Molecular analysis of ancestry informative markers (AIMs-INDELs) in a high altitude Ecuadorian mestizo population affected with breast cancer

López‐Cortés, Andrés; Echeverría‐Garcés, Gabriela; Burgos, Germán; Zambrano, Ana Karina; Cabrera-Andrade, Alejandro; Garcí­a-Cárdenas, Jennyfer M.; Salazar, Carolina; Leone, Paola; Paz‐y‐Miño, César

doi:10.1016/j.fsigss.2017.09.102

Cited by 3 publications

(2 citation statements)

References 6 publications

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“…Ancestry informative markers (AIMs) are some of the most useful tools in addressing population, biomedical, forensics, and evolutionary questions that remain in use today [8,[31][32][33]. However it is unclear to what extent known AIMs are applicable to ancient genomic data, characterized by high missingness and haploidy [1].…”

Section: Discussionmentioning

confidence: 99%

Ancient ancestry informative markers for identifying fine-scale ancient population structure in Eurasians

Esposito

Das

Pirooznia

et al. 2018

Preprint

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The rapid accumulation of ancient human genomes from various areas and time periods potentially allows the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for modern-day populations known to misrepresent the population structure. Past studies addressed these problems using ancestry informative markers (AIMs). However, it is unclear whether AIMs derived from contemporary human genomes can capture ancient population structure and whether AIM finding methods are applicable to ancient DNA (aDNA) provided that the high missingness rates in ancient, oftentimes haploid, DNA can also distort the population structure. Here, we define ancient AIMs (aAIMs) and develop a framework to evaluate established and novel AIM-finding methods in identifying the most informative markers. We show that aAIMs identified by a novel principal component analysis (PCA)-based method outperforms all competing methods in classifying ancient individuals into populations and identifying admixed individuals. In some cases, predictions made using the aAIMs were more accurate than those made with a complete marker set. We discuss the features of the ancient Eurasian population structure and strategies to identify aAIMs. This work informs the design of population microarrays and the interpretation of aDNA results.

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Section: Discussionmentioning

confidence: 99%

Ancient ancestry informative markers for identifying fine-scale ancient population structure in Eurasians

Esposito

Das

Pirooznia

et al. 2018

Preprint

View full text Add to dashboard Cite

show abstract

“…Ancestry informative markers are some of the most useful tools in addressing population, biomedical, forensics, and evolutionary questions that remain in use today [9,48,49,50]. However, it is unclear to what extent known AIMs are applicable to ancient genomic data, which are characterized by high missingness and haploidy [1].…”

Section: Discussionmentioning

confidence: 99%

Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians

Esposito

Das

Syed

et al. 2018

Genes

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The rapid accumulation of ancient human genomes from various areas and time periods potentially enables the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for modern-day populations, which are known to misrepresent the population structure. Past studies addressed these problems by using ancestry informative markers (AIMs). It is, however, unclear whether AIMs derived from contemporary human genomes can capture ancient population structures, and whether AIM-finding methods are applicable to aDNA. Further the high missingness rates in ancient—and oftentimes haploid—DNA can also distort the population structure. Here, we define ancient AIMs (aAIMs) and develop a framework to evaluate established and novel AIM-finding methods in identifying the most informative markers. We show that aAIMs identified by a novel principal component analysis (PCA)-based method outperform all of the competing methods in classifying ancient individuals into populations and identifying admixed individuals. In some cases, predictions made using the aAIMs were more accurate than those made with a complete marker set. We discuss the features of the ancient Eurasian population structure and strategies to identify aAIMs. This work informs the design of single nucleotide polymorphism (SNP) microarrays and the interpretation of aDNA results, which enables a population-wide testing of primordialist theories.

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Genetic basis and spatial distribution of glucose-6-phosphate dehydrogenase deficiency in ecuadorian ethnic groups: a malaria perspective

Atarihuana,

Gallardo-Condor,

López-Cortés

et al. 2023

Malar J

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Background Glucose-6-phosphate dehydrogenase deficiency (G6PDd) is an X-linked disorder affecting over 400 million people worldwide. Individuals with molecular variants associated with reduced enzymatic activity are susceptible to oxidative stress in red blood cells, thereby increasing the risk of pathophysiological conditions and toxicity to anti-malarial treatments. Globally, the prevalence of G6PDd varies among populations. Accordingly, this study aims to characterize G6PDd distribution within the Ecuadorian population and to describe the spatial distribution of reported malaria cases. Methods Molecular variants associated with G6PDd were genotyped in 581 individuals from Afro-Ecuadorian, Indigenous, Mestizo, and Montubio ethnic groups. Additionally, spatial analysis was conducted to identify significant malaria clusters with high incidence rates across Ecuador, using data collected from 2010 to 2021. Results The A- c.202G > A and A- c.968T > C variants underpin the genetic basis of G6PDd in the studied population. The overall prevalence of G6PDd was 4.6% in the entire population. However, this frequency increased to 19.2% among Afro-Ecuadorian people. Spatial analysis revealed 12 malaria clusters, primarily located in the north of the country and its Amazon region, with relative risks of infection of 2.02 to 87.88. Conclusions The findings of this study hold significant implications for public health interventions, treatment strategies, and targeted efforts to mitigate the burden of malaria in Ecuador. The high prevalence of G6PDd among Afro-Ecuadorian groups in the northern endemic areas necessitates the development of comprehensive malaria eradication strategies tailored to this geographical region.

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Molecular analysis of ancestry informative markers (AIMs-INDELs) in a high altitude Ecuadorian mestizo population affected with breast cancer

Cited by 3 publications

References 6 publications

Ancient ancestry informative markers for identifying fine-scale ancient population structure in Eurasians

Ancient ancestry informative markers for identifying fine-scale ancient population structure in Eurasians

Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians

Genetic basis and spatial distribution of glucose-6-phosphate dehydrogenase deficiency in ecuadorian ethnic groups: a malaria perspective

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