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12. Genome-wide Scan of Archaic Hominin Introgressions in Eurasians Reveals Complex Admixture History

Author

Hu, Ya, Wang, Yi, Ding, Qiliang, He, Yungang, Wang, Minxian, Wang, Jiucun, Xu, Shuhua, and Jin, Li

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Introgressions from Neanderthals and Denisovans were detected in modern humans. Introgressions from other archaic hominins were also implicated, however, identification of which poses a great technical challenge. Here, we introduced an approach in identifying introgressions from all possible archaic hominins in Eurasian genomes, without referring to archaic hominin sequences. We focused on mutations emerged in archaic hominins after their divergence from modern humans (denoted as archaic-specific mutations), and identified introgressive segments which showed significant enrichment of archaic-specific mutations over the rest of the genome. Furthermore, boundaries of introgressions were identified using a dynamic programming approach to partition whole genome into segments which contained different levels of archaic-specific mutations. We found that detected introgressions shared more archaic-specific mutations with Altai Neanderthal than they shared with Denisovan, and 60.3% of archaic hominin introgressions were from Neanderthals. Furthermore, we detected more introgressions from two unknown archaic hominins whom diverged with modern humans approximately 859 and 3,464 thousand years ago. The latter unknown archaic hominin contributed to the genomes of the common ancestors of modern humans and Neanderthals. In total, archaic hominin introgressions comprised 2.4% of Eurasian genomes. Above results suggested a complex admixture history among hominins. The proposed approach could also facilitate admixture research across species., Comment: 42 Pages, 1 Table, 4 Figures, 1 Supplementary Table, and 10 Supplementary Figures

Published
2014

13. The DRD4 Exon III VNTR, Bupropion, and Associations With Prospective Abstinence

Author

Bergen, Andrew W, Javitz, Harold S, Su, Li, He, Yungang, Conti, David V, Benowitz, Neal L, Tyndale, Rachel F, Lerman, Caryn, and Swan, Gary E

Subjects
Epidemiology, Public Health, Health Sciences, Behavioral and Social Science, Depression, Genetics, Clinical Trials and Supportive Activities, Prevention, Mental Health, Brain Disorders, Clinical Research, Neurosciences, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Good Health and Well Being, Adult, Bupropion, Cognitive Behavioral Therapy, Exons, Female, Humans, Longitudinal Studies, Male, Middle Aged, Minisatellite Repeats, Pharmacogenetics, Receptors, Dopamine D4, Regression Analysis, Smoking Cessation, Treatment Outcome, Clinical Sciences, Public Health and Health Services, Marketing, Public health
Abstract

IntroductionDRD4 Exon III Variable Number of Tandem Repeat (VNTR) variation was found to interact with bupropion to influence prospective smoking abstinence, in a recently published longitudinal analyses of N = 331 individuals from a randomized double-blind placebo-controlled trial of bupropion and intensive cognitive-behavioral mood management therapy.MethodsWe used univariate, multivariate, and longitudinal logistic regression to evaluate gene, treatment, time, and interaction effects on point prevalence and continuous abstinence at end of treatment, 6 months, and 12 months, respectively, in N = 416 European ancestry participants in a double-blind pharmacogenetic efficacy trial randomizing participants to active or placebo bupropion. Participants received 10 weeks of pharmacotherapy and 7 sessions of behavioral therapy, with a target quit date 2 weeks after initiating both therapies. VNTR genotypes were coded with the long allele dominant resulting in 4 analysis categories. Covariates included demographics, dependence measures, depressive symptoms, and genetic ancestry. We also performed genotype-stratified secondary analyses.ResultsWe observed significant effects of time in longitudinal analyses of both abstinence outcomes, of treatment in individuals with VNTR long allele genotypes for both abstinence outcomes, and of covariates in some analyses. We observed non-significantly larger differences in active versus placebo effect sizes in individuals with VNTR long allele genotypes than in individuals without the VNTR long allele, in the directions previously reported.ConclusionsVNTR by treatment interaction differences between these and previous analyses may be attributable to insufficient size of the replication sample. Analyses of multiple randomized clinical trials will enable identification and validation of factors mediating treatment response.

Published
2013

14. Dopamine Genes and Nicotine Dependence in Treatment-Seeking and Community Smokers

Author

Bergen, Andrew W, Conti, David V, Van Den Berg, David, Lee, Wonho, Liu, Jinghua, Li, Dalin, Guo, Nan, Mi, Huaiyu, Thomas, Paul D, Lessov-Schlaggar, Christina N, Krasnow, Ruth, He, Yungang, Nishita, Denise, Jiang, Ruhong, McClure, Jennifer B, Tildesley, Elizabeth, Hops, Hyman, Tyndale, Rachel F, Benowitz, Neal L, Lerman, Caryn, and Swan, Gary E

