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association study of NDST3 gene for schizophrenia,bipolar disorder,major depressive disorder in the Han Chinese population

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Association study of NDST3 gene for schizophrenia,bipolar di...

2017中国长三角遗传学大会

作者： Bio-X Institutes,Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders(Ministry of Education),the Collaborative Innovation Center for Brain Science,Shanghai Jiao Tong University Bio-X Institutes Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders(Ministry of Education)the Collaborative Innovation Center for Brain ScienceShanghai Jiao Tong University

The NDST3 gene at 4 q26 was a functional candidate gene for mental disorders.Recently,a novel genome-wide significant risk locus at chromosome4 q26 was identified and the top single nucleotide polymorphism rs11098403 in the vicinity of NDST3 gene was reported to confer risk of schizophrenia in Caucasian.Nevertheless,association between NDST3 gene polymorphisms and schizophrenia,bipolar disorder or major depressive disorders has not been well studied in the Han Chinese population.To further investigate whether NDST3 is a risk gene for these mental disorders,we genotyped and analyzed 8 tag SNPs(rs11098403,rs10857057,rs2389521,rs4833564,rs6837896,rs7689157,rs3817274,rs609512) covering NDST3 gene in 1248 schizophrenia cases,1056 major depression cases,1344 bipolar disorder cases,and 1248 controls of Chinese origin.However,there was no significant difference in allelic or genotypic frequency observed between each case group and healthy controls.Accordingly,our study does not support that the NDST3 gene plays a major role in schizophrenia,bipolar disorder and major depressive disorder in the Han Chinese population.

关键词： association study NDST3 Schizophrenia Bipolar disorder Major depressive disorder Wang Lin

Nucleotide Variation in the NCED3 Region of Arabidopsis thaliana and its association study with Abscisic Acid Content under Drought Stress

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Journal of Integrative Plant Biology 2009年第2期51卷 175-183页

作者： Gang-Ping Hao Xiu-Hai Zhang Yong-Qin Wang Zhong-Yi Wu Cong-Lin Huang Beijing Agro-Biotechnology Research Center Beijing Academy of Agriculture and Forestry Sciences Beijing 100097 China Taishan Medical College Taian 271000 China

Drought tolerance is a comprehensive quantitative trait that is being understood further at the molecular genetic level. Abscisic acid （ABA） is the main drought-induced hormone that regulates the expression of many genes related to drought responses. 9-cis-epoxycarotenoid dioxygenase （NCED3） is thought to be a key enzyme in ABA biosynthesis. In this paper, we measured the ABA content increase under drought stress, and sequenced and compared the sequence of AtNCED3 among 22 Arabidopsis thaliana accessions. The results showed that the fold of ABA content increase under drought stress was highly variable among these accessions. High density single nucleotide polymorphism （SNP） and insertion/deletion （indel） were found in the AtNCED3 region, on average one SNP per 87.4 bp and one indel per 502 bp. Nucleotide diversity was significantly lower in the coding region than that in non-coding regions. The results of an association study with ANOVA analysis suggested that the 274th site （P←→S） and the 327th site （P←→R） amino acid variations might be the cause of ABA content increase of 163av accession under drought stress.

关键词： abscisic acid Arabidopsis thaliana association study drought stress NCED3 region nucleotide variation.

association between SLC17A7 gene polymorphisms and venlafaxine for major depressive disorder in a Chinese Han population:a prospective pharmacogenetic case-control study

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Journal of Bio-X Research 2021年第3期4卷 124-129页

