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Admixture mapping

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https://www.readbyqxmd.com/read/28715450/african-genetic-ancestry-interacts-with-body-mass-index-to-modify-risk-for-uterine-fibroids
#1
Ayush Giri, Todd L Edwards, Katherine E Hartmann, Eric S Torstenson, Melissa Wellons, Pamela J Schreiner, Digna R Velez Edwards
Race, specifically African ancestry, and obesity are important risk factors for uterine fibroids, and likely interact to provide the right conditions for fibroid growth. However, existing studies largely focus on the main-effects rather than their interaction. Here, we firstly provide evidence for interaction between categories of body mass index (BMI) and reported-race in relation to uterine fibroids. We then investigate whether the association between inferred local European ancestry and fibroid risk is modified by BMI in African American (AA) women in the Vanderbilt University Medical Center bio-repository (BioVU) (539 cases and 794 controls) and the Coronary Artery Risk Development in Young Adults study (CARDIA, 264 cases and 173 controls)...
July 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28696560/overview-of-admixture-mapping
#2
Daniel Shriner
Admixture mapping is a powerful method of gene mapping for diseases or traits that show differential risk by ancestry. Admixture mapping has been applied most often to Americans who trace ancestry to various combinations of Native Americans, Europeans, and West Africans. Recent developments in admixture mapping include improvements in methods and the reference data needed to make inferences about ancestry, as well as extensions of the mapping approach in the framework of linear mixed models. In this unit, the key concepts of admixture mapping are outlined...
July 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28662691/the-wolf-reference-genome-sequence-canis-lupus-lupus-and-its-implications-for-canis-spp-population-genomics
#3
Shyam Gopalakrishnan, Jose A Samaniego Castruita, Mikkel-Holger S Sinding, Lukas F K Kuderna, Jannikke Räikkönen, Bent Petersen, Thomas Sicheritz-Ponten, Greger Larson, Ludovic Orlando, Tomas Marques-Bonet, Anders J Hansen, Love Dalén, M Thomas P Gilbert
BACKGROUND: An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data - that of a boxer dog (Canis lupus familiaris). We generated the first de novo wolf genome (Canis lupus lupus) as an additional choice of reference, and explored what implications may arise when previously published dog and wolf resequencing data are remapped to this reference...
June 29, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28657151/joint-genotype-and-ancestry-based-genome-wide-association-studies-in-admixed-populations
#4
Piotr Szulc, Malgorzata Bogdan, Florian Frommlet, Hua Tang
In genome-wide association studies (GWAS) genetic loci that influence complex traits are localized by inspecting associations between genotypes of genetic markers and the values of the trait of interest. On the other hand, admixture mapping, which is performed in case of populations consisting of a recent mix of two ancestral groups, relies on the ancestry information at each locus (locus-specific ancestry). Recently it has been proposed to jointly model genotype and locus-specific ancestry within the framework of single marker tests...
June 28, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28582460/admixture-mapping-of-pelvic-organ-prolapse-in-african-americans-from-the-women-s-health-initiative-hormone-therapy-trial
#5
Ayush Giri, Katherine E Hartmann, Melinda C Aldrich, Renee M Ward, Jennifer M Wu, Amy J Park, Mariaelisa Graff, Lihong Qi, Rami Nassir, Robert B Wallace, Mary J O'Sullivan, Kari E North, Digna R Velez Edwards, Todd L Edwards
Evidence suggests European American (EA) women have two- to five-fold increased odds of having pelvic organ prolapse (POP) when compared with African American (AA) women. However, the role of genetic ancestry in relation to POP risk is not clear. Here we evaluate the association between genetic ancestry and POP in AA women from the Women's Health Initiative Hormone Therapy trial. Women with grade 1 or higher classification, and grade 2 or higher classification for uterine prolapse, cystocele or rectocele at baseline or during follow-up were considered to have any POP (N = 805) and moderate/severe POP (N = 156), respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28523639/association-mapping-of-yield-and-yield-related-traits-under-reproductive-stage-drought-stress-in-rice-oryza-sativa-l
#6
B P Mallikarjuna Swamy, Noraziyah Abd Aziz Shamsudin, Site Noorzuraini Abd Rahman, Ramil Mauleon, Wickneswari Ratnam, Ma Teressa Sta Cruz, Arvind Kumar
BACKGROUND: The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS: The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%...
December 2017: Rice
https://www.readbyqxmd.com/read/28444387/meiotic-genes-are-enriched-in-regions-of-reduced-archaic-ancestry
#7
B Jégou, S Sankararaman, A D Rolland, D Reich, F Chalmel
About 1-6% of the genetic ancestry of modern humans today originates from admixture with archaic humans. It has recently been shown that autosomal genomic regions with a reduced proportion of Neanderthal and Denisovan ancestries are significantly enriched in genes that are more expressed in testis than in other tissues. To determine whether a cellular segregation pattern would exist, we combined maps of archaic introgression with a cross-analysis of three transcriptomic datasets deciphering the transcriptional landscape of human gonadal cell types...
April 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28408710/local-ancestry-association-admixture-mapping-and-ongoing-challenges
#8
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
#9
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
#10
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
#11
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
#12
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 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
#13
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
#14
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
#15
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...
July 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
#16
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
#17
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
#18
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
#19
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
#20
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
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