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https://www.readbyqxmd.com/read/29784950/genome-wide-association-study-identified-new-susceptible-genetic-variants-in-hla-class-i-region-for-hepatitis-b-virus-related-hepatocellular-carcinoma
#1
Hiromi Sawai, Nao Nishida, Seik-Soon Khor, Masao Honda, Masaya Sugiyama, Natsumi Baba, Kayoko Yamada, Norie Sawada, Shoichiro Tsugane, Kazuhiko Koike, Yuji Kondo, Hiroshi Yatsuhashi, Shinya Nagaoka, Akinobu Taketomi, Moto Fukai, Masayuki Kurosaki, Namiki Izumi, Jong-Hon Kang, Kazumoto Murata, Keisuke Hino, Sohji Nishina, Akihiro Matsumoto, Eiji Tanaka, Naoya Sakamoto, Koji Ogawa, Kazuhide Yamamoto, Akihiro Tamori, Osamu Yokosuka, Tatsuo Kanda, Isao Sakaida, Yoshito Itoh, Yuichiro Eguchi, Satoshi Oeda, Satoshi Mochida, Man-Fung Yuen, Wai-Kay Seto, Yong Poovorawan, Nawarat Posuwan, Masashi Mizokami, Katsushi Tokunaga
We have performed a genome-wide association study (GWAS) including 473 Japanese HBV (hepatitis B virus)-positive HCC (hepatocellular carcinoma) patients and 516 HBV carriers including chronic hepatitis and asymptomatic carrier individuals to identify new host genetic factors associated with HBV-derived HCC in Japanese and other East Asian populations. We identified 65 SNPs with P values < 10-4 located within the HLA class I region and three SNPs were genotyped in three independent population-based replication sets...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784899/pathway-based-analysis-of-genome-wide-association-study-of-circadian-phenotypes
#2
Di-di Zhu, Jia-Min Yuan, Rui Zhu, Yao Wang, Zhi-Yong Qian, Jian-Gang Zou
Sleepiness affects normal social life, which attracts more and more attention. Circadian phenotypes contribute to obvious individual differences in susceptibility to sleepiness. We aimed to identify candidate single nucleotide polymorphisms (SNPs) which may cause circadian phenotypes, elucidate the potential mechanisms, and generate corresponding SNP-gene-pathways. A genome-wide association studies (GWAS) dataset of circadian phenotypes was utilized in the study. Then, the Identify Candidate Causal SNPs and Pathways analysis was employed to the GWAS dataset after quality control filters...
November 1, 2017: Journal of Biomedical Research
https://www.readbyqxmd.com/read/29783944/estimates-of-genomic-heritability-and-genome-wide-association-study-for-fatty-acids-profile-in-santa-in%C3%A3%C2%AAs-sheep
#3
G A Rovadoscki, S F N Pertile, A B Alvarenga, A S M Cesar, F Pértille, J Petrini, V Franzo, W V B Soares, G Morota, M L Spangler, L F B Pinto, G G P Carvalho, D P D Lanna, L L Coutinho, G B Mourão
BACKGROUND: Despite the health concerns and nutritional importance of fatty acids, there is a relative paucity of studies in the literature that report genetic or genomic parameters, especially in the case of sheep populations. To investigate the genetic architecture of fatty acid composition of sheep, we conducted genome-wide association studies (GWAS) and estimated genomic heritabilities for fatty acid profile in Longissimus dorsi muscle of 216 male sheep. RESULTS: Genomic heritability estimates for fatty acid content ranged from 0...
May 21, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29783072/association-of-tnfaip3-and-tnip1-polymorphisms-with-systemic-lupus-erythematosus-risk-a-meta-analysis
#4
Liu Xiao, Qin Haihong, Wu Jinfeng, Xu Jinhua
OBJECT: With the development of GWAS, both TNFAIP3 and TNIP1 were revealed to be susceptibility genes of SLE. However, some other studies revealed no association between TNFAIP3, TNIP1 and SLE susceptibility. In order to estimate such association more precisely and systemically, a meta-analysis was conducted. METHOD: Studies on the association between TNFAIP3 rs2230926, TNIP1 rs7708392 and SLE risk were carefully selected via searching 3 databases (Pubmed, Embase, and Web of Science)...
May 18, 2018: Gene
https://www.readbyqxmd.com/read/29782705/wild-gwas-association-mapping-in-natural-populations
#5
Anna W Santure, Dany Garant
The increasing affordability of sequencing and genotyping technologies has transformed the field of molecular ecology in recent decades. By correlating marker variants with trait variation using association analysis, large-scale genotyping and phenotyping of individuals from wild populations has enabled the identification of genomic regions that contribute to phenotypic differences among individuals. Such 'gene mapping' studies are enabling us to better predict evolutionary potential and the ability of populations to adapt to challenges, such as changing environment...