作者： Liangile Liu Decheng Ren Fan Yuan Yan Bi Zhenming Guo Gaini Ma Fei Xu Binyin Hou Lei Ji Zhixuan Chen Lin An Naixin Zhang Tao Yu Xingwang Li Fengping Yang Xueli Sun Zaiquan Dong Shunying Yu Zhenghui Yi Yifeng Xu Lin He Shaochang Wu Longyou Zhao Changqun Cai Guang He Yi Shi Bio-X Institutes Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersWuhuAnhui ProvinceChina Shanghai Key Laboratory of Psychotic Disorders and Brain Science and Technology Research CenterShanghai Jiao Tong UniversityWuhuAnhui ProvinceChina Shanghai Center for Women and Children's Health ShanghaiWuhuAnhui ProvinceChina Psychological Center West China HospitalSichuan UniversityChengduSichuan ProvinceWuhuAnhui ProvinceChina Lishui No.2 People's Hospital LishuiZhejiang ProvinceWuhuAnhui ProvinceChina Wuhu No.4 People's Hospital WuhuAnhui ProvinceChina

Objective: Venlafaxine is a common antidepressant and its therapeutic effect varies among people with different genetic backgrounds. The aim of this study was to investigate whether single nucleotide polymorphisms (SNPs) in theSLC17A7 gene are associated with the treatment outcome of venlafaxine in a Chinese Han population with major depressive disorder.Methods: This prospective pharmacogenetic case-control study that involved genotyping of four SNPs ofSLC17A7 was conducted on 175 major depressive disorder patients of Chinese Han origin, aged 18 to 65 years, participated in the study from April 2005 to September 2006. Comparisons of allele and genotype frequencies of all SNPs were performed between the responder/remission group and the nonresponder/nonremission group. This study was approved by the Institutional Ethics Committee of Sichuan University (approval No. 20151112-265).Results: The allele and genotype frequencies of the four candidate SNPs inSCL17A7 showed no significant difference between responders and nonresponders. Meanwhile, no significant difference was detected in the four investigatedSLC17A7 SNPs between patients who did and did not exhibit remission. Although one of the investigatedSLC17A7 variants (rs1578944) demonstrated a significant association (P=0.022) with a response to venlafaxine after 6 weeks of treatment in the survival analysis, the association was unclear after a Bonferroni multiple comparisons test was conducted.Conclusion: No significant association exists between the four candidate SNPs (rs1043558, rs1320301, rs1578944, and rs74174284) inSLC17A7 and venlafaxine treatment in the Chinese Han population.

关键词： association study major depression pharmacogenomics SLC17A7 gene venlafaxine treatment

Mapping loci controlling fatty acid profiles and contents of oil and protein by genome-wide association study in Brassica napus

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Mapping loci controlling fatty acid profiles and contents of...

2018全国植物生物学大会

作者： Minqiang Tang Yuanyuan Zhang Yueying Liu Chaobo Tong Xiaohui Cheng Wei Zhu Junyan Huang Shengyi Liu The Key Laboratory of Biology and Genetic Improvement of Oil Crops The Ministry of Agriculture of PRCOil Crops Research InstituteChinese Academy of Agriculture Sciences

Optimal profile and quantity of fatty acids in rapeseed are very critical for maximizing thevalue of edible oil and biodiesel.Genome-wide association study(GWAS) could efficiently identify the genes and their network underlying complex traits and provide molecular markers to accelerate breeding.In this study,weperformed GWAS todissect the genetic variations of eightseed quality traits in a rapeseed population comprising370 diverse accessions.Seven common SNPs for the contents of seed oiland proteinwere detected on five chromosomes,and five genes orthologous to functionknown Arabidopsis genes were predicted as candidate genes.Genomic region of reduced variation aroundFAE1 loci onA08 and C03 chromosomes controlling the content of erucic acid showed that these two regions were strongly selected during breeding.With the re-sequencing data,we found,except the known haplotypes combination of the variations of BnaA.FAE1 and BnaC.FAE,three accessions contained an additional haplotype combination controlling the moderate content of erucic acid.This study reveals the genetic variations and complex correlations of eight quality traits,which may inform breeding selection strategies for traits in crops.

关键词： association study fatty acid profiles candidate genes Brassica napus

The association study of polymorphisms in three selenoprotein genes and Kashin-Beck disease susceptibility in a Chinese Tibetan population

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The association study of polymorphisms in three selenoprotei...

中华医学会第九次全国检验医学学术会议暨中国医院协会临床...

