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9p21.3

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https://read.qxmd.com/read/30747408/clinicopathological-significance-of-overall-frequency-of-allelic-loss-ofal-in-lesions-derived-from-thyroid-follicular-cell
#1
Monika Migdalska-Sęk, Karolina H Czarnecka, Michał Kusiński, Dorota Pastuszak-Lewandoska, Ewa Nawrot, Krzysztof Kuzdak, Ewa Brzeziańska-Lasota
BACKGROUND: Loss of heterozygosity (LOH) and microsatellite instability (MSI) are frequent molecular events in thyroid tumor etiopathogenesis occurring in several chromosomal critical areas, including 3p12-25.3, 7q21-31, 10q22-24, and 15q11-13, with loci of tumor suppressor genes. OBJECTIVE: We evaluated the usefulness of LOH/MSI as a diagnostic/prognostic biomarker in lesions derived from thyroid follicular cells: follicular thyroid carcinoma (FTC); follicular adenoma (FA), papillary thyroid carcinoma (PTC), and nodular goiter (NG)...
February 11, 2019: Molecular Diagnosis & Therapy
https://read.qxmd.com/read/30735646/unraveling-difficult-answers-from-genotype-to-phenotype-in-coronary-artery-disease
#2
Tarek Magdy, Paul W Burridge
Genome-wide association studies (GWASs) have robustly found a correlation between coronary artery disease (CAD) and an intergenic region at locus 9p21.3. However, the mechanistic implication of this association is unknown. Recently in Cell, Lo Sardo et al. used hiPSC genome editing to demonstrate how this locus contributes to CAD predisposition.
February 7, 2019: Cell Stem Cell
https://read.qxmd.com/read/30635552/cdkn2b-downregulation-and-other-genetic-characteristics-in-t-acute-lymphoblastic-leukemia
#3
Woori Jang, Joonhong Park, Ahlm Kwon, Hayoung Choi, Jiyeon Kim, Gun Dong Lee, Eunhee Han, Dong Wook Jekarl, Hyojin Chae, Kyungja Han, Jae-Ho Yoon, Seok Lee, Nack-Gyun Chung, Bin Cho, Myungshin Kim, Yonggoo Kim
We identified principal genetic alterations in 97.1% (99/102) of patients with T-acute lymphoblastic leukemia (T-ALL) using integrative genetic analyses, including massive parallel sequencing and multiplex ligation-dependent probe amplification (MLPA). A total of 133 mutations were identified in the following genes in descending order: NOTCH1 (66.7%), FBXW7 (19.6%), PHF6 (15.7%), RUNX1 (12.7%), NRAS (10.8%), and DNMT3A (9.8%). Copy number alterations were most frequently detected in CDKN2B, CDKN2A, and genes on 9p21...
January 11, 2019: Experimental & Molecular Medicine
https://read.qxmd.com/read/30604909/a-functional-variant-rs1537373-in-9p21-3-region-is-associated-with-pancreatic-cancer-risk
#4
Beibei Zhu, Ying Zhu, Jianbo Tian, Na Shen, Jiaoyuan Li, Jiao Lou, Juntao Ke, Yang Yang, Yajie Gong, Jing Gong, Jiang Chang, Xiaoping Miao, Rong Zhong
9p21.3 has been identified as an unexpected hot point in multiple diseases GWAS including cancers, and we performed a two-stage case-control studies integrating functional assay strategy to find the potential functional variants modified susceptibility to pancreatic cancer (PC). An expanded Illumina HumanExome Beadchip of PC including 943 cases and 3908 controls was used to examine 39 tagSNPs in 9p21.3 and the promising single nucleotide polymorphism (SNP) was validated in stage 2 comprising 624 cases and 1048 controls...
January 3, 2019: Molecular Carcinogenesis
https://read.qxmd.com/read/30600348/dietary-patterns-interact-with-chromosome-9p21-rs1333048-polymorphism-on-the-risk-of-obesity-and-cardiovascular-risk-factors-in-apparently-healthy-tehrani-adults
#5
Mehdi Mollahosseini, Mohammad Hossein Rahimi, Mir Saeed Yekaninejad, Zhila Maghbooli, Khadijeh Mirzaei
PURPOSE: Gene-dietary patterns may contribute to determining body composition and related biochemical indices. The aim of this study was to evaluate interactions between rs1333048 polymorphism and major dietary patterns on body fat percentage, general and central obesity, and related biochemical measurements. METHODS: This cross-sectional study was conducted on 265 healthy Tehrani adults with mean age of 35 years (47.5% men, 52.5% women). Dietary patterns (DPs) were extracted by factor analysis...
