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Prostate cancer SNP

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https://www.readbyqxmd.com/read/28614061/a-genetic-variant-in-slc28a3-rs56350726-is-associated-with-progression-to-castration-resistant-prostate-cancer-in-a-korean-population-with-metastatic-prostate-cancer
#1
Jung Ku Jo, Jong Jin Oh, Yong Tae Kim, Hong Sang Moon, Hong Yong Choi, Seunghyun Park, Jin-Nyoung Ho, Sungroh Yoon, Hae Young Park, Seok-Soo Byun
BACKGROUND: Genetic variation which related with progression to castration-resistant prostate cancer (CRPC) during androgen-deprivation therapy (ADT) has not been elucidated in patients with metastatic prostate cancer (mPCa). Therefore, we assessed the association between genetic variants in mPCa and progression to CRPC. RESULTS: Analysis of exome genotypes revealed that 42 SNPs were significantly associated with mPCa. The top five polymorphisms were statistically significantly associated with metastatic disease...
May 30, 2017: Oncotarget
https://www.readbyqxmd.com/read/28580135/snp-snp-interactions-as-risk-factors-for-aggressive-prostate-cancer
#2
Venkatesh Vaidyanathan, Vijay Naidu, Nishi Karunasinghe, Anower Jabed, Radha Pallati, Gareth Marlow, Lynnette R Ferguson
Prostate cancer (PCa) is one of the most significant male health concerns worldwide. Single nucleotide polymorphisms (SNPs) are becoming increasingly strong candidate biomarkers for identifying susceptibility to PCa. We identified a number of SNPs reported in genome-wide association analyses (GWAS) as risk factors for aggressive PCa in various European populations, and then defined SNP-SNP interactions, using PLINK software, with nucleic acid samples from a New Zealand cohort. We used this approach to find a gene x environment marker for aggressive PCa, as although statistically gene x environment interactions can be adjusted for, it is highly impossible in practicality, and thus must be incorporated in the search for a reliable biomarker for PCa...
2017: F1000Research
https://www.readbyqxmd.com/read/28578017/functional-polymorphism-at-the-mir-502-binding-site-in-the-3-untranslated-region-of-the-setd8-gene-increased-the-risk-of-prostate-cancer-in-a-sample-of-iranian-population
#3
Behzad Narouie, Seyed Amir Mohsen Ziaee, Abbas Basiri, Mohammad Hashemi
MicroRNAs (miRNAs), a class of non-coding RNAs, bind to the 3' untranslated regions (3'-UTRs) of target mRNAs and regulate gene expression. Genetic variations in miRNA binding domains influence the susceptibility to several diseases such as cancer. Several studies investigated the impact of single-nucleotide polymorphism (SNP) rs16917496 T>C within the 3'-UTR of SETD8 on cancer susceptibility, but the results were controversial. In addition, no study has been conducted to inspect the impact of this SNP in prostate cancer (PCa)...
May 31, 2017: Gene
https://www.readbyqxmd.com/read/28555354/contiguous-gene-deletion-of-chromosome-2p16-3-p21-as-a-cause-of-lynch-syndrome
#4
Erin E Salo-Mullen, Patricio B Lynn, Lu Wang, Michael Walsh, Anuradha Gopalan, Jinru Shia, Christina Tran, Fung Ying Man, Sean McBride, Mark Schattner, Liying Zhang, Martin R Weiser, Zsofia K Stadler
Lynch syndrome is an autosomal dominant condition caused by pathogenic mutations in the DNA mismatch repair (MMR) genes. Although commonly associated with clinical features such as intellectual disability and congenital anomalies, contiguous gene deletions may also result in cancer predisposition syndromes. We report on a 52-year-old male with Lynch syndrome caused by deletion of chromosome 2p16.3-p21. The patient had intellectual disability and presented with a prostatic adenocarcinoma with an incidentally identified synchronous sigmoid adenocarcinoma that exhibited deficient MMR with an absence of MSH2 and MSH6 protein expression...