作者： Huang Lulin Center for Human Molecular Biology & Genetics, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital,Chengdu,Sichuan, 610072,China

Objectives:To investigate the association of three selenoprotein genes GPX1(rs 1050450,rs1800668 and rs3811699),TrxR2(rs5748469) and DI02 (rs225014) and Kashin-Beck disease(KBD) in a Tibetan Chinese population.To furt... 详细信息

关键词： Kashin-Beck disease selenoprotein association study selenium iodine

Multi-locus association study of schizophrenia susceptibility genes with a posterior probability method

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Science China(Life Sciences) 2005年第3期48卷 263-269页

作者： SUN Xiangqing JIA Yanbin ZHANG Xuegong XU Qi SHEN Yan LI Yanda Ministry of Education(MOE)Key Laboratory of Bioinformatics at Tsinghua University Department of AutomationTsinghua UniversityBeijing 100084China National Laboratory of Medical Molecular Biology Institute of Basic Medical SciencesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100005China

Schizophrenia is a serious neuropsychiatric illness affecting about 1% of the world’s population. It is considered a complex inheritance disorder. A number of genes are involved in combination in the etiology of the disorder. Evidence implicates the altered dopaminergic trans- mission in schizophrenia. In the present study, in order to identify susceptibility genes for schizophrenia in dopaminergic metabolism, we analyzed 59 single nucleotide polymorphisms (SNPs) in 24 genes of the dopaminergic pathway among 82 unrelated patients with schizophre- nia and 108 matched normal controls. Considering that traditional single-locus association stud- ies ignore the multigenic nature of complex diseases and do not take into account possible in- teractions between susceptibility genes, we proposed a multi-locus analysis method, using the posterior probability of morbidity as a measure of absolute disease risk for a multi-locus genotype combination, and developed an algorithm based on perturbation and average to detect the sus- ceptibility multi-locus genotype combinations, as well as to repress noise and avoid false positive results at our best. A three-locus SNP genotype combination involved in the interactions of COMT and ALDH3B1 genes was detected to be significantly susceptible to schizophrenia.

关键词： posterior probability of morbidity schizophrenia association study multi-locus genotype combination.

A post-GWAS replication study confirming the association of C14H8orf33 gene with milk production traits in dairy cattle

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Frontiers of Agricultural Science and Engineering 2014年第4期1卷 321-330页

作者： Shaohua YANG Chao QI Yan XIE Xiaogang CUI Yahui GAO Jianping JIANG Li JIANG Shengli ZHANG Qin ZHANG Dongxiao SUN Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture National Engineering Laboratory of Animal BreedingCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China

Genome-wide association studies with an Illumina Bovine50K chip have detected 105 SNPs associated with one or multiple milk production traits in the Chinese Holstein population.Of these,38 significant SNPs detected with high confidence by both L1-TDT and MMRA methods were selected to further mine potential key genes affecting milk yield and milk composition.By blasting the flanking sequences of these 38 SNPs with the bovine genome sequence combined with comparative genomics analysis,26 genes were found to contain or be near to such SNPs.Among them,the C14H8orf33 gene is merely 87 bp away from the significant SNP,Hapmap30383-BTC-005848.Hence,we report herein genotype-phenotype associations to further validate the genetic effects of the C14H8orf33 gene.By pooled DNA sequencing of 14 unrelated Holstein sires,a total of 18 with seven novel SNPs were identified.Among them,nine SNPs were in the 5′regulatory region,one in exon 6 and the other in the 3′UTR and 3′regulatory region.A total of nine of these identified SNPs were successfully genotyped and analyzed by mass spectrometry for association with five milk production traits in an independent resource population.The results showed that these SNPs were statistically significant for more than two traits[Passociation of C14H8orf33 variants with milk yield and milk composition traits and may be applied in Chinese Holstein breeding programs.