May 21, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29779033/genome-wide-association-study-of-renal-function-traits-results-from-the-japan-multi-institutional-collaborative-cohort-study
#6
Asahi Hishida, Masahiro Nakatochi, Masato Akiyama, Yoichiro Kamatani, Takeshi Nishiyama, Hidemi Ito, Isao Oze, Yuichiro Nishida, Megumi Hara, Naoyuki Takashima, Tanvir Chowdhury Turin, Miki Watanabe, Sadao Suzuki, Rie Ibusuki, Ippei Shimoshikiryo, Yohko Nakamura, Haruo Mikami, Hiroaki Ikezaki, Norihiro Furusyo, Kiyonori Kuriki, Kaori Endoh, Teruhide Koyama, Daisuke Matsui, Hirokazu Uemura, Kokichi Arisawa, Tae Sasakabe, Rieko Okada, Sayo Kawai, Mariko Naito, Yukihide Momozawa, Michiaki Kubo, Kenji Wakai
BACKGROUND: Chronic kidney disease (CKD) is a rapidly growing, worldwide public health problem. Recent advances in genome-wide-association studies (GWAS) revealed several genetic loci associated with renal function traits worldwide. METHODS: We investigated the association of genetic factors with the levels of serum creatinine (SCr) and the estimated glomerular filtration rate (eGFR) in Japanese population-based cohorts analyzing the GWAS imputed data with 11,221 subjects and 12,617,569 variants, and replicated the findings with the 148,829 hospital-based Japanese subjects...
May 18, 2018: American Journal of Nephrology
https://www.readbyqxmd.com/read/29777226/genetic-contribution-to-waist-to-hip-ratio-in-mexican-children-and-adolescents-based-on-12-loci-validated-in-european-adults
#7
Michelle Turcotte, Arkan Abadi, Jesus Peralta-Romero, Fernando Suarez, Hudson Reddon, Jaime Gomez-Zamudio, Ana I Burguete-Garcia, Miguel Cruz, David Meyre
BACKGROUND/OBJECTIVES: The prevalence of abdominal obesity in Mexican children has risen dramatically in the past decade. Genome-wide association studies (GWAS) for waist-to-hip ratio (WHR) performed predominantly in European descent adult  populations have identified multiple single-nucleotide polymorphisms (SNPs) with larger effects in women. The contribution of these SNPs to WHR in non-European children is unknown. SUBJECTS/METHODS: Mexican children and adolescents (N = 1421, 5-17 years) were recruited in Mexico City...
March 13, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29777097/gwas-on-family-history-of-alzheimer-s-disease
#8
Riccardo E Marioni, Sarah E Harris, Qian Zhang, Allan F McRae, Saskia P Hagenaars, W David Hill, Gail Davies, Craig W Ritchie, Catharine R Gale, John M Starr, Alison M Goate, David J Porteous, Jian Yang, Kathryn L Evans, Ian J Deary, Naomi R Wray, Peter M Visscher
Alzheimer's disease (AD) is a public health priority for the 21st century. Risk reduction currently revolves around lifestyle changes with much research trying to elucidate the biological underpinnings. We show that self-report of parental history of Alzheimer's dementia for case ascertainment in a genome-wide association study of 314,278 participants from UK Biobank (27,696 maternal cases, 14,338 paternal cases) is a valid proxy for an AD genetic study. After meta-analysing with published consortium data (n = 74,046 with 25,580 cases across the discovery and replication analyses), three new AD-associated loci (P < 5 × 10-8 ) are identified...
May 18, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29776329/convaq-a-web-tool-for-copy-number-variation-based-association-studies
#9
Simon Jonas Larsen, Luisa Matos do Canto, Silvia Regina Rogatto, Jan Baumbach
BACKGROUND: Copy number variations (CNVs) are large segments of the genome that are duplicated or deleted. Structural variations in the genome have been linked to many complex diseases. Similar to how genome-wide association studies (GWAS) have helped discover single-nucleotide polymorphisms linked to disease phenotypes, the extension of GWAS to CNVs has aided the discovery of structural variants associated with human traits and diseases. RESULTS: We present CoNVaQ, an easy-to-use web-based tool for CNV-based association studies...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29776327/utility-of-whole-genome-sequence-data-for-across-breed-genomic-prediction
#10
Biaty Raymond, Aniek C Bouwman, Chris Schrooten, Jeanine Houwing-Duistermaat, Roel F Veerkamp
BACKGROUND: Genomic prediction (GP) across breeds has so far resulted in low accuracies of the predicted genomic breeding values. Our objective was to evaluate whether using whole-genome sequence (WGS) instead of low-density markers can improve GP across breeds, especially when markers are pre-selected from a genome-wide association study (GWAS), and to test our hypothesis that many non-causal markers in WGS data have a diluting effect on accuracy of across-breed prediction. METHODS: Estimated breeding values for stature and bovine high-density (HD) genotypes were available for 595 Jersey bulls from New Zealand, 957 Holstein bulls from New Zealand and 5553 Holstein bulls from the Netherlands...
