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Genome-wide association studies: inherent limitations and future challenges
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《医学前沿(英文)》 2012年 第6卷 第4期 页码 444-450 doi: 10.1007/s11684-012-0225-3
Genome-wide association studies (GWAS) have achieved great success in identifying genetic variants related to complex human diseases such as cancer and have provided valuable insights into their genetic architecture. Recently, GWAS is quite the fashion in China. However, there are issues related to its nature. Enormous work needs to be done in the post-GWAS era. Deep sequencing followed by functional studies will be needed to elucidate the underpinning biological mechanisms and further translate GWAS findings into medical practice. Along with pharmacogenomics, the success of GWAS in identifying genetic risk factors and genetic differences in drug response has been gradually enabling personalized medicine. In this article, we used hepatocellular carcinoma (HCC) as an example to demonstrate some of the inherent limitations and summarized future challenges of GWAS.
关键词: genome-wide association studies (GWAS) genetic variant cancer limitation challenge
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《医学前沿(英文)》 2015年 第9卷 第2期 页码 146-161 doi: 10.1007/s11684-014-0373-8
Obesity prevalence has increased in recent years. Lifestyle change fuels obesity, but genetic factors cause more than 50% of average variations in obesity. The advent of genome-wide association studies (GWAS) has hastened the progress of polygenic obesity research. As of this writing, more than 73 obesity susceptibility loci have been identified in ethnic groups through GWAS. The identified loci explain only 2% to 4% of obesity heritability, thereby indicating that a large proportion of loci remain undiscovered. Thus, the next step is to identify and confirm novel loci, which may exhibit smaller effects and lower allele frequencies than established loci. However, achieving these tasks has been difficult for researchers. GWAS help researchers discover the causal loci. Moreover, numerous biological studies have been performed on the polygenic effects on obesity, such as studies on fat mass- and obesity-associated gene (FTO), but the role of these polygenic effects in the mechanism of obesity remains unclear. Thus, obesity-causing variations should be identified, and insights into the biology of polygenic effects on obesity are needed.
关键词: obesity genetics genome-wide association studies body mass index fat mass- and obesity-associated gene
A genome-wide association study of five meat quality traits in Yorkshire pigs
Qian DONG,Huiying LIU,Xinyun LI,Wei WEI,Shuhong ZHAO,Jianhua CAO
《农业科学与工程前沿(英文)》 2014年 第1卷 第2期 页码 137-143 doi: 10.15302/J-FASE-2014014
关键词: Pig GWAS meat quality trait SNP
Genome-wide association study of the backfat thickness trait in two pig populations
Dandan ZHU,Xiaolei LIU,Rothschild MAX,Zhiwu ZHANG,Shuhong ZHAO,Bin FAN
《农业科学与工程前沿(英文)》 2014年 第1卷 第2期 页码 91-95 doi: 10.15302/J-FASE-2014005
关键词: backfat thickness SNP chip genome-wide association study compressed mixed linear model pig
Xingwang WANG, Rongrong DING, Jianping QUAN, Linxue YANG, Ming YANG, Enqin ZHENG, Dewu LIU, Gengyuan CAI, Zhenfang WU, Jie YANG
《农业科学与工程前沿(英文)》 2017年 第4卷 第3期 页码 335-341 doi: 10.15302/J-FASE-2017152
关键词: Duroc pigs genome-wide association analysis intramuscular fat
Systems understanding of plant–pathogen interactions through genome-wide protein–protein interaction
Hong LI,Ziding ZHANG
《农业科学与工程前沿(英文)》 2016年 第3卷 第2期 页码 102-112 doi: 10.15302/J-FASE-2016100
关键词: plant–pathogen interactions systems biology omics plant immunity protein–protein interaction network
Transcriptome resources and genome-wide marker development for Japanese larch (
Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG
《农业科学与工程前沿(英文)》 2014年 第1卷 第1期 页码 77-84 doi: 10.15302/J-FASE-2014010
关键词: Larix transcriptome age wood formation somatic embryogenesis molecular marker
Song-Song XU, Meng-Hua LI
《农业科学与工程前沿(英文)》 2017年 第4卷 第3期 页码 279-288 doi: 10.15302/J-FASE-2017151
关键词: sheep high-throughput screening productive traits genome-wide studies
QIN Lunxiu, TANG Zhaoyou, GUAN Xinyuan, YE Qinghai, JIA Huliang, REN Ning
《医学前沿(英文)》 2008年 第2卷 第3期 页码 211-215 doi: 10.1007/s11684-008-0041-y
关键词: sensitive genome-wide prediction genome-wide microsatellite frequency Hepatocellular carcinoma
Genetic Study Identifies CBLN4 as a Novel Susceptibility Gene for Accident Proneness
Shu-lin Zhang,Hui-qing Jin,Yang Song,Wan-sheng Yu,Liang-dan Sun
《工程管理前沿(英文)》 2016年 第3卷 第1期 页码 30-38 doi: 10.15302/J-FEM-2016008
