Read by QxMD icon Read

Prediction snp

Christian Rellstab, Stefan Zoller, Lorenz Walthert, Isabelle Lesur, Andrea R Pluess, René Graf, Catherine Bodénès, Christoph Sperisen, Antoine Kremer, Felix Gugerli
Testing how populations are locally adapted and predicting their response to their future environment is of key importance in view of climate change. Landscape genomics is a powerful approach to investigate genes and environmental factors involved in local adaptation. In a pooled amplicon sequencing approach of 94 genes in 71 populations, we tested if >3'500 single nucleotide polymorphisms (SNPs) in the three most common oak species in Switzerland (Quercus petraea, Q. pubescens, Q. robur) show an association with abiotic factors related to local topography, historical climate, and soil characteristics...
October 19, 2016: Molecular Ecology
Priyanka Srivastava, Himani Pandey, Divya Agarwal, Kausik Mandal, Shubha R Phadke
We describe three consanguineous Indian families with a distinct form of spondyloepiphyseal dysplasia (SED Omani type). It is an autosomal recessive disorder due to mutation in CHST3 gene. CHST3 gene encodes the enzyme chondroitin 6-O-sulfotransferase-1 (C6ST-1) which mediates the sulfation of proteoglycans, (chondroitin sulfate), in the extracellular matrix of cartilage. CHST3 gene was sequenced in probands from three different families with SED. In two families missense mutations (c.904G>C predicting the substitution D302H) and c...
October 18, 2016: American Journal of Medical Genetics. Part A
Fen Wei, Jie Chen, Xinye Chen, Baolong Bao
Flatfish with left-right eye asymmetry are the most significant among vertebrates. However, the genetic basis for the control of this characteristic is still unclear. We propose that the gene(s) for eye asymmetry initially control minor differences in cell number in the tissues around the eyes during development. This minor difference is then amplified, causing eye migration during metamorphosis. Therefore, comparing the neurula transcriptomes between flatfish species with different eye-reversal mutants may provide very useful information to screen for genes involved in eye asymmetry...
October 14, 2016: Gene
Rong-Miao Zhou, Yan Li, Na Wang, Xi Huang, Shi-Ru Cao, Bao-En Shan
Programmed death-1 (PD-1) is an immunoinhibitory receptor belonging to the CD28 family. This study was designed to investigate the association of PD-1 rs36084323:A>G, rs2227981:C>T, rs2227982:C>T and rs10204525:A>G single nucleotide polymorphisms (SNPs) with the risk and prognosis of esophageal squamous cell carcinoma (ESCC) in a high-incidence population from Northern China. These four SNPs were genotyped by polymerase chain reaction ligase detection reaction (PCR-LDR) method in 584 ESCC patients and 585 healthy controls...
September 2016: Cancer Genetics
Liang Li, Jian-Wei Zhang, Gregory Jenkins, Fang Xie, Erin E Carlson, Brooke L Fridley, William R Bamlet, Gloria M Petersen, Robert R McWilliams, Liewei Wang
BACKGROUND: Pancreatic cancer is a rapidly fatal disease with gemcitabine remaining the first-line therapy. We performed a genotype-phenotype association study to identify biomarkers for predicting gemcitabine treatment outcome. MATERIALS AND METHODS: We selected the top 200 single nucleotide polymorphisms (SNPs) identified from our previous genome-wide association study to associate with overall survival using 400 patients treated with/or without gemcitabine, followed by imputation analysis for regions around the identified SNPs and a replication study using an additional 537 patients by the TaqMan genotyping assay...
October 4, 2016: Pharmacogenetics and Genomics
Wen Xu, Di Liu, Yang Yang, Xi Ding, Yifeng Sun, Baohong Zhang, Jinfu Xu, Bo Su
BACKGROUND: Cell cycle checkpoint kinase 2 (CHEK2) plays an essential role in the repair of DNA damage. Single nucleotide polymorphisms (SNPs) in DNA repair genes are thought to influence treatment effects and survival of cancer patients. This study aimed to investigate the relationship between polymorphisms in the CHEK2 gene and efficacy of platinum-based doublet chemotherapy in never-smoking Chinese female patients with advanced non-small-cell lung cancer (NSCLC). METHODS: Using DNA from blood samples of 272 Chinese advanced NSCLC non-smoking female patients treated with first-line platinum-based chemotherapy, we have analyzed the relationships between four SNPs in the CHEK2 gene and clinical outcomes...
