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5. Genomic and physiological mechanisms of high-altitude adaptation in Ethiopian highlanders: a comparative perspective.

Author

Seifu, Wubalem Desta, Bekele-Alemu, Abreham, and Zeng, Changqing

Subjects
PHYSIOLOGY, OXYGEN saturation, ETHIOPIANS, EVIDENCE gaps, NATURAL selection
Abstract

High-altitude adaptation is a remarkable example of natural selection, yet the genomic and physiological adaptation mechanisms of Ethiopian highlanders remain poorly understood compared to their Andean and Tibetan counterparts. Ethiopian populations, such as the Amhara and Oromo, exhibit unique adaptive strategies characterized by moderate hemoglobin levels and enhanced arterial oxygen saturation, indicating distinct mechanisms of coping with chronic hypoxia. This review synthesizes current genomic insights into Ethiopian high-altitude adaptation, identifying key candidate genes involved in hypoxia tolerance and examining the influence of genetic diversity and historical admixture on adaptive responses. Furthermore, the review highlights significant research gaps, particularly the underrepresentation of Ethiopian populations in global genomic studies, the lack of comprehensive genotype-phenotype analyses, and inconsistencies in research methodologies. Addressing these gaps is crucial for advancing our understanding of the genetic basis of human adaptation to extreme environments and for developing a more complete picture of human physiological resilience. This review offers a comparative perspective with Tibetan and Andean highlanders, emphasizing the need for expanding genomic representation and refining methodologies to uncover the genetic mechanisms underlying high-altitude adaptation in Ethiopian populations. [ABSTRACT FROM AUTHOR]

Published
2025
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7. Scleral HIF-1α is a prominent regulatory candidate for genetic and environmental interactions in human myopia pathogenesis

Author

Zhao, Fei, Zhang, Dake, Zhou, Qingyi, Zhao, Fuxin, He, Mingguang, Yang, Zhenglin, Su, Yongchao, Zhai, Ying, Yan, Jiaofeng, Zhang, Guoyun, Xue, Anquan, Tang, Jing, Han, Xiaotong, Shi, Yi, Zhu, Yun, Liu, Tianzi, Zhuang, Wenjuan, Huang, Lulin, Hong, Yaqiang, Wu, Deng, Li, Yingxiang, Lu, Qinkang, Chen, Wei, Jiao, Shiming, Wang, Qiongsi, Srinivasalu, Nethrajeith, Wen, Yingying, Zeng, Changqing, Qu, Jia, and Zhou, Xiangtian

Published
2020
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8. Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome

Author

Du, Zhenglin, Ma, Liang, Qu, Hongzhu, Chen, Wei, Zhang, Bing, Lu, Xi, Zhai, Weibo, Sheng, Xin, Sun, Yongqiao, Li, Wenjie, Lei, Meng, Qi, Qiuhui, Yuan, Na, Shi, Shuo, Zeng, Jingyao, Wang, Jinyue, Yang, Yadong, Liu, Qi, Hong, Yaqiang, Dong, Lili, Zhang, Zhewen, Zou, Dong, Wang, Yanqing, Song, Shuhui, Liu, Fan, Fang, Xiangdong, Chen, Hua, Liu, Xin, Xiao, Jingfa, and Zeng, Changqing

Published
2019
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9. Scleral hypoxia is a target for myopia control

Author

Wu, Hao, Chen, Wei, Zhao, Fei, Zhou, Qingyi, Reinach, Peter S., Deng, Lili, Ma, Li, Luo, Shumeng, Srinivasalu, Nethrajeith, Pan, Miaozhen, Hu, Yang, Pei, Xiaomeng, Sun, Jing, Ren, Ran, Xiong, Yinghui, Zhou, Zhonglou, Zhang, Sen, Tian, Geng, Fang, Jianhuo, Zhang, Lina, Lang, Jidong, Wu, Deng, Zeng, Changqing, Qu, Jia, and Zhou, Xiangtian

Published
2018

13. Searching across-cohort relatives in 54,092 GWAS samples via encrypted genotype regression.

Author

Zhang, Qi-Xin, Liu, Tianzi, Guo, Xinxin, Zhen, Jianxin, Yang, Meng-yuan, Khederzadeh, Saber, Zhou, Fang, Han, Xiaotong, Zheng, Qiwen, Jia, Peilin, Ding, Xiaohu, He, Mingguang, Zou, Xin, Liao, Jia-Kai, Zhang, Hongxin, He, Ji, Zhu, Xiaofeng, Lu, Daru, Chen, Hongyan, and Zeng, Changqing

