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9p21.3

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https://www.readbyqxmd.com/read/30098783/oncogenic-drivers-in-11q13-associated-with-prognosis-and-response-to-therapy-in-advanced-oropharyngeal-carcinomas
#1
M C Barros-Filho, L A Reis-Rosa, M Hatakeyama, F A Marchi, T Chulam, C Scapulatempo-Neto, U R Nicolau, A L Carvalho, C A L Pinto, S A Drigo, L P Kowalski, S R Rogatto
OBJECTIVES: To identify potential molecular drivers associated with prognosis and response to treatment in advanced oropharyngeal squamous cell carcinomas (OPSCC). MATERIALS AND METHODS: Thirty-three OPSCC biopsies from untreated Brazilian patients were evaluated for human papilloma virus genotyping, genome wide copy number alterations and gene expression profiling. Data were integrated using CONEXIC algorithm. Validation with TCGA dataset and confirmation by RT-qPCR of candidate genes were performed...
August 2018: Oral Oncology
https://www.readbyqxmd.com/read/30072947/mediating-effect-of-diabetes-mellitus-on-the-association-between-chromosome-9p21-3-locus-and-myocardial-infarction-risk-a-case-control-study-in-shanghai-china
#2
Zhijun Wu, Haihui Sheng, Xiuxiu Su, Xiang Gao, Lin Lu, Wei Jin
Background: Previous genome-wide association studies revealed that the chromosome 9p21.3 locus is associated with an increased risk of myocardial infarction (MI) and diabetes mellitus (DM). However, it is unclear whether the 9p21.3-MI association is direct or mediated by pathways related to DM. Study Design: We applied mediation analysis to examine the potential mediating effect of DM on the association between the 9p21.3 genetic risk score (GRS; ranged from 0 to 8) and MI in a case-control study of 865 MI patients and 927 controls without coronary artery disease (CAD)...
2018: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/30050779/genome-wide-copy-number-analyses-of-samples-from-lace-bio-project-identify-novel-prognostic-and-predictive-markers-in-early-stage-non-small-cell-lung-cancer
#3
Federico Rotolo, Chang-Qi Zhu, Elisabeth Brambilla, Stephen L Graziano, Ken Olaussen, Thierry Le-Chevalier, Jean-Pierre Pignon, Robert Kratzke, Jean-Charles Soria, Frances A Shepherd, Lesley Seymour, Stefan Michiels, Ming-Sound Tsao
Background: Adjuvant chemotherapy (ACT) provides modest benefit in resected non-small cell lung cancer (NSCLC) patients. Genome-wide studies have identified gene copy number aberrations (CNA), but their prognostic implication is unknown. Methods: DNA from 1,013 FFPE tumor samples from three pivotal multicenter randomized trials (ACT vs. control) in the LACE-Bio consortium (median follow-up: 5.2 years) was successfully extracted, profiled using a molecular inversion probe SNP assay, normalized relative to a pool of normal tissues and segmented...
June 2018: Translational Lung Cancer Research
https://www.readbyqxmd.com/read/30018130/machine-learning-for-better-prognostic-stratification-and-driver-gene-identification-using-somatic-copy-number-variations-in-anaplastic-oligodendroglioma
#4
Shai Rosenberg, Francois Ducray, Agusti Alentorn, Caroline Dehais, Nabila Elarouci, Aurelie Kamoun, Yannick Marie, Marie-Laure Tanguy, Aurélien De Reynies, Karima Mokhtari, Dominique Figarella-Branger, Jean-Yves Delattre, Ahmed Idbaih
BACKGROUND: 1p/19q-codeleted anaplastic gliomas have variable clinical behavior. We have recently shown that the common 9p21.3 allelic loss is an independent prognostic factor in this tumor type. The aim of this study is to identify less frequent genomic copy number variations (CNVs) with clinical importance that may shed light on molecular oncogenesis of this tumor type. MATERIALS AND METHODS: A cohort of 197 patients with anaplastic oligodendroglioma was collected as part of the French POLA network...
