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Prostate cancer SNP

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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
#1
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
#2
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
#3
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...
March 1, 2017: Gene
https://www.readbyqxmd.com/read/28231280/alkbh7-variant-related-to-prostate-cancer-exhibits-altered-substrate-binding
#4
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
#5
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
#6
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
#7
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
#8
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...
December 30, 2016: 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
#9
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...
December 21, 2016: Oncotarget
https://www.readbyqxmd.com/read/27941040/genetic-predisposition-to-prostate-cancer
#10
REVIEW
S Benafif, R Eeles
INTRODUCTION: Prostate cancer (PrCa) is the commonest non-cutaneous cancer in men in the UK. Epidemiological evidence as well as twin studies points towards a genetic component contributing to aetiology. SOURCES OF DATA: Key recently published literature. AREAS OF AGREEMENT: A family history of PrCa doubles the risk of disease development in first-degree relatives. Linkage and genetic sequencing studies identified rare moderate-high-risk gene loci, which predispose to PrCa development when altered by mutation...
December 2016: British Medical Bulletin
https://www.readbyqxmd.com/read/27917368/sex-steroid-hormone-single-nucleotide-polymorphisms-pesticide-use-and-the-risk-of-prostate-cancer-a-nested-case-control-study-within-the-agricultural-health-study
#11
Carol H Christensen, Kathryn Hughes Barry, Gabriella Andreotti, Michael C R Alavanja, Michael B Cook, Scott P Kelly, Laurie A Burdett, Meredith Yeager, Laura E Beane Freeman, Sonja I Berndt, Stella Koutros
Experimental and epidemiologic investigations suggest that certain pesticides may alter sex steroid hormone synthesis, metabolism or regulation, and the risk of hormone-related cancers. Here, we evaluated whether single-nucleotide polymorphisms (SNPs) involved in hormone homeostasis alter the effect of pesticide exposure on prostate cancer risk. We evaluated pesticide-SNP interactions between 39 pesticides and SNPs with respect to prostate cancer among 776 cases and 1,444 controls nested in the Agricultural Health Study cohort...
2016: Frontiers in Oncology
https://www.readbyqxmd.com/read/27916838/prognostic-relevance-of-methylenetetrahydrofolate-reductase-polymorphisms-for-prostate-cancer
#12
Victor C Lin, Te-Ling Lu, Hsin-Ling Yin, Sheau-Fang Yang, Yung-Chin Lee, Chia-Chu Liu, Chao-Yuan Huang, Chia-Cheng Yu, Ta-Yuan Chang, Shu-Pin Huang, Bo-Ying Bao
Folate metabolism has been associated with cancers via alterations in nucleotide synthesis, DNA methylation, and DNA repair. We hypothesized that genetic variants in methylenetetrahydrofolate reductase (MTHFR), a key enzyme of folate metabolism, would affect the prognosis of prostate cancer. Three haplotype-tagging single-nucleotide polymorphisms (SNPs) across the MTHFR gene region were genotyped in a cohort of 458 patients with clinically localized prostate cancer treated with radical prostatectomy. One SNP, rs9651118, was associated with disease recurrence, and the association persisted after multivariate analyses adjusting for known risk factors...
November 29, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27916600/mapping-complex-traits-in-a-diversity-outbred-f1-mouse-population-identifies-germline-modifiers-of-metastasis-in-human-prostate-cancer
#13
Jean M Winter, Derek E Gildea, Jonathan P Andreas, Daniel M Gatti, Kendra A Williams, Minnkyong Lee, Ying Hu, Suiyuan Zhang, James C Mullikin, Tyra G Wolfsberg, Shannon K McDonnell, Zachary C Fogarty, Melissa C Larson, Amy J French, Daniel J Schaid, Stephen N Thibodeau, Gary A Churchill, Nigel P S Crawford
It is unclear how standing genetic variation affects the prognosis of prostate cancer patients. To provide one controlled answer to this problem, we crossed a dominant, penetrant mouse model of prostate cancer to Diversity Outbred mice, a collection of animals that carries over 40 million SNPs. Integration of disease phenotype and SNP variation data in 493 F1 males identified a metastasis modifier locus on Chromosome 8 (LOD = 8.42); further analysis identified the genes Rwdd4, Cenpu, and Casp3 as functional effectors of this locus...
January 25, 2017: Cell Systems
https://www.readbyqxmd.com/read/27906997/role-of-genetic-polymorphisms-in-the-development-and-prognosis-of-sporadic-and-familial-prostate-cancer
#14
Sabrina T Reis, Nayara I Viana, Katia R M Leite, Erico Diogenes, Alberto A Antunes, Alexandre Iscaife, Adriano J Nesrallah, Carlo C Passerotti, Victor Srougi, José Pontes-Junior, Mary Ellen Salles, William C Nahas, Miguel Srougi
BACKGROUNDS: Our aim was to evaluate the role of 20 genetic polymorphisms in the development and prognosis of sporadic and familial PC. A case-control study of 185 patients who underwent radical prostatectomy from 1997 to 2011. These patients were divided into two groups based on their family history. Gleason grade, PSA value and pathological TNM 2002 stage were used as prognostic factors. Blood samples from 70 men without PC were used as controls. The SNPs were genotyped using a TaqMan® SNP Genotyping Assay Kit...
