Amerindian Ancestry Influences Genetic Susceptibility to Chronic Obstructive Pulmonary Disease

Díaz‐Peña, Roberto; Boekstegers, Felix; Silva, Rafael S.; Jaime, Sergio Fernando; Hosgood, H. Dean; Miravitlles, Marc; Agustí, Àlvar; Bermejo, Justo Lorenzo; Olloquequi, Jordi

doi:10.3390/jpm10030093

Cited by 7 publications

(5 citation statements)

References 61 publications

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“…A total of 36 GWASs were included for full-text assessment ( Figure 1 ), but most of them were excluded for not/not directly about the etiology of COPD. The P value of 3 GWASs did not meet the threshold of 5 × 10 −8 [ 18 – 20 ], and in another 4 GWASs there was a lack of replication phases [ 21 – 24 ]. At last, 5 GWASs met the criteria for inclusion and reported 32 SNPs in or near 25 genes [ 25 – 29 ].…”

Section: Resultsmentioning

confidence: 99%

Genetic Variants Associated with Chronic Obstructive Pulmonary Disease Risk: Cumulative Epidemiological Evidence from Meta-Analyses and Genome-Wide Association Studies

Liu

Ran

et al. 2022

Canadian Respiratory Journal

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Background. Last two decades, many association studies on genetic variants and chronic obstructive pulmonary disease (COPD) risk have been published. But results from different studies are inconsistent. Therefore, we performed this article to systematically evaluate results from previous meta-analyses and genome-wide association studies (GWASs). Material and Methods. Firstly, we retrieved meta-analyses in PubMed, Embase, and China National Knowledge Infrastructure and GWASs in PubMed and GWAS catalog on or before April 7th, 2022. Then, data were extracted and screened. Finally, two main methods—Venice criteria and false-positive report probability test—were used to evaluate significant associations. Results. As a result, eighty-eight meta-analyses and 5 GWASs were deemed eligible for inclusion. Fifty variants in 26 genes obtained from meta-analyses were significantly associated with COPD risk. Cumulative epidemiological evidence of an association was graded as strong for 10 variants in 8 genes (GSTM1, CHRNA, ADAM33, SP-D, TNF-α, VDBP, HMOX1, and HHIP), moderate for 6 variants in 5 genes (PI, GSTM1, ADAM33, TNF-α, and VDBP), and weak for 40 variants in 23 genes. Five variants in 4 genes showed convincing evidence of no association with COPD risk in meta-analyses. Additionally, 29 SNPs identified in GWASs were proved to be noteworthy based on the FPRP test. Conclusion. In summary, more than half (52.38%) of genetic variants reported in previous meta-analyses showed no association with COPD risk. However, 13 variants in 9 genes had moderate to strong evidence for an association. This article can serve as a useful reference for further studies.

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Section: Resultsmentioning

confidence: 99%

Genetic Variants Associated with Chronic Obstructive Pulmonary Disease Risk: Cumulative Epidemiological Evidence from Meta-Analyses and Genome-Wide Association Studies

Liu

Ran

et al. 2022

Canadian Respiratory Journal

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“…One report evaluated the ancestral genetic contribution and SNPs associated with the risk of COPD in a Latin American population characterized by a higher proportion of European ancestry (55.93% ± 6.89) and Mapuche ancestry (35.11% ± 8.54); in this study, the authors reported alleles in PRDM15 associated with protection against COPD and SNPs in PPP1R12B associated with susceptibility [ 21 ].…”

