Admixture and population structure in Mexican-Mestizos based on paternal lineages

Martínez-Cortés, Gabriela; Salazar-Flores, Joel; Fernández-Rodríguez, Laura Gabriela; Rubí-Castellanos, Rodrigo; Rodríguez-Loya, Carmen; Velarde‐Félix, Jesús Salvador; Muñoz-Valle, J.F.; Parra‐Rojas, Isela; Rangel-Villalobos, Héctor

doi:10.1038/jhg.2012.67

Cited by 98 publications

(82 citation statements)

References 41 publications

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“…This could be because notwithstanding the Spanish Amerindian component, it is also likely that Chilean population has a greater European component 24 than Mexican population. 25 The results of this study, supported by previous studies, suggest that polymorphism 5557G>A in Mexican population in particular, and perhaps in Latin American population in general, confers an increase in the risk for breast cancer.…”

Section: Discussionsupporting

confidence: 80%

ATM polymorphisms IVS24-9delT, IVS38-8T>C, and 5557G>A in Mexican women with familial and/or early-onset breast cancer

Calderón-Zúñiga¹,

Ocampo-Gomez²,

López-Márquez³

et al. 2014

Salud Publica Mex

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ResumenObjetivo. Evaluar si en la población mexicana las frecuencias de los polimorfismos IVS-9delT, IVS38-8T>C y 5557G>A en casos de cáncer de mama y en controles sanos son diferentes de las encontradas en otros países. Material y métodos. Los polimorfismos IVS24-9delT, IVS38-8T>C y 5557G>A fueron analizados mediante PCR-RFLPs en 94 pacientes con CM de tipo familiar o de inicio temprano y 97 testigos seleccionadas de forma aleatoria. El análisis de la frecuencia alélica se hizo mediante χ 2 y equilibrio de HardyWeinberg. Resultados. Las frecuencias de heterocigotos fueron 5557G>A, 13% de casos, 0% de testigos (p=0.0009); IVS24-9delT, 21% de casos, 8% de testigos (p=0.0122); IVS38-8T>C, sólo un caso. 5557G>A y IVS24-9delT fueron más frecuentes en casos que en testigos. Las frecuencias alélicas encontradas en 5557G>A son similares a las descritas por González-Hormazábal en Chile. Conclusión. La similitud de resultados en este polimorfismo entre la población chilena y mexicana puede ser debida a que ambas son mestizas con un componente amerindio-español. Las diferencias encontradas podrían explicarse porque la población chilena tiene mayor componente europeo que la mexicana. AbstractObjective. To assess whether in Mexican population the frequencies of ATM polymorphisms IVS24-9delT, IVS38-8-T>C, and 5557G>A in breast cancer (BC) cases and healthy controls were different from those found in other countries. Materials and methods. Frequencies of polymorphisms conferring BC risk IVS24-9delT, IVS38-8T>C, and 5557G>A were analyzed by PCR-RFLP in 94 patients with familial and/or early onset BC, and 97 healthy controls randomly selected. Allele frequencies analysis was done using χ 2 and Hardy-Weinberg test. Results. Frequencies of heterozygous were: for 5557G>A, 13% cases, 0%controls (p=0.0009); for IVS24-9delT, 21% cases, 8% controls (p=0.0122); for IVS38-8T>C, only one case. 5557G>A and IVS24-9delT were more frequent in cases than in controls. The allelic frequencies found in 5557G>A are similar to those described by González-Hormazábal in Chile. Conclusion. The similarity of results in this polymorphism between Chilean and Mexican populations may be due to both being crossbred with an Amerindian-Spanish component, while differences may be due to fact that Chilean population has a greater European component than Mexican's.

