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JOURNAL ARTICLE
Eman A Badr, Nesreen G Elhelbawy, Alaa Osama Nagy, Amany A Sultan, Shereen S Elnaidany
BACKGROUND: There is no doubt about the cardiovascular complications of coronavirus disease 2019 (COVID-19). Several genetic studies have demonstrated an association between genetic variants in a region on chromosome 9p21 and in a region on chromosome 16q22 with myocardial infarction (MI) and atrial fibrillation (AF) accompanied by cerebral infarction (CI), respectively. OBJECTIVES: MI and CI susceptibility in patients with CDKN2B-AS1 and ZFHX3 polymorphisms, respectively, may have an effect on COVID-19 severity...
August 31, 2023: BMC Infectious Diseases
#22
JOURNAL ARTICLE
Yizhou Zhu, Seungjin Ryu, Archana Tare, Nir Barzilai, Gil Atzmon, Yousin Suh
Genome-wide association studies (GWAS) have pinpointed the chromosomal locus 9p21.3 as a genetic hotspot for various age-related disorders. Common genetic variants in this locus are linked to multiple traits, including coronary artery diseases, cancers, and diabetes. Centenarians are known for their reduced risk and delayed onset of these conditions. To investigate whether this evasion of disease risks involves diminished genetic risks in the 9p21.3 locus, we sequenced this region in an Ashkenazi Jewish centenarian cohort (centenarians: n = 450, healthy controls: n = 500)...
August 22, 2023: Aging Cell
#23
JOURNAL ARTICLE
Matthew R Orton, Evan Hann, Simon J Doran, Scott T C Shepherd, Derfel Ap Dafydd, Charlotte E Spencer, José I López, Víctor Albarrán-Artahona, Francesca Comito, Hannah Warren, Joshua Shur, Christina Messiou, James Larkin, Samra Turajlic, Dow-Mu Koh
BACKGROUND: The aim of this work is to evaluate the performance of radiomics predictions for a range of molecular, genomic and clinical targets in patients with clear cell renal cell carcinoma (ccRCC) and demonstrate the impact of novel feature selection strategies and sub-segmentations on model interpretability. METHODS: Contrast-enhanced CT scans from the first 101 patients recruited to the TRACERx Renal Cancer study (NCT03226886) were used to derive radiomics classification models to predict 20 molecular, histopathology and clinical target variables...
August 14, 2023: Cancer Imaging: the Official Publication of the International Cancer Imaging Society
#24
JOURNAL ARTICLE
Meral Unur, Zeynep Birsu Cincin, Tuncay Tanıs, Kivanc Bektas Kayhan, Murat Ulusan, Sinem Bireller, Bedia Cakmakoglu
OBJECTIVE: Oral squamous cell carcinoma (OSCC) is a severe form of cancer affecting different anatomic sites of the oral cavity. OSCC ranks as the sixth most common cancer type with an increasing prevalence globally. However, the mechanisms of OSCC process at later stages are not well understood. In this study, we aimed to determine genetic alternations in metastatic OSCC patients to identify genomic changes occurred at metastatic phase of the disease. MATERIAL AND METHODS: The Illumina CytoSNP-12 Array was used to determine copy number variations in OSCC cancer genome...
July 31, 2023: Journal of Stomatology, Oral and Maxillofacial Surgery
#25
JOURNAL ARTICLE
N M Bogari, R M Allam, A Dannoun, M Athar, A Bouazzaoui, O Elkhateeb, M Porqueddu, S A Amer, A Elsayed, G I Colombo
OBJECTIVE: We aim to investigate the relationship between genetic variation and biological function on a genomic scale, focusing on identifying genes responsible for complex diseases using single nucleotide polymorphisms. Specifically, the study explores the association between the rs2383206 gene located on chromosome 9p21.3 and the development of coronary artery disease (CAD) in a specific Saudi population. PATIENTS AND METHODS: This case-control study was conducted between September 2013 and May 2015 at King Abdullah Medical City (KAMC) and Al-Noor Specialist Hospital targeting the Saudi Population residing in the western region of Saudi Arabia...