July 17, 2018: Oncologist
https://www.readbyqxmd.com/read/30008256/loss-of-heterozygosity-of-key-tumor-suppressor-genes-in-advanced-renal-cancer-patients-treated-with-nivolumab
#5
Melissa Bersanelli, Letizia Gnetti, Cinzia Azzoni, Lorena Bottarelli, Nicola Sverzellati, Nicoletta Campanini, Elena Varotti, Michele Corrado, Raffaele Parziale, Elena Rapacchi, Giuseppe Caruso, Francesco Leonardi, Enrico Maria Silini, Sebastiano Buti
AIM: We studied the possible clinical significance of loss of heterozygosity (LOH) at key tumor suppressor genes loci in advanced renal cancer patients treated with nivolumab. METHODS: LOH study was performed on 3p14.2 (FHIT gene); 3p21.3-21.2; 9p21 (BDMF gene); 9p22 (SH3GL2 gene). RESULTS: Of 12 patients, 8 (67%) had LOH. The most affected gene was FHIT. All five patients with LOH at FHIT locus had good outcome, mean progression free survival of 6...
July 2018: Immunotherapy
https://www.readbyqxmd.com/read/30003307/genome-wide-association-study-of-coronary-artery-disease-among-individuals-with-diabetes-the-uk-biobank
#6
Tove Fall, Stefan Gustafsson, Marju Orho-Melander, Erik Ingelsson
AIMS/HYPOTHESIS: Coronary artery disease (CAD) is a common complication among individuals with diabetes. A better understanding of the genetic background of CAD in this population has the potential to suggest novel molecular targets for screening, risk assessment and drug development. METHODS: We performed a genome-wide association study of CAD in 15,666 unrelated individuals (3,968 CAD cases and 11,698 controls) of white British ancestry with diabetes at inclusion in the UK Biobank study...
July 12, 2018: Diabetologia
https://www.readbyqxmd.com/read/29924316/genome-wide-association-study-of-familial-lung-cancer
#7
Jinyoung Byun, Ann G Schwartz, Christine Lusk, Angela S Wenzlaff, Mariza de Andrade, Diptasri Mandal, Colette Gaba, Ping Yang, Ming You, Elena Y Kupert, Marshall W Anderson, Younghun Han, Yafang Li, David Qian, Adrienne Stilp, Cathy Laurie, Sarah Nelson, Wenying Zheng, Rayjean J Hung, Valerie Gaborieau, James Mckay, Paul Brennan, Neil E Caporaso, Maria Teresa Landi, Xifeng Wu, John R McLaughlin, Yonathan Brhane, Yohan Bossé, Susan M Pinney, Joan E Bailey-Wilson, Christopher I Amos
To identify genetic variation associated with lung cancer risk, we performed a genome-wide association analysis of 685 lung cancer cases that had a family history of two or more first or second degree relatives compared with 744 controls without lung cancer that were genotyped on an Illumina Human OmniExpressExome-8v1 array. To ensure robust results, we further evaluated these findings using data from six additional studies that were assembled through the Transdisciplinary Research on Cancer of the Lung Consortium comprising 1,993 familial cases and 33,690 controls...
June 19, 2018: Carcinogenesis
https://www.readbyqxmd.com/read/29876948/review-article-asia-pacific-consensus-recommendations-on-endoscopic-tissue-acquisition-for-biliary-strictures
#8
REVIEW
B Sun, J H Moon, Q Cai, R Rerknimitr, S Ma, S Lakhtakia, S Ryozawa, H Kutsumi, I Yasuda, H Shiomi, X Li, W Li, X Zhang, T Itoi, H-P Wang, D Qian, J Y Wong Lau, Z Yang, M Ji, B Hu
BACKGROUND: Pre-operative tissue diagnosis for suspected malignant biliary strictures remains challenging. AIM: To develop evidence-based consensus statements on endoscopic tissue acquisition for biliary strictures. METHODS: The initial draft of statements was prepared following a systematic literature review. A committee of 20 experts from Asia-Pacific region then reviewed, discussed, and modified the statements. Two rounds of independent voting were conducted to reach a final version...
