scholarly journals Comparison of Genome-Wide Association Scans for Quantitative and Observational Measures of Human Hair Curvature

2020 ◽  
Vol 23 (5) ◽  
pp. 271-277
Author(s):  
Yvonne Y. W. Ho ◽  
Angela Mina-Vargas ◽  
Gu Zhu ◽  
Mark Brims ◽  
Dennis McNevin ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Genetic Locus ◽  
Fibre Diameter ◽  
Quantitative Measure ◽  
High Linkage Disequilibrium ◽  
Self Report ◽  
Genome Wide Association ◽  
Observational Measures ◽  
Hair Morphology ◽  
Genome Wide

AbstractPrevious genetic studies on hair morphology focused on the overall morphology of the hair using data collected by self-report or researcher observation. Here, we present the first genome-wide association study (GWAS) of a micro-level quantitative measure of hair curvature. We compare these results to GWAS results obtained using a macro-level classification of observable hair curvature performed in the same sample of twins and siblings of European descent. Observational data were collected by trained observers, while quantitative data were acquired using an Optical Fibre Diameter Analyser (OFDA). The GWAS for both the observational and quantitative measures of hair curvature resulted in genome-wide significant signals at chromosome 1q21.3 close to the trichohyalin (TCHH) gene, previously shown to harbor variants associated with straight hair morphology in Europeans. All genetic variants reaching genome-wide significance for both GWAS (quantitative measure lead single-nucleotide polymorphism [SNP] rs12130862, p = 9.5 × 10–09; observational measure lead SNP rs11803731, p = 2.1 × 10–17) were in moderate to very high linkage disequilibrium (LD) with each other (minimum r2 = .45), indicating they represent the same genetic locus. Conditional analyses confirmed the presence of only one signal associated with each measure at this locus. Results from the quantitative measures reconfirmed the accuracy of observational measures.

scholarly journals Integration of a single-step genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Bingru Zhao ◽  
Hanpeng Luo ◽  
Xixia Huang ◽  
Chen Wei ◽  
Jiang Di ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genetic Improvement ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Fibre Diameter ◽  
Single Step ◽  
Genome Wide Association ◽  
Six Traits ◽  
Genome Wide

Abstract Background Genetic improvement of wool and growth traits is a major goal in the sheep industry, but their underlying genetic architecture remains elusive. To improve our understanding of these mechanisms, we conducted a weighted single-step genome-wide association study (WssGWAS) and then integrated the results with large-scale transcriptome data for five wool traits and one growth trait in Merino sheep: mean fibre diameter (MFD), coefficient of variation of the fibre diameter (CVFD), crimp number (CN), mean staple length (MSL), greasy fleece weight (GFW), and live weight (LW). Results Our dataset comprised 7135 individuals with phenotype data, among which 1217 had high-density (HD) genotype data (n = 372,534). The genotypes of 707 of these animals were imputed from the Illumina Ovine single nucleotide polymorphism (SNP) 54 BeadChip to the HD Array. The heritability of these traits ranged from 0.05 (CVFD) to 0.36 (MFD), and between-trait genetic correlations ranged from − 0.44 (CN vs. LW) to 0.77 (GFW vs. LW). By integrating the GWAS signals with RNA-seq data from 500 samples (representing 87 tissue types from 16 animals), we detected tissues that were relevant to each of the six traits, e.g. liver, muscle and the gastrointestinal (GI) tract were the most relevant tissues for LW, and leukocytes and macrophages were the most relevant cells for CN. For the six traits, 54 quantitative trait loci (QTL) were identified covering 81 candidate genes on 21 ovine autosomes. Multiple candidate genes showed strong tissue-specific expression, e.g. BNC1 (associated with MFD) and CHRNB1 (LW) were specifically expressed in skin and muscle, respectively. By conducting phenome-wide association studies (PheWAS) in humans, we found that orthologues of several of these candidate genes were significantly (FDR < 0.05) associated with similar traits in humans, e.g. BNC1 was significantly associated with MFD in sheep and with hair colour in humans, and CHRNB1 was significantly associated with LW in sheep and with body mass index in humans. Conclusions Our findings provide novel insights into the biological and genetic mechanisms underlying wool and growth traits, and thus will contribute to the genetic improvement and gene mapping of complex traits in sheep.

