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Admixture mapping

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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...
October 11, 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
#10
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
https://www.readbyqxmd.com/read/27708667/admixture-mapping-of-african-american-women-in-the-amber-consortium-identifies-new-loci-for-breast-cancer-and-estrogen-receptor-subtypes
#11
Edward A Ruiz-Narváez, Lara Sucheston-Campbell, Jeannette T Bensen, Song Yao, Stephen Haddad, Christopher A Haiman, Elisa V Bandera, Esther M John, Leslie Bernstein, Jennifer J Hu, Regina G Ziegler, Sandra L Deming, Andrew F Olshan, Christine B Ambrosone, Julie R Palmer, Kathryn L Lunetta
Recent genetic admixture coupled with striking differences in incidence of estrogen receptor (ER) breast cancer subtypes, as well as severity, between women of African and European ancestry, provides an excellent rationale for performing admixture mapping in African American women with breast cancer risk. We performed the largest breast cancer admixture mapping study with in African American women to identify novel genomic regions associated with the disease. We conducted a genome-wide admixture scan using 2,624 autosomal ancestry informative markers (AIMs) in 3,629 breast cancer cases (including 1,968 ER-positive, 1093 ER-negative, and 601 triple-negative) and 4,658 controls from the African American Breast Cancer Epidemiology and Risk (AMBER) Consortium, a collaborative study of four large geographically different epidemiological studies of breast cancer in African American women...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27687565/a-thousand-fly-genomes-an-expanded-drosophila-genome-nexus
#12
LETTER
Justin B Lack, Jeremy D Lange, Alison D Tang, Russell B Corbett-Detig, John E Pool
The Drosophila Genome Nexus is a population genomic resource that provides D. melanogaster genomes from multiple sources. To facilitate comparisons across data sets, genomes are aligned using a common reference alignment pipeline which involves two rounds of mapping. Regions of residual heterozygosity, identity-by-descent, and recent population admixture are annotated to enable data filtering based on the user's needs. Here, we present a significant expansion of the Drosophila Genome Nexus, which brings the current data object to a total of 1,121 wild-derived genomes...
December 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27662060/recent-advances-in-the-study-of-fine-scale-population-structure-in-humans
#13
REVIEW
John Novembre, Benjamin M Peter
Empowered by modern genotyping and large samples, population structure can be accurately described and quantified even when it only explains a fraction of a percent of total genetic variance. This is especially relevant and interesting for humans, where fine-scale population structure can both confound disease-mapping studies and reveal the history of migration and divergence that shaped our species' diversity. Here we review notable recent advances in the detection, use, and understanding of population structure...
December 2016: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/27609757/mtdna-diversity-in-human-populations-highlights-the-merit-of-haplotype-matching-in-gene-therapies
#14
E C Røyrvik, J P Burgstaller, I G Johnston
STUDY QUESTION: Does mitochondrial DNA (mtDNA) diversity in modern human populations potentially pose a challenge, via mtDNA segregation, to mitochondrial replacement therapies? SUMMARY ANSWER: The magnitude of mtDNA diversity in modern human populations is as high as in mammalian model systems where strong mtDNA segregation is observed; consideration of haplotype pairs and/or haplotype matching can help avoid these potentially deleterious effects. WHAT IS KNOWN ALREADY: In mammalian models, substantial proliferative differences are observed between different mtDNA haplotypes in cellular admixtures, with larger proliferative differences arising from more diverse haplotype pairings...
September 8, 2016: Molecular Human Reproduction
https://www.readbyqxmd.com/read/27546575/plumage-genes-and-little-else-distinguish-the-genomes-of-hybridizing-warblers
#15
David P L Toews, Scott A Taylor, Rachel Vallender, Alan Brelsford, Bronwyn G Butcher, Philipp W Messer, Irby J Lovette
When related taxa hybridize extensively, their genomes may become increasingly homogenized over time. This mixing via hybridization creates conservation challenges when it reduces genetic or phenotypic diversity and when it endangers previously distinct species via genetic swamping [1]. However, hybridization also facilitates admixture mapping of traits that distinguish each species and the associated genes that maintain distinctiveness despite ongoing gene flow [2]. We address these dual aspects of hybridization in the golden-winged/blue-winged warbler complex, two phenotypically divergent warblers that are indistinguishable using traditional molecular markers and that draw substantial conservation attention [3-5]...