Subjects
Biological Psychology, Pharmacology and Pharmaceutical Sciences, Biomedical and Clinical Sciences, Psychology, Tobacco Smoke and Health, Drug Abuse (NIDA only), Substance Misuse, Tobacco, Brain Disorders, Genetics, Clinical Research, Prevention, Good Health and Well Being, Adult, Analysis of Variance, Bupropion, Cohort Studies, DNA-Binding Proteins, Dopamine Plasma Membrane Transport Proteins, Dopamine Uptake Inhibitors, Female, Genetic Predisposition to Disease, Genotype, Humans, Linkage Disequilibrium, Male, Middle Aged, Nuclear Receptor Subfamily 4, Group A, Member 2, Polymorphism, Single Nucleotide, Receptors, Dopamine D3, Residence Characteristics, Smoking, Tobacco Use Disorder, Transcription Factors, White People, dopamine transporter, Fagerstrom Test for Nicotine Dependence, single nucleotide polymorphism, candidate gene, gene-gene interaction, Medical and Health Sciences, Psychology and Cognitive Sciences, Psychiatry, Neurosciences, Biological psychology
Abstract

We utilized a cohort of 828 treatment-seeking self-identified white cigarette smokers (50% female) to rank candidate gene single nucleotide polymorphisms (SNPs) associated with the Fagerström Test for Nicotine Dependence (FTND), a measure of nicotine dependence which assesses quantity of cigarettes smoked and time- and place-dependent characteristics of the respondent's smoking behavior. A total of 1123 SNPs at 55 autosomal candidate genes, nicotinic acetylcholine receptors and genes involved in dopaminergic function, were tested for association to baseline FTND scores adjusted for age, depression, education, sex, and study site. SNP P-values were adjusted for the number of transmission models, the number of SNPs tested per candidate gene, and their intragenic correlation. DRD2, SLC6A3, and NR4A2 SNPs with adjusted P-values

Published
2009

15. Data from IFNα Potentiates Anti–PD-1 Efficacy by Remodeling Glucose Metabolism in the Hepatocellular Carcinoma Microenvironment

Author

Hu, Bo, primary, Yu, Mincheng, primary, Ma, Xiaolu, primary, Sun, Jialei, primary, Liu, Chenglong, primary, Wang, Chunyan, primary, Wu, Suiyi, primary, Fu, Peiyao, primary, Yang, Zhen, primary, He, Yungang, primary, Zhu, Yuanyuan, primary, Huang, Cheng, primary, Yang, Xinrong, primary, Shi, Yinghong, primary, Qiu, Shuangjian, primary, Sun, Huichuan, primary, Zhu, Andrew X., primary, Zhou, Jian, primary, Xu, Yang, primary, Zhu, Di, primary, and Fan, Jia, primary

Published
2023
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16. Supplementary Figure from IFNα Potentiates Anti–PD-1 Efficacy by Remodeling Glucose Metabolism in the Hepatocellular Carcinoma Microenvironment

Author

Hu, Bo, primary, Yu, Mincheng, primary, Ma, Xiaolu, primary, Sun, Jialei, primary, Liu, Chenglong, primary, Wang, Chunyan, primary, Wu, Suiyi, primary, Fu, Peiyao, primary, Yang, Zhen, primary, He, Yungang, primary, Zhu, Yuanyuan, primary, Huang, Cheng, primary, Yang, Xinrong, primary, Shi, Yinghong, primary, Qiu, Shuangjian, primary, Sun, Huichuan, primary, Zhu, Andrew X., primary, Zhou, Jian, primary, Xu, Yang, primary, Zhu, Di, primary, and Fan, Jia, primary

Published
2023
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24. IFNα Potentiates Anti–PD-1 Efficacy by Remodeling Glucose Metabolism in the Hepatocellular Carcinoma Microenvironment

Author

Hu, Bo, primary, Yu, Mincheng, additional, Ma, Xiaolu, additional, Sun, Jialei, additional, Liu, Chenglong, additional, Wang, Chunyan, additional, Wu, Suiyi, additional, Fu, Peiyao, additional, Yang, Zhen, additional, He, Yungang, additional, Zhu, Yuanyuan, additional, Huang, Cheng, additional, Yang, Xinrong, additional, Shi, Yinghong, additional, Qiu, Shuangjian, additional, Sun, Huichuan, additional, Zhu, Andrew X., additional, Zhou, Jian, additional, Xu, Yang, additional, Zhu, Di, additional, and Fan, Jia, additional

Published
2022
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33. Additional file 11 of Characterization and modulation of endoplasmic reticulum stress response target genes in Kluyveromyces marxianus to improve secretory expressions of heterologous proteins

Author

Shi, Tianfang, Zhou, Jungang, Xue, Aijuan, Lu, Hong, He, Yungang, and Yu, Yao

Subjects
sense organs, skin and connective tissue diseases
Abstract

Additional file 11: Figure S1. Box plot of distributions of fold changes of transcript abundance under different treatment conditions.

