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Guixin Li, Mei Bai, Chenghao Guo, Linhao Zhu, Li Wang, Dongya Yuan, Tianbo Jin, Yongjun He
Schizophrenia (SCZ) is a highly heritable, chronic, severe psychiatric disorder associated with significant financial costs to families and societies. In this case-control study, we investigated the associations between seven SNPs in CHRNA3 gene and the risk of SCZ.A total of 1071 (384 cases and 687 controls) unrelated subjects were recruited for our association study. Seven candidate tagging SNPs in CHRNA3 gene (rs3743077, rs1317286, rs938682, rs12914385, rs2869546, rs3743075, rs8040868) selected in HapMap database were genotyped by Sequenom MassARRAY...
June 2018: Medicine (Baltimore)
Seung-Been Lee, Marsha M Wheeler, Karynne Patterson, Sean McGee, Rachel Dalton, Erica L Woodahl, Andrea Gaedigk, Kenneth E Thummel, Deborah A Nickerson
PURPOSE: Genotyping CYP2D6 is important for precision drug therapy because the enzyme it encodes metabolizes approximately 25% of drugs, and its activity varies considerably among individuals. Genotype analysis of CYP2D6 is challenging due to its highly polymorphic nature. Over 100 haplotypes (star alleles) have been defined for CYP2D6, some involving a gene conversion with its nearby nonfunctional but highly homologous paralog CYP2D7. We present Stargazer, a new bioinformatics tool that uses next-generation sequencing (NGS) data to call star alleles for CYP2D6 ( https://stargazer...
June 6, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Li Yu, Bo Yin, Kaiying Qu, Jingjing Li, Qiao Jin, Ling Liu, Chunlan Liu, Yuxing Zhu, Qi Wang, Xiaowei Peng, Jianda Zhou, Peiguo Cao, Ke Cao
In the present study, hereditary non-polyposis colorectal cancer (HNPCC) susceptibility genes were screened for using whole exome sequencing in 3 HNPCC patients from 1 family and using single nucleotide polymorphism (SNP) genotyping assays in 96 other colorectal cancer and control samples. Peripheral blood was obtained from 3 HNPCC patients from 1 family; the proband and the proband's brother and cousin. High-throughput sequencing was performed using whole exome capture technology. Sequences were aligned against the HAPMAP, dbSNP130 and 1,000 Genome Project databases...
June 2018: Oncology Letters
Feifei Pu, Fengxia Chen, Zhicai Zhang, Jing Feng, Ping Xia
Aim: Variants of TIM-3/HAVCR2 3'UTR miRNA binding sites are significantly associated with cancer; however, roles in post-transcriptional regulation have not been elucidated. Methods: The regulatory and coding region single nucleotide polymorphisms (SNPs) of TIM-3/HAVCR2 were identified using an online database. Single nucleotide polymorphism Function Prediction was used to predict potential functional relevance of miRNA binding sites. Results: The analysis indicated rs9313439, rs4704846, rs3087616 and rs1036199 affect possible miRNA binding sites in TIM-3/HAVCR2 3'UTR...
June 2018: Future Science OA
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
Sina Rüeger, Aaron McDaid, Zoltán Kutalik
As most of the heritability of complex traits is attributed to common and low frequency genetic variants, imputing them by combining genotyping chips and large sequenced reference panels is the most cost-effective approach to discover the genetic basis of these traits. Association summary statistics from genome-wide meta-analyses are available for hundreds of traits. Updating these to ever-increasing reference panels is very cumbersome as it requires reimputation of the genetic data, rerunning the association scan, and meta-analysing the results...
May 21, 2018: PLoS Genetics
Xiaowei Ma, Jia Huang, Difei Lu, Nan Gu, Ran Lu, Jianwei Zhang, Hong Zhang, Jianping Li, Junqing Zhang, Xiaohui Guo
Background: Glucose-dependent insulinotropic polypeptide (GIP) is closely related to diabetes and obesity, both of which are confirmed to increase the risk of coronary artery disease (CAD). Our study aimed to investigate whether the polymorphisms in GIP genes could affect the risk of cardiovascular disease in type 2 diabetic patients in the Chinese Han population. Methods: We selected and genotyped two haplotype-tagging single nucleotide polymorphisms (tag-SNPs) (rs2291725 C>T, rs8078510 G>A) of GIP gene based on CHB data in HapMap Phase II database ( r 2 < 0...
