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Gene, cancer, polymorphism

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https://www.readbyqxmd.com/read/28330108/identification-of-novel-snps-in-differentially-expressed-genes-and-its-association-with-horn-cancer-of-bos-indicus-bullocks-by-next-generation-sequencing
#1
P G Koringa, S J Jakhesara, D N Rank, C G Joshi
The use of polymorphic markers like SNPs promises to provide comprehensive tool for analysing genome and identifying genomic regions that contribute to cancer phenotype. Horn cancer is the most common cancer among Bos indicus animals. Increased expression of some genes due to polymorphisms increases risk of HC incidence. We successfully amplified 91 SNPs located in 69 genes in 52 samples, each of HC and HN. Equimolar concentration of amplicons from 69 PCR products of each sample was pooled and subjected to sequencing using Ion Torrent PGM...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329770/antigen-presentation-profiling-reveals-recognition-of-lymphoma-immunoglobulin-neoantigens
#2
Michael S Khodadoust, Niclas Olsson, Lisa E Wagar, Ole A W Haabeth, Binbin Chen, Kavya Swaminathan, Keith Rawson, Chih Long Liu, David Steiner, Peder Lund, Samhita Rao, Lichao Zhang, Caleb Marceau, Henning Stehr, Aaron M Newman, Debra K Czerwinski, Victoria E H Carlton, Martin Moorhead, Malek Faham, Holbrook E Kohrt, Jan Carette, Michael R Green, Mark M Davis, Ronald Levy, Joshua E Elias, Ash A Alizadeh
Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells. However, the personalized identification and validation of neoantigens remains a major challenge. Here we discover neoantigens in human mantle-cell lymphomas by using an integrated genomic and proteomic strategy that interrogates tumour antigen peptides presented by major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically characterize MHC ligands from 17 patients...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28328959/kras-and-vegf-gene-3-utr-single-nucleotide-polymorphisms-predicted-susceptibility-in-colorectal-cancer
#3
Minnan Yang, Xiuli Xiao, Xiaorui Xing, Xin Li, Tian Xia, Hanan Long
Single nucleotide polymorphisms (SNPs) in tumor-related genes have been reported to play important roles in cancer development. Recent studies have shown that 3'-untranslated regions (UTR) polymorphisms are associated with the occurrence and prognosis of cancers. The aim of this study is to analyze the association between KRAS and VEGF gene 3'-UTR SNPs and genetic susceptibility to colorectal cancer (CRC). In this case-control study of 371 CRC cases and 246 healthy controls, we analyzed the association between one SNP (rs1137188G > A) in the KRAS gene and four SNPs (rs3025039C > T, rs3025040C > T, rs3025053G > A and rs10434A > G) in the VEGF gene and CRC susceptibility by the improved multiplex ligase detection reaction (iMLDR) method...
2017: PloS One
https://www.readbyqxmd.com/read/28328801/influence-of-polymorphisms-in-the-wnt-%C3%AE-catenin-pathway-genes-on-hepatocellular-carcinoma-risk-in-a-chinese-han-population
#4
Qing-Min Li, Feng-Qin Zhang, Ya-Feng Li, Qing-Jie Xian, Yan-Qiang Zhang, Peng Li
The Wnt/β-catenin pathway plays a vital role in initiating and sustaining hepatocellular carcinoma (HCC). However, few studies have investigated polymorphisms in the Wnt/β-catenin signaling pathway genes in the Chinese Han population. The aim of the present retrospective study was to investigate the correlations between polymorphisms of the Wnt/β-catenin signaling pathway genes (CTNNB1 and WNT2) and HCC susceptibility, development, and progression.Twenty tagging single nucleotide polymorphisms were chosen from HapMap data and genotyped in 320 patients with HCC, 320 chronic hepatitis B virus (HBV)-infected patients without HCC (N-HCC, including 95 liver cirrhosis, 164 chronic hepatitis B, and 61 asymptomatic HBV carriers), and 320 healthy controls...