May 29, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28552848/meta-analysis-of-association-between-rs1447295-polymorphism-and-prostate-cancer-susceptibility
#5
Juan Zhou, Yang Yu, Anyou Zhu, Fengchao Wang, Shuxia Kang, Yunfeng Pei, Chunping Cao, Chen Ding, Duping Wang, Li Sun, Guoping Niu
AIMS: A number of studies have found that the single nucleotide polymorphisms (SNPs) within the 8q24 region of genome were associated with the susceptibility of prostate cancer. Association between 8q24 SNP variant rs1447295 and higher risk of prostate cancer had been investigated, but those studies were incomplete and the conclusions were obscure. METHODS: To better elucidate the relationship between rs1447295 polymorphism and the susceptibility of prostate cancer, we performed a more comprehensive meta-analysis about the association between rs1447295 polymorphism and prostate cancer susceptibility by collecting relevant articles published up to November, 2016 and excluding many replicated cohort data existing in previous reports, which made the conclusion more reliant and objective...
May 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28543179/genetic-ancestry-and-prostate-cancer-susceptibility-snps-in-puerto-rican-and-african-american-men
#6
Margarita Irizarry-Ramírez, Rick A Kittles, Xuemei Wang, Jeannette Salgado-Montilla, Graciela M Nogueras-González, Ricardo Sánchez-Ortiz, Lourdes Guerrios, Keila Rivera, Ebony Shah, Ina Prokhorova, Pamela Roberson, Patricia Troncoso, Curtis A Pettaway
BACKGROUND: The Puerto Rican (PR) population is a racially admixed population that has a high prostate cancer (PCa) mortality rate. We hypothesized in this pilot study that West African Ancestry (WAA) was associated with PCa in this heterogeneous (PR) population. METHODS: A case/case and case/control study was performed. Controls, 207 African American (AA) and 133 PR were defined as men with no PCa, a serum PSA < 2.5 ng/mL and a negative rectal examination...
May 24, 2017: Prostate
https://www.readbyqxmd.com/read/28471803/search-for-genetic-factor-association-with-cancer-free-prostate-specific-antigen-level-elevation-on-the-basis-of-a-genome-wide-association-study-in-the-korean-population
#7
Eun Kyung Choe, Young Lee, Jeong Yeon Cho, Seung Ho Choi, Boram Park, Jong-Eun Lee, Eun Young Cho
We investigated the genetic markers associated with elevated serum prostate-specific antigen (sPSA) levels to improve the predictive power of sPSA in screening for prostate cancer. A genome-wide association study was carried out among 4124 healthy Korean male adults using the Affymetrix Axiom Customized Biobank Genotyping Arrays for sPSA levels. A subgroup analysis for increased sPSA levels who underwent a prostate biopsy (n=64) was also carried out. We detected 11 single nucleotide polymorphisms (SNPs) near the Solute carrier family 45member 3, AGAP7P, MSMB, LOC101929917, and KLK3 genes associated with sPSA levels...
May 3, 2017: European Journal of Cancer Prevention
https://www.readbyqxmd.com/read/28422721/functional-analysis-implicating-the-snp-rs61552325-in-erbb2-as-an-effector-for-androgen-insensitive-prostate-cancer-cell-invasion
#8
Xianxiang Xin, Yinmin Gu, Yang Chen, Yuanjie Huang, Zengnan Mo, Yanling Hu
BACKGROUND: As one of the most common cancers in men, the pathogenesis of prostate cancer has been widely researched. Aberrant activation of the erb-b2 receptor tyrosine kinase 2 (ERBB2) has been found to play a critical role in metastatic prostate cancer. In our previous study, we demonstrated that rs61552325 (Pro1140Ala) located in ERBB2 is strongly correlated to prostate cancer. Therefore, we initially studied the effect of rs61552325 on androgen-independent prostate cancer cell metastasis...
