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Si Chen, Xiaoting Wen, Jing Li, Yuan Li, Liubing Li, Xinping Tian, Hui Yuan, Fengchun Zhang, Yongzhe Li
Takayasu arteritis (TA) is a chronic large-vessel vasculitis of unclear pathogenesis. A recent genome-wide association study (GWAS) has revealed that the FCGR2A/FCGR3A, EEFSEC, RPS9/LILRB3, RIPPLY2 and MLX genes confer susceptibility to TA. We investigated the linkage between presumptive TA-related genes (FCGR2A/FCGR3A, EEFSEC, RPS9/LILRB3, RIPPLY2 and MLX) and TA in the Han Chinese population. We performed a large case-control multi-center study of 412 Han Chinese TA patients and 597 ethnically matched healthy controls...
October 18, 2016: Oncotarget
Malik Nassan, Qingqin Li, Paul E Croarkin, Wenan Chen, Colin L Colby, Marin Veldic, Susan L McElroy, Gregory D Jenkins, Euijung Ryu, Julie M Cunningham, Marion Leboyer, Mark A Frye, Joanna M Biernacka
BACKGROUND: Although multiple genes have been implicated in bipolar disorder (BD), they explain only a small proportion of its heritability. Identifying additional BD risk variants may be impaired by phenotypic heterogeneity, which is usually not taken into account in genome-wide association studies (GWAS). BD with early age at onset is a more homogeneous familial form of the disorder associated with greater symptom severity. METHODS: We conducted a GWAS of early-onset BD (onset of mania/hypomania ≤19 years old) in a discovery sample of 419 cases and 1034 controls and a replication sample of 181 cases and 777 controls...
September 30, 2016: Journal of Affective Disorders
Pradipta Ranjan Rauta, Sarbani Ashe, Debasis Nayak, Bismita Nayak
Virulence-related outer membrane proteins (Omps) are expressed in bacteria (Gram-negative) such as V. cholerae and are vital to bacterial invasion in to eukaryotic cell and survival within macrophages that could be best candidate for development of vaccine against V. cholerae. Applying in silico approaches, the 3-D model of the Omp was developed using Swiss model server and validated byProSA and Procheck web server. The continuous stretch of amino acid sequences 26mer: RTRSNSGLLTWGDKQTITLEYGDPAL and 31mer: FFAGGDNNLRGYGYKSISPQDASGALTGAKY having B-cell binding sites were selected from sequence alignment after B cell epitopes prediction by BCPred and AAP prediction modules of BCPreds...
October 12, 2016: Computational Biology and Chemistry
Mala Ganesan, Sheikh Nizamuddin, Shiva Krishna Katkam, Konda Kumaraswami, Uday Kumar Hosad, Limmy Loret Lobo, Vijay Kumar Kutala, Kumarasamy Thangaraj
BACKGROUND: Coronary artery disease (CAD) is one of the leading causes of mortality worldwide. It is a multi-factorial disease and several studies have demonstrated that the genetic factors play a major role in CAD. Although variations in cholesteryl ester transfer protein (CETP) gene are reported to be associated with CAD, this gene has not been studied in South Indian populations. Hence we evaluated the CETP gene variations in CAD patients of South Indian origin. METHODS: We sequenced all the exons, exon-intron boundaries and UTRs of CETP in 323 CAD patients along with 300 ethnically and age matched controls...
2016: PloS One
P H Zaidi, K Seetharam, Girish Krishna, L Krishnamurthy, S Gajanan, Raman Babu, M Zerka, M T Vinayan, B S Vivek
An association mapping panel, named as CIMMYT Asia association mapping (CAAM) panel, involving 396 diverse tropical maize lines were phenotyped for various structural and functional traits of roots under drought and well-watered conditions. The experiment was conducted during Kharif (summer-rainy) season of 2012 and 2013 in root phenotyping facility at CIMMYT-Hyderabad, India. The CAAM panel was genotyped to generate 955, 690 SNPs through GBS v2.7 using Illumina Hi-seq 2000/2500 at Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA...
2016: PloS One
Nicole A Hawkins, Nicole J Zachwieja, Alison R Miller, Lyndsey L Anderson, Jennifer A Kearney
A substantial number of mutations have been identified in voltage-gated sodium channel genes that result in various forms of human epilepsy. SCN1A mutations result in a spectrum of severity ranging from mild febrile seizures to Dravet syndrome, an infant-onset epileptic encephalopathy. Dravet syndrome patients experience multiple seizures types that are often refractory to treatment, developmental delays, and elevated risk for SUDEP. The same sodium channel mutation can produce epilepsy phenotypes of varying clinical severity...
October 2016: PLoS Genetics
Kerry A Geiler-Samerotte, Yuan O Zhu, Benjamin E Goulet, David W Hall, Mark L Siegal
The protein-folding chaperone Hsp90 has been proposed to buffer the phenotypic effects of mutations. The potential for Hsp90 and other putative buffers to increase robustness to mutation has had major impact on disease models, quantitative genetics, and evolutionary theory. But Hsp90 sometimes contradicts expectations for a buffer by potentiating rapid phenotypic changes that would otherwise not occur. Here, we quantify Hsp90's ability to buffer or potentiate (i.e., diminish or enhance) the effects of genetic variation on single-cell morphological features in budding yeast...