Subjects
GENOTYPES, GENOME-wide association studies, RANDOM matrices, STATISTICAL power analysis, RELATIVES, DATA encryption, IMAGE encryption
Abstract

Explicitly sharing individual level data in genomics studies has many merits comparing to sharing summary statistics, including more strict QCs, common statistical analyses, relative identification and improved statistical power in GWAS, but it is hampered by privacy or ethical constraints. In this study, we developed encG-reg, a regression approach that can detect relatives of various degrees based on encrypted genomic data, which is immune of ethical constraints. The encryption properties of encG-reg are based on the random matrix theory by masking the original genotypic matrix without sacrificing precision of individual-level genotype data. We established a connection between the dimension of a random matrix, which masked genotype matrices, and the required precision of a study for encrypted genotype data. encG-reg has false positive and false negative rates equivalent to sharing original individual level data, and is computationally efficient when searching relatives. We split the UK Biobank into their respective centers, and then encrypted the genotype data. We observed that the relatives estimated using encG-reg was equivalently accurate with the estimation by KING, which is a widely used software but requires original genotype data. In a more complex application, we launched a finely devised multi-center collaboration across 5 research institutes in China, covering 9 cohorts of 54,092 GWAS samples. encG-reg again identified true relatives existing across the cohorts with even different ethnic backgrounds and genotypic qualities. Our study clearly demonstrates that encrypted genomic data can be used for data sharing without loss of information or data sharing barrier. Author summary: Estimating pairwise genetic relatedness within a single cohort is straightforward. However, in practice, related samples are often distributed across different cohorts, making it challenging to estimate inter-cohort relatedness. In this study, we propose a method called encrypted genotype regression (encG-reg), which provides an unbiased estimation of inter-cohort relatedness using encrypted genotypes. The genotype matrix of each cohort is masked by a random matrix, which acts similarly to a private key in a cryptographic scheme. This masking process produces encrypted genotypes, which are a projection of the original genotype matrix. We derive the expectation and particularly the sampling variance for encG-reg, the latter involves eighth-order moments calculation. encG-reg allows us to accurately identify relatedness across cohorts, even for large-scale biobank data. To demonstrate the efficacy of encG-reg, we verified it in a multi-ethnicity UK Biobank dataset comprising 485,158 samples. For this case, we successfully tracked down to the 1st-degree relatedness (such as full sibs and parent-offspring). Furthermore, we used encG-reg in a collaboration involving 9 Chinese cohorts, encompassing a total of 54,092 samples from 5 genomic centers. It is worth noting that if the number of effective markers is sufficient encG-reg has the potential to detect even more distant degrees of relatedness beyond what we demonstrated. [ABSTRACT FROM AUTHOR]

Published
2024
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19. A Proactive Intervention Study in Metabolic Syndrome High-Risk Populations Using Phenome-Based Actionable P4 Medicine Strategy

Author

Huang, Qiongrong, Hu, Zhiyuan, Zheng, Qiwen, Mao, Xuemei, Lv, Wenxi, Wu, Fei, Fu, Dapeng, Lu, Cuihong, Zeng, Changqing, Wang, Fei, Zeng, Qiang, Fang, Qiaojun, and Hood, Leroy

Abstract

The integration of predictive, preventive, personalized, and participatory (P4) healthcare advocates proactive intervention, including dietary supplements and lifestyle interventions for chronic disease. Personal profiles include deep phenotypic data and genetic information, which are associated with chronic diseases, can guide proactive intervention. However, little is known about how to design an appropriate intervention mode to precisely intervene with personalized phenome-based data. Here, we report the results of a 3-month study on 350 individuals with metabolic syndrome high-risk that we named the Pioneer 350 Wellness project (P350). We examined: (1) longitudinal (two times) phenotypes covering blood lipids, blood glucose, homocysteine (HCY), and vitamin D3(VD3), and (2) polymorphism of genes related to folic acid metabolism. Based on personalized data and questionnaires including demographics, diet and exercise habits information, coaches identified 'actionable possibilities', which combined exercise, diet, and dietary supplements. After a 3-month proactive intervention, two-thirds of the phenotypic markers were significantly improved in the P350 cohort. Specifically, we found that dietary supplements and lifestyle interventions have different effects on phenotypic improvement. For example, dietary supplements can result in a rapid recovery of abnormal HCY and VD3levels, while lifestyle interventions are more suitable for those with high body mass index (BMI), but almost do not help the recovery of HCY. Furthermore, although people who implemented only one of the exercise or diet interventions also benefited, the effect was not as good as the combined exercise and diet interventions. In a subgroup of 226 people, we examined the association between the polymorphism of genes related to folic acid metabolism and the benefits of folate supplementation to restore a normal HCY level. We found people with folic acid metabolism deficiency genes are more likely to benefit from folate supplementation to restore a normal HCY level. Overall, these results suggest: (1) phenome-based data can guide the formulation of more precise and comprehensive interventions, and (2) genetic polymorphism impacts clinical responses to interventions. Notably, we provide a proactive intervention example that is operable in daily life, allowing people with different phenome-based data to design the appropriate intervention protocol including dietary supplements and lifestyle interventions.

