry at 17q21.31 showed an opposite effect. Fine mapping pointed out 5 single nucleotide polymorphisms (SNPs) also associated in our replication cohort (rs10999948, rs373831475, rs8068257, rs6744555, and rs1520322). Our results suggest that genomic regions associated with ancestry may contribute to differences in lung function measurements in African American children in Brazil replicated in a cohort of Brazilian adults. The analysis strategy used in this work is especially important for phenotypes, such as lung function, which has considerable disparities in terms of measurements across different populations.

SUBMITTER: Fonseca H

PROVIDER: S-EPMC7565985 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Genomic Regions 10q22.2, 17q21.31, and 2p23.1 Can Contribute to a Lower Lung Function in African Descent Populations.

Fonseca Héllen H da Silva Thiago M TM Saraiva Mariana M Santolalla Meddly L ML Sant'Anna Hanaisa P HP Araujo Nathalia M NM Lima Natália P NP Rios Raimon R Tarazona-Santos Eduardo E Horta Bernardo L BL Cruz Alvaro A Barreto Mauricio L ML Figueiredo Camila A CA

Genes 20200904 9

Accumulated evidence supports the contribution of genetic factors in modulating airway function, especially ancestry. We investigated whether genetic polymorphisms can affect lung function in a mixed Brazilian child population using the admixture mapping strategy through RFMix software version 1.5.4 (Stanford University, Stanford, CA, USA), followed by fine mapping, to identify regions whereby local African or European ancestry is associated with lung function measured by the forced expiratory v ...[more]

PMID: 32899814

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Project description:Background: Predicting undiagnosed diabetes is a critical step toward addressing the diabetes epidemic in populations of African descent worldwide. Objective: To review characteristics of equations developed, tested, or modified to predict diabetes in African descent populations. Methods: Using PubMed, Scopus, and Embase databases, a scoping review yielded 585 research articles. After removal of duplicates (n = 205), 380 articles were reviewed. After title and abstract review 328 articles did not meet inclusion criteria and were excluded. Fifty-two articles were retained. However, full text review revealed that 44 of the 52 articles did not report findings by AROC or C-statistic in African descent populations. Therefore, eight articles remained. Results: The 8 articles reported on a total of 15 prediction equation studies. The prediction equations were of two types. Prevalence prediction equations (n = 9) detected undiagnosed diabetes and were based on non-invasive variables only. Non-invasive variables included demographics, blood pressure and measures of body size. Incidence prediction equations (n = 6) predicted risk of developing diabetes and used either non-invasive variables or both non-invasive and invasive. Invasive variables required blood tests and included fasting glucose, high density lipoprotein-cholesterol (HDL), triglycerides (TG), and A1C. Prevalence prediction studies were conducted in the United States, Africa and Europe. Incidence prediction studies were conducted only in the United States. In all these studies, the performance of diabetes prediction equations was assessed by area under the receiver operator characteristics curve (AROC) or the C-statistic. Therefore, we evaluated the efficacy of these equations based on standard criteria, specifically discrimination by either AROC or C-statistic were defined as: Poor (0.50 - 0.69); Acceptable (0.70 - 0.79); Excellent (0.80 - 0.89); or Outstanding (0.90 - 1.00). Prediction equations based only on non-invasive variables reported to have poor to acceptable detection of diabetes with AROC or C-statistic 0.64 - 0.79. In contrast, prediction equations which were based on both non-invasive and invasive variables had excellent diabetes detection with AROC or C-statistic 0.80 - 0.82. Conclusion: Equations which use a combination of non-invasive and invasive variables appear to be superior in the prediction of diabetes in African descent populations than equations that rely on non-invasive variables alone.

Project description:BackgroundThe ancestry of African-descended Americans is known to be drawn from three distinct populations: African, European, and Native American. While many studies consider this continental admixture, few account for the genetically distinct sources of ancestry within Africa--the continent with the highest genetic variation. Here, we dissect the within-Africa genetic ancestry of various populations of the Americas self-identified as having primarily African ancestry using uniparentally inherited mitochondrial DNA.Methods and principal findingsWe first confirmed that our results obtained using uniparentally-derived group admixture estimates are correlated with the average autosomal-derived individual admixture estimates (hence are relevant to genomic ancestry) by assessing continental admixture using both types of markers (mtDNA and Y-chromosome vs. ancestry informative markers). We then focused on the within-Africa maternal ancestry, mining our comprehensive database of published mtDNA variation (?5800 individuals from 143 African populations) that helped us thoroughly dissect the African mtDNA pool. Using this well-defined African mtDNA variation, we quantified the relative contributions of maternal genetic ancestry from multiple W/WC/SW/SE (West to South East) African populations to the different pools of today's African-descended Americans of North and South America and the Caribbean.ConclusionsOur analysis revealed that both continental admixture and within-Africa admixture may be critical to achieving an adequate understanding of the ancestry of African-descended Americans. While continental ancestry reflects gender-specific admixture processes influenced by different socio-historical practices in the Americas, the within-Africa maternal ancestry reflects the diverse colonial histories of the slave trade. We have confirmed that there is a genetic thread connecting Africa and the Americas, where each colonial system supplied their colonies in the Americas with slaves from African colonies they controlled or that were available for them at the time. This historical connection is reflected in different relative contributions from populations of W/WC/SW/SE Africa to geographically distinct Africa-derived populations of the Americas, adding to the complexity of genomic ancestry in groups ostensibly united by the same demographic label.

Dataset Information

Genomic Regions 10q22.2, 17q21.31, and 2p23.1 Can Contribute to a Lower Lung Function in African Descent Populations.

Publications

Genomic Regions 10q22.2, 17q21.31, and 2p23.1 Can Contribute to a Lower Lung Function in African Descent Populations.

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