Inferring the Most Likely Geographical Origin of mtDNA Sequence Profiles

Egeland, Thore; Bøvelstad, Hege; Storvik, Geir; Salas, Antonio

doi:10.1046/j.1529-8817.2004.00109.x

Cited by 35 publications

(32 citation statements)

References 20 publications

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“…For the examples in this paper, principal component analysis (PCA) and discriminant analysis, as explained in [17], is appropriate. A general disadvantage of PCA is the lack of scale invariance.…”

Section: Databases B = (B 1 …B G )mentioning

confidence: 99%

“…If this is not the case, scaling to unit variance is advisable. The first three examples deal with dichotomized mtDNA data (the data is on the form explained in ) [17] and the data should not be scaled prior to PCA. For the Y-chromosome data, the data matrix is scaled to have unit variance since the different markers are potentially on different scales (a transformation of the YSTRs profiles to a binary form could also be carried out, as in the case of the mtDNA data).…”

Section: Databases B = (B 1 …B G )mentioning

confidence: 99%

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Statistical Evaluation of Haploid Genetic Evidence

Egeland¹,

Salas²

2008

TOFORSJ

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A variety of forensic cases need to be based on haploid DNA. The statistical evaluation of the genetic evidence in such cases requires particular attention and methods. There may be considerable differences between databases and this must be accounted for when there is uncertainty about the population origin of the perpetrator. We here assume access to the relevant databases sampled from populations that the perpetrator may conceivably come from. Intuitively, if there are strong reasons to claim that a specific database is particularly relevant, the likelihood ratio should be influenced accordingly. Moreover, the haploid evidence is typically weaker than for nuclear DNA and there is therefore a greater need to assess uncertainty; here we have chosen the bootstrap method. We also discuss the ability of the proposed method to account for population stratification when computing the LR. A pilot implementation of the haploeve software is freely available.

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Section: Databases B = (B 1 …B G )mentioning

confidence: 99%

Section: Databases B = (B 1 …B G )mentioning

confidence: 99%

Statistical Evaluation of Haploid Genetic Evidence

Egeland¹,

Salas²

2008

TOFORSJ

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“…Several studies have indicated the feasibility of inferring the probable geographic origin of an individual from the sequence of the hypervariable regions (HV) of mitochondrial genome. These studies clearly demonstrate that the mitochondrial sequence alone does not determine one's ethnicity, by presenting exclusively maternal inheritance 1,10 .…”

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confidence: 79%

Relação entre a etnia auto-declarada, haplogrupo mitocondrial e ancestralidade genômica em indivíduos do sudeste brasileiro.

et al. 2013

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Cardena, MMSG; Santos, AR; Santos, S; Mansur, AJ; Pereira, AC; Fridman, C. Relação entre a etnia auto--declarada, haplogrupo mitocondrial e ancestralidade genômica em indivíduos do sudeste brasileiro. Saúde, Ética & Justiça. 2013;18(Ed. Especial):62-6. RESUMO:Em populações onde há um alto grau de miscigenação, como no Brasil, o uso exclusivo de informações da etnia auto-declarada não é um bom método de classifi cação étnica. Neste trabalho, nós avaliamos a relação entre as etnias auto-declaradas com ancestralidade genômica e haplogrupos mitocondriais em 492 indivíduos do Sudeste Brasileiro. Haplogrupos mitocondriais foram obtidos pela análise das regiões hipervariáveis do DNA mitocondrial (mtDNA) e a ancestralidade genômica foi obtida utilizando 48 marcadores autossômicos informativos de ancestralidade (AIM). Dos 492 indivíduos, 74,6% se auto-declararam brancos, 13,8% pardos e 10,4% pretos. Em relação aos haplogrupos mitocondriais, 46,3% apresentaram mtDNA Africano e a maior contribuição de ancestralidade genômica foi Europeia (57,4%). Quando realizamos a distribuição do mtDNA e ancestralidade genômica de acordo com as etnias auto-declaradas, dos 367 indivíduos auto-declarados brancos, encontramos 37,6% com mtDNA Africano, sendo observado maior contribuição de ancestralidade Europeia (63,3%). Dos 68 indivíduos auto-declarados pardos, 25% apresentaram mtDNA Ameríndio e pouca diferença na contribuição de ancestralidade Europeia e Africana. Dos 51 indivíduos auto-declarados pretos, 80,4% apresentaram mtDNA Africano e maior contribuição de ancestralidade Africana (55,6%). A população brasileira apresenta uma uniformidade de ancestralidade genômica Ameríndia, e apenas o uso de marcadores genéticos (autossômico e mitocondrial) foi capaz de capturar essa informação. Sugerimos que estudos epidemiológicos façam o uso associado destes métodos, pois poderiam fornecer informações complementares.