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Section: Discussionsupporting

confidence: 80%

ATM polymorphisms IVS24-9delT, IVS38-8T>C, and 5557G>A in Mexican women with familial and/or early-onset breast cancer

Calderón-Zúñiga¹,

Ocampo-Gomez²,

López-Márquez³

et al. 2014

Salud Publica Mex

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“…While the mean estimate of admixture time for the American group was somewhat higher than expected (980 years), the lower bound of 340 years ago is reasonable. The admixture fraction estimate for the American group is also consistent with existing literature [29], [30].…”

Section: Discussionsupporting

confidence: 78%

“…Inaccuracy in the rate might also be due to ascertainment bias or the incomplete detection of the mutations at the sequencing phase. While the mean estimate is slightly lower than is found in prior work [28], [29], [30], the 95% confidence interval overlaps estimates from the prior literature. The mean estimate of the admixture time t 1 was 48 generations with a 95% confidence interval of 17 to 150 generations.…”

Section: Real Snp Datacontrasting

confidence: 44%

Coalescent-Based Method for Learning Parameters of Admixture Events from Large-Scale Genetic Variation Data

Tsai¹,

Blelloch

Ravi

et al. 2013

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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Detecting and quantifying the timing and the genetic contributions of parental populations to a hybrid population is an important but challenging problem in reconstructing evolutionary histories from genetic variation data. With the advent of high throughput genotyping technologies, new methods suitable for large-scale data are especially needed. Furthermore, existing methods typically assume the assignment of individuals into subpopulations is known, when that itself is a difficult problem often unresolved for real data. Here we propose a novel method that combines prior work for inferring non-reticulate population structures with an MCMC scheme for sampling over admixture scenarios to both identify population assignments and learn divergence times and admixture proportions for those populations using genome-scale admixed genetic variation data. We validated our method using coalescent simulations and a collection of real bovine and human variation data. On simulated sequences, our methods show better accuracy and faster runtime than leading competitive methods in estimating admixture fractions and divergence times. Analysis on the real data further shows our methods to be effective at matching our best current knowledge about the relevant populations.

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“…To be selected, the publications had to meet the following criteria: (1) published in peer‐reviewed journals, (2) with independent data, and (3) written in English. We do not include studies based on mtDNA or Y‐chromosome markers, or studies using short tandem repeats, also known as STRs, such as those conducted by Martínez‐Cortés et al (2012), Rangel‐Villalobos et al (2008), and Salazar‐Flores et al (2010). …”

Section: Methodsmentioning

confidence: 99%

Analysis of admixture proportions in seven geographical regions of the state of Guerrero, Mexico

Cahua-Pablo

Cruz

Almaguer

et al. 2017

American J Hum Biol

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ObjectiveMexico's current population structure has been defined by admixture between European, Native American, and to some extent African, groups that started in the sixteenth century. The aim of this research was to analyze the relative contributions of these continental population groups to the seven regions of the state of Guerrero, Mexico.MethodsA total of 104 ancestry informative markers were analyzed in 480 unrelated women from the seven regions of the state of Guerrero. The individual ancestry proportions were estimated using the software ADMIXMAP v3.2.ResultsThe relative Native American, European and African ancestral contributions to the whole sample were estimated to be 69%, 27%, and 1.9%, respectively. We observed significant differences in admixture proportions across the regions. The highest average Native American ancestry was found in the Montaña region and the lowest in Costa Grande. Conversely, the highest European contribution was observed in Costa Grande. The highest African contributions were observed in the regions of Costa Chica and Costa Grande.ConclusionsThe genetic structure of the population of Guerrero reflects quite well the historical processes that have occurred in this state. Native American population settlements were mainly in the regions of Montaña, Norte, and Centro, where the highest indigenous genetic contribution is observed today. European settlers came from the center of the state to regions with significant agricultural and mining activities. The highest African contributions are observed in coastal regions, in agreement with historical evidence about slave trade routes in the Americas.

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Admixture and population structure in Mexican-Mestizos based on paternal lineages

Cited by 98 publications

References 41 publications

ATM polymorphisms IVS24-9delT, IVS38-8T>C, and 5557G>A in Mexican women with familial and/or early-onset breast cancer

ATM polymorphisms IVS24-9delT, IVS38-8T>C, and 5557G>A in Mexican women with familial and/or early-onset breast cancer

Coalescent-Based Method for Learning Parameters of Admixture Events from Large-Scale Genetic Variation Data

Analysis of admixture proportions in seven geographical regions of the state of Guerrero, Mexico

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