Published
2024
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20. How Placenta Promotes the Successful Reproduction in High-Altitude Populations: A Transcriptome Comparison between Adaptation and Acclimatization

Author

Wu, Deng, primary, Liu, Yunao, additional, Chen, Wei, additional, Shao, Jianming, additional, Zhuoma, Pubu, additional, Zhao, Dexiong, additional, Yu, Yang, additional, Liu, Tianzi, additional, Yu, Ruoxuan, additional, Gan, Yongna, additional, Yuzheng, Baima, additional, Huang, Yongshu, additional, Zhang, Haikun, additional, Bi, Xiaoman, additional, Tao, Chengcheng, additional, Lai, Shujuan, additional, Luo, Qiaoxia, additional, Zhang, Dake, additional, Wang, Hongmei, additional, Zhaxi, Pingcuo, additional, Zhang, Jianqing, additional, Qiao, Jie, additional, and Zeng, Changqing, additional

Published
2022
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21. Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data

Author

Tao, Yong, Ruan, Jue, Yeh, Shiou-Hwei, Lu, Xuemei, Wang, Yu, Zhai, Weiwei, Cai, Jun, Ling, Shaoping, Gong, Qiang, Chong, Zecheng, Qu, Zhengzhong, Li, Qianqian, Liu, Jiang, Yang, Jin, Zheng, Caihong, Zeng, Changqing, Wang, Hurng-Yi, Zhang, Jing, Wang, Sheng-Han, Hao, Lingtong, Dong, Lili, Li, Wenjie, Sun, Min, Zou, Wei, Yu, Caixia, Li, Chaohua, Liu, Guojing, Jiang, Lan, Xu, Jin, Huang, Huanwei, Li, Chunyan, Mi, Shuangli, Zhang, Bing, Chen, Baoxian, Zhao, Wenming, Hu, Songnian, Zhuang, Shi-Mei, Shen, Yang, Shi, Suhua, Brown, Christopher, White, Kevin P., Chen, Ding-Shinn, Chen, Pei-Jer, and Wu, Chung-I

Published
2011

22. Natural selection on EPAS1 (HIF2α) associated with low hemoglobin concentration in Tibetan highlanders

Author

Beall, Cynthia M., Cavalleri, Gianpiero L., Deng, Libin, Elston, Robert C., Gao, Yang, Knight, Jo, Li, Chaohua, Li, Jiang Chuan, Liang, Yu, McCormack, Mark, Montgomery, Hugh E., Pan, Hao, Robbins, Peter A., Shianna, Kevin V., Tam, Siu Cheung, Tsering, Ngodrop, Veeramah, Krishna R., Wang, Wei, Wangdui, Puchung, Weale, Michael E., Xu, Yaomin, Xu, Zhe, Yang, Ling, Zaman, M. Justin, Zeng, Changqing, Zhang, Li, Zhang, Xianglong, Zhaxi, Pingcuo, Zheng, Yong Tang, and Ellison, Peter T.

