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prostate cancer exome

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https://www.readbyqxmd.com/read/28790484/inherited-predisposition-to-prostate-cancer-from-gene-discovery-to-clinical-impact
#1
Kathleen A Cooney
Family history of prostate cancer is one of the three most important risk factors for the disease in addition to age and race. Yet despite the recognition of this significant heritable component, it has been challenging to identify the genes associated with prostate cancer predisposition. Initial approaches focused on the collection of multiplex prostate cancer families. However, despite more than 20 years of linkage studies, few genes have been identified that account for a significant number of hereditary prostate cancer families...
2017: Transactions of the American Clinical and Climatological Association
https://www.readbyqxmd.com/read/28789927/commentary-on-inherited-dna-repair-gene-mutations-in-men-with-metastatic-prostate-cancer-pritchard-cc-mateo-j-walsh-mf-de-sarkar-n-abida-w-beltran-h-garofalo-a-gulati-r-carreira-s-eeles-r-elemento-o-rubin-ma-robinson-d-lonigro-r-hussain-m-chinnaiyan-a-vinson
#2
Byron H Lee
BACKGROUND: Inherited mutations in DNA-repair genes such as BRCA2 are associated with increased risks of lethal prostate cancer. Although the prevalence of germline mutations in DNA-repair genes among men with localized prostate cancer who are unselected for family predisposition is insufficient to warrant routine testing, the frequency of such mutations in patients with metastatic prostate cancer has not been established. METHODS: We recruited 692 men with documented metastatic prostate cancer who were unselected for family history of cancer or age at diagnosis...
August 5, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28751446/gene-copy-number-estimation-from-targeted-next-generation-sequencing-of-prostate-cancer-biopsies-analytic-validation-and-clinical-qualification
#3
George Seed, Wei Yuan, Joaquin Mateo, Suzanne Carreira, Claudia Bertan, Maryou Lambros, Gunther Boysen, Roberta Ferraldeschi, Susana Miranda, Ines Figueiredo, Ruth Riisnaes, Mateus Crespo, Daniel Nava Rodrigues, Eric Talevich, Dan R Robinson, Lakshmi P Kunju, Yi-Mi Wu, Robert Lonigro, Shahneen Sandhu, Arul Chinnayan, Johann S de Bono
Abstract <p>Purpose</p> <p>Precise detection of copy number aberrations (CNAs) from tumor biopsies is critically important to the treatment of metastatic prostate cancer. The use of targeted panel next generation sequencing (NGS) is inexpensive, high throughput and easily feasible, allowing single nucleotide variant calls, but CNA estimation from this remains challenging..</p> <p>Experimental Design</p> <p>We evaluated CNVkit for CNA identification from amplicon-based targeted NGS in a cohort of 110 fresh castration resistant prostate cancer biopsies, and used capture based whole exome sequencing (WES), array comparative genomic hybridization (aCGH), and fluorescent in situ hybridization (FISH) to explore the viability of this approach...
July 27, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28694034/insertion-and-deletion-derived-tumour-specific-neoantigens-and-the-immunogenic-phenotype-a-pan-cancer-analysis
#4
Samra Turajlic, Kevin Litchfield, Hang Xu, Rachel Rosenthal, Nicholas McGranahan, James L Reading, Yien Ning S Wong, Andrew Rowan, Nnennaya Kanu, Maise Al Bakir, Tim Chambers, Roberto Salgado, Peter Savas, Sherene Loi, Nicolai J Birkbak, Laurent Sansregret, Martin Gore, James Larkin, Sergio A Quezada, Charles Swanton
BACKGROUND: The focus of tumour-specific antigen analyses has been on single nucleotide variants (SNVs), with the contribution of small insertions and deletions (indels) less well characterised. We investigated whether the frameshift nature of indel mutations, which create novel open reading frames and a large quantity of mutagenic peptides highly distinct from self, might contribute to the immunogenic phenotype. METHODS: We analysed whole-exome sequencing data from 5777 solid tumours, spanning 19 cancer types from The Cancer Genome Atlas...
