keyword
MENU ▼
Read by QxMD icon Read
search

Admixture mapping

keyword
https://www.readbyqxmd.com/read/29230682/association-of-functional-markers-with-flowering-time-in-lentil
#1
Jitendra Kumar, Sunanda Gupta, Revanappa S Biradar, Priyanka Gupta, Sonali Dubey, Narendra Pratap Singh
In the present study, a diverse panel of 96 accessions of lentil germplasm was used to study flowering time over environments and to identify simple sequence repeat markers associated with flowering time through association mapping. The study showed high broad sense heritability estimate (h 2 bs=0.93) for flowering time in lentil. Screening of 534 SSR markers resulted in an identification of 75 SSR polymorphic markers (13.9%) across studied genotypes. These markers amplified 266 loci and generated 697 alleles ranging from two to 16 alleles per locus...
December 11, 2017: Journal of Applied Genetics
https://www.readbyqxmd.com/read/29207956/a-microsatellite-diversity-analysis-and-the-development-of-core-set-germplasm-in-a-large-hulless-barley-hordeum-vulgare-l-collection
#2
Qijun Xu, Xingquan Zeng, Bin Lin, Zeqing Li, Hongjun Yuan, Yulin Wang, Zhasang, Nyima Tashi
BACKGROUND: Clarifying genetic diversity in a large germplasm resource plays important roles in experimental designs that provides flexible utility in fundamental research and breeding in crops. However, the work is limited due to small collections of barley that are insufficient representatives. RESULTS: In the present study, we collected 562 hulless barley (Hordeum vulgare L.) accessions with worldwide geographic origins and evaluated their genetic variability and relatedness based on 93 simple sequence repeat (SSR) markers...
December 6, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29202956/admixture-mapping-of-uterine-fibroid-size-and-number-in-african-american-women
#3
Michael J Bray, Todd L Edwards, Melissa F Wellons, Sarah H Jones, Katherine E Hartmann, Digna R Velez Edwards
OBJECTIVE: To evaluate the relationship between genetic ancestry and uterine fibroid characteristics. DESIGN: Cross-sectional study. SETTING: Not applicable. PATIENT(S): A total of 609 African American participants with image- or surgery-confirmed fibroids in a biorepository at Vanderbilt University electronic health record biorepository and the Coronary Artery Risk Development in Young Adults studies were included. INTERVENTION(S): None...
December 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/29155883/admixture-mapping-in-the-hispanic-community-health-study-study-of-latinos-reveals-regions-of-genetic-associations-with-blood-pressure-traits
#4
Tamar Sofer, Leslie J Baier, Sharon R Browning, Timothy A Thornton, Gregory A Talavera, Sylvia Wassertheil-Smoller, Martha L Daviglus, Robert Hanson, Sayuko Kobes, Richard S Cooper, Jianwen Cai, Daniel Levy, Alex P Reiner, Nora Franceschini
Admixture mapping can be used to detect genetic association regions in admixed populations, such as Hispanics/Latinos, by estimating associations between local ancestry allele counts and the trait of interest. We performed admixture mapping of the blood pressure traits systolic and diastolic blood pressure (SBP, DBP), mean arterial pressure (MAP), and pulse pressure (PP), in a dataset of 12,116 participants from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Hispanics/Latinos have three predominant ancestral populations (European, African, and Amerindian), for each of which we separately tested local ancestry intervals across the genome...
2017: PloS One
https://www.readbyqxmd.com/read/29124769/introgression-from-populus-balsamifera-underlies-adaptively-significant-variation-and-range-boundaries-in-p-%C3%A2-trichocarpa
#5
Adriana Suarez-Gonzalez, Charles A Hefer, Christian Lexer, Carl J Douglas, Quentin C B Cronk
Introgression can be an important source of adaptive phenotypes, although conversely it can have deleterious effects. Evidence for adaptive introgression is accumulating but information on the genetic architecture of introgressed traits lags behind. Here we determine trait architecture in Populus trichocarpa under introgression from P. balsamifera using admixture mapping and phenotypic analyses. Our results reveal that admixture is a key driver of clinal adaptation and suggest that the northern range extension of P...
November 10, 2017: New Phytologist
https://www.readbyqxmd.com/read/29118129/admixture-mapping-in-a-hybrid-zone-reveals-loci-associated-with-avian-feather-coloration
#6
Alan Brelsford, David P L Toews, Darren E Irwin
Identifying the genetic bases for colour patterns has provided important insights into the control and expression of pigmentation and how these characteristics influence fitness. However, much more is known about the genetic bases for traits based on melanin pigments than for traits based on another major class of pigments, carotenoids. Here, we use natural admixture in a hybrid zone between Audubon's and myrtle warblers (Setophaga coronata auduboni/S. c. coronata) to identify genomic regions associated with both types of pigmentation...