March 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28327944/a-phase-2-randomized-double-blind-placebo-%C3%A2-controlled-study-of-chemo-immunotherapy-combination-using-motolimod-with-pegylated-liposomal-doxorubicin-in-recurrent-or-persistent-ovarian-cancer-a-gynecologic-oncology-group-partners-study
#5
B J Monk, M F Brady, C Aghajanian, H A Lankes, T Rizack, J Leach, J M Fowler, R Higgins, P Hanjani, M Morgan, R Edwards, W Bradley, T Kolevska, P Foukas, E Swisher, K S Anderson, R Gottardo, J K Bryan, M Newkirk, K L Manjarrez, R S Mannel, R M Hershberg, G Coukos
Background: A phase 2, randomized, placebo-controlled trial was conducted in women with recurrent epithelial ovarian carcinoma to evaluate the efficacy and safety of motolimod-a Toll-like receptor 8 (TLR8) agonist that stimulates robust innate immune responses-combined with pegylated liposomal doxorubicin (PLD), a chemotherapeutic that induces immunogenic cell death. Patients and methods: Women with ovarian, fallopian tube, or primary peritoneal carcinoma were randomized 1 : 1 to receive PLD in combination with blinded motolimod or placebo...
February 21, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28327894/statistical-controversies-in-clinical-research-overlap-and-errors-in-the-meta-analyses-of-microrna-genetic-association-studies-in-cancers
#6
J H Park, M Eisenhut, H J Vliet, J I Shin
Background: : Various errors in the design, conduct, and analysis of medical and public health research studies can produce false results and waste valuable resources. While systematic reviews and meta-analyses are arguably considered the most dependable source of evidence-based medicine, increasing numbers of studies are indicating that, on the contrary to the public's belief, many of these investigations are redundant, erroneous, and even biased. Methods: 94 meta-analyses on microRNA polymorphism and risk of cancer were extracted from Pubmed database on August 2016...
January 24, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28327825/genotype-association-gstm1-null-and-gastric-cancer-evidence-based-meta-analysis
#7
Rívian Xavier Ribeiro, Cícera Isabella Leão Leite Nascimento, Antonio Márcio Teodoro Cordeiro Silva
BACKGROUND: Gastric cancer is the fourth most common cancer in men and the sixth among women, except for non-melanoma skin tumors, in Brazil. Epidemiological evidences reveal the multifactorial etiology of this cancer, highlighting risk factors such as: infection by the bacterium Helicobacter pylori, advanced age, smoking, chronic alcohol abuse, eating habits and genetic polymorphisms. Considering the context of genetic polymorphisms, there is the absence of the GSTM1 gene. The lack of GSTM1 function to detoxify xenobiotics and promote defense against oxidative stress leads to increased DNA damage, promoting gastric carcinogenesis...
March 16, 2017: Arquivos de Gastroenterologia
https://www.readbyqxmd.com/read/28326867/adverse-prognostic-impact-of-vascular-endothelial-growth-factor-gene-polymorphisms-in-patients-with-diffuse-large-b-cell-lymphoma
#8
Kyong-Ah Yoon, Min Kyeong Kim, Hyeon-Seok Eom, Hyewon Lee, Weon Seo Park, Ji Yeon Sohn, Man Jin Kim, Sun-Young Kong
Vascular endothelial growth factor (VEGF) plays an important role in angiogenesis and progression of cancer and its expression was associated with gene polymorphisms. Since the impact of polymorphisms of the VEGF on non-Hodgkin lymphoma prognosis has not been fully elucidated, we investigated 149 diffuse large B-cell lymphoma (DLBCL) patients treated with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) at the National Cancer Center, Korea. Five polymorphisms were analyzed with clinical characteristics as well as international prognostic index (IPI)...