May 18, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29775752/the-genetics-and-molecular-pathogenesis-of-systemic-lupus-erythematosus-sle-in-populations-of-different-ancestry
#11
REVIEW
George N Goulielmos, Maria I Zervou, Vassilis M Vazgiourakis, Yogita Ghodke-Puranik, Alexandros Garyfallos, Timothy B Niewold
Systemic lupus erythematosus (SLE; OMIM 152700) is a highly heterogeneous disorder, characterized by differences in autoantibody profile, serum cytokines, and a multi-system involvement commonly affecting the skin, renal, musculoskeletal, and hematopoetic systems clinical manifestations involving. Disease features range from mild manifestations, such as rash or arthritis, to life-threatening end-organ manifestations, such as glomerulonephritis or thrombosis, and it is difficult to predict which manifestations will affect a given patient...
May 15, 2018: Gene
https://www.readbyqxmd.com/read/29774533/analysis-of-type-2-diabetes-and-obesity-genetic-variants-in-mexican-pima-indians-marked-allelic-differentiation-among-amerindians-at-hla
#12
Wen-Chi Hsueh, Peter H Bennett, Julian Esparza-Romero, Rene Urquidez-Romero, Mauro E Valencia, Eric Ravussin, Robert C Williams, William C Knowler, Leslie J Baier, Leslie O Schulz, Robert L Hanson
Prevalence of diabetes and obesity in Mexican Pima Indians is low, while prevalence in US Pima Indians is high. Although lifestyle likely accounts for much of the difference, the role of genetic factors is not well explored. To examine this, we genotyped 359 single nucleotide polymorphisms, including established type 2 diabetes and obesity variants from genome-wide association studies (GWAS) and 96 random markers, in 342 Mexican Pimas. A multimarker risk score of obesity variants was associated with body mass index (BMI; β = 0...
May 17, 2018: Annals of Human Genetics
https://www.readbyqxmd.com/read/29774522/genome-wide-compound-heterozygosity-analysis-highlighted-four-novel-susceptibility-loci-for-congenital-heart-disease-in-chinese-population
#13
T Jiang, M Huang, T Jiang, Y Gu, Y Wang, Y Wu, H Ma, G Jin, J Dai, Z Hu
Genome-wide association studies (GWASs) have achieved great success in deciphering the genetic cause of congenital heart disease (CHD). However, the heritability of CHD remains to be clarified, and numerous genetic factors responsible for occurrence of CHD are yet unclear. In this study, we performed a genome-wide search for relaxed forms of compound heterozygosity (CH) in association with CHD using our existing GWAS data including 2,265 individuals (957 CHD cases and 1,308 controls). CollapsABEL was used to iteratively test the association between the CH genotype and CHD phenotype in a sliding window manner...
May 17, 2018: Clinical Genetics
https://www.readbyqxmd.com/read/29771388/gwas4d-multidimensional-analysis-of-context-specific-regulatory-variant-for-human-complex-diseases-and-traits
#14
Dandan Huang, Xianfu Yi, Shijie Zhang, Zhanye Zheng, Panwen Wang, Chenghao Xuan, Pak Chung Sham, Junwen Wang, Mulin Jun Li
Genome-wide association studies have generated over thousands of susceptibility loci for many human complex traits, and yet for most of these associations the true causal variants remain unknown. Tissue/cell type-specific prediction and prioritization of non-coding regulatory variants will facilitate the identification of causal variants and underlying pathogenic mechanisms for particular complex diseases and traits. By leveraging recent large-scale functional genomics/epigenomics data, we develop an intuitive web server, GWAS4D (http://mulinlab...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29771307/assessment-of-rosacea-symptom-severity-by-genome-wide-association-study-and-expression-analysis-highlights-immuno-inflammatory-and-skin-pigmentation-genes
#15
Jennifer L Aponte, Mathias N Chiano, Laura M Yerges-Armstrong, David A Hinds, Chao Tian, Akansha Gupta, Cong Guo, Dana J Fraser, Johannes M Freudenberg, Deepak K Rajpal, Margaret G Ehm, Dawn M Waterworth
Rosacea is a common, chronic skin disease of variable severity with limited treatment options. The cause of rosacea is unknown, but it is believed to be due to a combination of hereditary and environmental factors. Little is known about the genetics of the disease. We performed a genome-wide association study (GWAS) of rosacea symptom severity with data from 73,265 research participants of European ancestry from the 23andMe customer base. Seven loci had variants associated with rosacea at the genome-wide significance level (p≤5 × 10-8)...