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“…pcLOCATE is similar Fine-Scale Estimation of Birthplaceto the linear discriminant analysis method (Egeland et al 2004) recently employed to differentiate between several rural villages in three European countries (O'Dushlaine et al 2010). Like pcLOCATE, the method uses PCs for prediction and assumes that PC values are normally distributed in each town.…”

Section: Discussionmentioning

confidence: 99%

Fine-Scale Estimation of Location of Birth from Genome-Wide Single-Nucleotide Polymorphism Data

et al. 2012

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Systematic nonrandom mating in populations results in genetic stratification and is predominantly caused by geographic separation, providing the opportunity to infer individuals' birthplace from genetic data. Such inference has been demonstrated for individuals' country of birth, but here we use data from the Northern Finland Birth Cohort 1966 (NFBC1966) to investigate the characteristics of genetic structure within a population and subsequently develop a method for inferring location to a finer scale. Principal component analysis (PCA) shows that while the first PCs are particularly informative for location, there is also location information in the higher-order PCs, but it cannot be captured by a linear model. We introduce a new method, pcLOCATE, which is able to exploit this information to improve the accuracy of location inference. pcLOCATE uses individuals' PC values to estimate the probability of birth in each town and then averages over all towns to give an estimated longitude and latitude of birth using a fully Bayesian model. We apply pcLOCATE to the NFBC1966 data to estimate parental birthplace, testing with successively more PCs and finding the model with the top 23 PCs most accurate, with a median distance of 23 km between the estimated and the true location. pcLOCATE predicts the most recent residence of NFBC1966 individuals to a median distance of 47 km. We also apply pcLOCATE to Indian individuals from the London Life Sciences Prospective Population Study (LOLIPOP) data, and find that birthplace is predicated to a median distance of 54 km from the true location. A method with such accuracy is potentially valuable in population genetics and forensics. P RINCIPAL component analysis (PCA) has been used extensively to control for population structure and describe genetic diversity. It has been applied to worldwide allele frequency data of human populations (Cavalli-Sforza et al. 1993) and more recently to dense SNP data to illustrate population structure in Europe (Lao et al. 2008;, India (Reich et al. 2009), and China (Xu et al. 2009). Recent analyses of populations sampled across Europe demonstrated that genetic data could be used to predict place of birth to within a few hundred kilometers .Here we introduce a new Bayesian method, pcLOCATE, for predicting location of origin. We apply the method to the Northern Finland Birth Cohort 1966 (NFBC1966), which includes genome-wide data and location information on 2823 unrelated individuals born in 1966 in the two northernmost provinces of Finland, Oulu, and Lapland (Sabatti et al. 2008), and to The London Life Sciences Prospective Population Study (LOLIPOP), comprising genome-wide data and location data on 1574 individuals living in West London (UK) and born in India (Chambers et al. 2010 the accuracy of pcLOCATE with the approach of , in which linear models for longitude and latitude were employed with linear and quadratic effects for the first two PCs . PCA of the NFBC1966 data shows that higher-order PCs appear to contain information on loc...

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Inferring the Most Likely Geographical Origin of mtDNA Sequence Profiles

Cited by 35 publications

References 20 publications

Statistical Evaluation of Haploid Genetic Evidence

Statistical Evaluation of Haploid Genetic Evidence

Relação entre a etnia auto-declarada, haplogrupo mitocondrial e ancestralidade genômica em indivíduos do sudeste brasileiro.

Fine-Scale Estimation of Location of Birth from Genome-Wide Single-Nucleotide Polymorphism Data

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