Genome-wide Patterns of Population Structure and Ancestry Among Continental and Admixed Populations PDF Download
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Author: Katarzyna Bryc
Publisher:
ISBN:
Category :
Languages : en
Pages : 358
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Book Description
Population genetics seeks to use genetic data to illuminate patterns of human diversity, investigate how populations are related, and to provide insights into population history, such as migrations events and population sizes. Furthermore, an understanding of population genetics is necessary to disentangle population structure from genetic associations with traits, to learn how genes affect phenotype or to perform disease association mapping. I use high-density single nucleotide polyphorphism (SNP) data to examine population structure in humans among several world-wide populations. I show that principal components analysis (PCA) and STRUCTURE, a bayesian clustering method, are able to resolve structure both among continents as well as illuminate substructure within Europe, South Asia, and East Asia. In an analysis of 12 West African populations, I demonstrate that population structure within the West African samples reflects linguistic relationships and geographical distances, and also shows signals of the Bantu expansion. I proceed to focus on several questions involving populations of mixed ancestry, or admixed populations. First, I introduce a new method for inferring individual ancestry along the genome, or "local ancestry". This method leverages principal component analysis to allow computationally efficient ancestry estimation using high-density SNP data. I apply this method to a sample of African Americans and witness a large range of ancestry proportions across in- dividuals in this panel. I find that the African Americans have a greater propotion of African ancestry on the X chromosome versus the autosomes, consistent with a greater female African and male European ancestry contribution. Since previous studies have suggested a West African ancestral population of African Americans, I use estimates of African and European segments of the genome to examine which of 12 West African populations is closest to the African ancestral population. I find that, consistent with the West African results of previous studies and historical records, the African regions of African American genomes show the lowest genetic divergence to West African populations Igbo, Brong, and Yoruba, which are non-Bantu Niger-Kordofanian speaking populations. Hispanic/Latino (HL) populations possess a complex genetic structure reflecting recent admixture among Native American, European, and West African populations. I estimate ancestry among five Hispanic/Latino populations (Mexico, Ecuador, Colombia, Puerto Rico, and Dominican Republic) and illuminate patterns of ancestry among populations. These differences among HL populations reflect geographic proximity to slave trade routes and ports, European colonizations, and historical migrations. I show a consistent sex bias in ancestry proportions across all five HL populations with higher Native American and lower European ancestry on the X chromosome compared to the autosomes. The ancestry difference on the X versus the autosomes suggests a greater Native American female and European male ancestry contribution bias in all five HL populations, and is further supported by Y chromosome and mitochondrial DNA haplotyping. Lastly, I discuss challenges in identifying the closest Native American ancestral population to the HL populations, such as poor Native American population sampling or substructure within the Americas. However, I am able to show that the Nahua (for Meso-American populations) and the Quechua (for South American populations) are the two populations least differentiated from the Native American segments of the HL individuals.
Author: Katarzyna Bryc
Publisher:
ISBN:
Category :
Languages : en
Pages : 358
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Book Description
Population genetics seeks to use genetic data to illuminate patterns of human diversity, investigate how populations are related, and to provide insights into population history, such as migrations events and population sizes. Furthermore, an understanding of population genetics is necessary to disentangle population structure from genetic associations with traits, to learn how genes affect phenotype or to perform disease association mapping. I use high-density single nucleotide polyphorphism (SNP) data to examine population structure in humans among several world-wide populations. I show that principal components analysis (PCA) and STRUCTURE, a bayesian clustering method, are able to resolve structure both among continents as well as illuminate substructure within Europe, South Asia, and East Asia. In an analysis of 12 West African populations, I demonstrate that population structure within the West African samples reflects linguistic relationships and geographical distances, and also shows signals of the Bantu expansion. I proceed to focus on several questions involving populations of mixed ancestry, or admixed populations. First, I introduce a new method for inferring individual ancestry along the genome, or "local ancestry". This method leverages principal component analysis to allow computationally efficient ancestry estimation using high-density SNP data. I apply this method to a sample of African Americans and witness a large range of ancestry proportions across in- dividuals in this panel. I find that the African Americans have a greater propotion of African ancestry on the X chromosome versus the autosomes, consistent with a greater female African and male European ancestry contribution. Since previous studies have suggested a West African ancestral population of African Americans, I use estimates of African and European segments of the genome to examine which of 12 West African populations is closest to the African ancestral population. I find that, consistent with the West African results of previous studies and historical records, the African regions of African American genomes show the lowest genetic divergence to West African populations Igbo, Brong, and Yoruba, which are non-Bantu Niger-Kordofanian speaking populations. Hispanic/Latino (HL) populations possess a complex genetic structure reflecting recent admixture among Native American, European, and West African populations. I estimate ancestry among five Hispanic/Latino populations (Mexico, Ecuador, Colombia, Puerto Rico, and Dominican Republic) and illuminate patterns of ancestry among populations. These differences among HL populations reflect geographic proximity to slave trade routes and ports, European colonizations, and historical migrations. I show a consistent sex bias in ancestry proportions across all five HL populations with higher Native American and lower European ancestry on the X chromosome compared to the autosomes. The ancestry difference on the X versus the autosomes suggests a greater Native American female and European male ancestry contribution bias in all five HL populations, and is further supported by Y chromosome and mitochondrial DNA haplotyping. Lastly, I discuss challenges in identifying the closest Native American ancestral population to the HL populations, such as poor Native American population sampling or substructure within the Americas. However, I am able to show that the Nahua (for Meso-American populations) and the Quechua (for South American populations) are the two populations least differentiated from the Native American segments of the HL individuals.
