keyword
https://read.qxmd.com/read/38457761/-her2-gene-expression-levels-are-predictive-and-prognostic-in-patients-with-metastatic-colorectal-cancer-enrolled-in-calgb-swog-80405
#21
JOURNAL ARTICLE
Francesca Battaglin, Fang-Shu Ou, Xueping Qu, Howard S Hochster, Donna Niedzwiecki, Richard M Goldberg, Robert J Mayer, Karam Ashouri, Tyler J Zemla, Charles D Blanke, Alan P Venook, Omar Kabbarah, Heinz-Josef Lenz, Federico Innocenti
PURPOSE: The phase III Cancer and Leukemia Group B (CALGB)/SWOG 80405 trial found no difference in overall survival (OS) in patients with metastatic colorectal cancer receiving first-line chemotherapy in combination with either bevacizumab or cetuximab. We investigated the potential prognostic and predictive value of HER2 amplification and gene expression using next-generation sequencing (NGS) and NanoString data. PATIENTS AND METHODS: Primary tumor DNA from 559 patients was profiled for HER2 amplification by NGS (FoundationOne CDx)...
March 8, 2024: Journal of Clinical Oncology
https://read.qxmd.com/read/38456787/the-prevalence-and-radiologic-features-of-renal-cancers-associated-with-flcn-bap1-sdh-and-met-germline-mutations
#22
JOURNAL ARTICLE
Charlotte Charbel, Pamela I Causa Andrieu, Mohamed Soliman, Sungmin Woo, Junting Zheng, Marinela Capanu, Ines Nikolovski, Hebert A Vargas, Murad Abusamra, Maria I Carlo
Purpose To investigate the prevalence of FLCN, BAP1, SDH , and MET mutations in an oncologic cohort and determine the prevalence, clinical features, and imaging features of renal cell carcinoma (RCC) associated with these mutations. Secondarily, to determine the prevalence of encountered benign renal lesions. Materials and Methods From 25 220 patients with cancer who prospectively underwent germline analysis with a panel of more than 70 cancer-predisposing genes from 2015 to 2021, patients with FLCN, BAP1, SDH , or MET mutations were retrospectively identified...
March 2024: Radiology. Imaging cancer
https://read.qxmd.com/read/38455766/circulating-serum-mir-362-3p-and-mir-6721-5p-as-potential-biomarkers-for-classification-patients-with-adult-type-diffuse-glioma
#23
JOURNAL ARTICLE
Magdalena Niemira, Agnieszka Bielska, Karolina Chwialkowska, Justyna Raczkowska, Anna Skwarska, Anna Erol, Anna Zeller, Gabriela Sokolowska, Damian Toczydlowski, Iwona Sidorkiewicz, Zenon Mariak, Joanna Reszec, Tomasz Lyson, Marcin Moniuszko, Adam Kretowski
According to the fifth edition of the WHO Classification of Tumours of the Central Nervous System (CNS) published in 2021, grade 4 gliomas classification includes IDH-mutant astrocytomas and wild-type IDH glioblastomas. Unfortunately, despite precision oncology development, the prognosis for patients with grade 4 glioma remains poor, indicating an urgent need for better diagnostic and therapeutic strategies. Circulating miRNAs besides being important regulators of cancer development could serve as promising diagnostic biomarkers for patients with grade 4 glioma...
2024: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/38455414/clinical-implications-of-pd-l1-expression-and-pathway-related-molecular-subtypes-in-advanced-asian-colorectal-cancer-patients
#24
JOURNAL ARTICLE
Qingqing Qiu, Dan Tan, Qiaofeng Chen, Ru Zhou, Xiaokai Zhao, Wei Wen, Pengmin Yang, Jieyi Li, Ziying Gong, Daoyun Zhang, Mingliang Wang
The expression level of PD-L1 does not accurately predict the prognosis of advanced colorectal cancer (CRC) patients, but it still reflects the tumor microenvironment to some extent. By stratifying PD-L1 status, gene subtypes in PD-L1 positivity-related pathological pathways were analyzed for their relationship to MSI or TMB to provide more individualized treatment options for CRCs. A total of 752 advanced CRCs were included, and their genomic variance was measured by a targeted next generation sequencing panel in this study...
