keyword
MENU ▼
Read by QxMD icon Read
search

Admixture mapping

keyword
https://www.readbyqxmd.com/read/28408710/local-ancestry-association-admixture-mapping-and-ongoing-challenges
#1
EDITORIAL
Arya Mani
No abstract text is available yet for this article.
April 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/28408707/admixture-mapping-of-subclinical-atherosclerosis-and-subsequent-clinical-events-among-african-americans-in-2-large-cohort-studies
#2
Aditi Shendre, Howard Wiener, Marguerite R Irvin, Degui Zhi, Nita A Limdi, Edgar T Overton, Christina L Wassel, Jasmin Divers, Jerome I Rotter, Wendy S Post, Sadeep Shrestha
BACKGROUND: Local ancestry may contribute to the disproportionate burden of subclinical and clinical cardiovascular disease among admixed African Americans compared with other populations, suggesting a rationale for admixture mapping. METHODS AND RESULTS: We estimated local European ancestry (LEA) using Local Ancestry inference in adMixed Populations using Linkage Disequilibrium method (LAMP-LD) and evaluated the association with common carotid artery intima-media thickness (cCIMT) using multivariable linear regression analysis among 1554 African Americans from MESA (Multi-Ethnic Study of Atherosclerosis)...
April 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/28405389/mixing-of-porpoise-ecotypes-in-southwestern-uk-waters-revealed-by-genetic-profiling
#3
Michaël C Fontaine, Oliver Thatcher, Nicolas Ray, Sylvain Piry, Andrew Brownlow, Nicholas J Davison, Paul Jepson, Rob Deaville, Simon J Goodman
Contact zones between ecotypes are windows for understanding how species may react to climate changes. Here, we analysed the fine-scale genetic and morphological variation in harbour porpoises (Phocoena phocoena) around the UK by genotyping 591 stranded animals at nine microsatellite loci. The data were integrated with a prior study to map at high resolution the contact zone between two previously identified ecotypes meeting in the northern Bay of Biscay. Clustering and spatial analyses revealed that UK porpoises are derived from two genetic pools with porpoises from the southwestern UK being genetically differentiated, and having larger body sizes compared to those of other UK areas...
March 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28376731/ad-libs-inferring-ancestry-across-hybrid-genomes-using-low-coverage-sequence-data
#4
Nathan K Schaefer, Beth Shapiro, Richard E Green
BACKGROUND: Inferring the ancestry of each region of admixed individuals' genomes is useful in studies ranging from disease gene mapping to speciation genetics. Current methods require high-coverage genotype data and phased reference panels, and are therefore inappropriate for many data sets. We present a software application, AD-LIBS, that uses a hidden Markov model to infer ancestry across hybrid genomes without requiring variant calling or phasing. This approach is useful for non-model organisms and in cases of low-coverage data, such as ancient DNA...
April 4, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28332560/evaluating-genetic-susceptibility-to-staphylococcus-aureus-bacteremia-in-african-americans-using-admixture-mapping
#5
D D Cyr, A S Allen, G-J Du, F Ruffin, C Adams, J T Thaden, S A Maskarinec, M Souli, S Guo, D M Dykxhoorn, W K Scott, V G Fowler
The incidence of Staphylococcus aureus bacteremia (SAB) is significantly higher in African American (AA) than in European-descended populations. We used admixture mapping (AM) to test the hypothesis that genomic variations with different frequencies in European and African ancestral genomes influence susceptibility to SAB in AAs. A total of 565 adult AAs (390 cases with SAB; 175 age-matched controls) were genotyped for AM analysis. A case-only admixture score and a mixed χ(2)(1df) score (MIX) to jointly evaluate both single-nucleotide polymorphism (SNP) and admixture association (P<5...
March 23, 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28245265/admixture-mapping-in-two-mexican-samples-identifies-significant-associations-of-locus-ancestry-with-triglyceride-levels-in-the-bud13-znf259-apoa5-region-and-fine-mapping-points-to-rs964184-as-the-main-driver-of-the-association-signal
#6
Esteban J Parra, Andrew Mazurek, Christopher R Gignoux, Alexandra Sockell, Michael Agostino, Andrew P Morris, Lauren E Petty, Craig L Hanis, Nancy J Cox, Adan Valladares-Salgado, Jennifer E Below, Miguel Cruz
We carried out an admixture mapping study of lipid traits in two samples from Mexico City. Native American locus ancestry was significantly associated with triglyceride levels in a broad region of chromosome 11 overlapping the BUD13, ZNF259 and APOA5 genes. In our fine-mapping analysis of this region using dense genome-wide data, rs964184 is the only marker included in the 99% credible set of SNPs, providing strong support for rs964184 as the causal variant within this region. The frequency of the allele associated with increased triglyceride concentrations (rs964184-G) is between 30-40% higher in Native American populations from Mexico than in European populations...