July 2023: European Review for Medical and Pharmacological Sciences
#26
JOURNAL ARTICLE
Danielle Brandes, Layal Yasin, Karin Nebral, Jana Ebler, Dagmar Schinnerl, Daniel Picard, Anke K Bergmann, Jubayer Alam, Stefan Köhrer, Oskar A Haas, Andishe Attarbaschi, Tobias Marschall, Martin Stanulla, Arndt Borkhardt, Triantafyllia Brozou, Ute Fischer, Rabea Wagener
The mutational landscape of B-cell precursor acute lymphoblastic leukemia (BCP-ALL), the most common pediatric cancer, is not fully described partially because commonly applied short-read next generation sequencing has a limited ability to identify structural variations. By combining comprehensive analysis of structural variants (SVs), single-nucleotide variants (SNVs), and small insertions-deletions, new subtype-defining and therapeutic targets may be detected. We analyzed the landscape of somatic alterations in 60 pediatric patients diagnosed with the most common BCP-ALL subtypes, ETV6::RUNX1 + and classical hyperdiploid (HD), using conventional cytogenetics, single nucleotide polymorphism (SNP) array, whole exome sequencing (WES), and the novel optical genome mapping (OGM) technique...
August 2023: HemaSphere
#27
JOURNAL ARTICLE
Sergey Semaev, Elena Shakhtshneider, Liliya Shcherbakova, Pavel Orlov, Dinara Ivanoshchuk, Sofia Malyutina, Valery Gafarov, Mikhail Voevoda, Yuliya Ragino
The individual risk of an unfavorable cardiovascular outcome is determined by genetic factors in addition to lifestyle factors. This study was aimed at analyzing possible associations of several genetic factors with the risk of myocardial infarction (MI). For our study, we selected genes that have been significantly associated with MI in meta-analyses: the chromosomal region 9p21.3, the CETP gene, and the APOE gene. In total, 2286 randomly selected patients were included. Rs708272 and rs429358 and rs7412 were analyzed using RT-PCR via the TaqMan principle, and rs1333049 vas analyzed via a commercial KASP assay...
June 30, 2023: International Journal of Molecular Sciences
#28
JOURNAL ARTICLE
Chuan-Bao Zhang, Zhi-Liang Wang, Han-Jie Liu, Zheng Wang, Wang Jia
OBJECTIVE: Astrocytes constitute approximately 30% of cells in gliomas and play important roles in synapse construction and survival. Recently, JAK/STAT pathway activation associated with a new type of astrocyte was reported. However, the implications of these tumor-associated reactive astrocytes (TARAs) in glioma are not known. METHODS: We comprehensively assessed TARAs in gliomas, both in single cells and at the bulk tumor level, by analyzing five independent datasets...
2023: Frontiers in Neurology
#29
JOURNAL ARTICLE
Tong-Min Wang, Ruo-Wen Xiao, Yong-Qiao He, Wen-Li Zhang, Hua Diao, Minzhong Tang, Zhi-Ming Mai, Wen-Qiong Xue, Da-Wei Yang, Chang-Mi Deng, Ying Liao, Ting Zhou, Dan-Hua Li, Yan-Xia Wu, Xue-Yin Chen, Jiangbo Zhang, Xi-Zhao Li, Pei-Fen Zhang, Xiao-Hui Zheng, Shao-Dan Zhang, Ye-Zhu Hu, Yonglin Cai, Yuming Zheng, Zhe Zhang, Yifeng Zhou, Guangfu Jin, Jinxin Bei, Hai-Qiang Mai, Ying Sun, Jun Ma, Zhibin Hu, Jianjun Liu, Maria Li Lung, Hans-Olov Adami, Weimin Ye, Tai-Hing Lam, Hongbing Shen, Wei-Hua Jia
Large-scale genetic association studies have identified multiple susceptibility loci for nasopharyngeal carcinoma (NPC), but the underlying biological mechanisms remain to be explored. To gain insights into the genetic etiology of NPC, we conducted a follow-up study encompassing 6,907 cases and 10,472 controls and identified two additional NPC susceptibility loci, 9q22.33 (rs1867277; OR = 0.74, 95% CI = 0.68-0.81, p = 3.08 × 10-11 ) and 17q12 (rs226241; OR = 1.42, 95% CI = 1...