关键词： GWAS functional annotation Chinese Holstein milk production traits C14H8orf33 gene single nucleotide polymorphisms association study

Candidate genes for mastitis resistance in dairy cattle:a data integration approach

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Journal of Animal Science and Biotechnology 2023年第3期14卷 966-979页

作者： Zala Brajnik Jernej Ogorevc Biotechnical Faculty Department of Animal ScienceUniversity of LjubljanaGroblje 3Domzale SI‑1230Slovenia

Background Inflammation of the mammary tissue(mastitis)is one of the most detrimental health conditions in dairy ruminants and is considered the most economically important infectious disease of the dairy sector.Improving mastitis resistance is becoming an important goal in dairy ruminant breeding programmes.However,mastitis resistance is a complex trait and identification of mastitis-associated alleles in livestock is difficult.Currently,the only applicable approach to identify candidate loci for complex traits in large farm animals is to combine different information that supports the functionality of the identified genomic regions with respect to a complex trait.Methods To identify the most promising candidate loci for mastitis resistance we integrated heterogeneous data from multiple sources and compiled the information into a comprehensive database of mastitis-associated candidate loci.Mastitis-associated candidate genes reported in association,expression,and mouse model studies were collected by searching the relevant literature and databases.The collected data were integrated into a single database,screened for overlaps,and used for gene set enrichment analysis.Results The database contains candidate genes from association and expression studies and relevant transgenic mouse models.The 2448 collected candidate loci are evenly distributed across bovine chromosomes.Data integration and analysis revealed overlaps between different studies and/or with mastitis-associated QTL,revealing promising candidate genes for mastitis resistance.Conclusion Mastitis resistance is a complex trait influenced by numerous alleles.Based on the number of independent studies,we were able to prioritise candidate genes and propose a list of the 22 most promising.To our knowledge this is the most comprehensive database of mastitis associated candidate genes and could be helpful in selecting genes for functional validation studies.

关键词： association study Candidate genes Epigenetics Mammary gland Mastitis Quantitative trait loci

association between diacylglycerol kinase kappa variants and hypospadias susceptibility in a Han Chinese population

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Asian Journal of Andrology 2018年第1期20卷 85-89页

作者： Hua Xie Xiao-Ling Lin Song Zhang Ling Yu Xiao-Xi Li Yi-Chen Huang Yi-Qing Lyu Hai-Tao Chen Jianfeng Xu Fang Chen Department of Urology Shanghai Children's Hospital Shanghai Jiao Tong University Shanghai 200062 China Fudan Institute of Urology Huashan Hospital Fudan University Shanghai 200040 China State Key Laboratory of Genetic Engineering School of Life Sciences Fudan University Shanghai 200433 China Center for Genomic Translational Medicine and Prevention School of Public Health Fudan University Shanghai 200433 China Program for Personalized Cancer Care NorthShore University HealthSystem Evanston IL 60201 USA

Previous genome-wide association studies have identified variants in the diacylglycerol kinase kappa （DGKtO gene associated with hypospadias in populations of European descent. However, no variants of DGKKwere confirmed to be associated with hypospadias in a recent Han Chinese study population, likely due to the limited number of single-nucleotide polymorphisms （SNPs） included in the analysis. In this study, we aimed to address the inconsistent results and evaluate the association between DGKK and hypospadias in the Han Chinese population through a more comprehensive analysis of DGKK variants. We conducted association analyses for 17 SNPs in or downstream of DGKKwith hypospadias among 322 cases （58 mild, 113 moderate, 128 severe, and 23 unknown） and 1008 controls. Five SNPs （rs2211122, rs4554617, rs7058226, rs7063116, and rs5915254） in DGKK were significantly associated with hypospadias （P 〈 0.05）, with odds ratios （ORs） of 1.64-1.76. When only mild and moderate cases were compared to controls, 10 SNPs in DGKKwere significant （P〈 0.05）, with ORs of 1.56-2.13. No significant SNP was observed when only severe cases were compared to controls. This study successfully implicated DGKK variants in hypospadias risk among a Han Chinese population, especially for mild/moderate cases. Severe forms of hyposDadias are likely due to other genetic factors.

关键词： association study diacylglycerol kinase kappa hypospadias polymorphisms