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https://www.readbyqxmd.com/read/29610475/the-long-tail-of-oncogenic-drivers-in-prostate-cancer
#1
Joshua Armenia, Stephanie A M Wankowicz, David Liu, Jianjiong Gao, Ritika Kundra, Ed Reznik, Walid K Chatila, Debyani Chakravarty, G Celine Han, Ilsa Coleman, Bruce Montgomery, Colin Pritchard, Colm Morrissey, Christopher E Barbieri, Himisha Beltran, Andrea Sboner, Zafeiris Zafeiriou, Susana Miranda, Craig M Bielski, Alexander V Penson, Charlotte Tolonen, Franklin W Huang, Dan Robinson, Yi Mi Wu, Robert Lonigro, Levi A Garraway, Francesca Demichelis, Philip W Kantoff, Mary-Ellen Taplin, Wassim Abida, Barry S Taylor, Howard I Scher, Peter S Nelson, Johann S de Bono, Mark A Rubin, Charles L Sawyers, Arul M Chinnaiyan, Nikolaus Schultz, Eliezer M Van Allen
Comprehensive genomic characterization of prostate cancer has identified recurrent alterations in genes involved in androgen signaling, DNA repair, and PI3K signaling, among others. However, larger and uniform genomic analysis may identify additional recurrently mutated genes at lower frequencies. Here we aggregate and uniformly analyze exome sequencing data from 1,013 prostate cancers. We identify and validate a new class of E26 transformation-specific (ETS)-fusion-negative tumors defined by mutations in epigenetic regulators, as well as alterations in pathways not previously implicated in prostate cancer, such as the spliceosome pathway...
April 2, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29606109/neoadjuvant-degarelix-with-or-without-apalutamide-followed-by-radical-prostatectomy-for-intermediate-and-high-risk-prostate-cancer-arneo-a-randomized-double-blind-placebo-controlled-trial
#2
Lorenzo Tosco, Annouschka Laenen, Thomas Gevaert, Isabelle Salmon, Christine Decaestecker, Elai Davicioni, Christine Buerki, Frank Claessens, Johan Swinnen, Karolien Goffin, Raymond Oyen, Wouter Everaerts, Lisa Moris, Gert De Meerleer, Karin Haustermans, Steven Joniau
BACKGROUND: Recent retrospective data suggest that neoadjuvant androgen deprivation therapy can improve the prognosis of high-risk prostate cancer (PCa) patients. Novel androgen receptor pathway inhibitors are nowadays available for treatment of metastatic PCa and these compounds are promising for early stage disease. Apalutamide is a pure androgen antagonist with a very high affinity with the androgen receptor. The combination of apalutamide with degarelix, an LHRH antagonist, could increase the efficacy compared to degarelix alone...
April 2, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29535823/overexpression-of-p54-nrb-nono-induces-differential-epha6-splicing-and-contributes-to-castration-resistant-prostate-cancer-growth
#3
Ryuji Yamamoto, Tsuyoshi Osawa, Yusuke Sasaki, Shogo Yamamoto, Motonobu Anai, Kouji Izumi, Yoshihiro Matsumura, Juro Sakai, Hiroyuki Aburatani, Atsushi Mizokami, Tatsuhiko Kodama, Toshiya Tanaka
The non-POU domain-containing octamer binding protein p54nrb /NONO is a multifunctional nuclear protein involved in RNA splicing, processing, and transcriptional regulation of nuclear hormone receptors. Through chromosome copy number analysis via whole-exome sequencing, we revealed amplification of the chromosome Xq11.22-q21.33 locus containing the androgen receptor ( AR ) and NONO genes in androgen-independent, castration-resistant prostate cancer (CRPC)-like LNCaP-SF cells. Moreover, NONO was frequently amplified and overexpressed in patients with CRPC...