关键词: accident proneness genome-wide association study (GWAS) dopamine (DA) ACTH susceptibility gene traffic accident epidemiology accident prevention traffic safety three-dimensional model
Hongxia MIAO,Peiguang SUN,Yulu MIAO,Juhua LIU,Jianbin ZHANG,Caihong JIA,Jingyi WANG,Zhuo WANG,Zhiqiang JIN,Biyu XU
《农业科学与工程前沿(英文)》 2016年 第3卷 第4期 页码 346-356 doi: 10.15302/J-FASE-2016127
关键词: β-amylase banana genome-wide identification fruit development abiotic stress
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《医学前沿(英文)》 2015年 第9卷 第4期 页码 478-486 doi: 10.1007/s11684-015-0420-0
Telomeres play a critical role in biological ageing by maintaining chromosomal integrity and preventing chromosome ends fusion. Epidemiological studies have suggested that inter-individual differences of telomere length could affect predisposition to multiple cancers, but evidence regarding esophageal squamous cell carcinoma (ESCC) was still uncertain. Several telomere length-related single nucleotide polymorphisms (TL-SNPs) in Caucasians have been reported in genome-wide association studies. However, the effects of telomere length and TL-SNPs on ESCC development are unclear. Therefore, we conducted a case-control study (1045 ESCC cases and 1433 controls) to evaluate the associations between telomere length, TL-SNPs, and ESCC risk in Chinese population. As a result, ESCC cases showed overall shorter relative telomere length (RTL) (median: 1.34) than controls (median: 1.50, P<0.001). More interestingly, an evident nonlinear U-shaped association was observed between RTL and ESCC risk (P<0.001), with odds ratios (95% confidence interval) equal to 2.40 (1.84–3.14), 1.36 (1.03–1.79), 1.01 (0.76–1.35), and 1.37 (1.03–1.82) for individuals in the 1st (the shortest), 2nd, 3rd, and 5th (the longest) quintile, respectively, compared with those in the 4th quintile as reference group. No significant associations were observed between the eight reported TL-SNPs and ESCC susceptibility. These findings suggest that either short or extremely long telomeres may be risk factors for ESCC in the Chinese population.
关键词: esophageal squamous cell carcinoma telomere length genetic variants susceptibility genome-wide association study
Genome-wide search for candidate genes determining vertebrae number in pigs
Longchao ZHANG, Jingwei YUE, Xin LIU, Jing LIANG, Kebin ZHAO, Hua YAN, Na LI, Lei PU, Yuebo ZHANG, Huibi SHI, Ligang WANG, Lixian WANG
《农业科学与工程前沿(英文)》 2017年 第4卷 第3期 页码 327-334 doi: 10.15302/J-FASE-2017163
关键词: genome-wide association study number of vertebrae pig SSC7 TGFβ3
Caiyun LIU, Francisco PINTO, C. Mariano COSSANI, Sivakumar SUKUMARAN, Matthew P. REYNOLDS
《农业科学与工程前沿(英文)》 2019年 第6卷 第3期 页码 296-308 doi: 10.15302/J-FASE-2019269
The application of spectral reflectance indices (SRIs) as proxies to screen for yield potential (YP) and heat stress (HS) is emerging in crop breeding programs. Thus, a comparison of SRIs and their associations with grain yield (GY) under YP and HS conditions is important. In this study, we assessed the usefulness of 27 SRIs for indirect selection for agronomic traits by evaluating an elite spring wheat association mapping initiative (WAMI) population comprising 287 elite lines under YP and HS conditions. Genetic and phenotypic analysis identified 11 and 9 SRIs in different developmental stages as efficient indirect selection indices for yield in YP and HS conditions, respectively. We identified enhanced vegetation index (EVI) as the common SRI associated with GY under YP at booting, heading and late heading stages, whereas photochemical reflectance index (PRI) and normalized difference vegetation index (NDVI) were the common SRIs under booting and heading stages in HS. Genome-wide association study (GWAS) using 18704 single nucleotide polymorphisms (SNPs) from Illumina iSelect 90K identified 280 and 43 marker-trait associations for efficient SRIs at different developmental stages under YP and HS, respectively. Common genomic regions for multiple SRIs were identified in 14 regions in 9 chromosomes: 1B (60–62 cM), 3A (15, 85–90, 101–105 cM), 3B (132–134 cM), 4A (47–51 cM), 4B (71–75 cM), 5A (43–49, 56–60, 89–93 cM), 5B (124–125 cM), 6A (80–85 cM), and 6B (57–59, 71 cM). Among them, SNPs in chromosome 5A (89–93 cM) and 6A (80–85 cM) were co-located for yield and yield related traits. Overall, this study highlights the utility of SRIs as proxies for GY under YP and HS. High heritability estimates and identification of marker-trait associations indicate that SRIs are useful tools for understanding the genetic basis of agronomic and physiological traits.
