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Inferring the ancestry of parents and grandparents from genetic data [article]

Jingwen Pei, Rasmus Nielsen, Yufeng Wu
2018 bioRxiv   pre-print
Inference of admixture proportions is a classical statistical problem in population genetics. Standard methods implicitly assume that both parents of an individual have the same admixture fraction.  ...  As an illustration, we also apply the method on real data from the 1000 Genomes Project.  ...  We also thank Walter Krawec and Aaron Palmer for reading and helping to improve the manuscript.  ... 
doi:10.1101/308494 fatcat:z3afhvwrf5fizgowgrrrhat7am

Inferring the ancestry of parents and grandparents from genetic data

Jingwen Pei, Yiming Zhang, Rasmus Nielsen, Yufeng Wu, Sergei L. Kosakovsky Pond
2020 PLoS Computational Biology  
To illustrate the utility of the method, we apply it to real genetic data.  ...  Inference of admixture proportions is a classical statistical problem in population genetics. Standard methods implicitly assume that both parents of an individual have the same admixture fraction.  ...  The case of grandparents is more difficult because genetic data of grandparents is not available from the HapMap project.  ... 
doi:10.1371/journal.pcbi.1008065 pmid:32797037 fatcat:57g7y3dc3jf4jinmqvdhravegi

A genome-wide genetic signature of Jewish ancestry perfectly separates individuals with and without full Jewish ancestry in a large random sample of European Americans

Anna C Need, Dalia Kasperavičiūtė, Elizabeth T Cirulli, David B Goldstein
2009 Genome Biology  
No study however has yet assessed how accurately self-identified (Ashkenazi) Jewish ancestry can be inferred from genomic information, nor whether the degree of Jewish ancestry can be inferred among individuals  ...  It was recently shown that the genetic distinction between self-identified Ashkenazi Jewish and non-Jewish individuals is a prominent component of genome-wide patterns of genetic variation in European  ...  Acknowledgements Thanks to all the subjects that took part in this study. This work was funded by Duke IGSP start-up funding for DBG.  ... 
doi:10.1186/gb-2009-10-1-r7 pmid:19161619 pmcid:PMC2687795 fatcat:ft6gzw5jhfhetmvuugnqozs5cm

Spatial Localization of Recent Ancestors for Admixed Individuals

Wen-Yun Yang, Alexander Platt, Charleston Wen-Kai Chiang, Eleazar Eskin, John Novembre, Bogdan Pasaniuc
2014 G3: Genes, Genomes, Genetics  
infer the ancestry of the recent ancestors (e.g. grandparents) from genetic data.  ...  yield high accuracies in ancestry inference from genetic data.  ...  The parental inference is different from two ancestry inference, as the parental inference assumes that one haplotype is from paternal ancestry and one from maternal ancestry.  ... 
doi:10.1534/g3.114.014274 pmid:25371484 pmcid:PMC4267945 fatcat:trx4cvwwbbfn3brup3gq6rdndq

The genetic history of Greenlandic-European contact

Ryan K. Waples, Aviaja L. Hauptmann, Inge Seiding, Emil Jørsboe, Marit E. Jørgensen, Niels Grarup, Mette K. Andersen, Christina V.L. Larsen, Peter Bjerregaard, Garrett Hellenthal, Torben Hansen, Anders Albrechtsen (+1 others)
2021 Current Biology  
We combined dense SNP chip data from 3,972 Greenlanders and 8,275 Europeans from 14 countries and inferred the ancestry contribution from each of these 14 countries using haplotype-based methods.  ...  Consequently, the present-day Greenlandic population has ∼25% of its genetic ancestry from Europe.2 In this study, we investigated to what extent different European countries have contributed to this genetic  ...  Inference of European admixture sources Using the genetic data from the Greenlanders, we inferred admixture proportions (Figure S2 ; see also Data S1) and identified related individuals.  ... 
doi:10.1016/j.cub.2021.02.041 pmid:33711251 pmcid:PMC8284823 fatcat:nnum5shkwjak5oogkhrm4a354u

Spatial localization of recent ancestors for admixed individuals [article]

Wen-Yun Yang, Alexander Platt, Charleston Wen-Kai Chiang, Eleazar Eskin, John Novembre, Bogdan Pasaniuc
2014 biorxiv/medrxiv   pre-print
Ancestry analysis from genetic data plays a critical role in studies of human disease and evolution.  ...  Recent work has introduced explicit models for the geographic distribution of genetic variation and has shown that such explicit models yield superior accuracy in ancestry inference over non-model-based  ...  The parental inference is different from two ancestry inference, as the parental inference assumes that one haplotype is from paternal ancestry and one from maternal ancestry.  ... 
doi:10.1101/004713 fatcat:lsqhpnx6tjbhxjdp65zckmdk4y

What is ancestry?