February 13, 2018: Oncotarget
https://www.readbyqxmd.com/read/29520813/a-comprehensive-evaluation-of-chek2-germline-mutations-in-men-with-prostate-cancer
#4
Yishuo Wu, Hongjie Yu, S Lilly Zheng, Rong Na, Mufaddal Mamawala, Tricia Landis, Kathleen Wiley, Jacqueline Petkewicz, Sameep Shah, Zhuqing Shi, Kristian Novakovic, Michael McGuire, Charles B Brendler, Qiang Ding, Brian T Helfand, H Ballentine Carter, Kathleen A Cooney, William B Isaacs, Jianfeng Xu
BACKGROUND: Germline mutations in CHEK2 have been associated with prostate cancer (PCa) risk. Our objective is to examine whether germline pathogenic CHEK2 mutations can differentiate risk of lethal from indolent PCa. METHODS: A case-case study of 703 lethal PCa patients and 1455 patients with low-risk localized PCa of European, African, and Chinese origin was performed. Germline DNA samples from these patients were sequenced for CHEK2. Mutation carrier rates and their association with lethal PCa were analyzed using the Fisher exact test and Kaplan-Meier survival analysis...
June 2018: Prostate
https://www.readbyqxmd.com/read/29447163/paternal-lineage-early-onset-hereditary-ovarian-cancers-a-familial-ovarian-cancer-registry-study
#5
Kevin H Eng, J Brian Szender, John Lewis Etter, Jasmine Kaur, Samantha Poblete, Ruea-Yea Huang, Qianqian Zhu, Katherine A Grzesik, Sebastiano Battaglia, Rikki Cannioto, John J Krolewski, Emese Zsiros, Peter J Frederick, Shashikant B Lele, Kirsten B Moysich, Kunle O Odunsi
Given prior evidence that an affected woman conveys a higher risk of ovarian cancer to her sister than to her mother, we hypothesized that there exists an X-linked variant evidenced by transmission to a woman from her paternal grandmother via her father. We ascertained 3,499 grandmother/granddaughter pairs from the Familial Ovarian Cancer Registry at the Roswell Park Cancer Institute observing 892 informative pairs with 157 affected granddaughters. We performed germline X-chromosome exome sequencing on 186 women with ovarian cancer from the registry...
February 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29398457/genomic-heterogeneity-within-individual-prostate-cancer-foci-impacts-predictive-biomarkers-of-targeted-therapy
#6
David J VanderWeele, Richard Finney, Kotoe Katayama, Marc Gillard, Gladell Paner, Seiya Imoto, Rui Yamaguchi, David Wheeler, Justin Lack, Maggie Cam, Andrea Pontier, Yen Thi Minh Nguyen, Kazuhiro Maejima, Aya Sasaki-Oku, Kaoru Nakano, Hiroko Tanaka, Donald Vander Griend, Michiaki Kubo, Mark J Ratain, Satoru Miyano, Hidewaki Nakagawa
BACKGROUND: Most lethal prostate cancers progress from relapse of aggressive primary disease. Recently, the most significant advances in survival benefit from systemic therapy have come from moving the administration of therapy to an earlier disease state. There is movement toward using biomarkers from the intraprostatic index lesion to guide early systemic therapy. OBJECTIVE: To determine the genomic heterogeneity, including the heterogeneity of predictive biomarkers, within the index focus of treatment-naïve prostate cancer...
February 1, 2018: European Urology Focus
https://www.readbyqxmd.com/read/29367197/circulating-tumor-dna-genomics-correlate-with-resistance-to-abiraterone-and-enzalutamide-in-prostate-cancer
#7
Matti Annala, Gillian Vandekerkhove, Daniel Khalaf, Sinja Taavitsainen, Kevin Beja, Evan W Warner, Katherine Sunderland, Christian Kollmannsberger, Bernhard J Eigl, Daygen Finch, Conrad D Oja, Joanna Vergidis, Muhammad Zulfiqar, Arun A Azad, Matti Nykter, Martin E Gleave, Alexander W Wyatt, Kim N Chi
Primary resistance to androgen receptor (AR)-directed therapies in metastatic castration-resistant prostate cancer (mCRPC) is poorly understood. We randomized 202 patients with treatment-naïve mCRPC to abiraterone or enzalutamide and performed whole-exome and deep targeted 72-gene sequencing of plasma cell-free DNA prior to therapy. For these agents, which have never been directly compared, time to progression was similar. Defects in BRCA2 and ATM were strongly associated with poor clinical outcomes independently of clinical prognostic factors and circulating tumor DNA abundance...
