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Admixture mapping

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
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
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
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
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
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...
September 29, 2016: Molecular Biology and Evolution
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...
September 20, 2016: Current Opinion in Genetics & Development
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
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
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
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
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
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
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
A Manunza, T F Cardoso, A Noce, A Martínez, A Pons, L A Bermejo, V Landi, A Sànchez, J Jordana, J V Delgado, S Adán, J Capote, O Vidal, E Ugarte, J J Arranz, J H Calvo, J Casellas, M Amills
The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). We combined this dataset with Spanish ovine data previously reported by the International Sheep Genomics Consortium (N = 229). Multidimensional scaling and Admixture analyses revealed that Canaria de Pelo and, to a lesser extent, Roja Mallorquina, Latxa and Churra are clearly differentiated populations, while the remaining seven breeds (Ojalada, Castellana, Gallega, Xisqueta, Ripollesa, Rasa Aragonesa and Segureña) share a similar genetic background...
2016: Scientific Reports
Sharon R Browning, Kelsey Grinde, Anna Plantinga, Stephanie M Gogarten, Adrienne M Stilp, Robert C Kaplan, M Larissa Avilés-Santa, Brian L Browning, Cathy C Laurie
We estimated local ancestry on the autosomes and X chromosome in a large US-based study of 12,793 Hispanic/Latino individuals using the RFMix method, and we compared different reference panels and approaches to local ancestry estimation on the X chromosome by means of Mendelian inconsistency rates as a proxy for accuracy. We developed a novel and straightforward approach to performing ancestry-specific PCA after finding artifactual behavior in the results from an existing approach. Using the ancestry-specific PCA, we found significant population structure within African, European, and Amerindian ancestries in the Hispanic/Latino individuals in our study...
2016: G3: Genes—Genomes—Genetics
Jon E Hess, Joseph S Zendt, Amanda R Matala, Shawn R Narum
Migration traits are presumed to be complex and to involve interaction among multiple genes. We used both univariate analyses and a multivariate random forest (RF) machine learning algorithm to conduct association mapping of 15 239 single nucleotide polymorphisms (SNPs) for adult migration-timing phenotype in steelhead (Oncorhynchus mykiss). Our study focused on a model natural population of steelhead that exhibits two distinct migration-timing life histories with high levels of admixture in nature. Neutral divergence was limited between fish exhibiting summer- and winter-run migration owing to high levels of interbreeding, but a univariate mixed linear model found three SNPs from a major effect gene to be significantly associated with migration timing (p < 0...
May 11, 2016: Proceedings. Biological Sciences
Bridgett M vonHoldt, Roland Kays, John P Pollinger, Robert K Wayne
Hybrid zones typically contain novel gene combinations that can be tested by natural selection in a unique genetic context. Parental haplotypes that increase fitness can introgress beyond the hybrid zone, into the range of parental species. We used the Affymetrix canine SNP genotyping array to identify genomic regions tagged by multiple ancestry informative markers that are more frequent in an admixed population than expected. We surveyed a hybrid zone formed in the last 100 years as coyotes expanded their range into eastern North America...
June 2016: Molecular Ecology
Shubha Vij, Heiner Kuhl, Inna S Kuznetsova, Aleksey Komissarov, Andrey A Yurchenko, Peter Van Heusden, Siddharth Singh, Natascha M Thevasagayam, Sai Rama Sridatta Prakki, Kathiresan Purushothaman, Jolly M Saju, Junhui Jiang, Stanley Kimbung Mbandi, Mario Jonas, Amy Hin Yan Tong, Sarah Mwangi, Doreen Lau, Si Yan Ngoh, Woei Chang Liew, Xueyan Shen, Lawrence S Hon, James P Drake, Matthew Boitano, Richard Hall, Chen-Shan Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir Trifonov, Marsel Kabilov, Alexey Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J Sedlazeck, Gregory W Vurture, Gopikrishna Gopalapillai, Vinaya Kumar Katneni, Tansyn H Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R Jerry, Stephen J O'Brien, Michael C Schatz, Tamás Dalmay, Stephen W Turner, Si Lok, Alan Christoffels, László Orbán
We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range...
April 2016: PLoS Genetics
Hanim Kamis Norhalifah, Fatnin Hisham Syaza, Geoffrey Keith Chambers, Hisham Atan Edinur
This article explores the genetic history of the various sub-populations currently living in Peninsular Malaysia. This region has received multiple waves of migrants like the Orang Asli in prehistoric times and the Chinese, Indians, Europeans and Arabs during historic times. There are three highly distinct lineages that make up the Orang Asli; Semang, Senoi and Proto-Malays. The Semang, who have 'Negrito' characteristics, represent the first human settlers in Peninsular Malaysia arriving from about 50,000ya...
July 15, 2016: Gene
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