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Quang Tran, Shanshan Gao, Vinhthuy Phan
Efforts such as International HapMap Project and 1000 Genomes Project resulted in a catalog of millions of single nucleotides and insertion/deletion (INDEL) variants of the human population. Viewed as a reference of existing variants, this resource commonly serves as a gold standard for studying and developing methods to detect genetic variants. Our analysis revealed that this reference contained thousands of INDELs that were constructed in a biased manner. This bias occurred at the level of aligning short reads to reference genomes to detect variants...
October 6, 2016: BMC Bioinformatics
Herlander Marques, José Freitas, Rui Medeiros, Adhemar Longatto-Filho
Genetic variability in humans can explain many differences in disease risk factors. Polymorphism-related studies focus mainly on the single nucleotide polymorphisms (SNPs) of coding regions of the genes. SNPs on DNA binding motifs of the promoter region have been less explored. On a recent study of SNPs in patients with non-Hodgkin lymphomas we faced the problem of SNP selection from promoter regions and developed a practical methodology for clinical studies. The process consists in identifying SNPs in the coding and promoter regions of the antigen-processing system using the 'dbSNP' database...
2016: International Journal of Molecular Epidemiology and Genetics
Eun Yong Kang, Lisa Martin, Serghei Mangul, Warin Isvilanonda, Jennifer Zou, Eyal Ben-David, Buhm Han, Aldons J Lusis, Sagiv Shifman, Eleazar Eskin
The study of the genetics of gene expression is of considerable importance to understanding the nature of common, complex diseases. The most widely applied approach to identifying relationships between genetic variation and gene expression is the expression quantitative trait loci (eQTL) approach. Here we increase the computational power of eQTL with an alternative and complementary approach based on analyzing allele specific expression (ASE). We design a novel analytical method to identify cis-acting regulatory variants based on genome sequencing and measurements of ASE from RNA-seq data...
October 7, 2016: Genetics
Linna Zhao, Di Liu, Jing Xu, Zhaoyang Wang, Yang Chen, Changgui Lei, Ying Li, Guiyou Liu, Yongshuai Jiang
At present, understanding of DNA methylation at the population level is still limited. Here, we first extended the classical framework of population genetics, such as single nucleotide polymorphism allele frequency, linkage disequilibrium (LD), LD block and haplotype, to epigenetics. Then, as an example, we compared the DNA methylation disequilibrium (MD) maps between HapMap CEU (Caucasian residents of European ancestry from Utah) population and YRI (Yoruba people from Ibadan) population (lymphoblastoid cell lines)...
October 19, 2016: Briefings in Bioinformatics
G Y Ji, Y Wang, S Q Wu, Q Q Liu, J C Wu, M M Zhang, A J Sandford, J Q He
Anti-tuberculosis drug-induced hepatotoxicity (ATDH) is a serious adverse reaction to anti-tuberculosis (TB) treatment. Thioredoxin reductase 1 (TXNRD1), encoded by the TXNRD1 gene, is an important enzyme involved in oxidant challenge. TXNRD1 plays a key role in regulating cell growth and transformation, and protects cells against oxidative damage. We investigated the association between TXNRD1 polymorphisms and ATDH susceptibility. In this prospective study, 280 newly diagnosed TB patients were followed-up for 3 months after beginning anti-TB therapy...
September 2, 2016: Genetics and Molecular Research: GMR
William Leonardi, Leeor Zilbermintz, Luisa W Cheng, Josue Zozaya, Sharon H Tran, Jeffrey H Elliott, Kseniya Polukhina, Robert Manasherob, Amy Li, Xiaoli Chi, Dima Gharaibeh, Tara Kenny, Rouzbeh Zamani, Veronica Soloveva, Andrew D Haddow, Farooq Nasar, Sina Bavari, Michael C Bassik, Stanley N Cohen, Anastasia Levitin, Mikhail Martchenko
Diverse pathogenic agents often utilize overlapping host networks, and hub proteins within these networks represent attractive targets for broad-spectrum drugs. Using bacterial toxins, we describe a new approach for discovering broad-spectrum therapies capable of inhibiting host proteins that mediate multiple pathogenic pathways. This approach can be widely used, as it combines genetic-based target identification with cell survival-based and protein function-based multiplex drug screens, and concurrently discovers therapeutic compounds and their protein targets...
September 30, 2016: Scientific Reports
Zhe Wei, Jin-Wei He, Wen-Zhen Fu, Zhen-Lin Zhang
CONTEXT: Adefovir dipivoxil (ADV) was an important cause of adult-onset hypophosphatemic osteomalacia. However, its clinical characteristics and mechanisms have not been well defined. OBJECTIVE: The objective of the study was to summarize the clinical characteristics of ADV-induced osteomalacia and to explore the association between ADV-associated tubulopathy and polymorphisms in genes encoding drug transporters. DESIGN, SETTING, PATIENTS, AND MAIN OUTCOME MEASURE: Seventy-six affected patients were clinically studied...