Iain Mathieson, Aylwyn Scally, Jonathan Flint
2020 PLoS Genetics  
Acknowledgments We thank Richard Durbin, Joshua Schraiber and Jonathan Flint for helpful comments on an earlier version.  ...  inference from genetic data is unbiased.  ...  Genealogical ancestry probably reflects the most common and intuitive understanding of the term ancestry. Consider your parents, grandparents, or even great-grandparents.  ... 
doi:10.1371/journal.pgen.1008624 pmid:32150538 fatcat:xrijgsriwzdk3bbzdhizbqjx6i

Extracting transmission networks from phylogeographic data for epidemic and endemic diseases: Ebola virus in Sierra Leone, 2009 H1N1 pandemic influenza and polio in Nigeria

Michael Famulare, Hao Hu
2015 International Health  
We compare the transmission network generated by POTN with existing algorithms (BEAST and SeqTrack), and discuss the benefits and challenges of phylogeographic analysis on examples of epidemic and endemic  ...  We propose simple heuristic criteria to identify how sampling rates and disease dynamics interact to determine fundamental limitations of phylogeographic inference.  ...  It is thus common to identify redundant ancestry (grandparent-parent, parent-child, grandparent-child) because the pairwise algorithm is unable to detect when deeper relationships are better explained  ... 
doi:10.1093/inthealth/ihv012 pmid:25733563 pmcid:PMC4379986 fatcat:rq4fioe2crdttg5qlljtigivzy

Extracting transmission networks from phylogeographic data for epidemic and endemic diseases: Ebola virus in Sierra Leone, 2009 H1N1 pandemic influenza and polio in Nigeria

Michael Famulare, Hao Hu
2015 International Health  
We compare the transmission network generated by POTN with existing algorithms (BEAST and SeqTrack), and discuss the benefits and challenges of phylogeographic analysis on examples of epidemic and endemic  ...  We propose simple heuristic criteria to identify how sampling rates and disease dynamics interact to determine fundamental limitations of phylogeographic inference.  ...  It is thus common to identify redundant ancestry (grandparent-parent, parent-child, grandparent-child) because the pairwise algorithm is unable to detect when deeper relationships are better explained  ... 
doi:10.1093/inthealth/ihv031 pmid:26150555 pmcid:PMC4492342 fatcat:vqa57ysnmvhklnaayfpt2uvcdi

Identification of population substructure among Jews using STR markers and dependence on reference populations included

Jennifer B Listman, Deborah Hasin, Henry R Kranzler, Robert T Malison, Apiwat Mutirangura, Atapol Sughondhabirom, Efrat Aharonovich, Baruch Spivak, Joel Gelernter
2010 BMC Genetics  
Generally, for samples with a given grandparental country of birth, STRUCTURE assignment values to Northern, Southern, African and Asian clusters agreed with mitochondrial DNA and Y-chromosomal data from  ...  the absence of proxy parental populations, substructure within Jews was not detected.  ...  Acknowledgements We appreciate receiving helpful comments from Dr Jonathan Pritchard  ... 
doi:10.1186/1471-2156-11-48 pmid:20546593 pmcid:PMC2896335 fatcat:g65ygve3obbqfgstgfpbfusiqi

Comparing Genetic Ancestry and Self-Described Race in African Americans Born in the United States and in Africa

R. Yaeger, A. Avila-Bront, K. Abdul, P. C. Nolan, V. R. Grann, M. G. Birchette, S. Choudhry, E. G. Burchard, K. B. Beckman, P. Gorroochurn, E. Ziv, N. S. Consedine (+1 others)
2008 Cancer Epidemiology, Biomarkers and Prevention  
Genetic classifications of ancestry may provide a more objective and accurate method of defining homogenous populations for the investigation of specific population-disease associations.  ...  Our findings suggest that self-reported race and ancestry can predict ancestral clusters but do not reveal the extent of admixture.  ...  Bernard Weinstein for invaluable advise during the preparation of this article, Scott Huntsman for assistance in analyzing the AIM data, and Dr. Wendy K.  ... 
doi:10.1158/1055-9965.epi-07-2505 pmid:18559547 pmcid:PMC2507870 fatcat:howcjldth5fd5nvs3hg5lmnixy

