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Mutation analysis biomarkers cancer

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https://www.readbyqxmd.com/read/28915692/biomarker-analysis-of-the-phase-3-torch-trial-for-first-line-erlotinib-versus-chemotherapy-in-advanced-non-small-cell-lung-cancer-patients
#1
Lucia Kim, Mauro Saieg, Massimo Di Maio, Ciro Gallo, Charles Butts, Fortunato Ciardiello, Ronald Feld, Dengxiao Cheng, Vittorio Gebbia, Marco Angelo Burgio, Yasmin Alam, Simona Signoriello, Antonio Rossi, Natasha Leighl, Paolo Maione, Alessandro Morabito, Geoffrey Liu, Ming-Sound Tsao, Francesco Perrone, Cesare Gridelli
BACKGROUND: The TORCH phase III trial compared the efficacy of first-line erlotinib followed by chemotherapy at progression (experimental arm) with the reverse sequence (standard arm) in unselected advanced non-small cell lung cancer (NSCLC) patients. Here we report biomarker analyses. METHODS: EGFR and KRAS mutation, expression of EGFR family members and of cMET and PTEN and EGFR and ABCG2 germline polymorphisms were tested on tumor tissue or blood samples to either confirm previously proposed predictive role or describe it in an explorative setting...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28914717/the-relationship-between-mismatch-repair-deficiency-and-pd-l1-expression-in-breast-carcinoma
#2
Anne M Mills, Erik A Dill, Christopher A Moskaluk, Jaroslaw Dziegielewski, Tim N Bullock, Patrick M Dillon
Mismatch repair (MMR) deficiency in solid tumors has recently been linked to susceptibility to immunotherapies targeting the programmed cell death-1 (PD-1)/programmed cell death-1 ligand (PD-L1) axis. Loss of MMR proteins has been shown to correlate with tumoral PD-L1 expression in colorectal and endometrial carcinomas, but the association between expression of MMR proteins and PD-L1 has not previously been studied in breast carcinoma, where MMR deficiency is less common. We assessed the relationship between PD-L1 and MMR protein expression by immunohistochemistry in 245 primary and 40 metastatic breast carcinomas...
September 13, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28912405/-exploring-the-possibility-of-new-biomarkers-of-immune-checkpoint-inhibitors-for-non-small-cell-lung-cancer-nsclc
#3
Yuki Owada, Takuya Inoue, Yuzuru Watanabe, Mitsuro Fukuhara, Takumi Yamaura, Satoshi Muto, Yuki Matsumura, Takeo Hasegawa, Daisuke Tanaka, Ryo Kanno, Emi Ito, Hideaki Nanamiya, Junichi Imai, Takao Isogai, Shinya Watanabe, Hiroyuki Suzuki
Mutation burden in a tumor, presumably involving neo-antigens in the tumor tissue, is also thought to be one of the better predictors for the efficacy of immune checkpoint inhibitors. However, it is difficult to analyze the mutation burden routinely in the clinic. Here, we describe more convenient factors that can be used as surrogate markers of mutation burden. Ninety-four patients with NSCLC who underwent resection in our institution were recruited for this study. Mutation burden and major gene alterations were analyzed by using next generation sequencing...
September 2017: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/28912153/comprehensive-genomic-profiling-of-282-pediatric-low-and-high-grade-gliomas-reveals-genomic-drivers-tumor-mutational-burden-and-hypermutation-signatures
#4
Adrienne Johnson, Eric Severson, Laurie Gay, Jo-Anne Vergilio, Julia Elvin, James Suh, Sugganth Daniel, Mandy Covert, Garrett M Frampton, Sigmund Hsu, Glenn J Lesser, Kimberly Stogner-Underwood, Ryan T Mott, Sarah Z Rush, Jennifer J Stanke, Sonika Dahiya, James Sun, Prasanth Reddy, Zachary R Chalmers, Rachel Erlich, Yakov Chudnovsky, David Fabrizio, Alexa B Schrock, Siraj Ali, Vincent Miller, Philip J Stephens, Jeffrey Ross, John R Crawford, Shakti H Ramkissoon
BACKGROUND: Pediatric brain tumors are the leading cause of death for children with cancer in the U.S. Incorporating next-generation sequencing data for both pediatric low-grade (pLGGs) and high-grade gliomas (pHGGs) can inform diagnostic, prognostic, and therapeutic decision-making. MATERIALS AND METHODS: We performed comprehensive genomic profiling on 282 pediatric gliomas (157 pHGGs, 125 pLGGs), sequencing 315 cancer-related genes and calculating the tumor mutational burden (TMB; mutations per megabase [Mb])...