January 2, 2019: European Journal of Nutrition
https://read.qxmd.com/read/30587704/the-association-between-the-chromosome-9p21-cdkn2b-as1-gene-variants-and-the-lipid-metabolism-a-pre-diagnostic-biomarker-for-coronary-artery-disease
#6
Şehime Gülsün Temel, Mahmut Çerkez Ergören
OBJECTIVE: Recent genome-wide association studies have established that polymorphisms within CDKN2B-AS1 of chr9p21.3 locus increased susceptibility to coronary artery disease (CAD) or myocardial infarction. Common variants of CDKN2B-AS1 (including rs4977574 A>G and rs1333040 C>T) are determined to be directly associated with CADs in many populations worldwide and suggested biomarkers for the early detection of CAD. There is a lack of investigation for the association between CDKN2B-AS1 rs4977574 A>G and rs1333040 C>T genetic modifiers and CAD in a Turkish Cypriot population...
January 2019: Anatolian Journal of Cardiology
https://read.qxmd.com/read/30578714/non-leukemic-pediatric-mixed-phenotype-acute-leukemia-lymphoma-genomic-characterization-and-clinical-outcome-in-a-prospective-trial-for-pediatric-lymphoblastic-lymphoma
#7
Idoia Martin-Guerrero, Itziar Salaverria, Birgit Burkhardt, Catherine Chassagne-Clement, Monika Szczepanowski, Susanne Bens, Wolfram Klapper, Martin Zimmermann, Edita Kabickova, Yves Bertrand, Alfred Reiter, Reiner Siebert, Ilske Oschlies
Rare cases of hematological precursor neoplasms fulfill the diagnostic criteria of mixed phenotype acute leukemia (MPAL), characterized by expression patterns of at least two hematopoietic lineages, for which a highly aggressive behavior was reported. We present a series of 11 pediatric non-leukemic MPAL identified among 146 precursor lymphoblastic lymphomas included in the prospective trial Euro-LBL 02. Paraffin embedded biopsies of 10 cases were suitable for molecular analyses using OncoScan assay (n=7), fluorescence in situ hybridization (FISH) (n=7) or both (n=5)...
December 22, 2018: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30531171/the-association-between-the-chromosome-9p21-cdkn2b-as1-gene-variants-and-the-lipid-metabolism-a-pre-diagnostic-biomarker-for-coronary-artery-disease
#8
Şehime Gülsün Temel, Mahmut Çerkez Ergören
OBJECTIVE: Recent genome-wide association studies have established that polymorphisms within CDKN2B-AS1 of chr9p21.3 locus increased susceptibility to coronary artery disease (CAD) or myocardial infarction. Common variants of CDKN2B-AS1 (including rs4977574 A>G and rs1333040 C>T) are determined to be directly associated with CADs in many populations worldwide and suggested biomarkers for the early detection of CAD. There is a lack of investigation for the association between CDKN2B-AS1 rs4977574 A>G and rs1333040 C>T genetic modifiers and CAD in a Turkish Cypriot population...
December 7, 2018: Anatolian Journal of Cardiology
https://read.qxmd.com/read/30528432/unveiling-the-role-of-the-most-impactful-cardiovascular-risk-locus-through-haplotype-editing
#9
Valentina Lo Sardo, Pavel Chubukov, William Ferguson, Aditya Kumar, Evan L Teng, Michael Duran, Lei Zhang, Gregory Cost, Adam J Engler, Fyodor Urnov, Eric J Topol, Ali Torkamani, Kristin K Baldwin
The 9p21.3 cardiovascular disease locus is the most influential common genetic risk factor for coronary artery disease (CAD), accounting for ∼10%-15% of disease in non-African populations. The ∼60 kb risk haplotype is human-specific and lacks coding genes, hindering efforts to decipher its function. Here, we produce induced pluripotent stem cells (iPSCs) from risk and non-risk individuals, delete each haplotype using genome editing, and generate vascular smooth muscle cells (VSMCs). Risk VSMCs exhibit globally altered transcriptional networks that intersect with previously identified CAD risk genes and pathways, concomitant with aberrant adhesion, contraction, and proliferation...