July 2018: Alimentary Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/29868613/roles-of-the-chr-9p21-3-anril-locus-in-regulating-inflammation-and-implications-for-anti-inflammatory-drug-target-identification
#9
Ghazal Aarabi, Tanja Zeller, Guido Heydecke, Matthias Munz, Arne Schäfer, Udo Seedorf
Periodontitis (PD) is a common gingival infectious disease caused by an over-aggressive inflammatory reaction to dysbiosis of the oral microbiome. The disease induces a profound systemic inflammatory host response, that triggers endothelial dysfunction and pro-thrombosis and thus may aggravate atherosclerotic vascular disease and its clinical complications. Recently, a risk haplotype at the ANRIL / CDKN2B-AS1 locus on chromosome 9p21.3, that is not only associated with coronary artery disease / myocardial infarction (CAD/MI) but also with PD, could be identified by genome-wide association studies...
2018: Frontiers in Cardiovascular Medicine
https://www.readbyqxmd.com/read/29791233/association-of-a-chromosome-locus-9p21-3-cdkn2b-as1-variant-rs4977574-with-hypertension-the-tamrisk-study
#10
Tarja Kunnas, Jaakko Piesanen, Seppo T Nikkari
AIMS: Chromosome locus 9p21.3 CDKN2B antisense RNA 1 (CDKN2B-AS1) has been found to contain multiple genetic markers for coronary artery disease (CAD) by genome-wide association studies (GWAS). Of these, the association of variants rs4977574, rs10757274, and rs2383206 with hypertension was studied in the Tampere adult population cardiovascular risk study (TAMRISK). MATERIALS AND METHODS: A Finnish cohort of 336 subjects diagnosed with hypertension and 444 controls was analyzed...
May 2018: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/29779219/immunohistochemical-and-molecular-analysis-of-spitzoid-neoplasms-with-pulverocyte-subclones
#11
S M Amin, A M Haugh, J A Bubley, A E Verzì, E A Merkel, C Y Lee, V L Quan, E M Garfield, L M Sholl, B Zhang, P Gerami
BACKGROUND: Clonal naevi are characterized by a focal proliferation of pigmented melanocytes in an otherwise banal naevus. These subclones are often composed of aggregates of larger, epithelioid melanocytes with nuclear atypia and dusty-grey cytoplasmic pigmentation, which are referred to as 'pulverocytes', and this finding may lead to a misdiagnosis of malignant melanoma (MM). AIM: To characterize the significance of subclones of dusty-grey pigmented epithelioid melanocytes within spitzoid neoplasms...
May 20, 2018: Clinical and Experimental Dermatology
https://www.readbyqxmd.com/read/29778230/etv6-runx1-positive-childhood-acute-lymphoblastic-leukemia-all-the-spectrum-of-clonal-heterogeneity-and-its-impact-on-prognosis
#12
Μ Αmpatzidou, S I Papadhimitriou, G Paterakis, D Pavlidis, Κ Tsitsikas, I V Kostopoulos, V Papadakis, G Vassilopoulos, S Polychronopoulou
The prognostic significance of the ETV6/RUNX1-fusion and of the accompanying aberrations is disputable; whether co-existing sub-clones are responsible for delayed MRD-clearance and thus, moderate outcome, remains to be clarified. We studied, in a paediatric cohort of 119 B-ALLs, the relation between the ETV6/RUNX1 aberration and the co-existing subclones with (a) presenting clinical/biological features, (b) early response to treatment(MRD) and (c) long-term outcome over a 12-year period. Patients were homogeneously treated according to BFM-based-protocols...