September 14, 2017: Oncologist
https://www.readbyqxmd.com/read/28904888/routine-clinical-use-of-circulating-tumor-cells-for-diagnosis-of-mutations-and-chromosomal-rearrangements-in-non-small-cell-lung-cancer-ready-for-prime-time
#5
REVIEW
Emma Pailler, Vincent Faugeroux, Marianne Oulhen, Cyril Catelain, Françoise Farace
In non-small cell lung cancer (NSCLC), diagnosis of predictive biomarkers for targeted therapies is currently done in small tumor biopsies. However, tumor biopsies can be invasive, in some cases associated with risk, and tissue adequacy, both in terms of quantity and quality is often insufficient. The development of efficient and non-invasive methods to identify genetic alterations is a key challenge which circulating tumor cells (CTCs) have the potential to be exploited for. CTCs are extremely rare and phenotypically diverse, two characteristics that impose technical challenges and impact the success of robust molecular analysis...
August 2017: Translational Lung Cancer Research
https://www.readbyqxmd.com/read/28892905/an-immunohistochemical-study-of-anaplastic-lymphoma-kinase-and-epidermal-growth-factor-receptor-mutation-in-non-small-cell-lung-carcinoma
#6
Sonal Verma, Madhu Kumar, Malti Kumari, Raj Mehrotra, R A S Kushwaha, Madhumati Goel, Ashutosh Kumar, Surya Kant
INTRODUCTION: Lung cancer is one of the leading causes of cancer related death. Targeted treatment for specific markers may help in reducing the cancer related morbidity and mortality. AIM: To study expression of Anaplastic Lymphoma Kinase (ALK)and Epidermal Growth Factor Receptor (EGFR) mutations in patients of Non-Small Cell Lung Cancer NSCLC, that are the targets for specific ALK inhibitors and EGFR tyrosine kinase inhibitors. MATERIALS AND METHODS: Total 69 cases of histologically diagnosed NSCLC were examined retrospectively for immunohistochemical expression of EGFR and ALK, along with positive control of normal placental tissue and anaplastic large cell lymphoma respectively...
July 2017: Journal of Clinical and Diagnostic Research: JCDR
https://www.readbyqxmd.com/read/28891048/identifying-actionable-variants-using-next-generation-sequencing-in-patients-with-a-historical-diagnosis-of-undifferentiated-pleomorphic-sarcoma
#7
Jeremy Lewin, Swati Garg, Beatrice Y Lau, Brendan C Dickson, Frank Traub, Nalan Gokgoz, Anthony M Griffin, Peter C Ferguson, Irene L Andrulis, Hao-Wen Sim, Suzanne Kamel-Reid, Tracy L Stockley, Lillian Siu, Jay S Wunder, Albiruni Ra Razak
There are limited data regarding the molecular characterization of undifferentiated pleomorphic sarcomas (UPS; formerly malignant fibrous histiocytoma). This study aimed to investigate the utility of next generation sequencing (NGS) in UPS to identify subsets of patients who harbour actionable mutations. Patients diagnosed with UPS underwent pathological re-evaluation by a pathologist specializing in sarcoma. Tumor DNA was isolated from archived fresh frozen tissue samples and genotyped using NGS with the Illumina MiSeq TruSeq Amplicon Cancer Panel (48 genes, 212 amplicons)...