scholarly journals Correction: Novel Genetic Locus Implicated for HIV-1 Acquisition with Putative Regulatory Links to HIV Replication and Infectivity: A Genome-Wide Association Study

PLoS ONE ◽  
2015 ◽  
Vol 10 (5) ◽  
pp. e0129671
Author(s):  
Eric O. Johnson ◽  
Dana B. Hancock ◽  
Nathan C. Gaddis ◽  
Joshua L. Levy ◽  
Grier Page ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genetic Locus ◽  
Genome Wide Association ◽  
Hiv Replication ◽  
Genome Wide ◽  
A Genome ◽  
Hiv 1

scholarly journals Genome-wide association study of early-onset bipolar I disorder in the Han Taiwanese population

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lawrence Shih-Hsin Wu ◽  
Ming-Chyi Huang ◽  
Cathy Shen-Jang Fann ◽  
Hsien-Yuan Lane ◽  
Chian-Jue Kuo ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Association Study ◽  
Early Onset ◽  
Genome Wide Association Study ◽  
Genetic Locus ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Chinese Descent

AbstractThe search for susceptibility genes underlying the heterogeneous bipolar disorder has been inconclusive, often with irreproducible results. There is a hope that narrowing the phenotypes will increase the power of genetic analysis. Early-onset bipolar disorder is thought to be a genetically homogeneous subtype with greater symptom severity. We conducted a genome-wide association study (GWAS) for this subtype in bipolar I (BPI) disorder. Study participants included 1779 patients of Han Chinese descent with BPI disorder recruited by the Taiwan Bipolar Consortium. We conducted phenotype assessment using the Chinese version of the Schedules for Clinical Assessment in Neuropsychiatry and prepared a life chart with graphic depiction of lifetime clinical course for each of the BPI patient recruited. The assessment of onset age was based on this life chart with early onset defined as ≤20 years of age. We performed GWAS in a discovery group of 516 early-onset and 790 non-early-onset BPI patients, followed by a replication study in an independent group of 153 early-onset and 320 non-early-onset BPI patients and a meta-analysis with these two groups. The SNP rs11127876, located in the intron of CADM2, showed association with early-onset BPI in the discovery cohort (P = 7.04 × 10−8) and in the test of replication (P = 0.0354). After meta-analysis, this SNP was demonstrated to be a new genetic locus in CADM2 gene associated with early-onset BPI disorder (P = 5.19 × 10−8).

scholarly journals Genome-Wide Association Study Identifies GPC5 as a Novel Genetic Locus Protective against Sudden Cardiac Arrest

PLoS ONE ◽  
2010 ◽  
Vol 5 (3) ◽  
pp. e9879 ◽  
Author(s):  
Dan E. Arking ◽  
Kyndaron Reinier ◽  
Wendy Post ◽  
Jonathan Jui ◽  
Gina Hilton ◽  
...  
Keyword(s):  
Cardiac Arrest ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Genetic Locus ◽  
Sudden Cardiac Arrest ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Genome-wide association study reveals novel genetic locus associated with intra-individual variability in response time

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Ari Pinar ◽  
Ziarih Hawi ◽  
Tarrant Cummins ◽  
Beth Johnson ◽  
Marc Pauper ◽  
...  
Keyword(s):  
Response Time ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Genetic Locus ◽  
Individual Variability ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Novel Genetic Locus Implicated for HIV-1 Acquisition with Putative Regulatory Links to HIV Replication and Infectivity: A Genome-Wide Association Study

PLoS ONE ◽  
2015 ◽  
Vol 10 (3) ◽  
pp. e0118149 ◽  
Author(s):  
Eric O. Johnson ◽  
Dana B. Hancock ◽  
Nathan C. Gaddis ◽  
Joshua L. Levy ◽  
Grier Page ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genetic Locus ◽  
Genome Wide Association ◽  
Hiv Replication ◽  
Genome Wide ◽  
A Genome ◽  
Hiv 1

scholarly journals Genome-wide association and functional interrogation identified a variant at 3p26.1 modulating ovarian cancer survival among Chinese women