August 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29708279/cdkn2a-loss-and-pik3ca-mutation-in-myoepithelial-like-metaplastic-breast-cancer
#13
Stephan Bartels, Jana Lisa van Luttikhuizen, Matthias Christgen, Lavinia Mägel, Angelina Luft, Sonja Hänzelmann, Ulrich Lehmann, Brigitte Schlegelberger, Fabian Leo, Doris Steinemann, Hans Kreipe
Metaplastic breast carcinoma comprises a heterogeneous group of tumours with poorly understood pathogenesis. A subset of metaplastic breast cancers show myoepithelial differentiation and constitute a morphological spectrum with ill-defined borders from fibromatosis-like spindle cell carcinoma to myoepithelial carcinoma. In a series of 34 metaplastic breast cancers with spindle cell and myoepithelial differentiation, we found recurrent genetic aberrations, which set them apart from other metaplastic breast cancers and suggest a unique pathogenesis...
July 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29691299/undifferentiated-sarcomas-in-children-harbor-clinically-relevant-oncogenic-fusions-and-gene-copy-number-alterations-a-report-from-the-children-s-oncology-group
#14
Theodore W Laetsch, Angshumoy Roy, Lin Xu, Jennifer O Black, Cheryl M Coffin, Yueh-Yun Chi, Jing Tian, Sheri L Spunt, Douglas S Hawkins, Julia A Bridge, D Williams Parsons, Stephen X Skapek
Purpose: A comprehensive analysis of the genomics of undifferentiated sarcomas (UDS) is lacking. We analyzed copy-number alterations and fusion status in patients with UDS prospectively treated on Children's Oncology Group protocol ARST0332. Experimental Design: Copy-number alterations were assessed by OncoScan FFPE Express on 32 UDS. Whole-exome and transcriptome libraries from eight tumors with sufficient archived material were sequenced on HiSeq (2 × 100 bp). Targeted RNA-sequencing using Archer chemistry was performed on two additional cases...
April 24, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29663171/prognostic-relevance-of-mutations-and-copy-number-alterations-assessed-with-targeted-next-generation-sequencing-in-idh-mutant-grade-ii-glioma
#15
Maarten M J Wijnenga, Pim J French, Hendrikus J Dubbink, Winand N M Dinjens, Peggy N Atmodimedjo, Johan M Kros, Ruth Fleischeuer, Clemens M F Dirven, Arnaud J P E Vincent, Martin J van den Bent
BACKGROUND: At current prognostication of low grade glioma remains suboptimal and might be improved with additional markers. These may guide treatment decisions, in particular on early adjuvant therapy versus wait and see after surgery. METHODS: We used a targeted Next-Generation Sequencing panel to assess mutational and copy number status of selected genes and chromosomes in a consecutive series of adult grade II supratentorial glioma, and assessed the impact of molecular markers of interest on overall survival...
April 16, 2018: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/29581871/positive-urinary-fluorescence-in-situ-hybridization-indicates-poor-prognosis-in-patients-with-upper-tract-urothelial-carcinoma
#16
Bao Guan, Yicong Du, Xiaohong Su, Zhenpeng Cao, Yifan Li, Yonghao Zhan, Ding Peng, Gengyan Xiong, Dong Fang, Yi Ding, Shiming He, Yanqing Gong, Qun He, Xuesong Li, Liqun Zhou
Here, we evaluated the potential contribution of fluorescent in situ hybridization (FISH) as a prognostic risk factor of bladder recurrence and survival in patients with upper tract urothelial carcinoma (UTUC). A total of 159 UTUC patients were enrolled in this study from January 2012 to May 2016. The 159 voided urine samples before surgery were analyzed using the UroVysion® kit to detect the copy numbers of chromosomes 3, 7, 17 and 9p21 (p16). Patients were classified using an optimal cutoff value of chromosomes 3, 7, 17, and 9p21...
March 6, 2018: Oncotarget
https://www.readbyqxmd.com/read/29577646/performance-of-the-urovysion-%C3%A2-fish-assay-for-the-diagnosis-of-malignant-effusions-using-two-cutoff-strategies
#17
Débora C B Rosolen, Daniel K Faria, Caroline S Faria, Leila Antonangelo
The cytological examination of cavity fluids has limited sensitivity in the diagnosis of malignancy. Aneuploidy, which is commonly observed in neoplastic cells, could potentially be used as an ancillary diagnostic tool. To evaluate the detection of aneuploid cells in cavitary effusion samples using the fluorescence in situ hybridization (FISH) assay UroVysion® with some adaptations and two different cutoff strategies. Seventy samples of pleural or peritoneal fluid with positive (n = 40), negative (n = 15), or suspicious (n = 15) oncotic cytology were subjected to FISH assay with the multitarget UroVysion® kit, which is composed of probes that hybridize to the centromeric region of chromosomes 3, 7, and 17 and to the locus 9p21...
