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Admixture mapping

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https://www.readbyqxmd.com/read/29016599/coronary-collateralization-shows-sex-and-racial-ethnic-differences-in-obstructive-artery-disease-patients
#1
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
#2
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
#3
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
#4
Yadu Gautam, Mekbib 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...
September 26, 2017: Genetics
https://www.readbyqxmd.com/read/28941494/current-understanding-of-the-genetic-causes-of-keloid-formation
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
MULTICENTER STUDY
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
#16
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
#17
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 (NA and DA) 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...
August 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28408710/local-ancestry-association-admixture-mapping-and-ongoing-challenges
#18
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
#19
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
#20
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
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