August 2017: Lancet Oncology
https://www.readbyqxmd.com/read/28659719/somatic-mutation-analyses-in-studies-of-the-clonal-evolution-and-diagnostic-targets-of-prostate-cancer
#5
REVIEW
Dmitry S Mikhaylenko, Gennady D Efremov, Vladimir V Strelnikov, Dmitry V Zaletaev, Boris Y Alekseev
Prostate cancer (PC) is the most common uro-oncological disease in the global population and still requires a more efficient laboratory diagnosis. Point mutations of oncogenes and tumor sup-pressor genes are the most frequent molecular genetic events in carcinogenesis. The mutations are re-sponsible, to a great extent, for the clonal evolution of cancer and can be considered as primary candi-date molecular markers of PC. Using next-generation sequencing to analyze the mutations in PC, the main molecular PC subtypes were identified, which depended on the presence of fusion genes and FOXA1, CHD1, and SPOP point mutations; other driver mutations responsible for the progression of PC subclones were also characterized...
June 2017: Current Genomics
https://www.readbyqxmd.com/read/28623072/commentary-on-integrative-clinical-genomics-of-advanced-prostate-cancer-robinson-d-van-allen-em-wu-ym-schultz-n-lonigro-rj-mosquera-jm-montgomery-b-taplin-me-pritchard-cc-attard-g-beltran-h-abida-w-bradley-rk-vinson-j-cao-x-vats-p-kunju-lp-hussain-m-feng-fy
#6
Stephen J Freedland, William J Aronson
Toward development of a precision medicine framework for metastatic, castration-resistant prostate cancer (mCRPC), we established a multi-institutional clinical sequencing infrastructure to conduct prospective whole-exome and transcriptome sequencing of bone or soft tissue tumor biopsies from a cohort of 150 mCRPC affected individuals. Aberrations of AR, ETS genes, TP53, and PTEN were frequent (40%-60% of cases), with TP53 and AR alterations enriched in mCRPC compared to primary prostate cancer. We identified new genomic alterations in PIK3CA/B, R-spondin, BRAF/RAF1, APC, β-catenin, and ZBTB16/PLZF...
June 13, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28623070/commentary-on-inherited-dna-repair-gene-mutations-in-men-with-metastatic-prostate-cancer-pritchard-cc-mateo-j-walsh-mf-de-sarkar-n-abida-w-beltran-h-garofalo-a-gulati-r-carreira-s-eeles-r-elemento-o-rubin-ma-robinson-d-lonigro-r-hussain-m-chinnaiyan-a-vinson
#7
Stephen J Freedland, William J Aronson
BACKGROUND: Inherited mutations in DNA-repair genes such as BRCA2 are associated with increased risks of lethal prostate cancer. Although the prevalence of germline mutations in DNA-repair genes among men with localized prostate cancer who are unselected for family predisposition is insufficient to warrant routine testing, the frequency of such mutations in patients with metastatic prostate cancer has not been established. METHODS: We recruited 692 men with documented metastatic prostate cancer who were unselected for family history of cancer or age at diagnosis...
June 13, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28618400/genetic-risk-score-to-predict-biochemical-recurrence-after-radical-prostatectomy-in-prostate-cancer-prospective-cohort-study
#8
Jong Jin Oh, Seunghyun Park, Sang Eun Lee, Sung Kyu Hong, Sangchul Lee, Tae Jin Kim, In Jae Lee, Jin-Nyoung Ho, Sungroh Yoon, Seok-Soo Byun
PURPOSE: To investigate the genetic risk score (GRS) from a large-scale exome-wide association study as a tool of prediction for biochemical recurrence (BCR) after radical prostatectomy (RP) in prostate cancer (PCa). RESULTS: The 16 SNPs were selected as significant predictors of BCR. The GRS in men experiencing BCR was -1.21, significantly higher than in non-BCR patients (-2.43) (p < 0.001). The 10-year BCR-free survival rate was 46.3% vs. 81.8% in the high-versus low GRS group, respectively (p < 0...