September 10, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28889351/multidimensional-phenotyping-of-breast-cancer-cell-lines-to-guide-preclinical-research
#8
Jodi M Saunus, Chanel E Smart, Jamie R Kutasovic, Rebecca L Johnston, Priyakshi Kalita-de Croft, Mariska Miranda, Esdy N Rozali, Ana Cristina Vargas, Lynne E Reid, Eva Lorsy, Sibylle Cocciardi, Tatjana Seidens, Amy E McCart Reed, Andrew J Dalley, Leesa F Wockner, Julie Johnson, Debina Sarkar, Marjan E Askarian-Amiri, Peter T Simpson, Kum Kum Khanna, Georgia Chenevix-Trench, Fares Al-Ejeh, Sunil R Lakhani
PURPOSE: Cell lines are extremely useful tools in breast cancer research. Their key benefits include a high degree of control over experimental variables and reproducibility. However, the advantages must be balanced against the limitations of modelling such a complex disease in vitro. Informed selection of cell line(s) for a given experiment now requires essential knowledge about molecular and phenotypic context in the culture dish. METHODS: We performed multidimensional profiling of 36 widely used breast cancer cell lines that were cultured under standardised conditions...
September 9, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28886477/detection-of-8-hydroxydeoxyguanosine-8-ohdg-as-a-biomarker-of-oxidative-damage-in-peripheral-leukocyte-dna-by-uhplc-ms-ms
#9
Danni Wu, Baodong Liu, Junfa Yin, Tian Xu, Shuli Zhao, Qun Xu, Xi Chen, Hailin Wang
8-Hydroxydeoxyguanosine (8-OHdG) is a widely-used biomarker of oxidative DNA damages. 8-OHdG in peripheral blood leukocyte is associated with mutation and cancer risk. The level of 8-OHdG in peripheral blood leukocytes can indicate a long-term response to oxidative stress rather than that in urine. Accurate identification and quantification of leukocyte 8-OHdG are essential for understanding its mechanism of formation, repair, and biological consequences. In this study, a fast and accurate ultra-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method was developed and validated to detect 8-OHdG in human peripheral leukocyte...
August 26, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28860825/akt-inhibition-is-an-effective-treatment-strategy-in-arid1a-deficient-gastric-cancer-cells
#10
Dakeun Lee, Eun Ji Yu, In-Hye Ham, Hoon Hur, You-Sun Kim
BACKGROUND: The At-rich interactive domain 1A (ARID1A) is frequently mutated in gastric cancers (GCs) with a poor prognosis. Growing evidence indicates that loss of ARID1A expression leads to activation of the phosphatidylinositol 3-kinase (PI3K)/AKT pathway by AKT phosphorylation. We aim to investigate the different sensitivity for the AKT inhibitor in ARID1A-deficient GC cells. METHODS: After transfection using siRNA or shRNA, the effect of ARID1A knockdown on the PI3K/AKT signaling pathway was evaluated by Western blot analysis...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28854564/epigenome-wide-analysis-of-dna-methylation-in-lung-tissue-shows-concordance-with-blood-studies-and-identifies-tobacco-smoke-inducible-enhancers
#11
Theresa Ryan Stueve, Wen-Qing Li, Jianxin Shi, Crystal N Marconett, Tongwu Zhang, Chenchen Yang, Daniel Mullen, Chunli Yan, William Wheeler, Xing Hua, Beiyun Zhou, Zea Borok, Neil E Caporaso, Angela C Pesatori, Jubao Duan, Ite A Laird-Offringa, Maria Teresa Landi
Smoking-associated DNA hypomethylation has been observed in blood cells and linked to lung cancer risk. However, its cause and mechanistic relationship to lung cancer remain unclear. We studied the association between tobacco smoking and epigenome-wide methylation in non-tumor lung (NTL) tissue from 237 lung cancer cases in the Environment And Genetics in Lung cancer Etiology study, using the Infinium HumanMethylation450 BeadChip. We identified seven smoking-associated hypomethylated CpGs (P < 1.0 × 10-7), which were replicated in NTL data from The Cancer Genome Atlas...