September 21, 2016: Bone
David Porubsky, Ashley D Sanders, Niek van Wietmarschen, Ester Falconer, Mark Hills, Diana C J Spierings, Marianna R Bevova, Victor Guryev, Peter Michael Lansdorp
Haplotypes are fundamental to fully characterize the diploid genome of an individual, yet methods to directly chart the unique genetic makeup of each parental chromosome are lacking. Here we introduce single cell DNA template strand sequencing (Strand-seq) as a novel approach to phasing diploid genomes along the entire length of all chromosomes. We demonstrate this by building a complete haplotype for HapMap individual (NA12878) at high accuracy (concordance 99.3%), without using generational information or statistical inference...
September 19, 2016: Genome Research
Amanda M Hulse-Kemp, Hamid Ashrafi, Joerg Plieske, Jana Lemm, Kevin Stoffel, Theresa Hill, Hartmut Luerssen, Charit L Pethiyagoda, Cindy T Lawley, Martin W Ganal, Allen Van Deynze
The Capsicum genus (Pepper) is a part of the Solanacae family. It has been important in many cultures worldwide for its key nutritional components and uses as spices, medicines, ornamentals and vegetables. Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land. These conditions require increased efficiency in pepper breeding to deal with these imminent challenges. Through resequencing of inbred lines we have completed a valuable haplotype map (HapMap) for the pepper genome based on single-nucleotide polymorphisms (SNP)...
2016: Horticulture Research
Christian Loret de Mola, Fernando Pires Hartwig, Helen Gonçalves, Luciana de Avila Quevedo, Ricardo Pinheiro, Denise Petrucci Gigante, Janaína Vieira Dos Santos Motta, Alexandre C Pereira, Fernando C Barros, Bernardo Lessa Horta
BACKGROUND: Evidence suggests that there is an association between ethnicity/skin color and depression; however, many contextual and individual variables, like sense of discrimination and socioeconomic position (SEP), might influence the direction of this association. We assessed the association between African ancestry and major depression among young adults that have been followed-up since birth in a Southern Brazilian city, and the mediating effect of SEP and discrimination. METHODS: In 1982, all hospital deliveries in Pelotas (Southern Brazil) were identified; liveborns were examined and their mothers interviewed (n = 5914)...
2016: BMC Psychiatry
Kaname Kojima, Yosuke Kawai, Naoki Nariai, Takahiro Mimori, Takanori Hasegawa, Masao Nagasaki
BACKGROUND: Two types of approaches are mainly considered for the repeat number estimation in short tandem repeat (STR) regions from high-throughput sequencing data: approaches directly counting repeat patterns included in sequence reads spanning the region and approaches based on detecting the difference between the insert size inferred from aligned paired-end reads and the actual insert size. Although the accuracy of repeat numbers estimated with the former approaches is high, the size of target STR regions is limited to the length of sequence reads...
2016: BMC Genomics
Xu Zhang, Binal N Shah, Wei Zhang, Santosh L Saraf, Galina Miasnikova, Adelina Sergueeva, Tatiana Ammosova, Xiaomei Niu, Mehdi Nouraie, Sergei Nekhai, Oswaldo Castro, Mark T Gladwin, Josef T Prchal, Joe G N Garcia, Roberto F Machado, Victor R Gordeuk
Blood erythropoietin (EPO) increases primarily to hypoxia. In sickle cell anemia (homozygous HBB(E6V); HbSS), plasma EPO is elevated due to hemolytic anemia-related hypoxia. Hydroxyurea treatment reduces hemolysis and anemia by increasing fetal hemoglobin, which leads to lower hypoxic transcriptional responses in blood mononuclear cells but paradoxically further increases EPO. To investigate this apparent hypoxia-independent EPO regulation, we assessed two sickle cell disease (SCD) cohorts for genetic associations with plasma EPO, by prioritizing 237,079 quantitative trait loci for expression level and/or transcript isoform variations of 12,727 genes derived from SCD blood mononuclear cells...
August 30, 2016: Human Molecular Genetics
Rozi Zohra, M S Song, Nizam Iliham, Mamatyusupu Dolikun
OBJECTIVE: To investigate the characterizations of genetic recombination hotspots and linkage disequilibrium (LD) patterns in peroxisome proliferative activated receptor gamma (PPARG) gene in Kirgiz and Uyghur ethnic groups. METHODS: Blood samples were collected from 100 Kirgiz (50 healthy controls and 50 patients with type 2 diabetes mellitus) residents in Halajun County, Artux City, Kizilsu Kirgiz Autonomous Prefecture, Xinjiang in August 2013, and 50 healthy Uyghur residents in Hotan Prefecture of Xinjiang Uygur Autonomous Region in May 2012...