July 6, 2023: American Journal of Human Genetics
#30
JOURNAL ARTICLE
Yizhou Zhu, Cagdas Tazearslan, Michael G Rosenfeld, Andras Fiser, Yousin Suh
Glaucoma is a leading cause of irreversible blindness, with advanced age being the single most significant risk factor. However, the mechanisms underlying the relationship between aging and glaucoma remain unclear. Genome-wide association studies (GWAS) have successfully identified genetic variants strongly associated with increased glaucoma risk. Understanding how these variants function in pathogenesis is crucial for translating genetic associations into molecular mechanisms and, ultimately, clinical applications...
June 22, 2023: Aging Cell
#31
Yizhou Zhu, Cagdas Tazearslan, Michael G Rosenfeld, Andras Fiser, Yousin Suh
Glaucoma is a leading cause of irreversible blindness, with advanced age being the single most significant risk factor. However, the mechanisms underlying the relationship between aging and glaucoma remain unclear. Genome-wide association studies (GWAS) have successfully identified genetic variants strongly associated with increased glaucoma risk. Understanding how these variants function in pathogenesis is crucial for translating genetic associations into molecular mechanisms and, ultimately, clinical applications...
May 22, 2023: bioRxiv
#32
JOURNAL ARTICLE
Nur P Damayanti, M Reza Saadatzadeh, Erika Dobrota, Josue D Ordaz, Barbara J Bailey, Pankita H Pandya, Khadijeh Bijangi-Vishehsaraei, Harlan E Shannon, Anthony Alfonso, Kathy Coy, Melissa Trowbridge, Anthony L Sinn, Zhong-Yin Zhang, Rosa I Gallagher, Julia Wulfkuhle, Emanuel Petricoin, Angela M Richardson, Mark S Marshall, Alex Lion, Michael J Ferguson, Karl E Balsara, Karen E Pollok
Pleomorphic xanthoastrocytoma (PXA) is a rare subset of primary pediatric glioma with 70% 5-year disease free survival. However, up to 20% of cases present with local recurrence and malignant transformation into more aggressive type anaplastic PXA (AXPA) or glioblastoma. The understanding of disease etiology and mechanisms driving PXA and APXA are limited, and there is no standard of care. Therefore, development of relevant preclinical models to investigate molecular underpinnings of disease and to guide novel therapeutic approaches are of interest...
June 6, 2023: Scientific Reports
#33
JOURNAL ARTICLE
Jaimie M Mayner, Evan M Masutani, Elena Demeester, Aditya Kumar, Gail Macapugay, Pranjali Beri, Valentina Lo Sardo, Adam J Engler
9p21.3 locus polymorphisms have the strongest correlation with coronary artery disease, but as a noncoding locus, disease connection is enigmatic. The lncRNA ANRIL found in 9p21.3 may regulate vascular smooth muscle cell (VSMC) phenotype to contribute to disease risk. We observed significant heterogeneity in induced pluripotent stem cell-derived VSMCs from patients homozygous for risk versus isogenic knockout or nonrisk haplotypes. Subpopulations of risk haplotype cells exhibited variable morphology, proliferation, contraction, and adhesion...