September 12, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/27535931/nationwide-genomic-study-in-denmark-reveals-remarkable-population-homogeneity
#16
Georgios Athanasiadis, Jade Y Cheng, Bjarni J Vilhjálmsson, Frank G Jørgensen, Thomas D Als, Stephanie Le Hellard, Thomas Espeseth, Patrick F Sullivan, Christina M Hultman, Peter C Kjærgaard, Mikkel H Schierup, Thomas Mailund
Denmark has played a substantial role in the history of Northern Europe. Through a nationwide scientific outreach initiative, we collected genetic and anthropometrical data from ∼800 high school students and used them to elucidate the genetic makeup of the Danish population, as well as to assess polygenic predictions of phenotypic traits in adolescents. We observed remarkable homogeneity across different geographic regions, although we could still detect weak signals of genetic structure reflecting the history of the country...
October 2016: Genetics
https://www.readbyqxmd.com/read/27438321/genetic-investigation-into-the-differential-risk-of-atrial-fibrillation-among-black-and-white-individuals
#17
Jason D Roberts, Donglei Hu, Susan R Heckbert, Alvaro Alonso, Thomas A Dewland, Eric Vittinghoff, Yongmei Liu, Bruce M Psaty, Jeffrey E Olgin, Jared W Magnani, Scott Huntsman, Esteban G Burchard, Dan E Arking, Kirsten Bibbins-Domingo, Tamara B Harris, Marco V Perez, Elad Ziv, Gregory M Marcus
IMPORTANCE: White persons have a higher risk of atrial fibrillation (AF) compared with black individuals despite a lower prevalence of risk factors. This difference may be due, at least in part, to genetic factors. OBJECTIVES: To determine whether 9 single-nucleotide polymorphisms (SNPs) associated with AF account for this paradoxical differential racial risk for AF and to use admixture mapping to search genome-wide for loci that may account for this phenomenon...
July 1, 2016: JAMA Cardiology
https://www.readbyqxmd.com/read/27393700/what-ancestry-can-tell-us-about-the-genetic-origins-of-inter-ethnic-differences-in-asthma-expression
#18
REVIEW
Natalia Hernandez-Pacheco, Carlos Flores, Sam S Oh, Esteban G Burchard, Maria Pino-Yanes
Differences in asthma prevalence have been described across different populations, suggesting that genetic ancestry can play an important role in this disease. In fact, several studies have demonstrated an association between African ancestry with increased asthma susceptibility and severity, higher immunoglobulin E levels, and lower lung function. In contrast, Native American ancestry has been shown to have a protective role for this disease. Genome-wide association studies have allowed the identification of population-specific genetic variants with varying allele frequency among populations...
July 2016: Current Allergy and Asthma Reports
https://www.readbyqxmd.com/read/27324549/-research-advances-in-gene-polymorphisms-in-biological-pathways-of-drugs-for-asthma
#19
REVIEW
Dan-Dan Guo, Xiang-Rong Zheng
The studies on gene polymorphisms in biological pathways of the drugs for the treatment of asthma refer to the studies in which pharmacogenetic methods, such as genome-wide association studies, candidate gene studies, genome sequencing, admixture mapping analysis, and linkage disequilibrium, are used to identify, determine, and repeatedly validate the effect of one or more single nucleotide polymorphisms on the efficacy of drugs. This can provide therapeutic strategies with optimal benefits, least side effects, and lowest costs to patients with asthma, and thus realize individualized medicine...
June 2016: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
https://www.readbyqxmd.com/read/27297995/resolving-the-etiology-of-atopic-disorders-by-using-genetic-analysis-of-racial-ancestry
#20
REVIEW
Jayanta Gupta, Elisabet Johansson, Jonathan A Bernstein, Ranajit Chakraborty, Gurjit K Khurana Hershey, Marc E Rothenberg, Tesfaye B Mersha
Atopic dermatitis (AD), food allergy, allergic rhinitis, and asthma are common atopic disorders of complex etiology. The frequently observed atopic march from early AD to asthma, allergic rhinitis, or both later in life and the extensive comorbidity of atopic disorders suggest common causal mechanisms in addition to distinct ones. Indeed, both disease-specific and shared genomic regions exist for atopic disorders. Their prevalence also varies among races; for example, AD and asthma have a higher prevalence in African Americans when compared with European Americans...
September 2016: Journal of Allergy and Clinical Immunology
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