Genetic Ancestry and Risk Factors for Breast Cancer among Latinas in the San Francisco Bay Area

E. Ziv, E. M. John, S. Choudhry, J. Kho, W. Lorizio, E. J. Perez-Stable, E. G. Burchard
2006 Cancer Epidemiology, Biomarkers and Prevention  
(95% CI) associated with a 25% increase in Indigenous American ancestry, adjusting for age, education, and the participant's and grandparents' place of birth.  ...  We measured genetic ancestry among Latinas in a population-based case-control study of breast cancer and tested the association between ancestry and known breast cancer risk factors.  ...  A further question, not directly assessed in this study, is whether self-report of grandparents' or parents' ethnicity (e.g., European, Indigenous, and African) is a reliable estimate of genetic ancestry  ... 
doi:10.1158/1055-9965.epi-06-0092 pmid:17035394 pmcid:PMC5033763 fatcat:rb23dp3ndvaxpbcqetvn4wcwsm

Genetic admixture patterns in Argentinian Patagonia

María Laura Parolin, Ulises F. Toscanini, Irina F. Velázquez, Cintia Llull, Gabriela L. Berardi, Alfredo Holley, Camila Tamburrini, Sergio Avena, Francisco R. Carnese, José L. Lanata, Noela Sánchez Carnero, Lucas F. Arce (+4 others)
2019 PLoS ONE  
the origin of the participants and their ancestors for the correct interpretation and contextualization of the genetic information.  ...  As in other Latin American populations, Argentinians are the result of the admixture amongst different continental groups, mainly from America and Europe, and to a lesser extent from Sub-Saharan Africa  ...  and Marcelo Furque), the hemotherapys' technical teams for their support in collecting the samples, and Freya Chappell for carefully reviewing the writing.  ... 
doi:10.1371/journal.pone.0214830 pmid:31206551 pmcid:PMC6576754 fatcat:wqrueeov6fgwpktaq66wtuflx4

Variation in Genetic Relatedness Is Determined by the Aggregate Recombination Process

Carl Veller, Nathaniel B. Edelman, Pavitra Muralidhar, Martin A. Nowak
2020 Genetics  
For the relationships of grandparent-grandoffspring and siblings, the variance of genetic relatedness is a simple decreasing function of r̄, the average proportion of locus pairs that recombine in meiosis  ...  Our methods further allow us to calculate the neutral variance of ancestry among F2s in a hybrid cross, enabling precise statistical inference in F2-based tests for various kinds of selection.  ...  Acknowledgements We are grateful to Nicolas Bierne, Erin Calfee, Shai Carmi, Graham Coop, Jim Mallet, Molly Schumer, Sivan Yair, and the anonymous referees for helpful discussions and comments. This  ... 
doi:10.1534/genetics.120.303680 pmid:33109528 pmcid:PMC7768252 fatcat:k2dwce5gdfckdlp5p4q2peqqvi

Genetic admixture patterns in Argentinian Patagonia [article]

María Laura Parolin, Ulises F Toscanini, Irina F Velázquez, Cintia Llull, Gabriela L Berardi, Alfredo Holley, Camila Tamburrini, Sergio Avena, Francisco R Carnese, José L Lanata, Noela Sánchez Carnero, Lucas F Arce (+3 others)
2019 bioRxiv   pre-print
the origin of the participants and their ancestors for the correct interpretation and contextualization of the genetic information.  ...  AbstractAs for other Latin American populations, Argentinians are the result of the admixture amongst different continental groups, mainly from America and Europe, and to a lesser extent from Sub-Saharan  ...  This information allowed for investigating possible associations between 125 genetic ancestries inferred by the 46 AIMs panel and the geographic origin of the 126 participants. 127 The knowledge of the  ... 
doi:10.1101/586610 fatcat:vczuhljifrd73p5iemempfg4r4
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