April 2018: Cancer Discovery
https://www.readbyqxmd.com/read/29359367/truncating-mutations-of-tp53aip1-gene-predispose-to-cutaneous-melanoma
#8
Meriem Benfodda, Steven Gazal, Vincent Descamps, Nicole Basset-Seguin, Lydia Deschamps, Luc Thomas, Celeste Lebbe, Philippe Saiag, Roberto Zanetti, Lidia Sacchetto, Giovanna Chiorino, Maria Scatolini, Bernard Grandchamp, Armand Bensussan, Nadem Soufir
Genetic predisposition to cutaneous malignant melanoma (CMM) involves highly penetrant predisposing genes and low and intermediate penetrant predisposing alleles. However, the missing heritability in (CMM) is still high. For such and in order to identify new genetic factors for CMM, we conducted an exome sequencing study in high-risk CMM patients. Two rounds of exome sequencing were successively performed in 33 and 27 high-risk patients. We focused on genes carrying rare nonsense, frameshift, and splice variants (allelic frequency <1%) that were present in both series of exomes...
June 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29357011/immunogenomics-a-negative-prostate-cancer-outcome-associated-with-tcr-%C3%AE-%C3%AE-recombinations
#9
Yaping N Tu, Wei Lue Tong, John M Yavorski, George Blanck
We developed a scripted algorithm, based on previous, earlier editions of the algorithm, to mine prostate cancer exome files for T-cell receptor (TcR) recombination reads: Reads representing TcR gene recombinations were identified in 497 prostate cancer exome files from the cancer genome atlas (TCGA). As has been reported for melanoma, co-detection of productive TcR-α and TcR-β recombination reads correlated with an RNA expression signature representing T-cell exhaustion, particularly with high RNA levels for PD-1 and PD-L1, in comparison to several different control sets of samples...
January 22, 2018: Cancer Microenvironment: Official Journal of the International Cancer Microenvironment Society
https://www.readbyqxmd.com/read/29297493/the-genomics-of-prostate-cancer-emerging-understanding-with-technologic-advances
#10
Mark A Rubin, Francesca Demichelis
With the advent of next-generation sequencing technologies and large whole-exome and genome studies in prostate and other cancers, our understanding of the landscape of genomic alterations has dramatically been refined. In additional to well-known alterations in genomic regions involving 8p, 8q, 10q23, common ETS translocations and androgen receptor amplifications, newer technology have uncovered recurrent mutations in SPOP, FOXA1, MED12, IDH and complex large scale genomic alterations (eg, chromoplexy). This review surveys the enhanced landscape of genomic alterations in clinically localized and advanced prostate cancer...
January 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29229583/integrative-genomic-analysis-of-coincident-cancer-foci-implicates-ctnnb1-and-pten-alterations-in-ductal-prostate-cancer
#11
Marc Gillard, Justin Lack, Andrea Pontier, Divya Gandla, David Hatcher, Adam G Sowalsky, Jose Rodriguez-Nieves, Donald Vander Griend, Gladell Paner, David VanderWeele
BACKGROUND: Ductal adenocarcinoma of the prostate is an aggressive subtype, with high rates of biochemical recurrence and overall poor prognosis. It is frequently found coincident with conventional acinar adenocarcinoma. The genomic features driving evolution to its ductal histology and the biology associated with its poor prognosis remain unknown. OBJECTIVE: To characterize genomic features distinguishing ductal adenocarcinoma from coincident acinar adenocarcinoma foci from the same patient...
