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Mutation analysis biomarkers cancer

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https://www.readbyqxmd.com/read/29138235/brip1-overexpression-is-correlated-with-clinical-features-and-survival-outcome-of-luminal-breast-cancer-subtypes
#1
Ishita Gupta, Allal Ouhtit, Adil Al-Ajmi, Syed Gauhar A Rizvi, Hamad Al-Riyami, Marwa Al-Riyami, Yahya Tamimi
In Oman, breast cancer is most common, representing approximately more than 25% of all cancers in women. Relatively younger populations of patients (25 to 40 years) present surprisingly with an aggressive phenotype and advanced tumor stages. In this study, we investigated differential gene expressions in Luminal-A, Luminal-B, Triple negative and Her2+ breast cancer subtypes and compared data to benign tumor samples. We identified a potential candidate gene BRIP1, showing differential expression in the four breast cancer subtypes examined, suggesting that BRIP1 has the profile of a useful diagnostic marker, suitable for targeted therapeutic intervention...
November 14, 2017: Endocrine Connections
https://www.readbyqxmd.com/read/29132830/characterizing-recurrent-and-lethal-small-renal-masses-in-clear-cell-renal-cell-carcinoma-using-recurrent-somatic-mutations
#2
Brandon J Manley, Ed Reznik, Mazyar Ghanaat, Mahyar Kashan, Maria F Becerra, Jozefina Casuscelli, Daniel Tennenbaum, Almedina Redzematovic, Maria I Carlo, Yusuke Sato, Maria Arcila, Martin H Voss, Darren R Feldman, Robert J Motzer, Paul Russo, Jonathan Coleman, James J Hsieh, Ari A Hakimi
INTRODUCTION: Small renal masses (SRMs) with evidence of clear cell renal cell carcinoma (ccRCC) are understudied. Current algorithms for the management of SRMs include surgical resection, ablation, and active surveillance. We sought to identify genomic biomarkers that could potentially refine the management of ccRCC in SRMs, especially in patients being evaluated for active surveillance. METHODS: We identified patients who had SRMs (4cm or less) at time of surgery, had sequencing performed on their primary tumor and had a diagnosis of ccRCC...
November 10, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/29113157/lack-of-microsatellite-instability-in-gastrointestinal-stromal-tumors
#3
Nathália C Campanella, Cristovam Scapulatempo-Neto, Lucas Faria Abrahão-Machado, Antônio Talvane Torres De Oliveira, Gustavo N Berardinelli, Denise Peixoto Guimarães, Rui M Reis
The microsatellite instability (MSI) phenotype may constitute an important biomarker for patient response to immunotherapy, particularly to anti-programmed death-1 inhibitors. MSI is a type of genomic instability caused by a defect in DNA mismatch repair (MMR) proteins, which is present mainly in colorectal cancer and its hereditary form, hereditary nonpolyposis colorectal cancer. Gastrointestinal stromal tumor (GIST) development is associated with activating mutations of KIT proto-oncogene receptor tyrosine kinase (KIT) or platelet-derived growth factor receptor α (PDGFRA), which are oncogenes that predict the response to imatinib mesylate...
November 2017: Oncology Letters
https://www.readbyqxmd.com/read/29110152/low-pten-levels-and-pik3ca-mutations-predict-resistance-to-neoadjuvant-lapatinib-and-trastuzumab-without-chemotherapy-in-patients-with-her2-over-expressing-breast-cancer
#4
Mothaffar F Rimawi, Carmine De Angelis, Alejandro Contreras, Fresia Pareja, Felipe C Geyer, Kathleen A Burke, Sabrina Herrera, Tao Wang, Ingrid A Mayer, Andres Forero, Rita Nanda, Matthew P Goetz, Jenny C Chang, Ian E Krop, Antonio C Wolff, Anne C Pavlick, Suzanne A W Fuqua, Carolina Gutierrez, Susan G Hilsenbeck, Marilyn M Li, Britta Weigelt, Jorge S Reis-Filho, C Kent Osborne, Rachel Schiff
PURPOSE: Aberrant activation of the PI3K pathway has been implicated in resistance to HER2-targeted therapy, but results of clinical trials are confounded by the co-administration of chemotherapy. We investigated the effect of perturbations of this pathway in breast cancers from patients treated with neoadjuvant anti-HER2-targeted therapy without chemotherapy. PATIENTS AND METHODS: Baseline tumor samples from patients with HER2-positive breast cancer enrolled in TBCRC006 (NCT00548184), a 12-week neoadjuvant clinical trial with lapatinib plus trastuzumab [plus endocrine therapy for estrogen receptor (ER)-positive tumors], were assessed for PTEN status by immunohistochemistry and PIK3CA mutations by sequencing...