November 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29073141/genomic-regions-associated-with-susceptibility-to-barrett-s-esophagus-and-esophageal-adenocarcinoma-in-african-americans-the-cross-betrnet-admixture-study
#7
Xiangqing Sun, Apoorva K Chandar, Marcia I Canto, Prashanthi N Thota, Malcom Brock, Nicholas J Shaheen, David G Beer, Jean S Wang, Gary W Falk, Prasad G Iyer, Julian A Abrams, Medha Venkat-Ramani, Martina Veigl, Alexander Miron, Joseph Willis, Deepa T Patil, Ilke Nalbantoglu, Kishore Guda, Sanford D Markowitz, Xiaofeng Zhu, Robert Elston, Amitabh Chak
BACKGROUND: Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC) are far more prevalent in European Americans than in African Americans. Hypothesizing that this racial disparity in prevalence might represent a genetic susceptibility, we used an admixture mapping approach to interrogate disease association with genomic differences between European and African ancestry. METHODS: Formalin fixed paraffin embedded samples were identified from 54 African Americans with BE or EAC through review of surgical pathology databases at participating Barrett's Esophagus Translational Research Network (BETRNet) institutions...
2017: PloS One
https://www.readbyqxmd.com/read/29037167/ancestry-inference-using-principal-component-analysis-and-spatial-analysis-a-distance-based-analysis-to-account-for-population-substructure
#8
Jinyoung Byun, Younghun Han, Ivan P Gorlov, Jonathan A Busam, Michael F Seldin, Christopher I Amos
BACKGROUND: Accurate inference of genetic ancestry is of fundamental interest to many biomedical, forensic, and anthropological research areas. Genetic ancestry memberships may relate to genetic disease risks. In a genome association study, failing to account for differences in genetic ancestry between cases and controls may also lead to false-positive results. Although a number of strategies for inferring and taking into account the confounding effects of genetic ancestry are available, applying them to large studies (tens thousands samples) is challenging...
October 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29016599/coronary-collateralization-shows-sex-and-racial-ethnic-differences-in-obstructive-artery-disease-patients
#9
Zhi Liu, Margaret A Pericak-Vance, Pascal Goldschmidt-Clermont, David Seo, Liyong Wang, Tatjana Rundek, Gary W Beecham
BACKGROUND: Coronary collateral circulation protects cardiac tissues from myocardial infarction damage and decreases sudden cardiac death. So far, it is unclear how coronary collateralization varies by race-ethnicity groups and by sex. METHODS: We assessed 868 patients with obstructive CAD. Patients were assessed for collateral grades based on Rentrop grading system, as well as other covariates. DNA samples were genotyped using the Affymetrix 6.0 genotyping array...
2017: PloS One
https://www.readbyqxmd.com/read/28980262/the-analysis-of-ethnic-mixtures
#10
Xiaofeng Zhu, Heming Wang
Population of ethnic mixtures can be useful in genetic studies. Admixture mapping, or mapping by admixture linkage disequilibrium (MALD), is specially developed for admixed populations and can supplement traditional genome-wide association analyses in the search for genetic variants underlying complex traits. Admixture mapping tests the association between a trait and locus-specific ancestries. The locus-specific ancestries are in linkage disequilibrium (LD), which is generated by an admixture process between genetically distinct ancestral populations...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28955604/genetic-diversity-and-population-structure-of-cucumis-sativus-l-by-using-ssr-markers
#11
Aejaz Ahmad Dar, Reetika Mahajan, Padma Lay, Susheel Sharma
The genetic variation, marker attributes and population structure was assessed in 104 genotypes of cucumber using 23 SSR primer pairs. The total number of alleles produced was 67 with an average of 2.91 per locus. Allele frequency was in the range of 0.215 to 0.561 with mean value of 0.403, polymorphic information content ranged from 0.158 to 0.495 with the mean of 0.333, marker index ranged from 0.316 to 1.54 with an average value of 0.954 and resolving power ranged from 0.346 to 2.692 with mean of 1.392...
October 2017: 3 Biotech
https://www.readbyqxmd.com/read/28951529/admixpower-statistical-power-and-sample-size-estimation-for-mapping-genetic-loci-in-admixed-populations
#12
Yadu Gautam, Mekibib Altaye, Changchun Xie, Tesfaye B Mersha
Admixed populations result from recent admixture of two or more ancestral populations with divergent allele frequencies. The genome of each admixed individual is a mosaic of haplotypes inherited from the ancestral populations. Despite the substantial work to assess power and sample size requirements for association mapping in genetically homogeneous populations of European ancestry, power and sample size estimation methods for mapping genes in genetically heterogeneous admixed populations such as African Americans are lacking...