关键词: genome-wide association study (GWAS) heat tolerance spectral reflectance spring wheat
Construction, characterization and application of a genome-wide promoter library in
Ting Yuan,Yakun Guo,Junkai Dong,Tianyi Li,Tong Zhou,Kaiwen Sun,Mei Zhang,Qingyu Wu,Zhen Xie,Yizhi Cai,Limin Cao,Junbiao Dai
《化学科学与工程前沿(英文)》 2017年 第11卷 第1期 页码 107-116 doi: 10.1007/s11705-017-1621-7
关键词: synthetic biology yeast promoter activity metabolic engineering xylose utilization
标题 作者 时间 类型 操作
Advancement in genetic variants conferring obesity susceptibility from genome-wide association studies
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期刊论文
A genome-wide association study of five meat quality traits in Yorkshire pigs
Qian DONG,Huiying LIU,Xinyun LI,Wei WEI,Shuhong ZHAO,Jianhua CAO
期刊论文
Genome-wide association study of the backfat thickness trait in two pig populations
Dandan ZHU,Xiaolei LIU,Rothschild MAX,Zhiwu ZHANG,Shuhong ZHAO,Bin FAN
期刊论文
Genome-wide association analysis reveals genetic loci and candidate genes associated with intramuscular
Xingwang WANG, Rongrong DING, Jianping QUAN, Linxue YANG, Ming YANG, Enqin ZHENG, Dewu LIU, Gengyuan CAI, Zhenfang WU, Jie YANG
期刊论文
Systems understanding of plant–pathogen interactions through genome-wide protein–protein interaction
Hong LI,Ziding ZHANG
期刊论文
Transcriptome resources and genome-wide marker development for Japanese larch (
Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG
期刊论文
Recent advances in understanding genetic variants associated with economically important traits in sheep (
Song-Song XU, Meng-Hua LI
期刊论文
The predictive value of chromosome 8p deletion for metastasis of hepatocellular carcinoma: a summary of works in 10 years
QIN Lunxiu, TANG Zhaoyou, GUAN Xinyuan, YE Qinghai, JIA Huliang, REN Ning
期刊论文
Genetic Study Identifies CBLN4 as a Novel Susceptibility Gene for Accident Proneness
Shu-lin Zhang,Hui-qing Jin,Yang Song,Wan-sheng Yu,Liang-dan Sun
期刊论文
Genome-wide identification and expression analysis of the β-amylase genes strongly associated with fruit
Hongxia MIAO,Peiguang SUN,Yulu MIAO,Juhua LIU,Jianbin ZHANG,Caihong JIA,Jingyi WANG,Zhuo WANG,Zhiqiang JIN,Biyu XU
期刊论文
U-shaped association between telomere length and esophageal squamous cell carcinoma risk: a case-control
null
期刊论文
Genome-wide search for candidate genes determining vertebrae number in pigs
Longchao ZHANG, Jingwei YUE, Xin LIU, Jing LIANG, Kebin ZHAO, Hua YAN, Na LI, Lei PU, Yuebo ZHANG, Huibi SHI, Ligang WANG, Lixian WANG
期刊论文
Spectral reflectance indices as proxies for yield potential and heat stress tolerance in spring wheat: heritability estimates and marker-trait associations
Caiyun LIU, Francisco PINTO, C. Mariano COSSANI, Sivakumar SUKUMARAN, Matthew P. REYNOLDS
期刊论文