2016: PloS One
https://www.readbyqxmd.com/read/27900359/homozygous-inactivation-of-chek2-is-linked-to-a-familial-case-of-multiple-primary-lung-cancer-with-accompanying-cancers-in-other-organs
#15
Yoji Kukita, Jiro Okami, Noriko Yoneda-Kato, Ikuko Nakamae, Takeshi Kawabata, Masahiko Higashiyama, Junya Kato, Ken Kodama, Kikuya Kato
In clinical practice, there are a number of cancer patients with clear family histories, but the patients lack mutations in known familial cancer syndrome genes. Recent advances in genomic technologies have enhanced the possibility of identifying causative genes in such cases. Two siblings, an elder sister and a younger brother, were found to have multiple primary lung cancers at the age of 60. The former subsequently developed breast cancer and had a history of uterine myoma. The latter had initially developed prostate cancer at the age of 59 and had a history of colon cancer...
November 2016: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/27889279/vitamin-k-epoxide-reductase-expression-and-prostate-cancer-risk
#16
Ben Yi Tew, Sumanta K Pal, Miaoling He, Tommy Tong, Huiqing Wu, JoAnn Hsu, Xueli Liu, Susan L Neuhausen, Jeremy O Jones
PURPOSE: Increasing evidence has demonstrated that men taking the anticoagulant warfarin have a lower risk of developing prostate cancer. This phenomenon is not observed in other cancers. We sought to determine if the target of warfarin, vitamin K epoxide reductase (VKOR), is expressed in benign and cancerous prostate tissues and if a functional single nucleotide polymorphism (SNP) in the VKOR gene is associated with prostate cancer risk. MATERIALS AND METHODS: The expression of VKOR was quantified by immunohistochemistry in an institutional series of 54 radical prostatectomy samples and metastatic biopsies, as well as in 40 other cancers and matched benign tissues on a tissue microarray...
March 2017: Urologic Oncology
https://www.readbyqxmd.com/read/27863482/in-silico-snp-analysis-of-the-breast-cancer-antigen-ny-br-1
#17
Zeynep Kosaloglu, Julia Bitzer, Niels Halama, Zhiqin Huang, Marc Zapatka, Andreas Schneeweiss, Dirk Jäger, Inka Zörnig
BACKGROUND: Breast cancer is one of the most common malignancies with increasing incidences every year and a leading cause of death among women. Although early stage breast cancer can be effectively treated, there are limited numbers of treatment options available for patients with advanced and metastatic disease. The novel breast cancer associated antigen NY-BR-1 was identified by SEREX analysis and is expressed in the majority (>70%) of breast tumors as well as metastases, in normal breast tissue, in testis and occasionally in prostate tissue...
November 18, 2016: BMC Cancer
https://www.readbyqxmd.com/read/27647999/prognostic-value-of-prostaglandin-endoperoxide-synthase-2-polymorphisms-in-prostate-cancer-recurrence-after-radical-prostatectomy
#18
Cheng-Hsueh Lee, Jiunn-Bey Pao, Te-Ling Lu, Hong-Zin Lee, Yung-Chin Lee, Chia-Chu Liu, Chao-Yuan Huang, Victor C Lin, Chia-Cheng Yu, Hsin-Ling Yin, Shu-Pin Huang, Bo-Ying Bao
UNLABELLED: Backgroud: Increasing evidence suggests the involvement of chronic inflammation in the progression of prostate cancer, and prostaglandin-endoperoxide synthase 2 (PTGS2), also known as cyclooxygenase-2, catalyzes the rate-limiting steps of the pathway. We hypothesized that genetic variants of PTGS2 can influence the outcome of prostate cancer patients. METHODS: We genotyped five haplotype-tagging single-nucleotide polymorphisms (SNPs) to detect common genetic variations across the PTGS2 region in 458 prostate cancer patients treated with radical prostatectomy...
2016: International Journal of Medical Sciences
https://www.readbyqxmd.com/read/27624283/mdm2-promoter-snp55-rs2870820-affects-risk-of-colon-cancer-but-not-breast-lung-or-prostate-cancer
#19
Reham Helwa, Liv B Gansmo, Pål Romundstad, Kristian Hveem, Lars Vatten, Bríd M Ryan, Curtis C Harris, Per E Lønning, Stian Knappskog
Two functional SNPs (SNP285G > C; rs117039649 and SNP309T > G; rs2279744) have previously been reported to modulate Sp1 transcription factor binding to the promoter of the proto-oncogene MDM2, and to influence cancer risk. Recently, a third SNP (SNP55C > T; rs2870820) was also reported to affect Sp1 binding and MDM2 transcription. In this large population based case-control study, we genotyped MDM2 SNP55 in 10,779 Caucasian individuals, previously genotyped for SNP309 and SNP285, including cases of colon (n = 1,524), lung (n = 1,323), breast (n = 1,709) and prostate cancer (n = 2,488) and 3,735 non-cancer controls, as well as 299 healthy African-Americans...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27565647/a-prostate-cancer-risk-snp-upregulates-the-tumorigenic-lncrna-pcat1
#20
(no author information available yet)
The prostate cancer risk SNP rs7463708 promotes transformation via upregulation of PCAT1 lncRNA.
October 2016: Cancer Discovery
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