May 26, 2017: Oncotarget
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
#9
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/28515055/exome-sequencing-of-african-american-prostate-cancer-reveals-loss-of-function-erf-mutations
#10
Franklin W Huang, Juan Miguel Mosquera, Andrea Garofalo, Coyin Oh, Maria Baco, Ali Amin-Mansour, Bokang Rabasha, Samira Bahl, Stephanie A Mullane, Brian D Robinson, Saud Aldubayan, Francesca Khani, Beerinder Karir, Eejung Kim, Jeremy Chimene-Weiss, Matan Hofree, Alessandro Romanel, Joseph R Osborne, Jong Wook Kim, Gissou Azabdaftari, Anna Woloszynska-Read, Karen Sfanos, Angelo M De Marzo, Francesca Demichelis, Stacey Gabriel, Eliezer M Van Allen, Jill Mesirov, Pablo Tamayo, Mark A Rubin, Isaac J Powell, Levi A Garraway
African-American men have the highest incidence and mortality from prostate cancer. Whether a biological basis exists for this disparity remains unclear. Exome sequencing (n=102) and targeted validation (n = 90) of localized primary hormone-naïve prostate cancer in African-American men identified several gene mutations not previously observed in this context, including recurrent loss-of-function mutations in ERF, an ETS transcriptional repressor, in 5% of cases. Analysis of existing prostate cancer cohorts revealed ERF deletions in 3% of primary prostate cancers and mutations or deletions in ERF in 3-5% of lethal castration-resistant prostate cancers...
May 17, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28453432/multiregional-radiogenomic-assessment-of-prostate-microenvironments-with-multiparametric-mr-imaging-and-dna-whole-exome-sequencing-of-prostate-glands-with-adenocarcinoma
#11
Neema Jamshidi, Daniel J Margolis, Steven Raman, Jiaoti Huang, Robert E Reiter, Michael D Kuo
Purpose To assess the underlying genomic variation of prostate gland microenvironments of patients with prostate adenocarcinoma in the context of colocalized multiparametric magnetic resonance (MR) imaging and histopathologic assessment of normal and abnormal regions by using whole-exome sequencing. Materials and Methods Six patients with prostate adenocarcinoma who underwent robotic prostatectomy with whole-mount preservation of the prostate were identified, which enabled spatial mapping between preoperative multiparametric MR imaging and the gland...
July 2017: Radiology
https://www.readbyqxmd.com/read/28450425/circulating-free-dna-to-guide-prostate-cancer-treatment-with-parp-inhibition
#12
Jane Goodall, Joaquin Mateo, Wei Yuan, Helen Mossop, Nuria Porta, Susana Miranda, Raquel Perez-Lopez, David Dolling, Dan R Robinson, Shahneen Sandhu, Gemma Fowler, Berni Ebbs, Penny Flohr, George Seed, Daniel Nava Rodrigues, Gunther Boysen, Claudia Bertan, Mark Atkin, Matthew Clarke, Mateus Crespo, Ines Figueiredo, Ruth Riisnaes, Semini Sumanasuriya, Pasquale Rescigno, Zafeiris Zafeiriou, Adam Sharp, Nina Tunariu, Diletta Bianchini, Alexa Gillman, Christopher J Lord, Emma Hall, Arul M Chinnaiyan, Suzanne Carreira, Johann S de Bono
Biomarkers for a more precise patient care are needed in metastatic prostate cancer (mPC). We have reported a Phase II trial (TOPARP-A) of the poly(ADP)-ribose polymerase (PARP) inhibitor olaparib in mPC, demonstrating antitumor activity associating with homologous recombination DNA repair defects. We now report targeted and whole exome sequencing of serial circulating-free DNA (cfDNA) samples collected during this trial. Decreases in cfDNA concentration independently associated with outcome in multivariable analyses (HR for overall survival at week 8: 0...