Published
2021
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36. Subtyping of type A influenza by sequencing the variable regions of HA gene specifically amplified with RT-PCR

Author

Yan, An, Ding, GuoHui, Zhou, ZhenFeng, Dong, Hui, Zhang, YaKun, Zhu, Lei, He, YunGang, Zhang, GuoQing, Li, YiXue, Sun, Bing, Huang, Zhong, Lan, Ke, Jin, Li, Wang, HongYan, Wang, XiaoNing, Yang, Zhong, Zhong, Yang, Dai, JianXin, Guo, YaJun, Wang, Hao, Che, XiaoYan, Wu, Fan, Yuan, ZhenGan, Zhang, Xi, Cao, ZhiWei, Zhou, XiaoNong, Zhou, JiaHai, Ma, ZhiYong, Tong, GuangZhi, Zhao, GuoPing, Jin, WeiRong, and Xiong, Hui

Published
2009
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40. Genetic evidence supports demic diffusion of Han culture

Author

Wen, Bo, Li, Hui, Lu, Daru, Song, Xiufeng, Zhang, Feng, He, Yungang, Li, Feng, Gao, Yang, Mao, Xianyun, Zhang, Liang, Qian, Ji, Tan, Jingze, Jin, Jianzhong, Huang, Wei, Deka, Ranjan, Su, Bing, Chakraborty, Ranajit, and Jin, Li

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

Author(s): Bo Wen [1, 2]; Hui Li [1]; Daru Lu [1]; Xiufeng Song [1]; Feng Zhang [1]; Yungang He [1]; Feng Li [1]; Yang Gao [1]; Xianyun Mao [1]; Liang [...]

Published
2004
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43. Structure modeling and spatial epitope analysis for HA protein of the novel H1N1 influenza virus

Author

Wu, Di, Xu, TianLei, Sun, Jing, Dai, JianXin, Ding, GuoHui, He, Yungang, Zhou, ZhengFeng, Xiong, Hui, Dong, Hui, Jin, WeiRong, Bian, Chao, Jin, Li, Wang, HongYan, Wang, XiaoNing, Yang, Zhong, Zhong, Yang, Wang, Hao, Che, XiaoYan, Huang, Zhong, Lan, Ke, Sun, Bing, Wu, Fan, Yuan, ZhenAn, Zhang, Xi, Zhou, XiaoNong, Zhou, JiaHai, Ma, ZhiYong, Tong, GuangZhi, Guo, YaJun, Zhao, GuoPing, Li, YiXue, and Cao, ZhiWei

Published
2009
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44. The mutation network for the hemagglutinin gene from the novel influenza A (H1N1) virus

Author

He, YunGang, Ding, GuoHui, Bian, Chao, Huang, Zhong, Lan, Ke, Sun, Bing, Wang, XueCai, Li, YiXue, Wang, HongYan, Wang, XiaoNing, Yang, Zhong, Zhong, Yang, Jin, WeiRong, Xiong, Hui, Dai, JianXin, Guo, YaJun, Wang, Hao, Che, XiaoYan, Wu, Fan, Yuan, ZhenAn, Zhang, Xi, Cao, ZhiWei, Zhou, XiaoNong, Zhou, JiaHai, Ma, ZhiYong, Tong, GuangZhi, Zhao, GuoPing, and Jin, Li

Published
2009
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45. CMTTdb: the cancer molecular targeted therapy database

Author

Bai, Xue, primary, Yang, Xiaobo, additional, Wu, Liangcai, additional, Zuo, Bangyou, additional, Lin, Jianzhen, additional, Wang, Shanshan, additional, Bian, Jin, additional, Sang, Xinting, additional, He, Yungang, additional, Yang, Zhen, additional, and Zhao, Haitao, additional

Published
2019
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50. Detection for gene-gene co-association via kernel canonical correlation analysis

Author

Yuan Zhongshang, Gao Qingsong, He Yungang, Zhang Xiaoshuai, Li Fangyu, Zhao Jinghua, and Xue Fuzhong

Subjects
Genome-wide association study (GWAS), Gene-gene co-association, Gene-gene interaction (GGI), Kernel canonical correlation analysis (KCCA), Genetics, QH426-470
Abstract

Abstract Background Currently, most methods for detecting gene-gene interaction (GGI) in genomewide association studies (GWASs) are limited in their use of single nucleotide polymorphism (SNP) as the unit of association. One way to address this drawback is to consider higher level units such as genes or regions in the analysis. Earlier we proposed a statistic based on canonical correlations (CCU) as a gene-based method for detecting gene-gene co-association. However, it can only capture linear relationship and not nonlinear correlation between genes. We therefore proposed a counterpart (KCCU) based on kernel canonical correlation analysis (KCCA). Results Through simulation the KCCU statistic was shown to be a valid test and more powerful than CCU statistic with respect to sample size and interaction odds ratio. Analysis of data from regions involving three genes on rheumatoid arthritis (RA) from Genetic Analysis Workshop 16 (GAW16) indicated that only KCCU statistic was able to identify interactions reported earlier. Conclusions KCCU statistic is a valid and powerful gene-based method for detecting gene-gene co-association.

Published
2012
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