October 2016: PLoS Biology
Meng-Bo Hu, Hua Xu, Ji-Meng Hu, Wen-Hui Zhu, Tian Yang, Qiang Ding
Leptin and adiponectin signaling was associated with development and progression of various cancers. The present study aimed to clarify the role of genetic variants in leptin, adiponectin and their receptors in prostate cancer. After comprehensive search and manuscript scanning, a total of 49 genetic variants were enrolled and examined for their relations to cancer risk and aggressiveness. In the meta-analysis, LEP rs7799039 (allele contrast: OR 1.133, 95%CI 1.024-1.254), ADIPOQ rs2241766 (allele contrast: OR 1...
October 19, 2016: Oncotarget
Bang-Shun He, Tao Xu, Yu-Qin Pan, Han-Jin Wang, William C Cho, Kang Lin, Hui-Ling Sun, Tian-Yi Gao, Shu-Kui Wang
Polymorphisms in nucleotide excision repair (NER) pathway genes are associated with the risk of breast cancer, but the relevance of these associations appeared to vary according to the ethnicity of the subjects. To systemically evaluate the potential associations between NER polymorphisms and breast cancer risk in a Chinese population, we carried out a case-control study on 450 breast cancer patients and 430 healthy controls. Sequenom MassARRAY was used for genotyping, and immunohistochemistry was performed to detect estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER-2) expression in tumor tissue...
October 19, 2016: Oncotarget
Josip Crnjac, Petar Ozretić, Siniša Merkaš, Martina Ratko, Mateja Lozančić, Marina Korolija, Maja Popović, Gordan Mršić
X chromosome STR typing has emerged recently as a powerful tool, complementary to autosomal STR typing, in solving complex forensic and missing person cases. Investigator® Argus X-12 is a commercial product that allows co-amplification of 12 X chromosomal markers belonging to four linkage groups (LGs). In this study, we analyzed by capillary electrophoresis blood samples from 100 females and 102 males from a population of northern Croatia. Statistical analysis included calculation of allele and haplotype frequencies, as well as forensic parameters...
October 20, 2016: Genetics and Molecular Biology
Cristina Rodríguez, Tomás Sobrino, Jesús Agulla, Verónica Bobo-Jiménez, María E Ramos-Araque, Juan J Duarte, José C Gómez-Sánchez, Juan P Bolaños, José Castillo, Ángeles Almeida
Intracerebral hemorrhage (ICH) is a devastating subtype of stroke that lacks effective therapy and reliable prognosis. Neovascularization following ICH is an essential compensatory response that mediates brain repair and modulates the clinical outcome of stroke patients. However, the mechanism that dictates this process is unknown. Bone marrow-derived endothelial progenitor cells (EPCs) promote endothelial repair and contribute to ischemia-induced neovascularization. The human Tp53 gene harbors a common single-nucleotide polymorphism (SNP) at codon 72, which yields an arginine-to-proline amino-acidic substitution (Arg72Pro) that modulates the apoptotic activity of the p53 protein...
October 21, 2016: Cell Death and Differentiation
Christina Mitropoulou, Vasilios Fragoulakis, Ljiljana B Rakicevic, Mirjana M Novkovic, Athanassios Vozikis, Dragan M Matic, Nebojsa M Antonijevic, Dragica P Radojkovic, Ron H van Schaik, George P Patrinos
INTRODUCTION: Clopidogrel, which is activated by the CYP2C19 enzyme, is among the drugs for which all major regulatory agencies recommend genetic testing to be performed to identify a patient's CYP2C19 genotype in order to determine the optimal antiplatelet therapeutic scheme. The CYP2C19*2 and CYP2C19*3 variants are loss-of-function alleles, leading to abolished CYP2C19 function and thus have the risk of thrombotic events for carriers of these alleles on standard dosages, while the CYP2C19*17 allele results in CYP2C19 hyperactivity...
October 21, 2016: Pharmacogenomics
Vinicius A Sortica, Juliana D Lindenau, Maristela G Cunha, Maria DO Ohnishi, Ana Maria R Ventura, Ândrea Kc Ribeiro-Dos-Santos, Sidney Eb Santos, Luciano Sp Guimarães, Mara H Hutz
BACKGROUND: Chloroquine/primaquine is the current therapy to eliminate Plasmodium vivax infection in the Amazon region. AIMS: This study investigates CYP1A2, CYP2C8, CYP2C9, CYP3A4 and CYP3A5 genetic polymorphisms influence on cloroquine/primaquine treatment. PATIENTS & METHODS: Generalized estimating equations analyses were performed to determine the genetic influence in parasitemia and/or gametocytemia clearance over treatment time in 164 patients...