April 27, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28448495/dysregulation-of-inf2-mediated-mitochondrial-fission-in-spop-mutated-prostate-cancer
#13
Xiaofeng Jin, Jie Wang, Kun Gao, Pingzhao Zhang, Longfang Yao, Yan Tang, Lisha Tang, Jian Ma, Jiantao Xiao, Enceng Zhang, Jie Zhu, Bin Zhang, Shi-Min Zhao, Yao Li, Shancheng Ren, Haojie Huang, Long Yu, Chenji Wang
Next-generation sequencing of the exome and genome of prostate cancers has identified numerous genetic alternations. SPOP (Speckle-type POZ Protein) was one of the most frequently mutated genes in primary prostate cancer, suggesting SPOP is a potential driver of prostate cancer development and progression. However, how SPOP mutations contribute to prostate cancer pathogenesis remains poorly understood. SPOP acts as an adaptor protein of the CUL3-RBX1 E3 ubiquitin ligase complex that generally recruits substrates for ubiquitination and subsequent degradation...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28380453/exome-based-genome-wide-association-study-and-risk-assessment-using-genetic-risk-score-to-prostate-cancer-in-the-korean-population
#14
Jong Jin Oh, Soo Ji Lee, Joo-Yeon Hwang, Dokyoon Kim, Sang Eun Lee, Sung Kyu Hong, Jin-Nyoung Ho, Sungroh Yoon, Joohon Sung, Wun-Jae Kim, Seok-Soo Byun
PURPOSE: To investigate exome-wide genetic variants associated with prostate cancer (PCa) in Koreans and evaluate the discriminative ability by the genetic risk score (GRS). PATIENTS AND METHODS: We prospectively recruited 1,001 PCa cases from a tertiary hospital and conducted a case-control study including 2,641 healthy men (Stage I). Participants were analyzed using HumanExome BeadChip. For the external validation, additionally enrolled 514 PCa cases and 548 controls (independent cohort) were analyzed for the identified single nucleotide polymorphisms (SNPs) of Stage I (Stage II)...
July 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28228136/circulating-tumor-cells-capture-disease-evolution-in-advanced-prostate-cancer
#15
Justin Lack, Marc Gillard, Maggie Cam, Gladell P Paner, David J VanderWeele
BACKGROUND: Genetic analysis of advanced cancer is limited by availability of representative tissue. Biopsies of prostate cancer metastasized to bone are invasive with low quantity of tumor tissue. The prostate cancer genome is dynamic, however, with temporal heterogeneity requiring repeated evaluation as the disease evolves. Circulating tumor cells (CTCs) offer an alternative, "liquid biopsy", though single CTC sequencing efforts are laborious with high failure rates. METHODS: We performed exome sequencing of matched treatment-naïve tumor tissue, castrate resistant tumor tissue, and pooled CTC samples, and compared mutations identified in each...
February 23, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28119368/gleason-score-7-prostate-cancers-emerge-through-branched-evolution-of-clonal-gleason-pattern-3-and-4
#16
Adam G Sowalsky, Haydn T Kissick, Sean J Gerrin, Rachel J Schaefer, Zheng Xia, Joshua W Russo, M Simo Arredouani, Glenn J Bubley, Martin G Sanda, Wei Li, Huihui Ye, Steven P Balk
Purpose: The molecular features that account for the distinct histology and aggressive biological behavior of Gleason pattern 4 (Gp4) versus Gp3 prostate cancer, and whether Gp3 tumors progress directly to Gp4, remain to be established.Experimental Design: Whole-exome sequencing and transcriptome profiling of laser capture-microdissected adjacent Gp3 and cribiform Gp4 were used to determine the relationship between these entities.Results: Sequencing confirmed that adjacent Gp3 and Gp4 were clonal based on multiple shared genomic alterations...