September 2016: Journal of Thoracic Disease
Lixia Li, Yujie Luo, Biyun Chen, Kun Xu, Fugui Zhang, Hao Li, Qian Huang, Xin Xiao, Tianyao Zhang, Jihong Hu, Feng Li, Xiaoming Wu
Rapeseed (Brassica napus L.) is one of the most important oil crops in the world. However, the yield and quality of rapeseed were largely decreased by clubroot (Plasmodiophora brassicae Woronin). Therefore, it is of great importance for screening more resistant germplasms or genes and improving the resistance to P. brassicae in rapeseed breeding. In this study, a massive resistant identification for a natural global population was conducted in two environments with race/pathotype 4 of P. brassicae which was the most predominant in China, and a wide range of phenotypic variation was found in the population...
2016: Frontiers in Plant Science
Abdullah M Alhadheq, Jilani Purusottapatnam Shaik, Abdullah Alamri, Abdulrahman M Aljebreen, Othman Alharbi, Majid A Almadi, Faten Alhadeq, Nahla A Azzam, Abdelhabib Semlali, Mohammad Alanazi, Mohammad D Bazzi, Narasimha Reddy Parine
Background. DNA repair systems are essential for each cell to repair and maintain the genome integrity. Base excision repair pathway is one of the crucial pathways to maintain genome integrity and PARP-1 plays a key role in BER pathway. The purpose of this study is to evaluate the association between polymorphisms in PARP-1 3'untranslated region (3'UTR) SNP rs8679 and its expression in colorectal cancer. Methods. Genotyping and gene expression were performed using TaqMan assays. The effects of age, gender, and tumor location were evaluated in cases and controls regarding the genotyping results...
2016: Disease Markers
Gretchen A Hoff, Johannes C Fischer, Katharine Hsu, Sarah Cooley, Jeffrey S Miller, Tao Wang, Michael Haagenson, Stephen Spellman, Stephanie J Lee, Markus Uhrberg, Jeffrey M Venstrom, Michael R Verneris
Natural Killer (NK) cells are important in graft versus leukemia responses following hematopoietic cell transplantation (HCT). A variety of surface receptors dictate NK cell function, including killer immunoglobulin receptor (KIR) recognition of HLA-C. Previous single center studies show that HLA-C epitopes, designated C1 and C2, were associated with allogeneic-HCT outcomes; specifically recipients homozygous for the C1 epitope (C1/C1) experienced a survival benefit. Additionally, mismatching at HLA-C was beneficial in recipients possessing at least one C2 allele, while the opposite was true for homozygous C1 (C1/C1) recipients where HLA-C mismatching resulted in worse outcomes...
October 13, 2016: Biology of Blood and Marrow Transplantation
L C Emebiri, M-K Tan, M El-Bouhssini, O Wildman, A Jighly, W Tadesse, F C Ogbonnaya
This research provides the first report of a major locus controlling wheat resistance to Sunn pest. It developed and validated SNP markers that will be useful for marker-assisted selection. Sunn pest (Eurygaster integriceps Puton) is the most destructive insect pest of bread wheat and durum wheat in West and Central Asia and East Europe. Breeding for resistance at the vegetative stage of growth is vital in reducing the damage caused by overwintered adult populations that feed on shoot and leaves of seedlings, and in reducing the next generation of pest populations (nymphs and adults), which can cause damage to grain quality by feeding on spikes...
October 15, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Elfriede Bollschweiler, Arnulf H Hölscher, Till Herbold, Ralf Metzger, Hakan Alakus, Henner Schmidt, Uta Drebber, Ute Warnecke-Eberz
OBJECTIVE: The aim of this study was to evaluate the predictive value of a single or combination of biomarker(s) for histopathologic non-response to neoadjuvant chemoradiation in esophageal cancer. SUMMARY OF BACKGROUND DATA: Patients without response to neoadjuvant chemoradiation for esophageal cancer have no prognostic benefits, but experience time delays and risk side effects. METHODS: Inclusion criteria for this prospective diagnostic study were patients with cT3,Nx,M0, esophageal squamous cell or adenocarcinoma and planned neoadjuvant chemoradiation (5- fluorouracil, cisplatin, 40Gy) followed by 2-field transthoracic esophagectomy...