March 22, 2017: Leukemia & Lymphoma
https://www.readbyqxmd.com/read/28326835/polymorphisms-of-cancer-stem-cell-marker-gene-cd133-are-associated-with-susceptibility-and-prognosis-of-gastric-cancer
#9
Zhi-Fang Jia, Yan-Hua Wu, Dong-Hui Cao, Xue-Yuan Cao, Jing Jiang, Bao-Sen Zhou
AIM: This study was aimed to investigate the associations between single nucleotide polymorphisms of cancer stem cell marker genes, CD44 and CD133, and susceptibility and prognosis of gastric cancer. PATIENTS & METHODS: Five single nucleotide polymorphisms in CD44 and CD133 genes were genotyped in 898 gastric cancer cases and 992 controls. RESULTS: The A/C or C/C genotypes of CD133 rs2240688 were associated with decreased risk of gastric cancer comparing with the A/A genotype (odds ratio: 0...
February 24, 2017: Future Oncology
https://www.readbyqxmd.com/read/28321154/host-pathogen-interactions-in-helicobacter-pylori-related-gastric-cancer
#10
EDITORIAL
Magdalena Chmiela, Zuzanna Karwowska, Weronika Gonciarz, Bujana Allushi, Paweł Stączek
Helicobacter pylori (H. pylori), discovered in 1982, is a microaerophilic, spiral-shaped gram-negative bacterium that is able to colonize the human stomach. Nearly half of the world's population is infected by this pathogen. Its ability to induce gastritis, peptic ulcers, gastric cancer and mucosa-associated lymphoid tissue lymphoma has been confirmed. The susceptibility of an individual to these clinical outcomes is multifactorial and depends on H. pylori virulence, environmental factors, the genetic susceptibility of the host and the reactivity of the host immune system...
March 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28320150/additional-evidence-supports-association-of-common-genetic-variants-in-vti1a-and-etfa-with-increased-risk-of-glioma-susceptibility
#11
Ning Wang, Zhong Deng, Maode Wang, Ruichun Li, Gaofeng Xu, Gang Bao
BACKGROUND: VTI1A and ETFA were identified recently as susceptibility genes for non-glioblastoma (GBM) of glioma risk in European populations, but the genetic etiology and pathogenesis of glioma have not been fully elucidated. Here, we aimed to investigate whether common genetic variants in VTI1A and ETFA predispose Han Chinese individuals to glioma. METHODS: The association of thirteen common tagging single nucleotide polymorphisms (SNPs) in VTI1A and ETFA genes with glioma were assessed in a hospital-based case-control study including 473 non-GBM of glioma patients and 1046 cancer-free controls...
April 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28317869/genetic-association-between-the-cyclin-dependent-kinase-inhibitor-gene-p27-kip1-polymorphism-rs34330-and-cancer-susceptibility-a-meta-analysis
#12
Xiao-Ke Cheng, Xue-Jun Wang, Xiao-Dong Li, Xue-Qun Ren
The p27 rs34330 (-79C/T) polymorphism has been widely studied for human cancer susceptibility. The current findings, however, still remained controversial. Therefore, we performed the meta-analysis to provide a more accurate result. Eligible studies were identified from PubMed database up to June 2015. The association of p27 rs34330 polymorphism and cancer susceptibility was estimated with odds ratios and corresponding 95% confidence intervals. The meta-analysis was performed with Stata 12. A total of ten studies with 11,214 cases and more than 8,776 controls were included in the meta-analysis (including breast, lung, thyroid, endometrial, and hepatocellular cancer)...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28317149/association-between-variants-in-genes-involved-in-the-immune-response-and-prostate-cancer-risk-in-men-randomized-to-the-finasteride-arm-in-the-prostate-cancer-prevention-trial
#13
Danyelle A Winchester, Cathee Till, Phyllis J Goodman, Catherine M Tangen, Regina M Santella, Teresa L Johnson-Pais, Robin J Leach, Jianfeng Xu, S Lilly Zheng, Ian M Thompson, M Scott Lucia, Scott M Lippman, Howard L Parnes, William B Isaacs, Angelo M De Marzo, Charles G Drake, Elizabeth A Platz
BACKGROUND: We reported that some, but not all single nucleotide polymorphisms (SNPs) in select immune response genes are associated with prostate cancer, but not individually with the prevalence of intraprostatic inflammation in the Prostate Cancer Prevention Trial (PCPT) placebo arm. Here, we investigated whether these same SNPs are associated with risk of lower- and higher-grade prostate cancer in men randomized to finasteride, and with prevalence of intraprostatic inflammation among controls...