November 2017: Genetics
https://www.readbyqxmd.com/read/28941494/current-understanding-of-the-genetic-causes-of-keloid-formation
#13
REVIEW
Donald A Glass
Keloids are an exuberant response to cutaneous wound healing. Several lines of evidence suggest that keloid scarring is influenced by genetic factors. This review will discuss our current understanding of genetic influences on keloidal scarring via familial inheritance patterns; ethnic differences in prevalence; syndromes with keloid occurrence; linkage analysis, genome-wide association studies, and admixture mapping studies; transforming growth factor beta and p53 variant studies; and human leukocyte antigen polymorphisms...
October 2017: Journal of Investigative Dermatology. Symposium Proceedings
https://www.readbyqxmd.com/read/28900832/spatial-discrimination-of-glioblastoma-and-treatment-effect-with-histologically-validated-perfusion-and-diffusion-magnetic-resonance-imaging-metrics
#14
Melissa A Prah, Mona M Al-Gizawiy, Wade M Mueller, Elizabeth J Cochran, Raymond G Hoffmann, Jennifer M Connelly, Kathleen M Schmainda
The goal of this study is to spatially discriminate tumor from treatment effect (TE), within the contrast-enhancing lesion, for brain tumor patients at all stages of treatment. To this end, the diagnostic accuracy of MRI-derived diffusion and perfusion parameters to distinguish pure TE from pure glioblastoma (GBM) was determined utilizing spatially-correlated biopsy samples. From July 2010 through June 2015, brain tumor patients who underwent pre-operative DWI and DSC-MRI and stereotactic image-guided biopsy were considered for inclusion in this IRB-approved study...
September 12, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28843547/the-arms-race-between-man-and-mycobacterium-tuberculosis-time-to-regroup
#15
Eileen G Hoal, Anzaan Dippenaar, Craig Kinnear, Paul D van Helden, Marlo Möller
An arms race is an appropriate metaphor to use for the interaction of man and Mycobacterium tuberculosis (M.tb) through the millennia. Estimates of the time of infection of modern humans with M.tb often pre-date the Out-of-Africa migration. Humans have adapted to the changing environment during the migration with respect to climate, food sources and encounters with local pathogens. More recently, there has been adaptation to the demographic changes brought about in the majority of the human population by the Neolithic revolution...
August 23, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28743033/analysis-of-the-genetic-structure-of-the-malay-population-ancestry-informative-marker-snps-in-the-malay-of-peninsular-malaysia
#16
Padillah Yahya, Sarina Sulong, Azian Harun, Hatin Wan Isa, Nur-Shafawati Ab Rajab, Pongsakorn Wangkumhang, Alisa Wilantho, Chumpol Ngamphiw, Sissades Tongsima, Bin Alwi Zilfalil
Malay, the main ethnic group in Peninsular Malaysia, is represented by various sub-ethnic groups such as Melayu Banjar, Melayu Bugis, Melayu Champa, Melayu Java, Melayu Kedah Melayu Kelantan, Melayu Minang and Melayu Patani. Using data retrieved from the MyHVP (Malaysian Human Variome Project) database, a total of 135 individuals from these sub-ethnic groups were profiled using the Affymetrix GeneChip Mapping Xba 50-K single nucleotide polymorphism (SNP) array to identify SNPs that were ancestry-informative markers (AIMs) for Malays of Peninsular Malaysia...
September 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28731588/human-leukocyte-antigen-distribution-and-genomic-ancestry-in-brazilian-patients-with-sickle-cell-disease
#17
M C F da Silva-Malta, P S Rodrigues, L W Zuccherato, F C B de Souza, E M F L Domingues, V R Souza, E Tarazona-Santos, M L Martins
Hematopoietic stem-cell transplantation (HSCT) is currently the only established curative treatment for sickle cell disease (SCD), but is limited by donor availability. Ethnicity is thought to have an impact on the complications experienced by patients that undergo HSCT and on the likelihood of identifying an human leukocyte antigen (HLA) matched donor. In the present study, we investigated the genomic ancestry and the distribution of HLA allele groups in Brazilian patients with SCD, compared these HLA profiles to worldwide populations and evaluate the availability of HLA-matched donors...
July 21, 2017: HLA
https://www.readbyqxmd.com/read/28729877/genetic-diversity-population-structure-and-linkage-disequilibrium-of-an-association-mapping-panel-revealed-by-genome-wide-snp-markers-in-sesame
#18
Chengqi Cui, Hongxian Mei, Yanyang Liu, Haiyang Zhang, Yongzhan Zheng
The characterization of genetic diversity and population structure can be used in tandem to detect reliable phenotype-genotype associations. In the present study, we genotyped a set of 366 sesame germplasm accessions by using 89,924 single-nucleotide polymorphisms (SNPs). The number of SNPs on each chromosome was consistent with the physical length of the respective chromosome, and the average marker density was approximately 2.67 kb/SNP. The genetic diversity analysis showed that the average nucleotide diversity of the panel was 1...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28715450/african-genetic-ancestry-interacts-with-body-mass-index-to-modify-risk-for-uterine-fibroids
#19
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 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28696560/overview-of-admixture-mapping
#20
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
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"