Author: National Academy of Sciences
Publisher:
ISBN:
Category : Science
Languages : en
Pages : 388
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Book Description
The Arthur M. Sackler Colloquia of the National Academy of Sciences address scientific topics of broad and current interest, cutting across the boundaries of traditional disciplines. Each year, four or five such colloquia are scheduled, typically two days in length and international in scope. Colloquia are organized by a member of the Academy, often with the assistance of an organizing committee, and feature presentations by leading scientists in the field and discussions with a hundred or more researchers with an interest in the topic. Colloquia presentations are recorded and posted on the National Academy of Sciences Sackler colloquia website and published on CD-ROM. These Colloquia are made possible by a generous gift from Mrs. Jill Sackler, in memory of her husband, Arthur M. Sackler.
Author: Maxime Barakatt
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
"In this thesis, we apply and develop population genetics techniques to study admixed and spatially extended populations. We focus on the long haplotype patterns resulting from relatedness and recent admixture among the ancestors of a population. We use recently developed statistical methods to improve the inference of geographic origin of individual haplotypes in admixed population cohorts. We take advantage of these methods to address three problems in population and medical genetics. First, we perform an admixture mapping analysis to identify loci associated with the observed difference in heat pain sensitivity between African-Americans and European-Americans. Correcting for possible confounders, we identify one genome-wide significant genomic region containing the C10orf11 gene. Second, we studied the evolution of the pygmy phenotype by considering the correlation between ancestry and height among rainforest hunter-gatherers. Third, we studied the distribution of European, African, and Native American ancestry across the United States (US) in three different cohorts and find variation across cohorts and across regions consistent with sampling schemes and historical migrations. To interpret the latter results, we developed a non-parametric method that uses long shared haplotypes between individuals, or any other measure of relatedness, to infer migratory events in spatially extended populations. We apply our method to model African-American migrations in the US by analyzing the Health and Retirement Study (HRS) Cohort data. We identify migratory routes that are consistent with the historical event known as the Great Migration." --
Author: Wenfei Jin
Publisher: Springer
ISBN: 9401774080
Category : Medical
Languages : en
Pages : 126
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Book Description
In this thesis, Dr. Jin presents the distribution of ancestral chromosomal segments in the admixed genome, which could provide the information needed to explore population admixture dynamics. The author derives accurate population histories of African Americans and Mexicans using genome-wide single nucleotide polymorphisms (SNPs) data. Mapping the genetic background facilitates the study of natural selection in the admixed population, and the author identifies the signals of selection in African Americans since their African ancestors left for America. He further demonstrates that many of the selection signals were associated with African American-specific high-risk diseases such as prostate cancer and hypertension, suggesting an important role these disease-related genes might have played in adapting to their new environment. Lastly, the author reveals the complexity of natural selection in shaping human susceptibility to disease. The thesis significantly advances our understanding of the recent population admixture, adaptation to local environment and its health implications.
Author: Fouad Zakharia
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
The central theme of this work revolves around the genetics of admixed individuals--individuals who derive their ancestry from two or more different ancestral populations. The genomes of admixed individuals exhibit unique properties that make them both fascinating and challenging to study using existing statistical methods. Their uniqueness lies in their block-like structure, a feature that is the direct result of generations of recombination events. An important advance in the field of admixture genetics has been the development of algorithms capable of determining the ancestry of different regions in the admixed genome. As we will illustrate in this work, local ancestry information can readily be harnessed towards the investigation of subcontinental structure, by which we attempt to determine the specific ancestral populations that gave rise to the admixed genomes under study, and whether differences exist in the ancestral makeup of these admixed samples. The latter line of investigation is of particular relevance to genome-wide association studies, which are prone to confounding if structure in a population has not been explicitly corrected for. This work is thus divided into three parts. We first apply some straightforward multivariate statistical methods such as PCA to gain insights into the African ancestry of African Americans. To this end, we introduce a novel method for the study of specific components of admixture in admixed individuals. We then expand on this work to introduce more sophisticated algorithms for the study of admixed genomics. These methods entail the development of an improved method for local ancestry deconvolution, and the implementation of a PCA approach designed to handle large amounts of missing data. We illustrate the power of using these methods in conjunction with one another with the study of two Latino populations. Finally, we describe a novel phasing algorithm designed to incorporate sequencing information into the process of haplotype reconstruction--an important upstream step for many of the analyses described here.