August 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28842734/-resection-of-main-duct-and-mixed-type-ipmn-%C3%A2-5%C3%A2-mm
#12
REVIEW
G O Ceyhan, F Scheufele, H Friess
The incidence of cystic pancreatic lesions is steadily increasing due to the technical advances in imaging. Within the group of cystic pancreatic lesions intraductal papillary mucinous neoplasms (IPMNs) depict an important entity. Due to a possible progression to malignancy the clinical strategy has to be well chosen. For primary diagnostic work-up imaging by magnetic resonance imaging (MRI) with MR cholangiopancreatography (MRCP) and computed tomography (CT) scanning is recommended. Additional information can be gained by endosonography and a biopsy of the cystic lesion, allowing analysis of biomarkers, such as GNAS and KRAS mutation as wells as NLR...
August 25, 2017: Der Chirurg; Zeitschrift Für Alle Gebiete der Operativen Medizen
https://www.readbyqxmd.com/read/28842574/using-the-new-cellcollector-to-capture-circulating-tumor-cells-from-blood-in-different-groups-of-pulmonary-disease-a-cohort-study
#13
Yutong He, Jin Shi, Gaofeng Shi, Xiaoli Xu, Qingyi Liu, Congmin Liu, Zhaoyu Gao, Jiaoteng Bai, Baoen Shan
Circulating tumor cells (CTCs) are promising biomarkers for clinical application. Cancer screening with Low-Dose Computed Tomography (LDCT) and CTC detections in pulmonary nodule patients has never been reported. The aim of this study was to explore the effectiveness of the combined methods to screen lung cancer. Out of 8313 volunteers screened by LDCT, 32 ground-glass nodules (GGNs) patients and 19 healthy volunteers were randomly selected. Meanwhile, 15 lung cancer patients also enrolled. CellCollector, a new CTC capturing device, was applied for CTCs detection...
August 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28835386/tumor-mutational-burden-as-an-independent-predictor-of-response-to-immunotherapy-in-diverse-cancers
#14
Aaron M Goodman, Shumei Kato, Lyudmila Bazhenova, Sandip P Patel, Garrett M Frampton, Vincent Miller, Philip J Stephens, Gregory A Daniels, Razelle Kurzrock
Immunotherapy induces durable responses in a subset of patients with cancer. High TMB may be a response biomarker for PD-1/PD-L1 blockade in tumors such as melanoma and non-small cell lung cancer (NSCLC). Our aim was to examine the relationship between TMB and outcome in diverse cancers treated with various immunotherapies. We reviewed data on 1,638 patients who had undergone comprehensive genomic profiling and had TMB assessment. Immunotherapy-treated patients (N = 151) were analyzed for response rate (RR), progression-free and overall survival (PFS, OS)...
August 23, 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/28829813/clinical-validation-of-a-highly-sensitive-assay-to-detect-egfr-mutations-in-plasma-cell-free-dna-from-patients-with-advanced-lung-adenocarcinoma
#15
Yuping Li, Hanyan Xu, Shanshan Su, Junru Ye, Junjie Chen, Xuru Jin, Quan Lin, Dongqing Zhang, Caier Ye, Chengshui Chen
BACKGROUND: Circulating tumor DNA (ctDNA) is a promising biomarker for noninvasive epidermal growth factor receptor (EGFR) mutations detection in lung cancer patients, but the existing methods have limitations in sensitivity or in availability. In this study, we evaluated the performance of a novel assay called ADx-SuperARMS in detecting EGFR mutations in plasma cell-free DNA from patients with advanced lung adenocarcinoma. METHODS: A total of 109 patients with metastatic advanced adenocarcinoma were recruited who provided both blood samples and matched tumor tissue samples...
2017: PloS One
https://www.readbyqxmd.com/read/28810879/quantification-of-mutant-spop-proteins-in-prostate-cancer-using-mass-spectrometry-based-targeted-proteomics
#16
Hui Wang, Christopher E Barbieri, Jintang He, Yuqian Gao, Tujin Shi, Chaochao Wu, Athena A Schepmoes, Thomas L Fillmore, Sung-Suk Chae, Dennis Huang, Juan Miguel Mosquera, Wei-Jun Qian, Richard D Smith, Sudhir Srivastava, Jacob Kagan, David G Camp, Karin D Rodland, Mark A Rubin, Tao Liu
BACKGROUND: Speckle-type POZ protein (SPOP) is an E3 ubiquitin ligase adaptor protein that functions as a potential tumor suppressor, and SPOP mutations have been identified in ~10% of human prostate cancers. However, it remains unclear if mutant SPOP proteins can be utilized as biomarkers for early detection, diagnosis, prognosis or targeted therapy of prostate cancer. Moreover, the SPOP mutation sites are distributed in a relatively short region with multiple lysine residues, posing significant challenges for bottom-up proteomics analysis of the SPOP mutations...