December 8, 2017: European Urology Focus
https://www.readbyqxmd.com/read/29228579/a-genetic-variant-in-slc28a3-rs56350726-is-associated-with-progression-to-castration-resistant-prostate-cancer-in-a-korean-population-with-metastatic-prostate-cancer
#12
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 variats in mPCa and progession 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...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29219214/whole-exome-sequencing-identifies-a-germline-met-mutation-in-two-siblings-with-hereditary-wild-type-ret-medullary-thyroid-cancer
#13
Marialuisa Sponziello, Silvia Benvenuti, Alessandra Gentile, Valeria Pecce, Francesca Rosignolo, Anna Rita Virzì, Melissa Milan, Paolo M Comoglio, Eric Londin, Paolo Fortina, Agnese Barnabei, Marialuisa Appetecchia, Ferdinando Marandino, Diego Russo, Sebastiano Filetti, Cosimo Durante, Antonella Verrienti
Whole exome sequencing (WES) was used to investigate two Italian siblings with wild-type RET genotype, who developed medullary thyroid cancers (MTCs) and, later, primary prostate and breast cancers, respectively. The proband's MTC harbored a p.Met918Thr RET mutation; his sister's MTC was RET/RAS wild-type. Both siblings had a germline mutation (p.Arg417Gln) in the extracellular Sema domain of the proto-oncogene MET. Experiments involving ectopic expression of MET p.Arg417Gln in MET-negative T47D breast cancer cells documented the mutant receptor's functionality and its ability to enhance cell migration and invasion...
March 2018: Human Mutation
https://www.readbyqxmd.com/read/29206995/concordance-of-circulating-tumor-dna-and-matched-metastatic-tissue-biopsy-in-prostate-cancer
#14
Alexander W Wyatt, Matti Annala, Rahul Aggarwal, Kevin Beja, Felix Feng, Jack Youngren, Adam Foye, Paul Lloyd, Matti Nykter, Tomasz M Beer, Joshi J Alumkal, George V Thomas, Robert E Reiter, Matthew B Rettig, Christopher P Evans, Allen C Gao, Kim N Chi, Eric J Small, Martin E Gleave
Background: Real-time knowledge of the somatic genome can influence management of patients with metastatic castration-resistant prostate cancer (mCRPC). While routine metastatic tissue biopsy is challenging in mCRPC, plasma circulating tumor DNA (ctDNA) has emerged as a minimally invasive tool to sample the tumor genome. However, no systematic comparisons of matched "liquid" and "solid" biopsies have been performed that would enable ctDNA profiling to replace the need for direct tissue sampling...
December 1, 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29145505/spontaneous-development-of-epstein-barr-virus-associated-human-lymphomas-in-a-prostate-cancer-xenograft-program
#15
Alberto J Taurozzi, Ramprakash Beekharry, Michelle Wantoch, Marie-Christine Labarthe, Hannah F Walker, Robert I Seed, Matthew Simms, Greta Rodrigues, James Bradford, Geertje van der Horst, Gabri van der Pluijm, Anne T Collins
Prostate cancer research is hampered by the lack of in vivo preclinical models that accurately reflect patient tumour biology and the clinical heterogeneity of human prostate cancer. To overcome these limitations we propagated and characterised a new collection of patient-derived prostate cancer xenografts. Tumour fragments from 147 unsupervised, surgical prostate samples were implanted subcutaneously into immunodeficient Rag2-/-γC-/- mice within 24 hours of surgery. Histologic and molecular characterisation of xenografts was compared with patient characteristics, including androgen-deprivation therapy, and exome sequencing...
2017: PloS One
https://www.readbyqxmd.com/read/29109393/scalable-whole-exome-sequencing-of-cell-free-dna-reveals-high-concordance-with-metastatic-tumors
#16
Viktor A Adalsteinsson, Gavin Ha, Samuel S Freeman, Atish D Choudhury, Daniel G Stover, Heather A Parsons, Gregory Gydush, Sarah C Reed, Denisse Rotem, Justin Rhoades, Denis Loginov, Dimitri Livitz, Daniel Rosebrock, Ignaty Leshchiner, Jaegil Kim, Chip Stewart, Mara Rosenberg, Joshua M Francis, Cheng-Zhong Zhang, Ofir Cohen, Coyin Oh, Huiming Ding, Paz Polak, Max Lloyd, Sairah Mahmud, Karla Helvie, Margaret S Merrill, Rebecca A Santiago, Edward P O'Connor, Seong H Jeong, Rachel Leeson, Rachel M Barry, Joseph F Kramkowski, Zhenwei Zhang, Laura Polacek, Jens G Lohr, Molly Schleicher, Emily Lipscomb, Andrea Saltzman, Nelly M Oliver, Lori Marini, Adrienne G Waks, Lauren C Harshman, Sara M Tolaney, Eliezer M Van Allen, Eric P Winer, Nancy U Lin, Mari Nakabayashi, Mary-Ellen Taplin, Cory M Johannessen, Levi A Garraway, Todd R Golub, Jesse S Boehm, Nikhil Wagle, Gad Getz, J Christopher Love, Matthew Meyerson
Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing...