Published
2010

25. PDE4B Proposed as a High Myopia Susceptibility Gene in Chinese Population

Author

Zhao, Fuxin, primary, Chen, Wei, additional, Zhou, Hui, additional, Reinach, Peter S., additional, Wang, Yuhan, additional, Juo, Suh-Hang H., additional, Yang, Zhenglin, additional, Xue, Anquan, additional, Shi, Yi, additional, Liang, Chung-Ling, additional, Zeng, Changqing, additional, Qu, Jia, additional, and Zhou, Xiangtian, additional

Published
2022
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27. Exome-Wide Association Study Identifies East Asian-Specific Missense Variant MTHFR C136T Influencing Homocysteine Levels in Chinese Populations RH: ExWAS of tHCY in a Chinese Population

Author

Liu, Tianzi, primary, Momin, Mohetaboer, additional, Zhou, Huiyue, additional, Zheng, Qiwen, additional, Fan, Fangfang, additional, Jia, Jia, additional, Liu, Mengyuan, additional, Bao, Minghui, additional, Li, Jianping, additional, Huo, Yong, additional, Liu, Jialin, additional, Zhang, Yaning, additional, Mao, Xuemei, additional, Han, Xiao, additional, Hu, Zhiyuan, additional, Zeng, Changqing, additional, Liu, Fan, additional, and Zhang, Yan, additional

Published
2021
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32. TGFB3 downregulation causing chordomagenesis and its tumor suppression role maintained by Smad7

Author

Wang, Liang, primary, Guan, Xiaonan, additional, Hu, Qingtao, additional, Wu, Zhen, additional, Chen, Wei, additional, Song, Lairong, additional, Wang, Ke, additional, Tian, Kaibing, additional, Cao, Chunwei, additional, Zhang, Dake, additional, Ma, Junpeng, additional, Tong, Xiangjun, additional, Zhang, Bo, additional, Zhang, Junting, additional, and Zeng, Changqing, additional

Published
2021
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33. The International HapMap Project

Author

Gibbs, Richard A., Belmont, John W., Hardenbol, Paul, Willis, Thomas D., Yu, Fuli, Yang, Huanming, Ch'ang, Lan-Yang, Huang, Wei, Liu, Bin, Shen, Yan, Tam, Paul Kwong-Hang, Tsui, Lap-Chee, Waye, Mary Miu Yee, Wong, Jeffrey Tze-Fei, Zeng, Changqing, Zhang, Qingrun, Chee, Mark S., Galver, Luana M., Kruglyak, Semyon, Murray, Sarah S., Oliphant, Arnold R., Montpetit, Alexandre, Hudson, Thomas J., Chagnon, Fanny, Ferretti, Vincent, Leboeuf, Martin, Phillips, Michael S., Verner, Andrei, Kwok, Pui-Yan, Duan, Shenghui, Lind, Denise L., Miller, Raymond D., Rice, John P., Saccone, Nancy L., Taillon-Miller, Patricia, Xiao, Ming, Nakamura, Yusuke, Sekine, Akihiro, Sorimachi, Koki, Tanaka, Toshihiro, Tanaka, Yoichi, Tsunoda, Tatsuhiko, Yoshino, Eiji, Bentley, David R., Deloukas, Panos, Hunt, Sarah, Powell, Don, Altshuler, David, Gabriel, Stacey B., Zhang, Houcan, Matsuda, Ichiro, Fukushima, Yoshimitsu, Macer, Darryl R., Suda, Eiko, Rotimi, Charles N., Adebamowo, Clement A., Aniagwu, Toyin, Marshall, Patricia A., Matthew, Olayemi, Nkwodimmah, Chibuzor, Royal, Charmaine D. M., Leppert, Mark F., Dixon, Missy, Stein, Lincoln D., Cunningham, Fiona, Kanani, Ardavan, Thorisson, Gudmundur A., Chakravarti, Aravinda, Chen, Peter E., Cutler, David J., Kashuk, Carl S., Donnelly, Peter, Marchini, Jonathan, McVean, Gilean A. T., Myers, Simon R., Cardon, Lon R., Abecasis, Goncalo R., Morris, Andrew, Weir, Bruce S., Mullikin, James C., Sherry, Stephen T., Feolo, Michael, Daly, Mark J., Schaffner, Stephen F., Qiu, Renzong, Kent, Alastair, Dunston, Georgia M., Kato, Kazuto, Niikawa, Norio, Knoppers, Bartha M., Foster, Morris W., Clayton, Ellen Wright, Wang, Vivian Ota, Watkin, Jessica, Sodergren, Erica, Weinstock, George M., Wilson, Richard K., Fulton, Lucinda L., Rogers, Jane, Birren, Bruce W., Han, Hua, Wang, Hongguang, Godbout, Martin, Wallenburg, John C., L'Archeveque, Paul, Bellemare, Guy, Todani, Kazuo, Fujita, Takashi, Tanaka, Satoshi, Holden, Arthur L., Lai, Eric H., Collins, Francis S., Brooks, Lisa D., McEwen, Jean E., Guyer, Mark S., Jordan, Elke, Peterson, Jane L., Spiegel, Jack, Sung, Lawrence M., Zacharia, Lynn F., Kennedy, Karen, Dunn, Michael G., Seabrook, Richard, Shillito, Mark, Skene, Barbara, Stewart, John G., Cho, Mildred K., Duster, Troy, Jasperse, Marla, Licinio, Julio, Long, Jeffrey C., Ossorio, Pilar N., Spallone, Patricia, Terry, Sharon F., Boehnke, Michael, Douglas, Julie A., Hudson, Richard R., Kruglyak, Leonid, and Nussbaum, Robert L.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): The International HapMap Consortium ; (Participants are arranged alphabetically by institution, and then by principal investigator and alphabetically by last name.); ; Genotyping centres: Baylor College of Medicine and [...]