2024: American Journal of Cancer Research
https://read.qxmd.com/read/38455372/risk-stratification-for-radioactive-iodine-refractoriness-using-molecular-alterations-in-distant-metastatic-differentiated-thyroid-cancer
#25
JOURNAL ARTICLE
Zhuanzhuan Mu, Xin Zhang, Dongquan Liang, Jugao Fang, Ge Chen, Wenting Guo, Di Sun, Yuqing Sun, Zhentian Kai, Lisha Huang, Jun Liang, Yansong Lin
OBJECTIVE: Patients with radioactive iodine-refractory differentiated thyroid cancer (RAIR-DTC) are often diagnosed with delay and constrained to limited treatment options. The correlation between RAI refractoriness and the underlying genetic characteristics has not been extensively studied. METHODS: Adult patients with distant metastatic DTC were enrolled and assigned to undergo next-generation sequencing of a customized 26-gene panel (ThyroLead). Patients were classified into RAIR-DTC or non-RAIR groups to determine the differences in clinicopathological and molecular characteristics...
February 29, 2024: Chinese Journal of Cancer Research
https://read.qxmd.com/read/38454538/a-genome-wide-study-of-gastric-intramucosal-neoplasia-based-on-somatic-copy-number-alterations-gene-mutations-and-mrna-expression-patterns
#26
JOURNAL ARTICLE
Yoshihiko Koike, Mitsumasa Osakabe, Ryo Sugimoto, Noriyuku Uesugi, Takayuki Matsumoto, Hiromu Suzuki, Naoki Yanagawa, Tamotsu Sugai
We performed comprehensive analyses of somatic copy number alterations (SCNAs) and gene expression profiles of gastric intramucosal neoplasia (IMN) using array-based methods in 97 intestinal-type IMNs, including 39 low-grade dysplasias (LGDs), 37 high-grade dysplasias (HGDs), and 26 intramucosal carcinomas (IMCs) with stromal invasion of the lamina propria to identify the molecular mechanism of IMN. In addition, we examined gene mutations using gene panel analyses. We used cluster analyses for exclusion of arbitrariness to identify SCNA patterns and expression profiles...
March 2024: Journal of Pathology. Clinical Research
https://read.qxmd.com/read/38453438/-chinese-expert-consensus-on-second-line-treatment-for-non-small-cell-lung-cancer-with-negative-driver-gene-mutations
#27
JOURNAL ARTICLE
(no author information available yet)
For advanced non-small cell lung cancer (NSCLC) patients with negative driver gene mutations, chemotherapy has always been the standard treatment option, and immune checkpoint inhibitors (ICIs) provide other treatment option for these patients. At present, the first-line treatment can choose chemotherapy, anti-angiogenic drugs or immunotherapy. Although the initial treatment can achieve a certain clinical curative effect, disease progression or treatment failure is eventually unavoidable. The second-line and subsequent treatments have poor efficacy and more effective drugs are needed clinically...
February 20, 2024: Zhongguo Fei Ai za Zhi, Chinese Journal of Lung Cancer
https://read.qxmd.com/read/38452805/association-of-mutant-kras-alleles-with-morphology-and-clinical-outcomes-in-pancreatic-ductal-adenocarcinoma
#28
JOURNAL ARTICLE
Timothy Chao, Zi-Xuan Wang, Wilbur B Bowne, Clifford J Yudkoff, Ava Torjani, Vishal Swaminathan, Taylor R Kavanagh, Austin Roadarmel, Cyrus J Sholevar, Shawnna Cannaday, Geoffrey Krampitz, Tingting Zhan, Eliyahu Gorgov, Avinoam Nevler, Harish Lavu, Charles J Yeo, Stephen C Peiper, Wei Jiang
CONTEXT.—: Mutant KRAS is the main oncogenic driver in pancreatic ductal adenocarcinomas (PDACs). However, the clinical and phenotypic implications of harboring different mutant KRAS alleles remain poorly understood. OBJECTIVE.—: To characterize the potential morphologic and clinical outcome differences in PDACs harboring distinct mutant KRAS alleles. DESIGN.—: Cohort 1 consisted of 127 primary conventional PDACs with no neoadjuvant therapy, excluding colloid/mucinous, adenosquamous, undifferentiated, and intraductal papillary mucinous neoplasm-associated carcinomas, for which an in-house 42-gene mutational panel had been performed...