May 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28399564/interactions-between-genome-wide-significant-genetic-variants-and-circulating-concentrations-of-25-hydroxyvitamin-d-in-relation-to-prostate-cancer-risk-in-the-national-cancer-institute-bpc3
#9
Vasiliki I Dimitrakopoulou, Ruth C Travis, Irene M Shui, Alison Mondul, Demetrius Albanes, Jarmo Virtamo, Antonio Agudo, Heiner Boeing, H Bas Bueno-de-Mesquita, Marc J Gunter, Mattias Johansson, Kay-Tee Khaw, Kim Overvad, Domenico Palli, Antonia Trichopoulou, Edward Giovannucci, David J Hunter, Sara Lindström, Walter Willett, J Michael Gaziano, Meir Stampfer, Christine Berg, Sonja I Berndt, Amanda Black, Robert N Hoover, Peter Kraft, Timothy J Key, Konstantinos K Tsilidis
Genome-wide association studies (GWAS) have identified over 100 single nucleotide polymorphisms (SNPs) associated with prostate cancer. However, information on the mechanistic basis for some associations is limited. Recent research has been directed towards the potential association of vitamin D concentrations and prostate cancer, but little is known about whether the aforementioned genetic associations are modified by vitamin D. We investigated the associations of 46 GWAS-identified SNPs, circulating concentrations of 25-hydroxyvitamin D (25(OH)D), and prostate cancer (3,811 cases, 511 of whom died from the disease, compared with 2,980 controls-from 5 cohort studies that recruited participants over several periods beginning in the 1980s)...
March 15, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28376164/germline-mutations-in-the-kallikrein-6-region-and-predisposition-for-aggressive-prostate-cancer
#10
Laurent Briollais, Hilmi Ozcelik, Jingxiong Xu, Maciej Kwiatkowski, Emilie Lalonde, Dorota H Sendorek, Neil E Fleshner, Franz Recker, Cynthia Kuk, Ekaterina Olkhov-Mitsel, Tristan Juvet, Ioannis Prassas, John Trachtenberg, Ants Toi, Michael Fraser, Theodorus van der Kwast, Robert G Bristow, Bharati Bapat, Eleftherios P Diamandis, Paul C Boutros, Alexandre R Zlotta
Background: There is a need for markers that can specifically identify individuals at increased risk of harboring aggressive forms of prostate cancer (PCa). Methods: We surveyed the Kallikrein ( KLK ) region ( KLK 1-15) for single-nucleotide polymorphisms (SNPs) associated with aggressive PCa (Gleason Score ≥ 8) in 1858 PCa patients. Discovery cohorts (Swiss arm of the European Randomized Study of Screening for PCa, n = 379; Toronto, Canada, n = 540) and a validation cohort (Prostate, Lung, Colorectal and Ovarian [PLCO] screening trial, n = 939) were analyzed...
April 1, 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/28374791/prostate-cancer-in-a-snp-klk6-mutations-in-aggressive-disease
#11
Louise Stone
No abstract text is available yet for this article.
June 2017: Nature Reviews. Urology
https://www.readbyqxmd.com/read/28272408/computational-modeling-of-complete-hoxb13-protein-for-predicting-the-functional-effect-of-snps-and-the-associated-role-in-hereditary-prostate-cancer
#12
Gopalakrishnan Chandrasekaran, Eu Chang Hwang, Taek Won Kang, Dong Deuk Kwon, Kwangsung Park, Je-Jung Lee, Vinoth-Kumar Lakshmanan
The human HOXB13 gene encodes a 284 amino acid transcription factor belonging to the homeobox gene family containing a homeobox and a HoxA13 N-terminal domain. It is highly linked to hereditary prostate cancer, the majority of which is manifested as a result of a Single Nucleotide Polymorphism (SNP). In silico analysis of 95 missense SNP's corresponding to the non-homeobox region of HOXB13 predicted 21 nsSNP's to be potentially deleterious. Among 123 UTR SNPs analysed by UTRScan, rs543028086, rs550968159, rs563065128 were found to affect the UNR_BS, GY-BOX and MBE UTR signals, respectively...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28272245/single-nucleotide-polymorphism-rs1058205-of-klk3-is-associated-with-the-risk-of-prostate-cancer-a-case-control-study-of-han-chinese-men-in-northeast-china
#13
Chen Chen, Zhongqiu Xin
BACKGROUND: Prostate cancer (PCa) is a serious public health concern for men worldwide. However, the risk factors for PCa remain largely unclear. Aim of this study was to investigate statistical associations between the risk of prostate cancer and the rs1058205 single-nucleotide polymorphism (SNP) of the KLK3 gene, which encodes the prostate specific antigen (PSA), in a case-control study of Han Chinese men in Northeast China. METHODS: Using a high-resolution melting curve genotyping method, we determined the genotype and allele distributions of rs1058205 in 2 groups of Han Chinese men, consisting of 268 PCa patients and 298 healthy control subjects...