Published
2003
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36. Genome-Wide Association Studies Identify Multiple Genetic Loci Influencing Eyebrow Color Variation in Europeans

Author

Peng, Fuduan, Zhu, Gu, Hysi, Pirro G., Eller, Ryan J., Chen, Yan, Li, Yi, Hamer, Merel A., Zeng, Changqing, Hopkins, Racquel L., Jacobus, Case L., Wallace, Paige L., Uitterlinden, André G., Ikram, M. Arfan, Nijsten, Tamar, Duffy, David L., Medland, Sarah E., Spector, Timothy D., Walsh, Susan, Martin, Nicholas G., Liu, Fan, and Kayser, Manfred

Published
2019
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37. Dysfunction of VIPR2 leads to myopia in humans and mice

Author

Zhao, Fuxin, primary, Li, Qihang, additional, Chen, Wei, additional, Zhu, He, additional, Zhou, Dengke, additional, Reinach, Peter Sol, additional, Yang, Zhenglin, additional, He, Mingguang, additional, Xue, Anquan, additional, Wu, Deng, additional, Liu, Tianzi, additional, Fu, Qian, additional, Zeng, Changqing, additional, Qu, Jia, additional, and Zhou, Xiangtian, additional

Published
2020
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39. Integrating common and rare genetic variation in diverse human populations

Author

Altshuler, David M., Gibbs, Richard A., Peltonen, Leena, Dermitzakis, Emmanouil, Schaffner, Stephen F., Yu, Fuli, Bonnen, Penelope E., de Bakker, Paul I. W., Deloukas, Panos, Gabriel, Stacey B., Gwilliam, Rhian, Hunt, Sarah, Inouye, Michael, Jia, Xiaoming, Palotie, Aarno, Parkin, Melissa, Whittaker, Pamela, Yu, Fuli, Chang, Kyle, Hawes, Alicia, Lewis, Lora R., Ren, Yanru, Wheeler, David, Marie Muzny, Donna, Barnes, Chris, Darvishi, Katayoon, Hurles, Matthew, Korn, Joshua M., Kristiansson, Kati, Lee, Charles, McCarroll, Steven A., Nemesh, James, Keinan, Alon, Montgomery, Stephen B., Pollack, Samuela, Price, Alkes L., Soranzo, Nicole, Gonzaga-Jauregui, Claudia, Keinan, Alon, Anttila, Verneri, Brodeur, Wendy, Daly, Mark J., Leslie, Stephen, McVean, Gil, Moutsianas, Loukas, Nguyen, Huy, Schaffner, Stephen F., Zhang, Qingrun, Ghori, Mohammed J. R., McGinnis, Ralph, McLaren, William, Price, Alkes L., Schaffner, Stephen F., Takeuchi, Fumihiko, Grossman, Sharon R., Shlyakhter, Ilya, Hostetter, Elizabeth B., Sabeti, Pardis C., Adebamowo, Clement A., Foster, Morris W., Gordon, Deborah R., Licinio, Julio, Cristina Manca, Maria, Marshall, Patricia A., Matsuda, Ichiro, Ngare, Duncan, Ota Wang, Vivian, Reddy, Deepa, Rotimi, Charles N., Royal, Charmaine D., Sharp, Richard R., Zeng, Changqing, Brooks, Lisa D., and McEwen, Jean E.