2018: Journal of Diabetes Research
Xiu-Xiu Sun, Su-Su Li, Man Zhang, Qiao-Mei Xie, Jian-Hua Xu, Sheng-Xiu Liu, Yuan-Yuan Gu, Fa-Ming Pan, Jin-Hui Tao, Sheng-Qian Xu, Shuang Liu, Jing Cai, De-Guang Wang, Long Qian, Chun-Huai Wang, Li Lian, Hui Xiao, Pei-Ling Chen, Chun-Mei Liang, You-Bing Fang, Qiang Zhou, Hai-Liang Huang, Hong Su, Hai-Feng Pan, Dong-Qing Ye, Yan-Feng Zou
Objective: The aim of this study was to investigate the associations between HSP90B1 gene polymorphisms and the efficacy of glucocorticoids (GCs) and the improvement of health-related quality of life (HRQoL) in Anhui patients with systemic lupus erythematosus (SLE). Method: A total of 305 patients with SLE were recruited to the study. These patients were treated with GCs for 12 weeks and classified into two groups (sensitivity and insensitivity) according to the response to GCs measured by the scores on SLE disease activity index (SLEDAI)...
2018: American Journal of Clinical and Experimental Immunology
Lianping Xu, Jiao Li, Danyang Tian, Lu Chen, Lu Tang, Dongsheng Fan
Single-nucleotide polymorphisms (SNPs) in the Nogo-A receptor gene ( RTN4R ) have been associated with increased risk for sporadic amyotrophic lateral sclerosis (SALS) in the French population. In the present study, we investigated the associations between RTN4R tag SNPs and SALS in a large Chinese population. Four tag SNPs (rs854971, rs887765, rs696880 and rs1567871) in the RTN4R gene with an r 2 threshold of 0.8 and a minor allele frequency (MAF) greater than 0.2% were selected based on Chinese population data from HapMap...
2018: Frontiers in Aging Neuroscience
Jing Li, Chenghao Guo, Mengdan Yan, Fanglin Niu, Peng Chen, Bin Li, Tianbo Jin
Pharmacogenomics, the study of the role of genetics in drug response, has recently become a focal point of research. Previous studies showed that genes associated with drug detoxification vary among different populations. However, pharmacogenomic information of the Zhuang ethnic group is scarce. The aim of the present study was to screen members of the Zhuang ethnicity in southwestern China for genotype frequencies of very important pharmacogenomic (VIP) variants and to determine the differences between the Zhuang ethnicity and other human populations...
April 2018: Medicine (Baltimore)
Shuo Li, Xialiang Dou, Ruiqi Gao, Xinzhou Ge, Minping Qian, Lin Wan
Copy number variations (CNVs) are gain and loss of DNA sequence of a genome. High throughput platforms such as microarrays and next generation sequencing technologies (NGS) have been applied for genome wide copy number losses. Although progress has been made in both approaches, the accuracy and consistency of CNV calling from the two platforms remain in dispute. In this study, we perform a deep analysis on copy number losses on 254 human DNA samples, which have both SNP microarray data and NGS data publicly available from Hapmap Project and 1000 Genomes Project respectively...
2018: PloS One
Jing Guo, Hao Chen, Peng Yang, Yew Ti Lee, Min Wu, Teresa M Przytycka, Chee Keong Kwoh, Jie Zheng
BACKGROUND: Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulation could lead to serious human diseases such as birth defects. Although the regulatory mechanism of recombination events is still unclear, DNA sequence polymorphisms have been found to play crucial roles in the regulation of recombination hotspots...
April 20, 2018: BMC Medical Genomics
Khalid Al-Rubeaan, Mohthash Musambil, Salma Majid Wakil, Haya Al-Saud, Amr T M Saeb, Sara Al-Qasim, Dhekra Al-Naqeb
In the case of diabetes and other complex diseases, the challenge has always been to find genetic markers that explain the excess risk associated with development of the disease. In the last 12 years, advances in genotyping technology provided substantial development in the discovery of loci contributing to Type 2 diabetes (T2D) susceptibility. Therefore, the aim of this study is to custom design, for the first time in Arab world, an "Arab Diabetes Gene Centric Array" (ADGCA) that assays 643, 745 SNP markers including 50,617 diabetes associated SNPs...
July 15, 2018: Gene
Nan Gu, Xiaowei Ma, Jianwei Zhang, Mengmeng Jin, Nan Feng, Ruifen Deng, Ge Bai, Hong Zhang, Xiaohui Guo
Aims: Protein kinase-like endoplasmic reticulum kinase (PERK)/eukaryotic translation initiation factor 2 alpha ( eIF2α ) pathway mutations lead to failure of β -cell function. The aim of this article was to assess the association between eIF2α and the risk of glucose metabolism abnormalities. Methods: Two eIF2α SNPs (rs9840992 T>C and rs13072593 A>G) were selected based on CHB data from HapMap, and 1466 unrelated nondiabetes individuals were genotyped...