December 6, 2018: Cell
https://read.qxmd.com/read/30455436/dynamic-molecular-monitoring-reveals-that-swi-snf-mutations-mediate-resistance-to-ibrutinib-plus-venetoclax-in-mantle-cell-lymphoma
#10
Rishu Agarwal, Yih-Chih Chan, Constantine S Tam, Tane Hunter, Dane Vassiliadis, Charis E Teh, Rachel Thijssen, Paul Yeh, Stephen Q Wong, Sarah Ftouni, Enid Y N Lam, Mary Ann Anderson, Christiane Pott, Omer Gilan, Charles C Bell, Kathy Knezevic, Piers Blombery, Kathleen Rayeroux, Adrian Zordan, Jason Li, David C S Huang, Meaghan Wall, John F Seymour, Daniel H D Gray, Andrew W Roberts, Mark A Dawson, Sarah-Jane Dawson
Ibrutinib plus venetoclax is a highly effective combination in mantle cell lymphoma. However, strategies to enable the evaluation of therapeutic response are required. Our prospective analyses of patients within the AIM study revealed genomic profiles that clearly dichotomized responders and nonresponders. Mutations in ATM were present in most patients who achieved a complete response, while chromosome 9p21.1-p24.3 loss and/or mutations in components of the SWI-SNF chromatin-remodeling complex were present in all patients with primary resistance and two-thirds of patients with relapsed disease...
November 19, 2018: Nature Medicine
https://read.qxmd.com/read/30400960/microrna-31-5p-regulates-chemosensitivity-by-preventing-the-nuclear-location-of-parp1-in-hepatocellular-carcinoma
#11
Ke-Ting Que, Yun Zhou, Yu You, Zhen Zhang, Xiao-Ping Zhao, Jian-Ping Gong, Zuo-Jin Liu
BACKGROUND: MicroRNAs (miRNAs) posttranscriptionally regulate gene expression and thereby contribute to the modulation of numerous complex and disease-relevant cellular processes, including cell proliferation, cell motility, apoptosis and stress response. miRNA-31-5p is encoded on a genomic fragile site, 9p21.3, which is reportedly lost in many hepatocellular carcinoma (HCC) tumors. Based on previous findings, we hypothesized that miR-31-5p alters chemosensitivity and that miR-31-5p mimics may influence sensitivity to chemotherapeutics in HCC as well as in a variety of other cancers...
November 6, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://read.qxmd.com/read/30364300/interaction-between-a-variant-of-chromosome-9p21-3-locus-and-diet-antioxidant-capacity-on-metabolic-syndrome-in-tehrani-adults
#12
Atieh Mirzababaei, Mehdi Mollahosseini, Mohammad Hossein Rahimi, Mir Saeed Yekaninejad, Zhila Maghbooli, Reza Sobhani, Khadijeh Mirzaei
Background: Genome-wide association studies have shown that risk alleles on chromosome 9p21.3 locus, are associated with increasing the risk of cardiovascular diseases (CVDs). Several epidemiological studies have found that metabolic syndrome (MetS) is associated with CVDs. Dietary antioxidants also have shown to have potential favorable effects on MetS prevention. This study examined the interactions between rs1333048 genotypes on 9p21 genetic region and Total antioxidant capacity (TAC) on odds of MetS...
2018: Diabetology & Metabolic Syndrome
https://read.qxmd.com/read/30355083/genetics-of-human-longevity-within-an-eco-evolutionary-nature-nurture-framework
#13
Cristina Giuliani, Paolo Garagnani, Claudio Franceschi
Human longevity is a complex trait, and to disentangle its basis has a great theoretical and practical consequences for biomedicine. The genetics of human longevity is still poorly understood despite several investigations that used different strategies and protocols. Here, we argue that such rather disappointing harvest is largely because of the extraordinary complexity of the longevity phenotype in humans. The capability to reach the extreme decades of human lifespan seems to be the result of an intriguing mixture of gene-environment interactions...