June 13, 2023: Proceedings of the National Academy of Sciences of the United States of America
#34
JOURNAL ARTICLE
Stella Koutros, Lambertus A Kiemeney, Parichoy Pal Choudhury, Roger L Milne, Evangelina Lopez de Maturana, Yuanqing Ye, Vijai Joseph, Oscar Florez-Vargas, Lars Dyrskjøt, Jonine Figueroa, Diptavo Dutta, Graham G Giles, Michelle A T Hildebrandt, Kenneth Offit, Manolis Kogevinas, Elisabete Weiderpass, Marjorie L McCullough, Neal D Freedman, Demetrius Albanes, Charles Kooperberg, Victoria K Cortessis, Margaret R Karagas, Alison Johnson, Molly R Schwenn, Dalsu Baris, Helena Furberg, Dean F Bajorin, Olivier Cussenot, Geraldine Cancel-Tassin, Simone Benhamou, Peter Kraft, Stefano Porru, Angela Carta, Timothy Bishop, Melissa C Southey, Giuseppe Matullo, Tony Fletcher, Rajiv Kumar, Jack A Taylor, Philippe Lamy, Frederik Prip, Mark Kalisz, Stephanie J Weinstein, Jan G Hengstler, Silvia Selinski, Mark Harland, Mark Teo, Anne E Kiltie, Adonina Tardón, Consol Serra, Alfredo Carrato, Reina García-Closas, Josep Lloreta, Alan Schned, Petra Lenz, Elio Riboli, Paul Brennan, Anne Tjønneland, Thomas Otto, Daniel Ovsiannikov, Frank Volkert, Sita H Vermeulen, Katja K Aben, Tessel E Galesloot, Constance Turman, Immaculata De Vivo, Edward Giovannucci, David J Hunter, Chancellor Hohensee, Rebecca Hunt, Alpa V Patel, Wen-Yi Huang, Gudmar Thorleifsson, Manuela Gago-Dominguez, Pilar Amiano, Klaus Golka, Mariana C Stern, Wusheng Yan, Jia Liu, Shengchao Alfred Li, Shilpa Katta, Amy Hutchinson, Belynda Hicks, William A Wheeler, Mark P Purdue, Katherine A McGlynn, Cari M Kitahara, Christopher A Haiman, Mark H Greene, Thorunn Rafnar, Nilanjan Chatterjee, Stephen J Chanock, Xifeng Wu, Francisco X Real, Debra T Silverman, Montserrat Garcia-Closas, Kari Stefansson, Ludmila Prokunina-Olsson, Núria Malats, Nathaniel Rothman
BACKGROUND: Genomic regions identified by genome-wide association studies (GWAS) for bladder cancer risk provide new insights into etiology. OBJECTIVE: To identify new susceptibility variants for bladder cancer in a meta-analysis of new and existing genome-wide genotype data. DESIGN, SETTING, AND PARTICIPANTS: Data from 32 studies that includes 13,790 bladder cancer cases and 343,502 controls of European ancestry were used for meta-analysis...
July 2023: European Urology
#35
JOURNAL ARTICLE
Rui Li, Chaojie Wang, Zhenhua Zhang, Dongxiao Li, Lifeng Li, Ding Zhao, Zhaojie Xu
BACKGROUND: Subchromosomal deletions and duplications are the leading cause of congenital malformations and mental retardation in children. With the recent clinical application of genomic microarrays in the evaluation of patients with developmental delays and congenital malformations, it has led to the discovery of several new microdeletion and microduplication syndromes. However, there are no published reports involving patients with both microduplications in the 9p21.1-p24.3 region and microdeletions in the 7p22...
April 13, 2023: BMC Pediatrics
#36
JOURNAL ARTICLE
Marta Grau, Cristina López, Alba Navarro, Gerard Frigola, Ferran Nadeu, Guillem Clot, Gabriela Bastidas-Mora, Miguel Alcoceba, Maria Joao Baptista, Margarita Blanes, Dolors Colomer, Dolors Costa, Eva Domingo-Domènech, Anna Enjuanes, Lourdes Escoda, Pilar Forcada, Eva Giné, Mónica Lopez-Guerra, Olga Ramón, Alfredo Rivas-Delgado, Laura Vicente Folch, Andrew Wotherspoon, Fina Climent, Elias Campo, Armando López-Guillermo, Estella Matutes, Sílvia Beà
The genetic mechanisms associated with splenic marginal zone lymphoma (SMZL) transformation are not well defined. We studied 41 patients with SMZL that eventually underwent large B-cell lymphoma transformation. Tumor material was obtained either only at diagnosis (9 patients), at diagnosis and transformation (18 patients), and only at transformation (14 patients). Samples were categorized in 2 groups: (1) at diagnosis (SMZL, n = 27 samples), and (2) at transformation (SMZL-T, n = 32 samples). Using copy number arrays and a next-generation sequencing custom panel, we identified that the main genomic alterations in SMZL-T involved TNFAIP3, KMT2D, TP53, ARID1A, KLF2, 1q gains, and losses of 9p21...