November 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/29100285/genetic-risk-score-to-predict-biochemical-recurrence-after-radical-prostatectomy-in-prostate-cancer-prospective-cohort-study
#17
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...
September 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/29069303/a-prospective-genome-wide-study-of-prostate-cancer-metastases-reveals-association-of-wnt-pathway-activation-and-increased-cell-cycle-proliferation-with-primary-resistance-to-abiraterone-acetate-prednisone
#18
L Wang, S M Dehm, D W Hillman, H Sicotte, W Tan, M Gormley, V Bhargava, R Jimenez, F Xie, P Yin, S Qin, F Quevedo, B A Costello, H C Pitot, T Ho, A H Bryce, Z Ye, Y Li, P Eiken, P T Vedell, P Barman, B P McMenomy, T D Atwell, R E Carlson, M Ellingson, B W Eckloff, R Qin, F Ou, S N Hart, H Huang, J Jen, E D Wieben, K R Kalari, R M Weinshilboum, L Wang, M Kohli
Background: Genomic aberrations have been identified in metastatic castration-resistant prostate cancer (mCRPC), but molecular predictors of resistance to abiraterone acetate/prednisone (AA/P) treatment are not known. Patients and methods: In a prospective clinical trial, mCRPC patients underwent whole-exome sequencing (n = 82) and RNA sequencing (n = 75) of metastatic biopsies before initiating AA/P with the objective of identifying genomic alterations associated with resistance to AA/P...
February 1, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29030706/rare-adar-and-rnaseh2b-variants-and-a-type-i-interferon-signature-in-glioma-and-prostate-carcinoma-risk-and-tumorigenesis
#19
Ulrike Beyer, Frank Brand, Helge Martens, Julia Weder, Arne Christians, Natalie Elyan, Bettina Hentschel, Manfred Westphal, Gabriele Schackert, Torsten Pietsch, Bujung Hong, Joachim K Krauss, Amir Samii, Peter Raab, Anibh Das, Claudia A Dumitru, I Erol Sandalcioglu, Oliver W Hakenberg, Andreas Erbersdobler, Ulrich Lehmann, Guido Reifenberger, Michael Weller, Martin A M Reijns, Matthias Preller, Bettina Wiese, Christian Hartmann, Ruthild G Weber
In search of novel germline alterations predisposing to tumors, in particular to gliomas, we studied a family with two brothers affected by anaplastic gliomas, and their father and paternal great-uncle diagnosed with prostate carcinoma. In this family, whole-exome sequencing yielded rare, simultaneously heterozygous variants in the Aicardi-Goutières syndrome (AGS) genes ADAR and RNASEH2B co-segregating with the tumor phenotype. AGS is a genetically induced inflammatory disease particularly of the brain, which has not been associated with a consistently increased cancer risk to date...
October 13, 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/29023722/prevalence-and-clonality-of-synchronous-primary-carcinomas-in-the-bladder-and-prostate
#20
Ying Jing, Ruiyun Zhang, Pengfei Ma, Mei-Chun Cai, Guanglei Zhuang, Haige Chen
Incidental prostate adenocarcinoma (IPCa) has been frequently discovered during postoperative histopathological evaluation of radical cystoprostatectomy specimens in patients with bladder cancer (BCa). However, there is currently no conclusive study addressing the clinical significance of IPCa and the clonal relatedness of IPCa and BCa. Here, we performed a retrospective single-center review of 919 BCa cases and an additional meta-analysis including a total of 19 868 individuals who underwent radical cystectomy for bladder cancer...
January 2018: Journal of Pathology
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