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On the inference of ancestries in admixed populations
2008
Genome Research
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On the inference of ancestries in admixed populations Sriram Sankararaman, 1, 4 Inference of ancestral information in recently admixed populations, in which every individual is composed of a mixed ancestry ...
populations, and the inference of allele frequencies in one ancestral population given those in another. ...
The value of this SNP depends on the values of the jth alleles in haplotypes 2i מ 1 and 2i: We now replace all X variables in previous equations with Y, and instead of Equation 1 we use which can be ...
doi:10.1101/gr.072751.107
pmid:18353809
pmcid:PMC2279254
fatcat:lll4cf2syjflzaqwr4rvalvy4m
Inferring ancestry in admixed populations using microarray probe intensities
2012
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '12
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sequence of most likely ancestry states {f 1 , f 2 … f i … f n } at every marker, where f is one of m' states in F Distance Model • Find the set of ancestor intensities closest to the target sample's intensities ...
in F at every marker Note: m' ≥ number of clusters at each marker (different ancestors may fall within the same cluster) • Find:
Results We can refine breakpoints better v Results -Ancestry Inference ...
doi:10.1145/2382936.2382950
dblp:conf/bcb/FuWVM12
fatcat:qmy53j2dhraalexzbqp5dqy35i
On the Inference of Ancestries in Admixed Populations
[chapter]
Lecture Notes in Computer Science
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Inference of ancestral information in recently admixed populations, in which every individual is composed of a mixed ancestry (e.g., African Americans in the US), is a challenging problem. ...
populations, and the inference of allele frequencies in one ancestral population given those in another. ...
Our focus in the current paper is on the setting of recently admixed populations in which every individual is composed of a mixed ancestry (e.g., African Americans in the US, Hispanic populations, and ...
doi:10.1007/978-3-540-78839-3_37
dblp:conf/recomb/SankararamanKHJ08
fatcat:befj25b5c5g33cmzos6hx47hjq
Human genetic admixture through the lens of population genomics
[article]
2022
arXiv
pre-print
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We also outline some challenges for admixture population genetics, including limitations of applying methods designed for single-ancestry populations to the study of admixed populations. ...
The admixture process introduces unique patterns of genetic variation within and between populations, which in turn influences the inference of demographic histories, identification genetic targets of ...
As demonstrated in the bottom panel of Figure 1 , no individual locus in a genome from an admixed population will enable inference of the demographic history of the admixed group. ...
arXiv:2109.12190v2
fatcat:rj4k6ltnbvejfcicuqekxsupqi
RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference
2013
American Journal of Human Genetics
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Local-ancestry inference is an important step in the genetic analysis of fully sequenced human genomes. ...
RFMix is capable of learning from the admixed samples themselves to boost performance and autocorrect phasing errors. ...
Also, because local ancestry can be inferred on each chromosome in the genome independently, we describe the analysis of one chromosome in the genome. ...
doi:10.1016/j.ajhg.2013.06.020
pmid:23910464
pmcid:PMC3738819
fatcat:kixq4fkzjbcmxdam7vrki3jqeq
Models, methods and tools for ancestry inference and admixture analysis
2017
Quantitative Biology
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In this review, we provide an overview of models, methods, and tools for ancestry inference and admixture analysis. ...
Genetic admixture refers to the process or consequence of interbreeding between two or more previously isolated populations within a species. ...
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ...
doi:10.1007/s40484-017-0117-2
fatcat:bu7w65axxzgz5jhdcskhcbxljy
Efficient inference of local ancestry
2013
Bioinformatics
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Motivation: The inference of local ancestry of admixed individuals at every locus provides the basis for admixture mapping. ...
Results: In this study, we developed a statistical method, efficient inference of local ancestry (EILA), which uses fused quantile regression and k-means classifier to infer the local ancestry for admixed ...
Based on these assumptions, we infer local ancestry using three samples: one study sample of admixed individuals with unknown local ancestry and two reference samples from different ancestral populations ...
doi:10.1093/bioinformatics/btt488
pmid:23958727
pmcid:PMC3799480
fatcat:qvwsmr6m4fgm5eoxhpbadl5wze
Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations
2009
PLoS Genetics
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HAPMIX will be of particular utility for mapping disease genes in recently admixed populations, as its accurate estimates of local ancestry permit admixture and case-control association signals to be combined ...
Most methods require the use of unlinked markers; but, using all markers from genomewide scanning arrays, it should in principle be possible to infer the ancestry of even very small segments with exquisite ...
Details of haplotype-based inference of local ancestry Modeling genetic variation in admixed populations. ...
doi:10.1371/journal.pgen.1000519
pmid:19543370
pmcid:PMC2689842
fatcat:gvziywsgobc5zfsmqbaa2lgg7m
Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals
2014
PLoS Computational Biology
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Inferring the ancestry at each locus in the genome of recently admixed individuals (e.g., Latino Americans) plays a major role in medical and population genetic inferences, ranging from finding disease-risk ...