May 16, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29770990/pool-based-genome-wide-association-study-identified-novel-candidate-regions-on-bta9-and-14-for-oleic-acid-percentage-in-japanese-black-cattle
#16
Fuki Kawaguchi, Hiroto Kigoshi, Ayaka Nakajima, Yuta Matsumoto, Yoshinobu Uemoto, Moriyuki Fukushima, Emi Yoshida, Eiji Iwamoto, Takayuki Akiyama, Namiko Kohama, Eiji Kobayashi, Takeshi Honda, Kenji Oyama, Hideyuki Mannen, Shinji Sasazaki
Fatty acid composition is an important indicator of beef quality. The objective of this study was to search the potential candidate region for fatty acid composition. We performed pool-based genome-wide association studies (GWAS) for oleic acid percentage (C18:1) in a Japanese Black cattle population from the Hyogo prefecture. GWAS analysis revealed two novel candidate regions on BTA9 and BTA14. The most significant single nucleotide polymorphisms (SNPs) in each region were genotyped in a population (n = 899) to verify their effect on C18:1...
May 17, 2018: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/29770529/genome-wide-association-studies-identified-variants-for-taurine-concentration-in-japanese-black-beef
#17
Nanae Sasago, Masayuki Takeda, Tsuyoshi Ohtake, Tsuyoshi Abe, Hironori Sakuma, Takatoshi Kojima, Shinji Sasaki, Yoshinobu Uemoto
We performed genome-wide association studies (GWAS) using the BovineSNP50 array to detect significant single nucleotide polymorphisms (SNPs) that may affect the concentration of 22 free amino acids and three peptides in Japanese Black beef cattle. A total of 574 Japanese Black cattle and 40,657 SNPs from the array were used for this study. Genome-wide significant SNPs were detected for β-alanine (three SNPs on chromosomes 22 and 29) and taurine (26 SNPs on chromosome 22). Importantly, the top two SNPs for taurine were highly significant (p = 6...
May 16, 2018: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/29769702/fine-mapping-of-98-obesity-loci-in-mexican-children
#18
Hsin Yen Liu, Akram Alyass, Arkan Abadi, Jesus Peralta-Romero, Fernando Suarez, Jaime Gomez-Zamudio, Astride Audirac, Esteban J Parra, Miguel Cruz, David Meyre
BACKGROUND/OBJECTIVES: Mexico has one of the highest prevalence of childhood obesity in the world. Genome-wide association studies (GWAS) for obesity have identified multiple single-nucleotide polymorphisms (SNPs) in populations of European, East Asian, and African descent. The contribution of these loci to obesity in Mexican children is unclear. We assessed the transferability of 98 obesity loci in Mexican children and fine-mapped the association signals. SUBJECTS/METHODS: The study included 405 and 390 Mexican children with normal weight and obesity...
March 12, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29769521/thirty-loci-identified-for-heart-rate-response-to-exercise-and-recovery-implicate-autonomic-nervous-system
#19
Julia Ramírez, Stefan van Duijvenboden, Ioanna Ntalla, Borbala Mifsud, Helen R Warren, Evan Tzanis, Michele Orini, Andrew Tinker, Pier D Lambiase, Patricia B Munroe
Impaired capacity to increase heart rate (HR) during exercise (ΔHRex ), and a reduced rate of recovery post-exercise (ΔHRrec ) are associated with higher cardiovascular mortality rates. Currently, the genetic basis of both phenotypes remains to be elucidated. We conduct genome-wide association studies (GWASs) for ΔHRex and ΔHRrec in ~40,000 individuals, followed by replication in ~27,000 independent samples, all from UK Biobank. Six and seven single-nucleotide polymorphisms for ΔHRex and ΔHRrec , respectively, formally replicate...
May 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29768301/germline-genome-wide-association-studies-in-women-receiving-neoadjuvant-chemotherapy-with-or-without-bevacizumab
#20
James N Ingle, Krishna R Kalari, Donald Lawrence Wickerham, Gunter von Minckwitz, Peter A Fasching, Yoichi Furukawa, Taisei Mushiroda, Matthew P Goetz, Poulami Barman, Erin E Carlson, Priya Rastogi, Joseph P Costantino, Junmei Cairns, Soonmyung Paik, Harry D Bear, Michiaki Kubo, Liewei Wang, Norman Wolmark, Richard M Weinshilboum
Neoadjuvant chemotherapy (NAC) for breast cancer is widely utilized, and we performed genome-wide association studies (GWAS) to determine whether germ-line genetic variability was associated with benefit in terms of pathological complete response (pCR), disease-free survival, and overall survival in patients entered on the NSABP B-40 NAC trial, wherein patients were randomized to receive, or not, bevacizumab in addition to chemotherapy. Patient DNA samples were genotyped with the Illumina OmniExpress BeadChip...
June 2018: Pharmacogenetics and Genomics
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