March 20, 2017: Prostate
https://www.readbyqxmd.com/read/28315507/polymorphisms-and-mutations-in-gstp1-rad51-xrcc1-and-xrcc3-genes-in-breast-cancer-patients
#14
Mazhar Salim Al Zoubi, Katia Zavaglia, Chiara Mazanti, Mohammad Al Hamad, Khalid Al Batayneh, Alaa A A Aljabali, Generoso Bevilacqua
BACKGROUND: Genotoxic factors, including ionizing radiation and oxidative stress, are associated with genomic instability and development of breast cancer (BC). The homologous recombination DNA repair (HRR) pathway, base excision repair (BER) mechanism, and antioxidative enzymes are required as defense mechanisms against these DNA damaging agents. GSTP1, XRCC1, XRCC3 and RAD51 proteins are essential components of antioxidation, BER and HRR of DNA, respectively. Deficiencies in BER, HRR and antioxidation pathways are involved in the progression of cancer...
March 6, 2017: International Journal of Biological Markers
https://www.readbyqxmd.com/read/28315227/insulin-like-growth-factor-1-gene-polymorphism-in-women-with-breast-cancer
#15
Danylo Rafhael Costa-Silva, Maria da Conceição Barros-Oliveira, Rafael Soares Borges, Larysse Maira Campos-Verdes, João Paulo da Silva-Sampaio, Carla Solange Escorcio-Dourado, Luana Mota Martins, Airlane Pereira Alencar, Edmund Chada Baracat, Vladimir Costa Silva, Benedito Borges da Silva
Breast cancer is a disease of unknown etiology; however, the major risk factors are genetic alterations. Studies have demonstrated an association between insulin-like growth factor 1 (IGF-1) gene polymorphism and cell proliferation and reduced apoptosis, in addition to its role in breast cancer growth and aggressiveness. Two polymorphic variants of the IGF-1 gene are highlighted in association with breast cancer, rs6220 and rs7136446, although controversy exists as to this relationship. The current study included 137 women (68 breast cancer cases and 69 controls without breast cancer) who had 3 ml of peripheral blood drawn for the study of genomic DNA extracted from leukocytes using the genotyping technique by real-time polymerase chain reaction...
April 2017: Medical Oncology
https://www.readbyqxmd.com/read/28306219/characterization-of-a-novel-pold1-missense-founder-mutation-in-a-spanish-population
#16
Rosario Ferrer-Avargues, Virginia Díez-Obrero, Ester Martín-Tomás, Eva Hernández-Illán, María-Isabel Castillejo, Alan Codoñer-Alejos, Víctor-Manuel Barberá, Ana-Beatriz Sánchez-Heras, Ángel Segura, María-José Juan, Isabel Tena, Adela Castillejo, José-Luis Soto
BACKGROUND: We identified a new and a recurrent POLD1 mutation associated with predisposition to colorectal cancer (CRC). We characterized the molecular and clinical nature of the potential POLD1 founder mutation in families from Valencia (Spain). METHODS: Clinical and molecular data were collected from 4 independent families known to have a POLD1 Leu474Pro mutation. To establish its founder effect, haplotype construction was performed using 14 flanking POLD1 polymorphic markers...