2017: PloS One
https://www.readbyqxmd.com/read/28241052/osbpl10-rxra-and-lipid-metabolism-confer-african-ancestry-protection-against-dengue-haemorrhagic-fever-in-admixed-cubans
#7
Beatriz Sierra, Petr Triska, Pedro Soares, Gissel Garcia, Ana B Perez, Eglys Aguirre, Marisa Oliveira, Bruno Cavadas, Béatrice Regnault, Mayling Alvarez, Didye Ruiz, David C Samuels, Anavaj Sakuntabhai, Luisa Pereira, Maria G Guzman
Ethnic groups can display differential genetic susceptibility to infectious diseases. The arthropod-born viral dengue disease is one such disease, with empirical and limited genetic evidence showing that African ancestry may be protective against the haemorrhagic phenotype. Global ancestry analysis based on high-throughput genotyping in admixed populations can be used to test this hypothesis, while admixture mapping can map candidate protective genes. A Cuban dengue fever cohort was genotyped using a 2.5 million SNP chip...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28137830/admixture-mapping-identifies-an-amerindian-ancestry-locus-associated-with-albuminuria-in-hispanics-in-the-united-states
#8
Lisa A Brown, Tamar Sofer, Adrienne M Stilp, Leslie J Baier, Holly J Kramer, Ivica Masindova, Daniel Levy, Robert L Hanson, Ashley E Moncrieft, Susan Redline, Sylvia E Rosas, James P Lash, Jianwen Cai, Cathy C Laurie, Sharon Browning, Timothy Thornton, Nora Franceschini
Increased urine albumin excretion is highly prevalent in Hispanics/Latinos. Previous studies have found an association between urine albumin excretion and Amerindian ancestry in Hispanic/Latino populations. Admixture between racial/ethnic groups creates long-range linkage disequilibrium between variants with different allelic frequencies in the founding populations and it can be used to localize genes. Hispanic/Latino genomes are an admixture of European, African, and Amerindian ancestries. We leveraged this admixture to identify associations between urine albumin excretion (urine albumin-to-creatinine ratio [UACR]) and genomic regions harboring variants with highly differentiated allele frequencies among the ancestral populations...
January 30, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28135767/landscape-genetic-approaches-to-guide-native-plant-restoration-in-the-mojave-desert
#9
Daniel F Shryock, Caroline A Havrilla, Lesley A DeFalco, Todd C Esque, Nathan A Custer, Troy E Wood
Restoring dryland ecosystems is a global challenge due to synergistic drivers of disturbance coupled with unpredictable environmental conditions. Dryland plant species have evolved complex life-history strategies to cope with fluctuating resources and climatic extremes. Although rarely quantified, local adaptation is likely widespread among these species and potentially influences restoration outcomes. The common practice of reintroducing propagules to restore dryland ecosystems, often across large spatial scales, compels evaluation of adaptive divergence within these species...
October 5, 2016: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28126562/genetic-diversity-and-evolution-of-dengue-virus-serotype-3-a-comparative-genomics-study
#10
Vaishali P Waman, Mohan M Kale, Urmila Kulkarni-Kale
Dengue virus serotype 3 (DENV-3), one of the four serotypes of Dengue viruses, is geographically diverse. There are five distinct genotypes (I-V) of DENV-3. Emerging strains and lineages of DENV-3 are increasingly being reported. Availability of genomic data for DENV-3 strains provides opportunity to study its population structure. Complete genome sequences are available for 860 strains of four genotypes (I, II, III and V) isolated worldwide and were analyzed using population genetics and evolutionary approaches to map landscape of genomic diversity...
January 23, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28100184/cnvs-into-the-wild-screening-the-genomes-of-conifer-trees-picea-spp-reveals-fewer-gene-copy-number-variations-in-hybrids-and-links-to-adaptation
#11
Julien Prunier, Sébastien Caron, John MacKay
BACKGROUND: Copy number variations (CNVs) have been linked to different phenotypes in human, including many diseases. A genome-scale understanding of CNVs is available in a few plants but none are wild species, leaving a knowledge gap regarding their genome biology and evolutionary role. We developed a reliable CNV detection method for species lacking contiguous reference genome. We selected multiple probes within 14,078 gene sequences and developed comparative genome hybridization on arrays...