March 8, 2024: Archives of Pathology & Laboratory Medicine
https://read.qxmd.com/read/38452709/cancer-genetic-counselling-for-hereditary-breast-cancer-in-the-era-of-precision-oncology
#29
REVIEW
M Pensabene, A Calabrese, C von Arx, R Caputo, M De Laurentiis
A relevant percentage of breast cancers (BCs) are tied to pathogenetic (P)/likely pathogenetic (LP) variants in predisposing genes. The knowledge of P/LP variants is an essential element in the management of BC patients since the first diagnosis because it influences surgery and subsequent oncological treatments and follow-up. Moreover, patients with metastatic BCs can benefit from personalized treatment if carriers of P/LP in BRCA1/2 genes. Multigene panels allow the identification of other predisposing genes with an impact on management...
February 28, 2024: Cancer Treatment Reviews
https://read.qxmd.com/read/38452634/mutations-in-cancer-relevant-genes-are-ubiquitous-in-histologically-normal-endometrial-tissue
#30
JOURNAL ARTICLE
Deep Pandya, Shannon Tomita, Maria Padron Rhenals, Sabina Swierczek, Katherine Reid, Olga Camacho-Vanegas, Catalina Camacho, Kelsey Engelman, Stephanie Polukort, Jordan RoseFigura, Linus Chuang, Vaagn Andikyan, Samantha Cohen, Paul Fiedler, Steven Sieber, Ie-Ming Shih, Jean-Noël Billaud, Robert Sebra, Boris Reva, Peter Dottino, John A Martignetti
OBJECTIVE: Endometrial cancer (EndoCA) is the most common gynecologic cancer and incidence and mortality rate continue to increase. Despite well-characterized knowledge of EndoCA-defining mutations, no effective diagnostic or screening tests exist. To lay the foundation for testing development, our study focused on defining the prevalence of somatic mutations present in non-cancerous uterine tissue. METHODS: We obtained ≥8 uterine samplings, including separate endometrial and myometrial layers, from each of 22 women undergoing hysterectomy for non-cancer conditions...
March 6, 2024: Gynecologic Oncology
https://read.qxmd.com/read/38452310/target-a-randomized-noninferiority-trial-of-a-pretest-patient-driven-genetic-education-webtool-versus-genetic-counseling-for-prostate-cancer-germline-testing
#31
JOURNAL ARTICLE
Stacy Loeb, Scott W Keith, Heather H Cheng, Amy E Leader, Laura Gross, Tatiana Sanchez Nolasco, Nataliya Byrne, Rebecca Hartman, Lauren H Brown, Christopher Michael Pieczonka, Leonard G Gomella, William Kevin Kelly, Costas D Lallas, Nathan Handley, Patrick Johnston Mille, James Ryan Mark, Gordon Andrew Brown, Sameer Chopra, Alexandra McClellan, David R Wise, Lucas Hollifield, Veda N Giri
PURPOSE: Germline genetic testing (GT) is important for prostate cancer (PCA) management, clinical trial eligibility, and hereditary cancer risk. However, GT is underutilized and there is a shortage of genetic counselors. To address these gaps, a patient-driven, pretest genetic education webtool was designed and studied compared with traditional genetic counseling (GC) to inform strategies for expanding access to genetic services. METHODS: Technology-enhanced acceleration of germline evaluation for therapy (TARGET) was a multicenter, noninferiority, randomized trial (ClinicalTrials...
March 2024: JCO Precision Oncology
https://read.qxmd.com/read/38451242/circulating-cell-free-dna-based-biomarkers-for-prognostication-and-disease-monitoring-in-adrenocortical-carcinoma
#32
JOURNAL ARTICLE
Juliane Lippert, Gabrielle Smith, Silke Appenzeller, Laura-Sophie Landwehr, Alessandro Prete, Sonja Steinhauer, Miriam Asia, Hanna Urlaub, Yasir S Elhassan, Stefan Kircher, Wiebke Arlt, Martin Fassnacht, Barbara Altieri, Cristina L Ronchi
Adrenocortical carcinoma (ACC) is a rare aggressive cancer with heterogeneous behaviour. Disease surveillance relies on frequent imaging, which comes with significant radiation exposure. The aim of the study was to investigate the role of circulating cell-free DNA (ccfDNA)-related biomarkers (BM) for prognostication and monitoring of ACC. We investigated 34 patients with ACC and 23 healthy subjects (HS) as controls. ccfDNA was extracted by commercial kits and ccfDNA concentrations quantified by fluorimeter (BM1)...