November 2016: Annals of Surgery
Ahmed A Al-Qahtani, Mashael R Al-Anazi, Fahad A Al-Zoghaibi, Ayman A Abdo, Faisal M Sanai, Waleed K Al-Hamoudi, Khalid A Alswat, Hamad I Al-Ashgar, Mohammed Q Khan, Ali Albenmousa, Hanif Khalak, Mohammed N Al-Ahdal
:  Background. The protein encoded by PARK2 gene is a component of the ubiquitin-proteasome system that mediates targeting of proteins for the degradation pathway. Genetic variations at PARK2 gene were linked to various diseases including leprosy, typhoid and cancer. The present study investigated the association of single nucleotide polymorphisms (SNPs) in the PARK2 gene with the development of hepatitis C virus (HCV) infection and its progression to severe liver diseases. MATERIAL AND METHODS: A total of 800 subjects, including 400 normal healthy subjects and 400 HCV-infected patients, were analyzed in this study...
November 2016: Annals of Hepatology
Maria Rossing, Anders Albrechtsen, Anne-Bine Skytte, Uffe B Jensen, Lilian B Ousager, Anne-Marie Gerdes, Finn C Nielsen, Thomas vO Hansen
Pathogenic germline mutations in the folliculin (FLCN) tumor suppressor gene predispose to Birt-Hogg-Dubé (BHD) syndrome, a rare disease characterized by the development of cutaneous hamartomas (fibrofolliculomas), multiple lung cysts, spontaneous pneumothoraces and renal cell cancer. In this study, we report the identification of 13 variants and three polymorphisms in the FLCN gene in 143 Danish patients or families with suspected BHD syndrome. Functional mini-gene splicing analysis revealed that two intronic variants (c...
October 13, 2016: Journal of Human Genetics
Fengxia Chen, Haozhong Zhang, Feifei Pu
OBJECT: Variants of microRNA (miRNA)-binding sites in RAD51 gene's 3' untranslated region (3'UTR) are significantly associated with cancer risk, but the roles of these genetic variants in post-transcriptional regulation have not been elucidated. METHODS: The SNPs of RAD51 were identified both in the regulatory region and in the coding region by means of the online database. The bioinformatic tool SNP Function Prediction was used to predict the potential functional relevance of the miRNA-binding sites...
2016: SpringerPlus
Xiaochen Sun, Rohan Fernando, Jack Dekkers
BACKGROUND: Traditional genomic prediction models using multiple regression on single nucleotide polymorphisms (SNPs) genotypes exploit associations between genotypes of quantitative trait loci (QTL) and SNPs, which can be created by historical linkage disequilibrium (LD), recent co-segregation (CS) and pedigree relationships. Results from field data analyses show that prediction accuracy is usually much higher for individuals that are close relatives of the training population than for distantly related individuals...
October 11, 2016: Genetics, Selection, Evolution: GSE
İbrahim Ömer Barlas, Orhan Sezgin, Collet Dandara, Gözde Türköz, Emre Yengel, Zinhle Cindi, Handan Ankaralı, Semra Şardaş
Pharmacogenomics harnesses the utility of a patient's genome (n = 1) in decisions on which therapeutic drugs and in what amounts should be administered. Often, patients with shared ancestry present with comparable genetic profiles that predict drug response. However, populations are not static, thus, often, population mobility through migration, especially enmasse as is seen for refugees, changes the pharmacogenetic profiles of resultant populations and therefore observed responses to commonly used therapeutic drugs...
October 2016: Omics: a Journal of Integrative Biology
Marwa K Ibrahim, Hosny Salama, Mohamad Abd El Rahman, Reham M Dawood, Noha G Bader El Din, Heba F Salem, Mohamed E A Abdelrahim, Dalia Omran, Moataza H Omran, Khaled Helmi El-Wakeel, Tawfeek H Abdelhafez, Ahmed Khedr, Mostafa K El Awady
Hepatitis C virus (HCV) is the leading cause of liver fibrosis and hepatocellular carcinoma (HCC). At present, there is no predictive biomarker for the patients at high risk of developing HCC. In this study, we examined the association between single-nucleotide polymorphisms (SNPs) in 3 innate immunity genes [2'-5'oligoadenylate synthetase 1 (OAS1) rs10774671, interleukin 28B (IL28B) rs12979860, and low molecular mass polypeptide 7 (LMP-7) at codon 49] besides cytomegalovirus (CMV) coinfection and susceptibility to HCC in genotype 4 (GT4) chronically infected Egyptian patients...