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Hongji Dai ◽  
Xinlei Chu ◽  
Qian Liang ◽  
Mengyun Wang ◽  
Lian Li ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Long Range ◽  
Genome Wide Association Study ◽  
Cancer Survival ◽  
Genetic Locus ◽  
Regulatory Region ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Ovarian Cancer Survival

AbstractOvarian cancer survival varies considerably among patients, to which germline variation may also contribute in addition to mutational signatures. To identify genetic markers modulating ovarian cancer outcome, we performed a genome-wide association study in 2130 Chinese ovarian cancer patients and found a hitherto unrecognized locus at 3p26.1 to be associated with the overall survival (Pcombined = 8.90 × 10−10). Subsequent statistical fine-mapping, functional annotation, and eQTL mapping prioritized a likely casual SNP rs9311399 in the non-coding regulatory region. Mechanistically, rs9311399 altered its enhancer activity through an allele-specific transcription factor binding and a long-range interaction with the promoter of a lncRNA BHLHE40-AS1. Deletion of the rs9311399-associated enhancer resulted in expression changes in several oncogenic signaling pathway genes and a decrease in tumor growth. Thus, we have identified a novel genetic locus that is associated with ovarian cancer survival possibly through a long-range gene regulation of oncogenic pathways.

Genome-wide association study of patients with atrioventricular nodal reentry tachycardia

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
L Andreasen ◽  
G Ahlberg ◽  
J Hartmann ◽  
C Paludan-Mueller ◽  
H.K Jensen ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Electrophysiological Study ◽  
Genetic Locus ◽  
Disease Onset ◽  
Genome Wide Association ◽  
Funding Source ◽  
Genome Wide ◽  
A Genome ◽  
Reentry Tachycardia

Abstract Background Supraventricular tachycardias (SVTs) originate from the atria or the area close to the AV node. AV nodal reentry tachycardia (AVNRT) is one of the tachyarrhytmias comprising the group of SVTs. The typical patient is female, young at disease onset, with a structurally normal heart. At present we do not know the etiology of AVNRT. We therefore hypothesized that AVNRT might be caused by changes in the DNA. Methods DNA from purified blood was obtained from patients with AVNRT verified by an invasive electrophysiological study. Patients were recruited from five ablation centers in Denmark and individuals from the general population of Denmark (the BEFUS cohort) served as controls. DNA was subjected to chip genotyping, imputation and analyses in a genome-wide association study (GWAS) setup. Results A GWAS on 1,143 AVNRT patients and 3,004 controls revealed one locus close to the gene MYH6 to reach genome-wide significance for association with AVNRT (P=4.8x10–8). MYH6 encodes the α-isoform of the protein myosin heavy chain important for the contractile units of the heart, the sarcomeres. The gene is predominantly expressed in the atria. Additional subthreshold loci located close to other plausible arrhythmia genes were identified. Conclusion We report the first genetic locus to be associated with AVNRT close to the sarcomere gene MYH6. This is, to our knowledge, the first gene ever associated with AVNRT. Manhattan plot Funding Acknowledgement Type of funding source: Public hospital(s). Main funding source(s): Rigshospitalets Forskningspulje - 3 years PhD salary

scholarly journals A Genome-Wide Association Study Uncovers a Genetic Locus Associated with Thoracic-to-Hip Ratio in Koreans

PLoS ONE ◽  
2015 ◽  
Vol 10 (12) ◽  
pp. e0145220 ◽  
Author(s):  
Seongwon Cha ◽  
Ah Yeon Park ◽  
Changsoo Kang
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genetic Locus ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-wide Association Study Identification of a New Genetic Locus with Susceptibility to Osteoporotic Fracture in the Korean Population

2011 ◽  
Vol 9 (2) ◽  
pp. 52-58 ◽  
Author(s):  
Joo-Yeon Hwang ◽  
Seung-Hun Lee ◽  
Min-Jin Go ◽  
Beom-Jun Kim ◽  
Young-Jin Kim ◽  
...  
Keyword(s):  
Association Study ◽  
Osteoporotic Fracture ◽  
Genome Wide Association Study ◽  
Genetic Locus ◽  
Genome Wide Association ◽  
Korean Population ◽  
Genome Wide
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