July 15, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28068672/genomic-hallmarks-of-localized-non-indolent-prostate-cancer
#17
Michael Fraser, Veronica Y Sabelnykova, Takafumi N Yamaguchi, Lawrence E Heisler, Julie Livingstone, Vincent Huang, Yu-Jia Shiah, Fouad Yousif, Xihui Lin, Andre P Masella, Natalie S Fox, Michael Xie, Stephenie D Prokopec, Alejandro Berlin, Emilie Lalonde, Musaddeque Ahmed, Dominique Trudel, Xuemei Luo, Timothy A Beck, Alice Meng, Junyan Zhang, Alister D'Costa, Robert E Denroche, Haiying Kong, Shadrielle Melijah G Espiritu, Melvin L K Chua, Ada Wong, Taryne Chong, Michelle Sam, Jeremy Johns, Lee Timms, Nicholas B Buchner, Michèle Orain, Valérie Picard, Helène Hovington, Alexander Murison, Ken Kron, Nicholas J Harding, Christine P'ng, Kathleen E Houlahan, Kenneth C Chu, Bryan Lo, Francis Nguyen, Constance H Li, Ren X Sun, Richard de Borja, Christopher I Cooper, Julia F Hopkins, Shaylan K Govind, Clement Fung, Daryl Waggott, Jeffrey Green, Syed Haider, Michelle A Chan-Seng-Yue, Esther Jung, Zhiyuan Wang, Alain Bergeron, Alan Dal Pra, Louis Lacombe, Colin C Collins, Cenk Sahinalp, Mathieu Lupien, Neil E Fleshner, Housheng H He, Yves Fradet, Bernard Tetu, Theodorus van der Kwast, John D McPherson, Robert G Bristow, Paul C Boutros
Prostate tumours are highly variable in their response to therapies, but clinically available prognostic factors can explain only a fraction of this heterogeneity. Here we analysed 200 whole-genome sequences and 277 additional whole-exome sequences from localized, non-indolent prostate tumours with similar clinical risk profiles, and carried out RNA and methylation analyses in a subset. These tumours had a paucity of clinically actionable single nucleotide variants, unlike those seen in metastatic disease. Rather, a significant proportion of tumours harboured recurrent non-coding aberrations, large-scale genomic rearrangements, and alterations in which an inversion repressed transcription within its boundaries...
January 19, 2017: Nature
https://www.readbyqxmd.com/read/27902461/whole-exome-sequencing-in-75-high-risk-families-with-validation-and-replication-in-independent-case-control-studies-identifies-tango2-or5h14-and-chad-as-new-prostate-cancer-susceptibility-genes
#18
Danielle M Karyadi, Milan S Geybels, Eric Karlins, Brennan Decker, Laura McIntosh, Amy Hutchinson, Suzanne Kolb, Shannon K McDonnell, Belynda Hicks, Sumit Middha, Liesel M FitzGerald, Melissa S DeRycke, Meredith Yeager, Daniel J Schaid, Stephen J Chanock, Stephen N Thibodeau, Sonja I Berndt, Janet L Stanford, Elaine A Ostrander
Prostate cancer (PCa) susceptibility is defined by a continuum from rare, high-penetrance to common, low-penetrance alleles. Research to date has concentrated on identification of variants at the ends of that continuum. Taking an alternate approach, we focused on the important but elusive class of low-frequency, moderately penetrant variants by performing disease model-based variant filtering of whole exome sequence data from 75 hereditary PCa families. Analysis of 341 candidate risk variants identified nine variants significantly associated with increased PCa risk in a population-based, case-control study of 2,495 men...
January 3, 2017: Oncotarget
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
#19
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/27844240/identification-of-a-rare-germline-nbn-gene-mutation-by-whole-exome-sequencing-in-a-lung-cancer-survivor-from-a-large-family-with-various-types-of-cancer
#20
Makia J Marafie, Mohammed Dashti, Fahd Al-Mulla
Nijmegen breakage syndrome is an autosomal recessive disorder caused by biallelic mutation in NBN gene. It is characterized by microcephaly, growth retardation, immuno-deficiency and cancer predisposition. The monoallelic carriers of NBN gene are also reported to be at increased risk of developing various types of malignancy. We have investigated an individual with lung cancer from an extended family segregating different types of hereditary cancer over several generations, including lung, breast, ovarian, colon, prostate and renal cancers...
November 14, 2016: Familial Cancer
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