2018: International Journal of Endocrinology
Ruchira Menka Jha, Theresa A Koleck, Ava M Puccio, David O Okonkwo, Seo-Young Park, Benjamin E Zusman, Robert S B Clark, Lori A Shutter, Jessica S Wallisch, Philip E Empey, Patrick M Kochanek, Yvette P Conley
OBJECTIVE: ABCC8 encodes sulfonylurea receptor 1, a key regulatory protein of cerebral oedema in many neurological disorders including traumatic brain injury (TBI). Sulfonylurea-receptor-1 inhibition has been promising in ameliorating cerebral oedema in clinical trials. We evaluated whether ABCC8 tag single-nucleotide polymorphisms predicted oedema and outcome in TBI. METHODS: DNA was extracted from 485 prospectively enrolled patients with severe TBI. 410 were analysed after quality control...
April 19, 2018: Journal of Neurology, Neurosurgery, and Psychiatry
Erwen Huang, Changhui Liu, Jingjing Zheng, Xiaolong Han, Weian Du, Yuanjian Huang, Chengshi Li, Xiaoguang Wang, Dayue Tong, Xueling Ou, Hongyu Sun, Zhaoshu Zeng, Chao Liu
Differences among SNP panels for individual identification in SNP-selecting and populations led to few common SNPs, compromising their universal applicability. To screen all universal SNPs, we performed a genome-wide SNP mining in multiple populations based on HapMap and 1000Genomes databases. SNPs with high minor allele frequencies (MAF) in 37 populations were selected. With MAF from ≥0.35 to ≥0.43, the number of selected SNPs decreased from 2769 to 0. A total of 117 SNPs with MAF ≥0.39 have no linkage disequilibrium with each other in every population...
April 3, 2018: Scientific Reports
Nurgul Sikhayeva, Yerkebulan Talzhanov, Aisha Iskakova, Jarkyn Dzharmukhanov, Raushan Nugmanova, Elena Zholdybaeva, Erlan Ramanculov
Background: Ethnic differences exist in the frequencies of genetic variations that contribute to the risk of common disease. This study aimed to analyse the distribution of several genes, previously associated with susceptibility to type 2 diabetes and obesity-related phenotypes, in a Kazakh population. Methods: A total of 966 individuals belonging to the Kazakh ethnicity were recruited from an outpatient clinic. We genotyped 41 common single nucleotide polymorphisms (SNPs) previously associated with type 2 diabetes in other ethnic groups and 31 of these were in Hardy-Weinberg equilibrium...
2018: Clinical Interventions in Aging
Seyed Amir Malekpour, Hamid Pezeshk, Mehdi Sadeghi
Currently a few tools are capable of detecting genome-wide Copy Number Variations (CNVs) based on sequencing of multiple samples. Although aberrations in mate pair insertion sizes provide additional hints for the CNV detection based on multiple samples, the majority of the current tools rely only on the depth of coverage. Here, we propose a new algorithm (MSeq-CNV) which allows detecting common CNVs across multiple samples. MSeq-CNV applies a mixture density for modeling aberrations in depth of coverage and abnormalities in the mate pair insertion sizes...
March 5, 2018: Scientific Reports
Worachart Lert-Itthiporn, Bhoom Suktitipat, Harald Grove, Anavaj Sakuntabhai, Prida Malasit, Nattaya Tangthawornchaikul, Fumihiko Matsuda, Prapat Suriyaphol
BACKGROUND: Imputation involves the inference of untyped single nucleotide polymorphisms (SNPs) in genome-wide association studies. The haplotypic reference of choice for imputation in Southeast Asian populations is unclear. Moreover, the influence of SNP annotation on imputation results has not been examined. METHODS: This study was divided into two parts. In the first part, we applied imputation to genotyped SNPs from Southeast Asian populations from the Pan-Asian SNP database...
February 13, 2018: BMC Medical Genetics
Kristin McDonald Gibson, Addie Nesbitt, Kajia Cao, Zhenming Yu, Elizabeth Denenberg, Elizabeth DeChene, Qiaoning Guan, Elizabeth Bhoj, Xiangdong Zhou, Bo Zhang, Chao Wu, Holly Dubbs, Alisha Wilkens, Livija Medne, Emma Bedoukian, Peter S White, Jeffrey Pennington, Minjie Lou, Laura Conlin, Dimitri Monos, Mahdi Sarmady, Eric Marsh, Elaine Zackai, Nancy Spinner, Ian Krantz, Matt Deardorff, Avni Santani
PurposeThe objective of this study was to assess the ability of our laboratory's exome-sequencing test to detect known and novel sequence variants and identify the critical factors influencing the interpretation of a clinical exome test.MethodsWe developed a two-tiered validation strategy: (i) a method-based approach that assessed the ability of our exome test to detect known variants using a reference HapMap sample, and (ii) an interpretation-based approach that assessed our relative ability to identify and interpret disease-causing variants, by analyzing and comparing the results of 19 randomly selected patients previously tested by external laboratories...
March 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
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