Section: Discussionmentioning

confidence: 99%

Genetic Factors Associated with COPD Depend on the Ancestral Caucasian/Amerindian Component in the Mexican Population

et al. 2021

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Genetic variability influences the susceptibility to and severity of complex diseases; there is a lower risk of COPD in Hispanics than in non-Hispanic Caucasians. In this study, we included 830 Mexican-Mestizo subjects; 299 were patients with COPD secondary to tobacco smoking, and 531 were smokers without COPD. We employed a customized genotyping array of single nucleotide polymorphisms (SNPs). The population structure was evaluated by principal component analysis and allele association through a logistic regression model and haplotype identification. In this study, 118 individuals were identified with a high Caucasian component and 712 with a high Amerindian component. Independent of the ancestral contribution, two SNPs were associated with a reduced risk (p ≤ 0.01) of developing COPD in the CYP2A6 (rs4105144) and CYP2B6 (rs10426235) genes; however, a haplotype was associated with an increased risk of COPD (p = 0.007, OR = 2.47) in the CHRNA5-CHRNA3 loci among smokers with a high Caucasian component. In Mexican-Mestizo smokers, there are SNPs in genes that encode proteins responsible for the metabolism of nicotine associated with a lower risk of COPD; individuals with a high Caucasian component harboring a haplotype in the CHRNA5-CHRNA3 loci have a higher risk of suffering from COPD.

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“…Subsequent to DNA quality control, samples were genotyped using the Illumina Global Screening Array [ 60 ], which enabled genotyping of 754,159 genomic markers. We assessed the distribution of DMET variants considering the genetic ancestry, which was previously described and calculated [ 59 , 61 ]. After that, we compared the genotype frequencies in the Chilean population from Talca with those of five major populations from the 1000 Genomes Project ( , accessed on 1 March 2022) [ 8 ]: African, Amerindian, East and South Asian, and European.…”

Section: Methodsmentioning

confidence: 99%

Pharmacogenetic Variation and Its Clinical Relevance in a Latin American Rural Population

Olloquequi

Castro‐Santos

Díaz‐Peña

2022

IJMS

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Latin-American populations have been largely underrepresented in genomic studies of drug response and disease susceptibility. In this paper, we present a genome-wide Chilean dataset from Talca based on the Illumina Global Screening Array. This let us to compare the frequency of gene variants involved in response to drugs among our population and others, taking data from the 1000 Genomes Project. We found four single-nucleotide polymorphisms with low prevalence in Chileans when compared with African, Amerindian, East and South Asian, and European populations: rs2819742 (RYR2), rs2631367 (SLC22A5), rs1063320 (HLA-G), and rs1042522 (TP53). Moreover, two markers showed significant differences between lower and higher proportion of Mapuche ancestry groups: rs1719247 (located in an intergenic region in chromosome 15; p-value = 6.17 × 10−5, Bonferroni corrected p-value = 0.02) and rs738409 (A nonsynonymous gene variant in the PNPLA3 gene; p-value = 9.02 × 10−5, Bonferroni corrected p-value = 0.04). All of these polymorphisms have been shown to be associated with diverse pathologies, such as asthma, cancer, or chronic hepatitis B, or to be involved in a different response to drugs, such as metformin, HMG-CoA reductase inhibitors, or simvastatin. The present work provides a pharmacogenetic landscape of an understudied Latin American rural population and supports the notion that pharmacogenetic studies in admixed populations should consider ancestry for a higher accuracy of the results. Our study stresses the relevance of the pharmacogenomic research to provide guidance for a better choice of the best treatment for each individual in a population with admixed ancestry.

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Amerindian Ancestry Influences Genetic Susceptibility to Chronic Obstructive Pulmonary Disease

Cited by 7 publications

References 61 publications

Genetic Variants Associated with Chronic Obstructive Pulmonary Disease Risk: Cumulative Epidemiological Evidence from Meta-Analyses and Genome-Wide Association Studies

Genetic Variants Associated with Chronic Obstructive Pulmonary Disease Risk: Cumulative Epidemiological Evidence from Meta-Analyses and Genome-Wide Association Studies

Genetic Factors Associated with COPD Depend on the Ancestral Caucasian/Amerindian Component in the Mexican Population

Pharmacogenetic Variation and Its Clinical Relevance in a Latin American Rural Population

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