July 25, 2023: Blood Advances
#37
JOURNAL ARTICLE
Pablo Mozas, Cristina López, Marta Grau, Ferran Nadeu, Guillem Clot, Sara Valle, Marta Kulis, Alba Navarro, Joan Enric Ramis-Zaldivar, Blanca González-Farré, Alfredo Rivas-Delgado, Andrea Rivero, Gerard Frigola, Olga Balagué, Eva Giné, Julio Delgado, Neus Villamor, Estella Matutes, Laura Magnano, Ramón García-Sanz, Sarah Huet, Robert B Russell, Elías Campo, Armando López-Guillermo, Sílvia Beà
While some follicular lymphoma (FL) patients do not require treatment or experience prolonged responses, others relapse early, and little is known about genetic alterations specific to patients with a particular clinical behavior. We selected 56 grade 1-3A FL patients according to their need of treatment or timing of relapse: never treated (n = 7), non-relapsed (19), late relapse (14), early relapse or POD24 (11), and primary refractory (5). We analyzed 56 diagnostic and 12 paired relapse lymphoid tissue biopsies and performed copy number alteration (CNA) analysis and next generation sequencing (NGS)...
March 30, 2023: Hematological Oncology
#38
JOURNAL ARTICLE
G Tjitske Los-de Vries, Phylicia Stathi, Ryanne Rutkens, Nathalie J Hijmering, Jeroen A C W Luijks, Patricia J T A Groenen, Daphne de Jong, Bauke Ylstra, Margaretha G M Roemer
Large B-cell lymphoma of immune privileged sites (LBCL-IP) arise in immune sanctuaries including the testis and central nervous system. After initially reaching complete response, relapses occur in almost 50% of patients, typically at other immune privileged sites. Resolution of the clonal relationships and evolutionary patterns of LBCL-IP is required to understand the unique clinical behavior. We collected a unique set of 33 primary-relapse LBCL-IP sample pairs and performed next-generation sequencing for copy number, mutation, translocation and immunoglobulin clonality analysis...
March 27, 2023: Cancer Research
#39
JOURNAL ARTICLE
Sanna Kettunen, Anna-Kaisa Ruotsalainen, Tiit Örd, Tuisku Suoranta, Janne Heikkilä, Minna U Kaikkonen, Nihay Laham-Karam, Seppo Ylä-Herttuala
BACKGROUND: Several genome-wide association studies have reported a risk locus for coronary artery disease (CAD) in the 9p21. 3 chromosomal region. This region encodes a lncRNA in the INK4 locus ( ANRIL ) and its genetic variance has a strong association with CAD, but its mechanisms in atherogenesis remain unclear. OBJECTIVES: This study aimed to investigate the role of the murine ortholog of human 9p21.3 locus in atherogenesis in hypercholesterolemic mice. METHODS: Murine 9p21...
2023: Frontiers in Cardiovascular Medicine
#40
JOURNAL ARTICLE
Yen-Ting Liu, Celeste Romero, Xue Xiao, Lei Guo, Xiaoyun Zhou, Mark A Applebaum, Lin Xu, Stephen X Skapek
CDKN2A/B deletion or silencing is common across human cancer, reinforcing the general importance of bypassing its tumor suppression in cancer formation or progression. In rhabdomyosarcoma (RMS) and neuroblastoma, two common childhood cancers, the three CDKN2A/B transcripts are independently expressed to varying degrees, but one, ARF, is uniformly silenced. Although TGFβ induces certain CDKN2A/B transcripts in HeLa cells, it was unable to do so in five tested RMS lines unless the cells were pretreated with a broadly acting methyltransferase inhibitor, DZNep, or one targeting EZH2...
2023: Molecular and Cellular Biology
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