May 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29556024/the-subclonal-complexity-of-stil-tal1-t-cell-acute-lymphoblastic-leukaemia
#18
Caroline L Furness, Marcela B Mansur, Victoria J Weston, Luca Ermini, Frederik W van Delft, Sarah Jenkinson, Rosemary Gale, Christine J Harrison, Maria S Pombo-de-Oliveira, Marta Sanchez-Martin, Adolfo A Ferrando, Pamela Kearns, Ian Titley, Anthony M Ford, Nicola E Potter, Mel Greaves
Single-cell genetics were used to interrogate clonal complexity and the sequence of mutational events in STIL-TAL1+ T-ALL. Single-cell multicolour FISH was used to demonstrate that the earliest detectable leukaemia subclone contained the STIL-TAL1 fusion and copy number loss of 9p21.3 (CDKN2A/CDKN2B locus), with other copy number alterations including loss of PTEN occurring as secondary subclonal events. In three cases, multiplex qPCR and phylogenetic analysis were used to produce branching evolutionary trees recapitulating the snapshot history of T-ALL evolution in this leukaemia subtype, which confirmed that mutations in key T-ALL drivers, including NOTCH1 and PTEN, were subclonal and reiterative in distinct subclones...
March 20, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/29460007/diffuse-gliomas-classified-by-1p-19q-co-deletion-tert-promoter-and-idh-mutation-status-are-associated-with-specific-genetic-risk-loci
#19
Karim Labreche, Ben Kinnersley, Giulia Berzero, Anna Luisa Di Stefano, Amithys Rahimian, Ines Detrait, Yannick Marie, Benjamin Grenier-Boley, Khe Hoang-Xuan, Jean-Yves Delattre, Ahmed Idbaih, Richard S Houlston, Marc Sanson
Recent genome-wide association studies of glioma have led to the discovery of single nucleotide polymorphisms (SNPs) at 25 loci influencing risk. Gliomas are heterogeneous, hence to investigate the relationship between risk SNPs and glioma subtype we analysed 1659 tumours profiled for IDH mutation, TERT promoter mutation and 1p/19q co-deletion. These data allowed definition of five molecular subgroups of glioma: triple-positive (IDH mutated, 1p/19q co-deletion, TERT promoter mutated); TERT-IDH (IDH mutated, TERT promoter mutated, 1p/19q-wild-type); IDH-only (IDH mutated, 1p/19q wild-type, TERT promoter wild-type); triple-negative (IDH wild-type, 1p/19q wild-type, TERT promoter wild-type) and TERT-only (TERT promoter mutated, IDH wild-type, 1p/19q wild-type)...
May 2018: Acta Neuropathologica
https://www.readbyqxmd.com/read/29446543/cyclin-dependent-kinase-inhibitor-2a-b-gene-deletions-are-markers-of-poor-prognosis-in-indian-children-with-acute-lymphoblastic-leukemia
#20
Manisha Agarwal, Sameer Bakhshi, Sadanand N Dwivedi, Madhulika Kabra, Rashmi Shukla, Rachna Seth
BACKGROUND: Cyclin dependent kinase inhibitor 2A/B (CDKN2A/B) genes are implicated in many malignancies including acute lymphoblastic leukemia (ALL). These tumor suppressor genes, with a key regulatory role in cell cycle are located on chromosome 9p21.3. Previous studies involving CDKN2A/B gene deletions have shown mixed associations with survival outcome in childhood ALL. PROCEDURE: Hundred and four newly diagnosed children with ALL (1-14 years) were enrolled in this study...
June 2018: Pediatric Blood & Cancer
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