March 17, 2017: Journal of Gene Medicine
https://www.readbyqxmd.com/read/28304396/associations-between-genetic-variants-in-mrna-splicing-related-genes-and-risk-of-lung-cancer-a-pathway-based-analysis-from-published-gwass
#17
Yongchu Pan, Hongliang Liu, Yanru Wang, Xiaozheng Kang, Zhensheng Liu, Kouros Owzar, Younghun Han, Li Su, Yongyue Wei, Rayjean J Hung, Yonathan Brhane, John McLaughlin, Paul Brennan, Heike Bickeböller, Albert Rosenberger, Richard S Houlston, Neil Caporaso, Maria Teresa Landi, Joachim Heinrich, Angela Risch, Xifeng Wu, Yuanqing Ye, David C Christiani, Christopher I Amos, Qingyi Wei
mRNA splicing is an important mechanism to regulate mRNA expression. Abnormal regulation of this process may lead to lung cancer. Here, we investigated the associations of 11,966 single-nucleotide polymorphisms (SNPs) in 206 mRNA splicing-related genes with lung cancer risk by using the summary data from six published genome-wide association studies (GWASs) of Transdisciplinary Research in Cancer of the Lung (TRICL) (12,160 cases and 16,838 controls) and another two lung cancer GWASs of Harvard University (984 cases and 970 controls) and deCODE (1,319 cases and 26,380 controls)...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28303356/the-association-of-plasminogen-activator-inhibitor-type-1-pai-1-level-and-pai-1-4g-5g-gene-polymorphism-with-the-formation-and-the-grade-of-endometrial-cancer
#18
Malik Ejder Yıldırım, Savas Karakuş, Hande Küçük Kurtulgan, Hasan Kılıçgün, Serpil Erşan, Sevtap Bakır
Plasminogen activator inhibitor type 1 (PAI-1) is a serine protease inhibitor (Serpine 1), and it inhibits both tissue plasminogen activator and urokinase plasminogen activator which are important in fibrinolysis. We aimed to find whether there is a possible association between PAI-1 level, PAI-1 4G/5G polymorphism, and endometrial cancer. PAI-1 levels in peripheral blood were determined in 82 patients with endometrial carcinoma and 76 female healthy controls using an enzyme-linked immunoassay (ELISA). Then, the genomic DNA was extracted and screened by reverse hybridization procedure (Strip assay) to detect PAI 1 4G/5G polymorphism...
March 16, 2017: Biochemical Genetics
https://www.readbyqxmd.com/read/28302216/-association-of-indoor-air-pollution-single-nucleotide-polymorphism-of-hif-1%C3%AE-gene-with-susceptibility-to-lung-cancer-in-han-population-in-fujian-province
#19
Fei He, Qi Qi, Xu Li, Rendong Xiao, Qiuping Xu, Weimin Xiong, Zhiqiang Liu, Lin Cai
BACKGROUND: Hypoxia inducible factor-1α (HIF-1α) is associated with the progression and metastasis of lung cancer. There are, however, few studies on the relationship between the single nucleotide polymorphisms of HIF-1α and susceptibility to lung cancer. Therefore, we aimed to investigate the relationship between indoor air pollution, HIF-1α rs2057482, and the susceptibility to primary lung cancer of the Fujian Han population. METHODS: The present study is a hospital-based case-control study...
March 20, 2017: Zhongguo Fei Ai za Zhi, Chinese Journal of Lung Cancer
https://www.readbyqxmd.com/read/28302063/epigenetic-and-genetic-alterations-and-their-influence-on-gene-regulation-in-chronic-lymphocytic-leukemia
#20
Di Huang, Ivan Ovcharenko
BACKGROUND: To understand the changes of gene regulation in carcinogenesis, we explored signals of DNA methylation - a stable epigenetic mark of gene regulatory elements - and designed a computational model to profile loss and gain of regulatory elements (REs) during carcinogenesis. We also utilized sequencing data to analyze the allele frequency of single nucleotide polymorphisms (SNPs) and detected the cancer-associated SNPs, i.e., the SNPs displaying the significant allele frequency difference between cancer and normal samples...
March 16, 2017: BMC Genomics
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