Published
2010
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44. A Genome Sequence of Novel SARS-CoV Isolates: the Genotype, GD-Ins29, Leads to a Hypothesis of Viral Transmission in South China

Author

Qin, E’de, He, Xionglei, Tian, Wei, Liu, Yong, Li, Wei, Wen, Jie, Wang, Jingqiang, Fan, Baochang, Wu, Qingfa, Chang, Guohui, Cao, Wuchun, Xu, Zuyuan, Yang, Ruifu, Wang, Jing, Yu, Man, Li, Yan, Xu, Jing, Si, Bingyin, Hu, Yongwu, Peng, Wenming, Tang, Lin, Jiang, Tao, Shi, Jianping, Ji, Jia, Zhang, Yu, Ye, Jia, Wang, Cui’e, Han, Yujun, Zhou, Jun, Deng, Yajun, Li, Xiaoyu, Hu, Jianfei, Wang, Caiping, Yan, Chunxia, Zhang, Qingrun, Bao, Jingyue, Li, Guoqing, Chen, Weijun, Fang, Lin, Li, Changfeng, Lei, Meng, Li, Dawei, Tong, Wei, Tian, Xiangjun, Wang, Jin, Zhang, Bo, Zhang, Haiqing, Zhang, Yilin, Zhao, Hui, Zhang, Xiaowei, Li, Shuangli, Cheng, Xiaojie, Zhang, Xiuqing, Liu, Bin, Zeng, Changqing, Li, Songgang, Tan, Xuehai, Liu, Siqi, Dong, Wei, Wang, Jun, Wong, Gane Ka-Shu, Yu, Jun, Wang, Jian, Zhu, Qingyu, and Yang, Huanming

Published
2003
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45. Whole genome HBV deletion profiles and the accumulation of preS deletion mutant during antiviral treatment

Author

Zhang Dake, Dong Peiling, Zhang Ke, Deng Libin, Bach Christian, Chen Wei, Li Feifei, Protzer Ulrike, Ding Huiguo, and Zeng Changqing

Subjects
HBV, Deletion, PreS, Chronic hepatitis, Antiviral therapy, Nucleotide analog, Microbiology, QR1-502
Abstract

Abstract Background Hepatitis B virus (HBV), because of its error-prone viral polymerase, has a high mutation rate leading to widespread substitutions, deletions, and insertions in the HBV genome. Deletions may significantly change viral biological features complicating the progression of liver diseases. However, the clinical conditions correlating to the accumulation of deleted mutants remain unclear. In this study, we explored HBV deletion patterns and their association with disease status and antiviral treatment by performing whole genome sequencing on samples from 51 hepatitis B patients and by monitoring changes in deletion variants during treatment. Clone sequencing was used to analyze preS regions in another cohort of 52 patients. Results Among the core, preS, and basic core promoter (BCP) deletion hotspots, we identified preS to have the highest frequency and the most complex deletion pattern using whole genome sequencing. Further clone sequencing analysis on preS identified 70 deletions which were classified into 4 types, the most common being preS2. Also, in contrast to the core and BCP regions, most preS deletions were in-frame. Most deletions interrupted viral surface epitopes, and are possibly involved in evading immuno-surveillance. Among various clinical factors examined, logistic regression showed that antiviral medication affected the accumulation of deletion mutants (OR = 6.81, 95% CI = 1.296 ~ 35.817, P = 0.023). In chronic carriers of the virus, and individuals with chronic hepatitis, the deletion rate was significantly higher in the antiviral treatment group (Fisher exact test, P = 0.007). Particularly, preS2 deletions were associated with the usage of nucleos(t)ide analog therapy (Fisher exact test, P = 0.023). Dynamic increases in preS1 or preS2 deletions were also observed in quasispecies from samples taken from patients before and after three months of ADV therapy. In vitro experiments demonstrated that preS2 deletions alone were not responsible for antiviral resistance, implying the coordination between wild type and mutant strains during viral survival and disease development. Conclusions We present the HBV deletion distribution patterns and preS deletion substructures in viral genomes that are prevalent in northern China. The accumulation of preS deletion mutants during nucleos(t)ide analog therapy may be due to viral escape from host immuno-surveillance.