August 16, 2016: Zhonghua Yi Xue za Zhi [Chinese medical journal]
Peter Humburg, Narelle Maugeri, Wanseon Lee, Bert Mohr, Julian C Knight
BACKGROUND: The heat shock transcriptional response is essential to effective cellular function under stress. This is a highly heritable trait but the nature and extent of inter-individual variation in heat shock response remains unresolved. METHODS: We determined global transcription profiles of the heat shock response for a panel of lymphoblastoid cell lines established from 60 founder individuals in the Yoruba HapMap population. We explore the observed differentially expressed gene sets following heat shock, establishing functional annotations, underlying networks and nodal genes involving heat shock factor 1 recruitment...
2016: Genome Medicine
Shicai Wang, Mihaela A Mares, Yi-Ke Guo
MOTIVATION: High-throughput molecular profiling has greatly improved patient stratification and mechanistic understanding of diseases. With the increasing amount of data used in translational medicine studies in recent years, there is a need to improve the performance of data warehouses in terms of data retrieval and statistical processing. Both relational and Key Value models have been used for managing molecular profiling data. Key Value models such as SeqWare have been shown to be particularly advantageous in terms of query processing speed for large datasets...
August 13, 2016: Bioinformatics
Guy S Jacobs, Tim J Sluckin, Toomas Kivisild
During a selective sweep, characteristic patterns of linkage disequilibrium can arise in the genomic region surrounding a selected locus. These have been used to infer past selective sweeps. However, the recombination rate is known to vary substantially along the genome for many species. We here investigate the effectiveness of current (Kelly's [Formula: see text] and [Formula: see text]) and novel statistics at inferring hard selective sweeps based on linkage disequilibrium distortions under different conditions, including a human-realistic demographic model and recombination rate variation...
August 2016: Genetics
Renata Szalai, Kinga Hadzsiev, Bela Melegh
The cytochrome P450 drug metabolizing enzymes are highly polymorphic and show inter-individual differences in variability in drug response, which varies widely also with ethnicity. This study aimed to summarize the available data on genetic polymorphisms associated with cytochrome enzymes conducted in Roma populations. Our goal was to compare the frequency of the variant alleles, genotypes and predicted phenotypes with corresponding rates from other populations. We carried out a systematic review including the papers published on the pharmacogenetically relevant variants of cytochrome P450 genes related to Roma population...
August 8, 2016: Current Medicinal Chemistry
Y L Chen, Y M Jia, Y T Xie, Y Li, W G Fang, X X Tian
OBJECTIVE: To study the effects of single nucleotide polymorphisms (SNP) in Plasminogen activator inhibitor 1(PAI-1) on breast cancer susceptibility and patients' prognosis among a Chinese Han women population. METHODS: Six tag SNP (tSNP) of PAI-1 were selected according to HapMap CHB population, and TaqMan realtime PCR method was used to genotype the 6 tSNP in 1 160 breast cancer cases and 1 318 age-matched controls among Chinese Han women. Haplotypes and diplotypes were inferred according to genotyping data and linkage disequilibrium...
August 8, 2016: Zhonghua Bing Li Xue za Zhi Chinese Journal of Pathology
Dan Ye, Yang Fei, Qi Ling, Weiwei Xu, Zhe Zhang, Jing Shu, Chengjiang Li, Fengqin Dong
This study aimed to investigate the possible association between diabetes susceptibility gene transcription factor 7-like 2 (TCF7L2) and gestational diabetes mellitus (GDM) in a Chinese Han population. A total of 556 GDM patients and 500 Non-GDM were included. Eighteen single nucleotide polymorphisms (SNPs) were evaluated. Fifteen tag SNPs were selected from HapMap CHB database with a minor allele frequency of >0.2 and r(2) of >0.8. Three additional SNPs were also chosen because these SNPs are associated with type 2 diabetes in East Asians...
2016: Scientific Reports
Jin Zining, Xu Lu, He Caiyun, Yuan Yuan
mTOR regulates several cellular processes that are critical for tumorigenesis. However, previous studies on the association of mTOR polymorphisms with predisposition to different cancer types are somewhat contradictory. Therefore, we performed a systematic review and updated meta-analysis of the available evidence regarding the relationship between mTOR single nucleotide polymorphisms (SNPs) and cancer risk. Up to November 2015, 23 original publications were identified covering 20 mTOR SNPs, of which seven SNPs (rs2536, rs2295080, rs1883965, rs1034528, rs17036508, rs3806317 and rs1064261) were included in the final meta-analysis...
July 24, 2016: Oncotarget
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