March 7, 2024: European Journal of Endocrinology
https://read.qxmd.com/read/38448490/a-long-read-sequencing-strategy-with-overlapping-linkers-on-adjacent-fragments-olaf-seq-for-targeted-resequencing-and-enrichment
#33
JOURNAL ARTICLE
Lahari Uppuluri, Christina Huan Shi, Dharma Varapula, Eleanor Young, Rachel L Ehrlich, Yilin Wang, Danielle Piazza, Joshua Chang Mell, Kevin Y Yip, Ming Xiao
In this report, we present OLAF-Seq, a novel strategy to construct a long-read sequencing library such that adjacent fragments are linked with end-terminal duplications. We use the CRISPR-Cas9 nickase enzyme and a pool of multiple sgRNAs to perform non-random fragmentation of targeted long DNA molecules (> 300kb) into smaller library-sized fragments (about 20 kbp) in a manner so as to retain physical linkage information (up to 1000 bp) between adjacent fragments. DNA molecules targeted for fragmentation are preferentially ligated with adaptors for sequencing, so this method can enrich targeted regions while taking advantage of the long-read sequencing platforms...
March 7, 2024: Scientific Reports
https://read.qxmd.com/read/38447012/targeted-dna-sequencing-of-high-grade-serous-ovarian-carcinoma-reveals-association-of-tp53-mutations-with-platinum-resistance-when-combined-with-gene-expression
#34
JOURNAL ARTICLE
Petr Holý, Viktor Hlaváč, Karolína Šeborová, Simona Šůsová, Tereza Tesařová, Lukáš Rob, Martin Hruda, Jiří Bouda, Alena Bartáková, Marcela Mrhalová, Kateřina Kopečková, Mohammad Al Obeed Allah, Jiří Špaček, Iva Sedláková, Pavel Souček, Radka Václavíková
High-grade serous ovarian carcinoma (HGSC) is the most common subtype of ovarian cancer and is among the most fatal gynecological malignancies worldwide, due to late diagnosis at advanced stages and frequent therapy resistance. In 47 HGSC patients, we assessed somatic and germline genetic variability of a custom panel of 144 known or suspected HGSC-related genes by high-coverage targeted DNA sequencing to identify the genetic determinants associated with resistance to platinum-based therapy. In the germline, the most mutated genes were DNAH14 (17%), RAD51B (17%), CFTR (13%), BRCA1 (11%), and RAD51 (11%)...
March 6, 2024: International Journal of Cancer. Journal International du Cancer
https://read.qxmd.com/read/38446389/identification-of-gene-variation-feature-for-targeted-therapy-of-non-small-cell-lung-cancer-through-combined-method-of-dna-and-rna-sequencing
#35
JOURNAL ARTICLE
Wenguang Pang, Longlong Gong, Wangpan Shi, Hongbo Zheng, Min Ye, Jiarong Chen, Ronggang Li, Xin Zhang, Dong Ren, Zheng Wang
Next generation sequencing (NGS) is typically used to reveal tumor gene variation feature for targeted therapy of various types of human cancers, including non-small cell lung cancer (NSCLC). Here, we report the role and potential applicable value of combining DNA and RNA sequencing in gene variation detection in NSCLC. 386 NSCLC patients with stage II-IV were enrolled and detected using NGS sequencing of DNA and RNA panels that covered all well-documented target driver genes from the Chinese Society of Clinical Oncology (CSCO)...
March 6, 2024: Discover. Oncology
https://read.qxmd.com/read/38442470/up-regulation-of-extracellular-matrix-and-inflammation-related-genes-in-oral-squamous-cell-carcinoma
#36
JOURNAL ARTICLE
Vaidehi P Thakore, Kinjal D Patel, Hemangini H Vora, Prabhudas S Patel, Nayan K Jain
OBJECTIVE: Oral squamous cell carcinoma (OSCC) is the most prevalent malignancy with late-presentation, site-specific heterogeneity, and high-propensity for recurrence/metastasis that has shown rise in mortality. Lately, research emphasize on dynamic interactions between tumor-cells and extracellular-matrix components within tumor-microenvironment that promote tissue integrity loss and carcinogenesis. Therefore, OSCC clinical-management is still challenging. DESIGN: Present study validated clinical utility of a 13 gene-panel in two chief sub-sites of OSCC: Buccal mucosa squamous cell carcinoma (BMSCC) (N = 50) and Tongue squamous cell carcinoma (TSCC) (N = 52) using qRT-PCR...