Published
2012
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46. Genome-wide association studies and CRISPR/Cas9-mediated gene editing identify regulatory variants influencing eyebrow thickness in humans

Author

Wu, Sijie, Zhang, Manfei, Yang, Xinzhou, Peng, Fuduan, Zhang, Juan, Tan, Jingze, Yang, Yajun, Wang, Lina, Hu, Yanan, Peng, Qianqian, Li, Jinxi, Li, Yu, Guan, Yaqun, Chen, Chen, Hamer, Merel, Nijsten, Tamar, Zeng, Changqing, Adhikari, Kaustubh, Gallo, Carla, Poletti, Giovanni, Schuler-Faccini, Lavinia, Bortolini, Maria-Cátira, Canizales-Quinteros, Samuel, Rothhammer, Francisco, Bedoya, Gabriel, González-José, Rolando, Hu, Hui, Krutmann, Jean, Li, Fan, Kayser, Manfred, Li, Lina, Tan, Kun, Xu, Shuhua, Zhang, Liang, Li, Li, Wang, Sijia, Cooper, Gregory, Central South University [Changsha], Beijing Institute of Technology (BIT), Chinese Academy of Agricultural Sciences (CAAS), Ministry of Agriculture of the People's Republic of China (MOA), Modélisation, Information et Systèmes - UR UPJV 4290 (MIS), Université de Picardie Jules Verne (UPJV), Institut National de l'Environnement Industriel et des Risques (INERIS), Laboratorio de Genética Molecular, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], Unit of Molecular Biology and Genomic Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán - National Institute of Medical Science and Nutrition Salvador Zubiran [Mexico], Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Laboratoire Images, Signaux et Systèmes Intelligents (LISSI), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Forensic Molecular Biology, ErasmusMC, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-École Supérieure Chimie Physique Électronique de Lyon-Centre National de la Recherche Scientifique (CNRS), University of Peking, Peking University [Beijing], Graduate School for Integrative Sciences and Engineering, Ingénierie et biologie cellulaire et tissulaire (IBCT (ex IFR133)), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS [Bourgogne-Franche-Comté])-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Harvard FAS Center for Systems Biology, Université de Lyon-Université de Lyon-École Supérieure de Chimie Physique Électronique de Lyon (CPE)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Ruiz-Linares, Andres

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

47. Genome-wide association meta-analysis of individuals of European ancestry identifies new loci explaining a substantial fraction of hair color variation and heritability

Author

Valdes, Ana M., Hysi, Pirro G., Liu, Fan, Furlotte, Nicholas A., Evans, David M., Bataille, Veronique, Visconti, Alessia, Hemani, Gibran, McMahon, George, Ring, Susan M., Smith, George Davey, Duffy, David L., Zhu, Gu, Gordon, Scott D., Medland, Sarah E., Lin, Bochao D., Willemsen, Gonneke, Hottenga, Jouke Jan, Vuckovic, Dragana, Girotto, Giorgia, Gandin, Ilaria, Sala, Cinzia, Pina Concas, Maria, Brumat, Marco, Gasparini, Paolo, Toniolo, Daniela, Cocca, Massimiliano, Robino, Antonietta, Yazar, Seyhan, Hewitt, Alex W., Chen, Yan, Zeng, Changqing, Uitterlinden, Andre G., Arfan Ikram, M., Hamer, Merel A., van Duijn, Cornelia M., Nijsten, Tamar, Mackey, David A., Falchi, Mario, Boomsma, Dorret I., Martin, Nicholas G., Hinds, David A., Kayser, Manfred, Spector, Timothy D., and International Visible Trait Genetics Consortium

Subjects
integumentary system, sense organs
Abstract

© 2018 The Author(s). Hair color is one of the most recognizable visual traits in European populations and is under strong genetic control. Here we report the results of a genome-wide association study meta-analysis of almost 300,000 participants of European descent. We identified 123 autosomal and one X-chromosome loci significantly associated with hair color; all but 13 are novel. Collectively, single-nucleotide polymorphisms associated with hair color within these loci explain 34.6% of red hair, 24.8% of blond hair, and 26.1% of black hair heritability in the study populations. These results confirm the polygenic nature of complex phenotypes and improve our understanding of melanin pigment metabolism in humans.