January 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28078323/genetic-architecture-of-age-related-cognitive-decline-in-african-americans
#12
Towfique Raj, Lori B Chibnik, Cristin McCabe, Andus Wong, Joseph M Replogle, Lei Yu, Sujuan Gao, Frederick W Unverzagt, Barbara Stranger, Jill Murrell, Lisa Barnes, Hugh C Hendrie, Tatiana Foroud, Anna Krichevsky, David A Bennett, Kathleen S Hall, Denis A Evans, Philip L De Jager
OBJECTIVE: To identify genetic risk factors associated with susceptibility to age-related cognitive decline in African Americans (AAs). METHODS: We performed a genome-wide association study (GWAS) and an admixture-mapping scan in 3,964 older AAs from 5 longitudinal cohorts; for each participant, we calculated a slope of an individual's global cognitive change from neuropsychological evaluations. We also performed a pathway-based analysis of the age-related cognitive decline GWAS...
February 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28077191/genome-wide-analysis-in-endangered-populations-a-case-study-in-barbaresca-sheep
#13
S Mastrangelo, B Portolano, R Di Gerlando, R Ciampolini, M Tolone, M T Sardina
Analysis of genomic data is becoming increasingly common in the livestock industry and the findings have been an invaluable resource for effective management of breeding programs in small and endangered populations. In this paper, with the goal of highlighting the potential of genomic analysis for small and endangered populations, genome-wide levels of linkage disequilibrium, measured as the squared correlation coefficient of allele frequencies at a pair of loci, effective population size, runs of homozygosity (ROH) and genetic diversity parameters, were estimated in Barbaresca sheep using Illumina OvineSNP50K array data...
January 12, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28076865/gene-mapping-in-admixed-families-a-cautionary-note-on-the-interpretation-of-the-transmission-disequilibrium-test-and-a-possible-solution
#14
Xuexia Wang, Rui Xiao, Xiaofeng Zhu, Mingyao Li
A family-based study design is commonly used in gene mapping studies of complex human diseases. Most family-based studies use the transmission of alleles to assess evidence of association. It is generally believed that the transmission disequilibrium test (TDT) is robust against spurious association due to population stratification or admixture. While this is true when population stratification is due to discrete population structure, one should use the TDT-type methods with caution when they are applied to admixed populations in which population structure exists in local genomic regions...
2016: Human Heredity
https://www.readbyqxmd.com/read/27905875/a-nonsense-mutation-in-the-col7a1-gene-causes-epidermolysis-bullosa-in-vorderwald-cattle
#15
Hubert Pausch, Simon Ammermüller, Christine Wurmser, Henning Hamann, Jens Tetens, Cord Drögemüller, Ruedi Fries
BACKGROUND: The widespread use of individual sires for artificial insemination promotes the propagation of recessive conditions. Inadvertent matings between unnoticed carriers of deleterious alleles may result in the manifestation of fatal phenotypes in their progeny. Breeding consultants and farmers reported on Vorderwald calves with a congenital skin disease. The clinical findings in affected calves were compatible with epidermolysis bullosa. RESULTS: Pedigree analysis indicated autosomal recessive inheritance of epidermolysis bullosa in Vorderwald cattle...
December 1, 2016: BMC Genetics
https://www.readbyqxmd.com/read/27870264/a-hot-topic-the-genetics-of-adaptation-to-geothermal-vents-in-mimulus-guttatus
#16
Kathleen G Ferris
Identifying the individual loci and mutations that underlie adaptation to extreme environments has long been a goal of evolutionary biology. However, finding the genes that underlie adaptive traits is difficult for several reasons. First, because many traits and genes evolve simultaneously as populations diverge, it is difficult to disentangle adaptation from neutral demographic processes. Second, finding the individual loci involved in any trait is challenging given the respective limitations of quantitative and population genetic methods...