Finally, we generalize CSVs to sub-continental population-specific variants (sCSVs) and show that in some cases it is possible to determine the sub-continental ancestry for short chromosomal segments on ...
Acknowledgments We would like to acknowledge Kirk Lohmueller, John Novembre, Diego Ortega, Gleb Kichaev and Wen-Yun Yang for useful discussion that has greatly improved the quality of this manuscript. ...
doi:10.1371/journal.pcbi.1003555
pmid:24743331
pmcid:PMC3990492
fatcat:cziauqxsyfhbncec7dfwdyavs4
A Continuous Correlated Beta Process Model for Genetic Ancestry in Admixed Populations
2016
PLoS ONE
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fixed in the admixed population. ...
Similar variation was detected in the mouse hybrid zone, with notable constancy in regions of excess ancestry among admixed populations. ...
Wrote the paper: ZG. Designed the software used in analysis: ZG. ...
doi:10.1371/journal.pone.0151047
pmid:26966908
pmcid:PMC4788345
fatcat:r55r6cmld5enxlbkbaln4xma2e
Human genetic admixture
2021
PLoS Genetics
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This process leads to subsequent shuffling of genetic ancestry through recombination, producing variation in ancestry between populations, among individuals in a population, and along the genome within ...
Recent methodological and empirical developments have elucidated the genomic signatures of this admixture process, bringing previously understudied admixed populations to the forefront of population and ...
Summaries of ancestry-such as the mean proportion of ancestry across individuals in a population, the proportion of ancestry at different genetic loci in a population, and the length of ancestry tracts ...
doi:10.1371/journal.pgen.1009374
pmid:33705374
pmcid:PMC7951803
fatcat:5prc4rr7qveejmunmw2i2lzlpa
Population Genetic Inference from Personal Genome Data: Impact of Ancestry and Admixture on Human Genomic Variation
2012
American Journal of Human Genetics
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We further infer that multiple periods of gene flow shaped the diversity of admixed populations in the Americas-70% of the European ancestry in today's African Americans dates back to European gene flow ...
This heterozygosity ranged from a high of one heterozygous site per kilobase in west African genomes to a low of 0.57 heterozygous sites per kilobase in segments inferred to have diploid Native American ...
De La Vega are or were employees of Life Technologies during this study. Archie Russell and Martin Reese are employees of Omicia. The Varimed database has been licensed to Personalis. ...
doi:10.1016/j.ajhg.2012.08.025
pmid:23040495
pmcid:PMC3484644
fatcat:mll2ikn2prb2ln73tmf6nqtg5q
Loter: A Software Package to Infer Local Ancestry for a Wide Range of Species
2018
Molecular biology and evolution
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Admixture studies rely on local ancestry inference for admixed individuals, which consists of computing at each locus the number of copies that originate from ancestral source populations. ...
Here, we introduce Loter, an open-source software package that does not require any biological parameter besides haplotype data in order to make local ancestry inference available for a wide range of species ...
We use the first 500, 000 SNPs of chromosome 6 to reconstruct ancestry tracts. We simulate 16 admixed individuals based on 20 genotypes from P. balsamifera and P. trichocarpa species. ...
doi:10.1093/molbev/msy126
pmid:29931083
pmcid:PMC6107063
fatcat:cbrhx2ykerhbrbvc2ibw3zqnoy
Loter: A software package to infer local ancestry for a wide range of species
[article]
2017
biorxiv/medrxiv
pre-print
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Admixture studies rely on local ancestry inference for admixed individuals, which consists of computing at each locus the number of copies that originate from ancestral source populations. ...
Here, we introduce Loter, an open-source software package that does not require any biological parameter besides haplotype data in order to make local ancestry inference available for a wide range of species ...
We use the first 500, 000 SNPs of chromosome 6 to reconstruct ancestry tracts. We simulate 16 admixed individuals based on 20 genotypes from P. balsamifera and P. trichocarpa species. ...
doi:10.1101/213728
fatcat:5k3fsj4cfrbzvbqidaftbdk7ke
XGMix: Local-Ancestry Inference With Stacked XGBoost
[article]
2020
bioRxiv
pre-print
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The severe under-representation of the majority of the world's populations in genetic association studies stems in part from an addressable algorithmic weakness: lack of simple, accurate, and easily trained ...
methods for identifying and annotating ancestry along the genome (local ancestry). ...
Fortunately, an algorithmic solution exists to the problem of complex genomic covariance structures in admixed and diverse populations: local ancestry inference (LAI) (figure 1). ...
doi:10.1101/2020.04.21.053876
fatcat:njcnjlxvwnewrfwuxzb4a6k2dy
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