Published
2018

48. Genome-wide association study in 176,678 Europeans reveals genetic loci for tanning response to sun exposure (Supplementary Data)

Author

Visconti, Alessia, Duffy, David L, Liu, Fan, Zhu, Gu, Wu, Wenting, Cheng, Yan, Hysi, Pirro G, Zeng, Changqing, Sanna, Marianna, Iles, Mark M, Kanetsky, Peter A, Demenais, Florence, Hamer, Merel A, Uitterlinden, Andre G, Ikram, M Arfan, Nijsten, Tamar, Martin, Nicholas G, Kayser, Manfred, Spector, Tim D, Han, Jiali, Bataille, Veronique, and Falchi, Mario

Subjects
GWAS, ease of skin tanning
Abstract

Supplementary Data for the manuscript entitled "Genome-wide association study in 176,678 Europeans reveals genetic loci for tanning response to sun exposure", Visconti et al. The association summary statistics for the 10,834 genome-wide significant SNPs are provided as Supplementary Data 1. Genomic coordinates are reported in GRCh37.p13. The association summary statistics for the SNPs associated in the UKBB non-melanoma skin cancer GWAS (P < 1x10-5) are provided as Supplementary Data 2. Genomic coordinates are reported in GRCh37.p13. The cis-eQTLs identified in the three studied skin tissues, and available within the GTEx project, are provided as Supplementary Data 3. &nbsp

Published
2018
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49. Haplo2Ped: a tool using haplotypes as markers for linkage analysis

Author

Zhang Yinan, Zhang Xianglong, Cheng Feng, Li Chaohua, and Zeng Changqing

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Generally, SNPs are abundant in the genome; however, they display low power in linkage analysis because of their limited heterozygosity. Haplotype markers, on the other hand, which are composed of many SNPs, greatly increase heterozygosity and have superiority in linkage statistics. Results Here we developed Haplo2Ped to automatically transform SNP data into haplotype markers and then to compute the logarithm (base 10) of odds (LOD) scores of regional haplotypes that are homozygous within the disease co-segregation haploid group. The results are reported as a hypertext file and a 3D figure to help users to obtain the candidate linkage regions. The hypertext file contains parameters of the disease linked regions, candidate genes, and their links to public databases. The 3D figure clearly displays the linkage signals in each chromosome. We tested Haplo2Ped in a simulated SNP dataset and also applied it to data from a real study. It successfully and accurately located the causative genomic regions. Comparison of Haplo2Ped with other existing software for linkage analysis further indicated the high effectiveness of this software. Conclusions Haplo2Ped uses haplotype fragments as mapping markers in whole genome linkage analysis. The advantages of Haplo2Ped over other existing software include straightforward output files, increased accuracy and superior ability to deal with pedigrees showing incomplete penetrance. Haplo2Ped is freely available at: http://bighapmap.big.ac.cn/software.html.

Published
2011
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50. Prevalent HBV point mutations and mutation combinations at BCP/preC region and their association with liver disease progression

Author

Zhang Dake, Ma Sufang, Zhang Xin, Zhao Hanqing, Ding Huiguo, and Zeng Changqing

Subjects
Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Mutations in the basic core promoter (BCP) and its adjacent precore (preC) region in HBV genome are common in chronic hepatitis B patients. However, the patterns of mutation combinations in these two regions during chronic infection are less understood. This study focused on single base mutations in BCP and preC region and the multi-mutation patterns observed in chronic HBV infection patients. Methods Total 192 blood samples of chronic HBV infection patients were included. Direct PCR sequencing on the target region of HBV genome was successfully conducted in 157 samples. The rest 35 samples were analyzed by clone sequencing. Only the nucleotide substitutions with their frequencies no less than 10% were included in multi-mutation analysis with the exception for the polymorphic sites between genotypes B and C. Results Five high frequency mutations (≥10%) were found in BCP and preC region. Thirteen types of multi-mutations in one fragment were observed, among which 3 types were common combinations (≥5%). The top three multi-mutations were A1762T/G1764A (36%), A1762T/G1764A/G1896A (11%) and T1753(A/C)/A1762T/G1764A/G1896A (8%). Patients with multi-mutations in viral genomes (≥3) were more likely to have liver cirrhosis or hepatocellular carcinoma (OR = 3.1, 95% CI: 1.6-6.0, P = 0.001). G1896A mutation seemed to be involved in liver disease progression independent of the patient age (OR = 3.6, 95% CI: 1.5-8.6; P = 0.004). In addition, patients with more viral mutations detected (≥3) were more likely to be HBeAg negative (OR = 2.7, 95% CI: 1.1-6.4; P = 0.027). Moreover, G1776A mutation was shown to contribute to HBeAg negativity in our study (OR = 8.6, 95% CI: 1.2-44.9; P = 0.01). Conclusions Patients with advanced liver diseases and with HBeAg negativity more likely have multi-mutations in HBV genomes but with different mutation combination patterns. G1896A mutation appears to be independent of infection history.

Published
2010
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