September 14, 2018: Circulation Research
https://read.qxmd.com/read/30352225/genetic-architecture-of-primary-open-angle-glaucoma-in-individuals-of-african-descent-the-african-descent-and-glaucoma-evaluation-study-iii
#14
Kent D Taylor, Xiuqing Guo, Linda M Zangwill, Jeffrey M Liebmann, Christopher A Girkin, Robert M Feldman, Harvey Dubiner, Yang Hai, Brian C Samuels, Joseph F Panarelli, John P Mitchell, Lama A Al-Aswad, Sung Chul Park, Celso Tello, Jeremy Cotliar, Rajendra Bansal, Paul A Sidoti, George A Cioffi, Dana Blumberg, Robert Ritch, Nicholas P Bell, Lauren S Blieden, Garvin Davis, Felipe A Medeiros, Swapan K Das, Jasmin Divers, Carl D Langefeld, Nicholette D Palmer, Barry I Freedman, Donald W Bowden, Maggie C Y Ng, Yii-Der Ida Chen, Radha Ayyagari, Jerome I Rotter, Robert N Weinreb
PURPOSE: To find genetic contributions to glaucoma in African Americans. DESIGN: Cross-sectional, case-control study. PARTICIPANTS: One thousand eight hundred seventy-five primary open-angle glaucoma (POAG) patients and 1709 controls, self-identified as being of African descent (AD), from the African Descent and Glaucoma Evaluation Study (ADAGES) III and Wake Forest School of Medicine. METHODS: MegaChip genotypes were imputed to Thousand Genomes data...
October 21, 2018: Ophthalmology
https://read.qxmd.com/read/30307677/array-based-cgh-of-primary-cutaneous-cd8-aggressive-epidermo-tropic-cytotoxic-t-cell-lymphoma
#15
Daniele Fanoni, Laura Corti, Silvia Alberti-Violetti, Cornelis P Tensen, Luigia Venegoni, Maarten Vermeer, Rein Willemze, Emilio Berti
Primary cutaneous CD8+ aggressive epidermotropic cytotoxic T-cell lymphoma (pcAECyTCL) is a rare provisionally categorized cutaneous lymphoma characterized by an aggressive course. Its pathogenesis and molecular mechanisms are still unknown, and only two individual cases have so far been molecularly characterized. The aim of this study was to define the pattern of numerical chromosomal alterations in tumor samples taken from 20 patients with pcAECyTCL at the time of diagnosis by means of array-comparative genomic hybridization (a-CGH)...
December 2018: Genes, Chromosomes & Cancer
https://read.qxmd.com/read/30169623/a-pediatric-intra-axial-malignant-smarcb1-deficient-desmoplastic-tumor-arising-in-meningioangiomatosis
#16
Sabrina Rossi, Monica Brenca, Lucia Zanatta, Elena Trincia, Angela Guerriero, Cristina Pizzato, Alessandro Fiorindi, Elisabetta Viscardi, Felice Giangaspero, Roberta Maestro, Angelo Paolo Dei Tos, Caterina Giannini
SMARCB1 inactivation is a well-established trigger event in atypical teratoid/rhabdoid tumor. Recently, a role for SMARCB1 inactivation has emerged as a mechanism of clonal evolution in other tumor types, including rare brain tumors. We describe an unusual malignant intra-axial SMARCB1-deficient spindle cell desmoplastic neoplasm, occurring in a 6-year-old child with meningioangiomatosis and a long history of seizures. Striking features of the tumor were a storiform pattern and strong CD34 expression. Undifferentiated round cell areas with isolated rhabdoid cells showing high mitotic index and focal necrosis with INI1 expression loss were present...
October 1, 2018: Journal of Neuropathology and Experimental Neurology
https://read.qxmd.com/read/30098783/oncogenic-drivers-in-11q13-associated-with-prognosis-and-response-to-therapy-in-advanced-oropharyngeal-carcinomas
#17
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://read.qxmd.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
#18
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://read.qxmd.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
#19
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://read.qxmd.com/read/30018130/machine-learning-for-better-prognostic-stratification-and-driver-gene-identification-using-somatic-copy-number-variations-in-anaplastic-oligodendroglioma
#20
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
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