August 15, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28796802/the-prognostic-value-of-kras-mutation-by-cell-free-dna-in-cancer-patients-a-systematic-review-and-meta-analysis
#17
Rongyuan Zhuang, Song Li, Qian Li, Xi Guo, Feng Shen, Hong Sun, Tianshu Liu
KRAS mutation has been found in various types of cancer. However, the prognostic value of KRAS mutation in cell-free DNA (cfDNA) in cancer patients was conflicting. In the present study, a meta-analysis was conducted to clarify its prognostic significance. Literature searches of Cochrane Library, EMBASE, PubMed and Web of Science were performed to identify studies related to KRAS mutation detected by cfDNA and survival in cancer patients. Two evaluators reviewed and extracted the information independently. Review Manager 5...
2017: PloS One
https://www.readbyqxmd.com/read/28790854/hypermethylation-of-secreted-frizzled-related-proteins-predicts-poor-prognosis-in-non-m3-acute-myeloid-leukemia
#18
Hong Guo, Ting-Juan Zhang, Xiang-Mei Wen, Jing-Dong Zhou, Ji-Chun Ma, Cui An, Wei Zhang, Zi-Jun Xu, Jiang Lin, Jun Qian
OBJECTIVE: Secreted frizzled-related proteins (SFRPs) as Wnt signaling antagonists have been found to be dysregulated by promoter hypermethylation in several cancers including acute myeloid leukemia (AML). This study aimed to investigate the methylated status of SFRPs promoter region and its clinical relevance in Chinese non-M3 AML patients. METHODS: SFRPs methylation in 139 primary non-M3 AML patients was determined using methylation-specific real-time quantitative polymerase chain reaction...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28790338/statistical-analysis-of-mutant-allele-frequency-level-of-circulating-cell-free-dna-and-blood-cells-in-healthy-individuals
#19
Ligang Xia, Zhoufang Li, Bo Zhou, Geng Tian, Lidong Zeng, Hongyu Dai, Xiaohua Li, Chaoyu Liu, Shixin Lu, Feiyue Xu, Xiaonian Tu, Fang Deng, Yuancai Xie, Weiren Huang, Jiankui He
Cell-free DNA (cfDNA) in plasma has emerged as a potential important biomarker in clinical diagnostics, particularly in cancer. However, somatic mutations are also commonly found in healthy individuals, which interfere with the effectiveness for cancer diagnostics. This study examined the background somatic mutations in white blood cells (WBC) and cfDNA in healthy controls based on sequencing data from 821 non-cancer individuals and several cancer samples with the aim of understanding the patterns of mutations detected in cfDNA...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28775303/molecular-characterization-of-breast-cancer-ctcs-associated-with-brain-metastasis
#20
Debasish Boral, Monika Vishnoi, Haowen N Liu, Wei Yin, Marc L Sprouse, Antonio Scamardo, David S Hong, Tuan Z Tan, Jean P Thiery, Jenny C Chang, Dario Marchetti
The enumeration of EpCAM-positive circulating tumor cells (CTCs) has allowed estimation of overall metastatic burden in breast cancer patients. However, a thorough understanding of CTCs associated with breast cancer brain metastasis (BCBM) is necessary for early identification and evaluation of treatment response to BCBM. Here we report that BCBM CTCs is enriched in a distinct sub-population of cells identifiable by their biomarker expression and mutational content. Deriving from a comprehensive analysis of CTC transcriptomes, we discovered a unique "circulating tumor cell gene signature" that is distinct from primary breast cancer tissues...
August 4, 2017: Nature Communications
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