October 11, 2016: Journal of Interferon & Cytokine Research
Vishal Kumar, Mehak Baweja, Puneet K Singh, Pratyoosh Shukla
Microorganisms play a crucial role in the sustainability of the various ecosystems. The characterization of various interactions between microorganisms and other biotic factors is a necessary footstep to understand the association and functions of microbial communities. Among the different microbial interactions in an ecosystem, plant-microbe interaction plays an important role to balance the ecosystem. The present review explores plant-microbe interactions using gene editing and system biology tools toward the comprehension in improvement of plant traits...
2016: Frontiers in Plant Science
Kayoko Matsunami, Nao Nishida, Naoko Kaneko, Kazuho Ikeo, Licht Toyo-Oka, Hiroshi Takeuchi, Kentaro Matsuura, Akihiro Tamori, Hideyuki Nomura, Hitoshi Yoshiji, Masatoshi Imamura, Naohiko Masaki, Tatsuro Hayakawa, Tatsuya Ide, Noritomo Shimada, Fusao Ikeda, Keisuke Hino, Shuhei Nishiguchi, Chiaki Okuse, Shunsuke Nojiri, Kazunobu Sawamoto, Katsushi Tokunaga, Takashi Joh, Yasuhito Tanaka
The therapeutic use of interferon (IFN) is known to cause depression that frequently interrupts treatment. To identify genetic variants associated with IFN-induced depression, we conducted a genome-wide association study (GWAS) of 224 Japanese chronic hepatitis C patients receiving IFN-based therapy in a multicenter prospective study and stratified them into two groups according to the Beck Depression Inventory, Second Edition (BDI-II) score. In the GWAS stage, we selected 42 candidate single nucleotide polymorphisms (SNPs) to perform replication analysis in an independent set of 160 subjects...
2016: PloS One
Angelica Macauda, Diego Calvetti, Giuseppe Maccari, Kari Hemminki, Asta Försti, Hartmut Goldschmidt, Niels Weinhold, Richard Houlston, Vibeke Andersen, Ulla Vogel, Gabriele Buda, Judit Varkonyi, Anna Sureda, Joaquin Martinez Lopez, Marzena Watek, Aleksandra Butrym, Maria Eugenia Sarasquete, Marek Dudziński, Artur Jurczyszyn, Agnieszka Druzd-Sitek, Marcin Kruszewski, Edyta Subocz, Mario Petrini, Elzbieta Iskierka-Jażdżewska, Malgorzata Raźny, Gergely Szombath, Herlander Marques, Daria Zawirska, Dominik Chraniuk, Janusz Halka, Svend Erik Hove Jacobsen, Grzegorz Mazur, Ramón García Sanz, Charles Dumontet, Victor Moreno, Anna Stępień, Katia Beider, Matteo Pelosini, Rui Manuel Reis, Malgorzata Krawczyk-Kulis, Marcin Rymko, Hervé Avet-Loiseau, Fabienne Lesueur, Norbert Grząśko, Olga Ostrovsky, Krzysztof Jamroziak, Annette J Vangsted, Andrés Jerez, Waldemar Tomczak, Jan Maciej Zaucha, Katalin Kadar, Juan Sainz Pérez, Arnon Nagler, Stefano Landi, Federica Gemignani, Federico Canzian
Multiple myeloma (MM) is a malignancy of plasma cells usually infiltrating the bone marrow, associated with the production of a monoclonal immunoglobulin (M protein) which can be detected in the blood and/or urine. Multiple lines of evidence suggest that genetic factors are involved in MM pathogenesis, and several studies have identified single nucleotide polymorphisms (SNPs) associated with the susceptibility to the disease. SNPs within miRNA-binding sites in target genes (miRSNPs) may alter the strength of miRNA-mRNA interactions, thus deregulating protein expression...
October 8, 2016: International Journal of Cancer. Journal International du Cancer
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"