March 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28259691/hotair-genetic-variants-are-associated-with-prostate-cancer-and-benign-prostate-hyperplasia-in-an-iranian-population
#14
Mohammad Taheri, Mohsen Habibi, Rezvan Noroozi, Azadeh Rakhshan, Shaghayegh Sarrafzadeh, Arezou Sayad, Mir Davood Omrani, Soudeh Ghafouri-Fard
Prostate cancer and benign prostate hyperplasia (BPH) are heterogeneous disorders with a wide array of clinical presentations and high prevalence among men. Several protein coding genes as well as non-coding genes have been shown to contribute in prostate cancer and BPH risk. Among non-coding genes whose contribution in tumorigenesis has been identified is HOX transcript antisense RNA (HOTAIR). In the present study we aimed at identification of the associations between three HOTAIR polymorphisms (rs12826786, rs1899663 and rs4759314) and risk of prostate cancer and BPH by the means of tetra-primer ARMS-PCR in a population of 128 Iranian prostate cancer patients, 143 BPH patients and 250 normal male controls...
May 20, 2017: Gene
https://www.readbyqxmd.com/read/28231280/alkbh7-variant-related-to-prostate-cancer-exhibits-altered-substrate-binding
#15
Alice R Walker, Pavel Silvestrov, Tina A Müller, Robert H Podolsky, Gregory Dyson, Robert P Hausinger, Gerardo Andrés Cisneros
The search for prostate cancer biomarkers has received increased attention and several DNA repair related enzymes have been linked to this dysfunction. Here we report a targeted search for single nucleotide polymorphisms (SNPs) and functional impact characterization of human ALKBH family dioxygenases related to prostate cancer. Our results uncovered a SNP of ALKBH7, rs7540, which is associated with prostate cancer disease in a statistically significantly manner in two separate cohorts, and maintained in African American men...
February 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28124475/genome-wide-two-locus-interaction-analysis-identifies-multiple-epistatic-snp-pairs-that-confer-risk-of-prostate-cancer-a-cross-population-study
#16
Jiawei Shen, Zhiqiang Li, Zhijian Song, Jianhua Chen, Yongyong Shi
Prostate cancer is one of the most common carcinomas among adult males. Recently, genome-wide association studies (GWAS) have identified several susceptibility genes of prostate cancer. However, these single locus results can only explain a small proportion of the genetic etiology. In order to understand how multiple genetic variants may contribute to the penetrance of prostate cancer, we conducted a genome-wide SNP-SNP interaction study in four populations, involving 5,269 cases and 5,289 controls. We exhaustively evaluated all pairs of SNP-SNP interactions for 661,658 SNPs that were consensus in all four groups, and then performed a meta-analysis to combine the results...
May 1, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28072499/in-silico-analysis-of-the-deleterious-nssnp-s-missense-in-the-homeobox-domain-of-human-hoxb13-gene-responsible-for-hereditary-prostate-cancer
#17
Gopalakrishnan Chandrasekaran, Eu Chang Hwang, Taek Won Kang, Dongdeuk Kwon, Kwangsung Park, Je-Jung Lee, Vinoth-Kumar Lakshmanan
The human HOXB13 gene encodes a transcription factor containing a DNA-binding homeobox domain and a HoxA13 N-terminal domain. SNP is considered to be the primary genetic cause for hereditary prostate cancer (PCa). The study of functional nsSNP's would give an insight into the exact cause underlying the onset of hereditary PCa and possible methodologies for the cure or early management of the disease. Several in silico tools were used to screen and map the deleterious nsSNP's to the protein structure for predicting the structure-function effects...
