Genetic ancestry, admixture and health determinants in Latin America
Abstract Background Modern Latin American populations were formed via genetic admixture among ancestral source populations from Africa, the Americas and Europe. We are interested in studying how combinations of genetic ancestry in admixed Latin American populations may impact genomic determinants of...
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| Format: | Article |
| Language: | English |
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BMC
2018-12-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-5195-7 |
| _version_ | 1818408644610359296 |
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| author | Emily T. Norris Lu Wang Andrew B. Conley Lavanya Rishishwar Leonardo Mariño-Ramírez Augusto Valderrama-Aguirre I. King Jordan |
| author_facet | Emily T. Norris Lu Wang Andrew B. Conley Lavanya Rishishwar Leonardo Mariño-Ramírez Augusto Valderrama-Aguirre I. King Jordan |
| author_sort | Emily T. Norris |
| collection | DOAJ |
| description | Abstract Background Modern Latin American populations were formed via genetic admixture among ancestral source populations from Africa, the Americas and Europe. We are interested in studying how combinations of genetic ancestry in admixed Latin American populations may impact genomic determinants of health and disease. For this study, we characterized the impact of ancestry and admixture on genetic variants that underlie health- and disease-related phenotypes in population genomic samples from Colombia, Mexico, Peru, and Puerto Rico. Results We analyzed a total of 347 admixed Latin American genomes along with 1102 putative ancestral source genomes from Africans, Europeans, and Native Americans. We characterized the genetic ancestry, relatedness, and admixture patterns for each of the admixed Latin American genomes, finding a spectrum of ancestry proportions within and between populations. We then identified single nucleotide polymorphisms (SNPs) with anomalous ancestry-enrichment patterns, i.e. SNPs that exist in any given Latin American population at a higher frequency than expected based on the population’s genetic ancestry profile. For this set of ancestry-enriched SNPs, we inspected their phenotypic impact on disease, metabolism, and the immune system. All four of the Latin American populations show ancestry-enrichment for a number of shared pathways, yielding evidence of similar selection pressures on these populations during their evolution. For example, all four populations show ancestry-enriched SNPs in multiple genes from immune system pathways, such as the cytokine receptor interaction, T cell receptor signaling, and antigen presentation pathways. We also found SNPs with excess African or European ancestry that are associated with ancestry-specific gene expression patterns and play crucial roles in the immune system and infectious disease responses. Genes from both the innate and adaptive immune system were found to be regulated by ancestry-enriched SNPs with population-specific regulatory effects. Conclusions Ancestry-enriched SNPs in Latin American populations have a substantial effect on health- and disease-related phenotypes. The concordant impact observed for same phenotypes across populations points to a process of adaptive introgression, whereby ancestry-enriched SNPs with specific functional utility appear to have been retained in modern populations by virtue of their effects on health and fitness. |
| first_indexed | 2024-12-14T09:47:01Z |
| format | Article |
| id | doaj.art-7066a60fd5ce4262b443c0d7c7415c5f |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T09:47:01Z |
| publishDate | 2018-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-7066a60fd5ce4262b443c0d7c7415c5f2022-12-21T23:07:36ZengBMCBMC Genomics1471-21642018-12-0119S8758710.1186/s12864-018-5195-7Genetic ancestry, admixture and health determinants in Latin AmericaEmily T. Norris0Lu Wang1Andrew B. Conley2Lavanya Rishishwar3Leonardo Mariño-Ramírez4Augusto Valderrama-Aguirre5I. King Jordan6School of Biological Sciences, Georgia Institute of TechnologySchool of Biological Sciences, Georgia Institute of TechnologyIHRC-Georgia Tech Applied Bioinformatics Laboratory (ABiL)School of Biological Sciences, Georgia Institute of TechnologyPanAmerican Bioinformatics InstitutePanAmerican Bioinformatics InstituteSchool of Biological Sciences, Georgia Institute of TechnologyAbstract Background Modern Latin American populations were formed via genetic admixture among ancestral source populations from Africa, the Americas and Europe. We are interested in studying how combinations of genetic ancestry in admixed Latin American populations may impact genomic determinants of health and disease. For this study, we characterized the impact of ancestry and admixture on genetic variants that underlie health- and disease-related phenotypes in population genomic samples from Colombia, Mexico, Peru, and Puerto Rico. Results We analyzed a total of 347 admixed Latin American genomes along with 1102 putative ancestral source genomes from Africans, Europeans, and Native Americans. We characterized the genetic ancestry, relatedness, and admixture patterns for each of the admixed Latin American genomes, finding a spectrum of ancestry proportions within and between populations. We then identified single nucleotide polymorphisms (SNPs) with anomalous ancestry-enrichment patterns, i.e. SNPs that exist in any given Latin American population at a higher frequency than expected based on the population’s genetic ancestry profile. For this set of ancestry-enriched SNPs, we inspected their phenotypic impact on disease, metabolism, and the immune system. All four of the Latin American populations show ancestry-enrichment for a number of shared pathways, yielding evidence of similar selection pressures on these populations during their evolution. For example, all four populations show ancestry-enriched SNPs in multiple genes from immune system pathways, such as the cytokine receptor interaction, T cell receptor signaling, and antigen presentation pathways. We also found SNPs with excess African or European ancestry that are associated with ancestry-specific gene expression patterns and play crucial roles in the immune system and infectious disease responses. Genes from both the innate and adaptive immune system were found to be regulated by ancestry-enriched SNPs with population-specific regulatory effects. Conclusions Ancestry-enriched SNPs in Latin American populations have a substantial effect on health- and disease-related phenotypes. The concordant impact observed for same phenotypes across populations points to a process of adaptive introgression, whereby ancestry-enriched SNPs with specific functional utility appear to have been retained in modern populations by virtue of their effects on health and fitness.http://link.springer.com/article/10.1186/s12864-018-5195-7Genetic ancestryAdmixtureAncestry-enrichmentAdaptive introgressionHealthDisease |
| spellingShingle | Emily T. Norris Lu Wang Andrew B. Conley Lavanya Rishishwar Leonardo Mariño-Ramírez Augusto Valderrama-Aguirre I. King Jordan Genetic ancestry, admixture and health determinants in Latin America BMC Genomics Genetic ancestry Admixture Ancestry-enrichment Adaptive introgression Health Disease |
| title | Genetic ancestry, admixture and health determinants in Latin America |
| title_full | Genetic ancestry, admixture and health determinants in Latin America |
| title_fullStr | Genetic ancestry, admixture and health determinants in Latin America |
| title_full_unstemmed | Genetic ancestry, admixture and health determinants in Latin America |
| title_short | Genetic ancestry, admixture and health determinants in Latin America |
| title_sort | genetic ancestry admixture and health determinants in latin america |
| topic | Genetic ancestry Admixture Ancestry-enrichment Adaptive introgression Health Disease |
| url | http://link.springer.com/article/10.1186/s12864-018-5195-7 |
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