February 22, 2024: Archives of Oral Biology
https://read.qxmd.com/read/38439815/comprehensive-germline-profiling-of-patients-with-breast-cancer-initial-experience-from-a-familial-cancer-clinic
#37
JOURNAL ARTICLE
Raja Pramanik, Sindhura Chitikela, S V S Deo, Ajay Gogia, Atul Batra, Akash Kumar, Ritu Gupta, Deepshi Thakral, Vedam L Ramprasad, Sandeep Mathur, D N Sharma, Aparna Sharma, Ashutosh Mishra, Babul Bansal
INTRODUCTION: Breast cancer is the most common cancer among Indian females. There is limited data on germline profiling of breast cancer patients from India. OBJECTIVE: The objective of the current study was to analyse the frequency and spectrum of germline variant profiles and clinicopathological characteristics of breast cancer patients referred to our Familial Cancer Clinic (FCC). MATERIALS AND METHODS: It is a single-centre audit of patients with a confirmed diagnosis of breast carcinoma referred to our FCC from January 2017 to 2020...
2024: Ecancermedicalscience
https://read.qxmd.com/read/38439030/assessing-the-genomic-feature-of-chinese-patients-with-ampullary-adenocarcinoma-potential-therapeutic-targets
#38
JOURNAL ARTICLE
Zhang Dong, Wan Chong, Chen Chen, Li Qi, Li Mengke, Dou Minghui, Yuan Jiawei, Quan Longxi, Liu Hengchao, Jia Liu, Geng Zhimin
BACKGROUNDS: Ampullary adenocarcinoma (AMPAC) is a rare malignancy, treated as pancreatic or intestinal cancer based on its histologic subtype. Little is known about the genomic features of Chinese patients with AMPAC. MATERIALS AND METHODS: We enrolled 145 Chinese AMPAC patients in our local cohort and performed a compressive somatic and germline genetic testing using a 156 gene panel. Expression of PD-L1 (clone 28 - 8) was also assessed in tumor specimens from 64 patients...
March 4, 2024: BMC Cancer
https://read.qxmd.com/read/38429519/digital-rna-sequencing-using-unique-molecular-identifiers-enables-ultrasensitive-rna-mutation-analysis
#39
JOURNAL ARTICLE
Manuel Luna Santamaría, Daniel Andersson, Toshima Z Parris, Khalil Helou, Tobias Österlund, Anders Ståhlberg
Mutation analysis is typically performed at the DNA level since most technical approaches are developed for DNA analysis. However, some applications, like transcriptional mutagenesis, RNA editing and gene expression analysis, require RNA analysis. Here, we combine reverse transcription and digital DNA sequencing to enable low error digital RNA sequencing. We evaluate yield, reproducibility, dynamic range and error correction rate for seven different reverse transcription conditions using multiplexed assays...
March 1, 2024: Communications Biology
https://read.qxmd.com/read/38424437/the-evolutionary-impact-of-childhood-cancer-on-the-human-gene-pool
#40
JOURNAL ARTICLE
Ulrik Kristoffer Stoltze, Jon Foss-Skiftesvik, Thomas van Overeem Hansen, Simon Rasmussen, Konrad J Karczewski, Karin A W Wadt, Kjeld Schmiegelow
Germline pathogenic variants associated with increased childhood mortality must be subject to natural selection. Here, we analyze publicly available germline genetic metadata from 4,574 children with cancer [11 studies; 1,083 whole exome sequences (WES), 1,950 whole genome sequences (WGS), and 1,541 gene panel] and 141,456 adults [125,748 WES and 15,708 WGS]. We find that pediatric cancer predisposition syndrome (pCPS) genes [n = 85] are highly constrained, harboring only a quarter of the loss-of-function variants that would be expected...
February 29, 2024: Nature Communications
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