January 10, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28046236/su-d-204-06-integration-of-machine-learning-and-bioinformatics-methods-to-analyze-genome-wide-association-study-data-for-rectal-bleeding-and-erectile-dysfunction-following-radiotherapy-in-prostate-cancer
#18
J Oh, S Kerns, H Ostrer, B Rosenstein, J Deasy
PURPOSE: We investigated whether integration of machine learning and bioinformatics techniques on genome-wide association study (GWAS) data can improve the performance of predictive models in predicting the risk of developing radiation-induced late rectal bleeding and erectile dysfunction in prostate cancer patients. METHODS: We analyzed a GWAS dataset generated from 385 prostate cancer patients treated with radiotherapy. Using genotype information from these patients, we designed a machine learning-based predictive model of late radiation-induced toxicities: rectal bleeding and erectile dysfunction...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28039167/snp-interaction-pattern-identifier-sipi-an-intensive-search-for-snp-snp-interaction-patterns
#19
Hui-Yi Lin, Dung-Tsa Chen, Po-Yu Huang, Yung-Hsin Liu, Augusto Ochoa, Jovanny Zabaleta, Donald E Mercante, Zhide Fang, Thomas A Sellers, Julio M Pow-Sang, Chia-Ho Cheng, Rosalind Eeles, Doug Easton, Zsofia Kote-Jarai, Ali Amin Al Olama, Sara Benlloch, Kenneth Muir, Graham G Giles, Fredrik Wiklund, Henrik Gronberg, Christopher A Haiman, Johanna Schleutker, Børge G Nordestgaard, Ruth C Travis, Freddie Hamdy, Nora Pashayan, Kay-Tee Khaw, Janet L Stanford, William J Blot, Stephen N Thibodeau, Christiane Maier, Adam S Kibel, Cezary Cybulski, Lisa Cannon-Albright, Hermann Brenner, Radka Kaneva, Jyotsna Batra, Manuel R Teixeira, Hardev Pandha, Yong-Jie Lu, Jong Y Park
Motivation: Testing SNP-SNP interactions is considered as a key for overcoming bottlenecks of genetic association studies. However, related statistical methods for testing SNP-SNP interactions are underdeveloped. Results: We propose the SNP Interaction Pattern Identifier (SIPI), which tests 45 biologically meaningful interaction patterns for a binary outcome. SIPI takes non-hierarchical models, inheritance modes and mode coding direction into consideration. The simulation results show that SIPI has higher power than MDR (Multifactor Dimensionality Reduction), AA_Full, Geno_Full (full interaction model with additive or genotypic mode) and SNPassoc in detecting interactions...
March 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28009986/conditionally-reprogrammed-normal-and-primary-tumor-prostate-epithelial-cells-a-novel-patient-derived-cell-model-for-studies-of-human-prostate-cancer
#20
Olga A Timofeeva, Nancy Palechor-Ceron, Guanglei Li, Hang Yuan, Ewa Krawczyk, Xiaogang Zhong, Geng Liu, Geeta Upadhyay, Aleksandra Dakic, Songtao Yu, Shuang Fang, Sujata Choudhury, Xueping Zhang, Andrew Ju, Myeong-Seon Lee, Han C Dan, Youngmi Ji, Yong Hou, Yun-Ling Zheng, Chris Albanese, Johng Rhim, Richard Schlegel, Anatoly Dritschilo, Xuefeng Liu
Our previous study demonstrated that conditional reprogramming (CR) allows the establishment of patient-derived normal and tumor epithelial cell cultures from a variety of tissue types including breast, lung, colon and prostate. Using CR, we have established matched normal and tumor cultures, GUMC-29 and GUMC-30 respectively, from a patient's prostatectomy specimen. These CR cells proliferate indefinitely in vitro and retain stable karyotypes. Most importantly, only tumor-derived CR cells (GUMC-30) produced tumors in xenografted SCID mice, demonstrating maintenance of the critical tumor phenotype...
April 4, 2017: Oncotarget
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