Author: Mark Jobling
Publisher: Garland Science
ISBN: 1317952251
Category : Medical
Languages : en
Pages : 1557
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Book Description
Human Evolutionary Genetics is a groundbreaking text which for the first time brings together molecular genetics and genomics to the study of the origins and movements of human populations. Starting with an overview of molecular genomics for the non-specialist (which can be a useful review for those with a more genetic background), the book shows h
Author: David George Hogarth
Publisher:
ISBN:
Category : Arabian Peninsula
Languages : en
Pages : 488
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Book Description
Record of the development of western knowledge concerning the Arabian peninsula.
Author: Chao Tian
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
There exists much variation in genetic ancestry within and between ethnic groups, which causes substantial population stratification to be present not only in recently admixed populations like African Americans but also in generally assumed homogeneous populations like European Americans. In Chapter One I reviewed the recent studies of measuring and using genetic ancestry in human complex disease studies. Genetics variations constitute an important basis for Admixture Mapping. Many complex diseases show population specific prevalence that could be due to the differences of particular disease-susceptible genes among founding populations of different ancestry. Statistical methods can be applied to infer the locus ancestry along the chromosome in admixed individuals and tests for the association of the locus ancestry with the disease in admixed population, so called admixture mapping. Admixture mapping requires a genome-wide panel of relatively evenly spaced markers that can distinguish the locus ancestral origins in admixed individuals. In Chapter Two and Chapter Three I introduced our defined genome-wide Single-Nucleotide-Polymorphism panels that can extract ancestry information mostly with the least markers for African American and Mexican American admixed populations. On the other hand, a consequence of population stratification is the potential for false allelic associations and thus the inconsistent reports across genome-wide association studies. Statistical methods can be applied to discern and correct for the individual ancestry differences using Genome-wide association panel. In Chapter Four I introduced our findings of the European substructures, which have significant genetic variation along the north to south and west to east geographic axis. One of our recent report showed that after accounting for genetic ancestry difference, some locus are no long associated to Rheumatoid Arthritis but they appeared as very strong candidates without accounting for the substructure. In Chapter Five I introduced our findings of the East Asian substructures. Our analysis showed that there exist genetic variations both between different East Asian groups and within the Han Chinese population. In Chapter Six I reviewed the current available methods and importance of accounting for ancestry in genome-wide association studies. In Chapter Seven, I discussed some implications and future research directions.
Author: Paul Maria Selzer
Publisher: Springer Science & Business Media
ISBN: 3540728007
Category : Science
Languages : en
Pages : 297
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Book Description
At last, here is a baseline book for anyone who is confused by cryptic computer programs, algorithms and formulae, but wants to learn about applied bioinformatics. Now, anyone who can operate a PC, standard software and the internet can also learn to understand the biological basis of bioinformatics, of the existence as well as the source and availability of bioinformatics software, and how to apply these tools and interpret results with confidence. This process is aided by chapters that introduce important aspects of bioinformatics, detailed bioinformatics exercises (including solutions), and to cap it all, a glossary of definitions and terminology relating to bioinformatics.
Author: Irene Dankwa-Mullan
Publisher: John Wiley & Sons
ISBN: 1119374812
Category : Science
Languages : en
Pages : 548
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Book Description
Integrates the various disciplines of the science of health disparities in one comprehensive volume The Science of Health Disparities Research is an indispensable source of up-to-date information on clinical and translational health disparities science. Building upon the advances in health disparities research over the past decade, this authoritative volume informs policies and practices addressing the diseases, disorders, and gaps in health outcomes that are more prevalent in minority populations and socially disadvantaged communities. Contributions by recognized scholars and leaders in the field—featuring contemporary research, conceptual models, and a broad range of scientific perspectives—provide an interdisciplinary approach to reducing inequalities in population health, encouraging community engagement in the research process, and promoting social justice. In-depth chapters help readers better understand the specifics of minority health and health disparities while demonstrating the importance of advancing theory, refining measurement, improving investigative methods, and diversifying scientific research. In 26 chapters, the book examines topics including the etiology of health disparities research, the determinants of population health, research ethics, and research in African American, Asians, Latino, American Indian, and other vulnerable populations. Providing a unified framework on the principles and applications of the science of health disparities research, this important volume: Defines the field of health disparities science and suggests new directions in scholarship and research Explains basic definitions, principles, and concepts for identifying, understanding and addressing health disparities Provides guidance on both conducting health disparities research and translating the results Examines how social, historical and contemporary injustices may influence the health of racial and ethnic minorities Illustrates the increasing national and global importance of addressing health disparities Discusses population health training, capacity-building, and the transdisciplinary tools needed to advance health equity A significant contribution to the field, The Science of Health Disparities Research is an essential resource for students and basic and clinical researchers in genetics, population genetics, and public health, health care policymakers, and epidemiologists, medical students, and clinicians, particularly those working with minority, vulnerable, or underserved populations.