November 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27768888/genetic-adaptation-and-neandertal-admixture-shaped-the-immune-system-of-human-populations
#17
Hélène Quach, Maxime Rotival, Julien Pothlichet, Yong-Hwee Eddie Loh, Michael Dannemann, Nora Zidane, Guillaume Laval, Etienne Patin, Christine Harmant, Marie Lopez, Matthieu Deschamps, Nadia Naffakh, Darragh Duffy, Anja Coen, Geert Leroux-Roels, Frederic Clément, Anne Boland, Jean-François Deleuze, Janet Kelso, Matthew L Albert, Lluis Quintana-Murci
Humans differ in the outcome that follows exposure to life-threatening pathogens, yet the extent of population differences in immune responses and their genetic and evolutionary determinants remain undefined. Here, we characterized, using RNA sequencing, the transcriptional response of primary monocytes from Africans and Europeans to bacterial and viral stimuli-ligands activating Toll-like receptor pathways (TLR1/2, TLR4, and TLR7/8) and influenza virus-and mapped expression quantitative trait loci (eQTLs)...
October 20, 2016: Cell
https://www.readbyqxmd.com/read/27766601/genetic-diversity-and-population-structure-of-rice-varieties-cultivated-in-temperate-regions
#18
Juan L Reig-Valiente, Juan Viruel, Ester Sales, Luis Marqués, Javier Terol, Marta Gut, Sophia Derdak, Manuel Talón, Concha Domingo
BACKGROUND: After its domestication, rice cultivation expanded from tropical regions towards northern latitudes with temperate climate in a progressive process to overcome limiting photoperiod and temperature conditions. This process has originated a wide range of diversity that can be regarded as a valuable resource for crop improvement. In general, current rice breeding programs have to deal with a lack of both germplasm accessions specifically adapted to local agro-environmental conditions and adapted donors carrying desired agronomical traits...
December 2016: Rice
https://www.readbyqxmd.com/read/27730503/exploratory-study-on-the-presence-of-gm-oilseed-rape-near-german-oil-mills
#19
J Franzaring, K Wedlich, A Fangmeier, S Eckert, J Zipperle, I Krah-Jentgens, C Hünig, W Züghart
Seed losses from imported oilseed rape (OSR) and the genetically modified (GM) admixtures therein may potentially lead to the establishment of transgenic plants and their hybridization with wild crucifers. The post-market environmental monitoring (PMEM) must therefore also address problems related to seed spillages of GM OSR. Since detailed information on imported commodity flows, GM contents, means of transport, downstream users and efficient containment of GM OSR was lacking, we performed a field study in the vicinity of large oil mills and seed processing industries at the harbours along the river Rhine...
November 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/27725671/a-continuum-of-admixture-in-the-western-hemisphere-revealed-by-the-african-diaspora-genome
#20
Rasika Ann Mathias, Margaret A Taub, Christopher R Gignoux, Wenqing Fu, Shaila Musharoff, Timothy D O'Connor, Candelaria Vergara, Dara G Torgerson, Maria Pino-Yanes, Suyash S Shringarpure, Lili Huang, Nicholas Rafaels, Meher Preethi Boorgula, Henry Richard Johnston, Victor E Ortega, Albert M Levin, Wei Song, Raul Torres, Badri Padhukasahasram, Celeste Eng, Delmy-Aracely Mejia-Mejia, Trevor Ferguson, Zhaohui S Qin, Alan F Scott, Maria Yazdanbakhsh, James G Wilson, Javier Marrugo, Leslie A Lange, Rajesh Kumar, Pedro C Avila, L Keoki Williams, Harold Watson, Lorraine B Ware, Christopher Olopade, Olufunmilayo Olopade, Ricardo Oliveira, Carole Ober, Dan L Nicolae, Deborah Meyers, Alvaro Mayorga, Jennifer Knight-Madden, Tina Hartert, Nadia N Hansel, Marilyn G Foreman, Jean G Ford, Mezbah U Faruque, Georgia M Dunston, Luis Caraballo, Esteban G Burchard, Eugene Bleecker, Maria Ilma Araujo, Edwin Francisco Herrera-Paz, Kimberly Gietzen, Wendy E Grus, Michael Bamshad, Carlos D Bustamante, Eimear E Kenny, Ryan D Hernandez, Terri H Beaty, Ingo Ruczinski, Joshua Akey, Kathleen C Barnes
The African Diaspora in the Western Hemisphere represents one of the largest forced migrations in history and had a profound impact on genetic diversity in modern populations. To date, the fine-scale population structure of descendants of the African Diaspora remains largely uncharacterized. Here we present genetic variation from deeply sequenced genomes of 642 individuals from North and South American, Caribbean and West African populations, substantially increasing the lexicon of human genomic variation and suggesting much variation remains to be discovered in African-admixed populations in the Americas...
October 11, 2016: Nature Communications
keyword
keyword
57059
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"