October 21, 2016: Pharmacogenomics
Ambily Sivadas, Parul Sharma, Vinod Scaria
AIM: Pharmacogenetic landscapes of commonly used antiplatelet drugs, warfarin and clopidogrel have been studied in-depth in many countries. However, there is a paucity of data to understand their patterns in the Arab populations. MATERIALS & METHODS: We analyzed the whole exome sequencing datasets of 100 Qatar individuals available in public domain with this perspective. RESULTS: We characterized the allelic distribution of variants routinely tested for warfarin and clopidogrel...
October 21, 2016: Pharmacogenomics
Shin Yup Lee, Cheng Cheng Jin, Jin Eun Choi, Mi Jeong Hong, Deuk Kju Jung, Sook Kyung Do, Sun Ah Baek, Hyo Jung Kang, Hyo-Gyoung Kang, Sun Ha Choi, Won Kee Lee, Yangki Seok, Eung Bae Lee, Ji Yun Jeong, Kyung Min Shin, Sukki Cho, Seung Soo Yoo, Jaehee Lee, Seung Ick Cha, Chang Ho Kim, You Mie Lee, In-Kyu Lee, Sanghoon Jheon, Jae Yong Park
This study was conducted to investigate whether polymorphisms of genes involved in glycolysis are associated with the prognosis of patients with non-small cell lung cancer (NSCLC) after surgical resection. Forty-four single nucleotide polymorphisms (SNPs) of 17 genes in glycolytic pathway were investigated in a total of 782 patients with NSCLC who underwent curative surgical resection. The association of the SNPs with overall survival (OS) and disease free survival (DFS) were analyzed. Among the 44 SNPs investigated, four SNPs (ENO1 rs2274971A > G, PFKM rs11168417C > T, PFKP rs1132173C > T, PDK2 rs3785921G > A) were significantly associated with survival outcomes in multivariate analyses...
October 21, 2016: Scientific Reports
Takumi Takeuchi, Mami Hattori-Kato, Yumiko Okuno, Atsushi Kanatani, Masayoshi Zaitsu, Koji Mikami
Various conditions including distal renal tubular acidosis (dRTA) can induce stone formation in the kidney. dRTA is characterized by an impairment of urine acidification in the distal nephron. dRTA is caused by variations in genes functioning in intercalated cells including SLC4A1/AE1/Band3 transcribing two kinds of mRNAs encoding the Cl(-)/HCO3(-) exchanger in erythrocytes and that expressed in α-intercalated cells (kAE1). With the acid-loading test, 25% of urolithiasis patients were diagnosed with incomplete dRTA...
October 21, 2016: Scientific Reports
Rola F Turki, Mourad Assidi, Huda A Banni, Hanan A Zahed, Sajjad Karim, Hans-Juergen Schulten, Muhammad Abu-Elmagd, Abdulrahim A Rouzi, Osama Bajouh, Hassan S Jamal, Mohammed H Al-Qahtani, Adel M Abuzenadah
BACKGROUND: Recurrent pregnancy loss (RPL) or recurrent spontaneous abortion is an obstetric complication that affects couples at reproductive age. Previous reports documented a clear relationship between parents with chromosomal abnormalities and both recurrent miscarriages and infertility. However, limited data is available from the Arabian Peninsula which is known by higher rates of consanguineous marriages. The main goal of this study was to determine the prevalence of chromosomal abnormalities and thrombophilic polymorphisms, and to correlate them with RPL and consanguinity in Saudi Arabia...
October 10, 2016: BMC Medical Genetics
Sajjad Karim, Hend Fakhri NourEldin, Heba Abusamra, Nada Salem, Elham Alhathli, Joel Dudley, Max Sanderford, Laura B Scheinfeldt, Sudhir Kumar
BACKGROUND: Genome-wide association studies (GWAS) have become a mainstay of biological research concerned with discovering genetic variation linked to phenotypic traits and diseases. Both discrete and continuous traits can be analyzed in GWAS to discover associations between single nucleotide polymorphisms (SNPs) and traits of interest. Associations are typically determined by estimating the significance of the statistical relationship between genetic loci and the given trait. However, the prioritization of bona fide, reproducible genetic associations from GWAS results remains a central challenge in identifying genomic loci underlying common complex diseases...
October 17, 2016: BMC Genomics
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
Brendan D Crawford, Christopher E Gillies, Catherine C Robertson, Matthias Kretzler, Edgar Otto, Virginia Vega-Wagner, Matthew G Sampson
BACKGROUND: More than 30 genes can harbor rare exonic variants sufficient to cause nephrotic syndrome (NS), and the number of genes implicated in monogenic NS continues to grow. However, outside the first year of life, the majority of affected patients, particularly in ancestrally mixed populations, do not have a known monogenic form of NS. Even in those children classified with a monogenic form of NS, there is phenotypic heterogeneity. Thus, we have only discovered a fraction of the heritability of NS-the underlying genetic factors contributing to phenotypic variation...
October 20, 2016: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
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