November 7, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29108264/lncrnas-pvt1-and-har1a-are-prognosis-biomarkers-and-indicate-therapy-outcome-for-diffuse-glioma-patients
#5
Hecun Zou, Lan-Xiang Wu, Yonglong Yang, Shuang Li, Ying Mei, Yong-Bin Liu, Lihua Zhang, Yu Cheng, Hong-Hao Zhou
Diffuse gliomas are well known malignant brain tumors. Long non-coding RNAs (lncRNAs), a type of RNA transcript with more than 200 nucleotides, involve in tumorigenesis and development of various cancers. This study focused on identifying differentially expressed lncRNAs in gliomas based on gene expression profiling, and chose certain lncRNAs PVT1, CYTOR, HAR1A and MIAT, which changed with significant differences. Further analysis of TCGA and GEO data revealed that the expressions of PVT1 and CYTOR were up-regulated, while HAR1A and MIAT expressions were down-regulated in gliomas...
October 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/29101156/mutation-load-offers-predictive-biomarker-in-sclc
#6
(no author information available yet)
Tumor mutation burden offers a promising predictive biomarker for patients with small cell lung cancer. An exploratory analysis presented at the World Conference on Lung Cancer showed that the patients with large numbers of mutations in their cancer cells were more likely to respond-and for a longer time-to a single checkpoint inhibitor or a combination of them than those with a low mutation load.
November 3, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/29100283/circulating-microparticles-are-prognostic-biomarkers-in-advanced-non-small-cell-lung-cancer-patients
#7
Chin-Chou Wang, Chia-Cheng Tseng, Huang-Chih Chang, Kuo-Tung Huang, Wen-Feng Fang, Yu-Mu Chen, Cheng-Ta Yang, Chang-Chun Hsiao, Meng-Chih Lin, Chi-Kung Ho, Hon-Kan Yip
We investigated whether circulating microparticles (MPs) could serve as prognostic biomarkers in non-small cell lung cancer (NSCLC) patients. We enrolled 25 control subjects and 136 NSCLC patients categorized into disease-progression (DP, n=42) and disease-control (DC, n=94) groups. Flow cytometric analysis showed that levels of four types of circulating microparticles (EDAc-MPs, EDAp-MPs, PDAc-MPs and PDAp-MPs) were higher in the study patients than the control subjects (P < 0.04). DP patients showed poor initially performance status and more non-adenocarcinomas than DC patients...
September 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/29098023/detection-of-somatic-mutations-in-the-mitochondrial-dna-control-region-d-loop-in-brain-tumors-the-first-report-in-malaysian-patients
#8
Abdul Aziz Mohamed Yusoff, Khairol Naaim Mohd Nasir, Khalilah Haris, Siti Zulaikha Nashwa Mohd Khair, Abdul Rahman Izaini Abdul Ghani, Zamzuri Idris, Jafri Malin Abdullah
Although the role of nuclear-encoded gene alterations has been well documented in brain tumor development, the involvement of the mitochondrial genome in brain tumorigenesis has not yet been fully elucidated and remains controversial. The present study aimed to identify mutations in the mitochondrial DNA (mtDNA) control region D-loop in patients with brain tumors in Malaysia. A mutation analysis was performed in which DNA was extracted from paired tumor tissue and blood samples obtained from 49 patients with brain tumors...
November 2017: Oncology Letters
https://www.readbyqxmd.com/read/29095543/background-current-role-and-potential-applications-of-radiogenomics
#9
Katja Pinker, Fuki Shitano, Evis Sala, Richard K Do, Robert J Young, Andreas G Wibmer, Hedvig Hricak, Elizabeth J Sutton, Elizabeth A Morris
With the genomic revolution in the early 1990s, medical research has been driven to study the basis of human disease on a genomic level and to devise precise cancer therapies tailored to the specific genetic makeup of a tumor. To match novel therapeutic concepts conceived in the era of precision medicine, diagnostic tests must be equally sufficient, multilayered, and complex to identify the relevant genetic alterations that render cancers susceptible to treatment. With significant advances in training and medical imaging techniques, image analysis and the development of high-throughput methods to extract and correlate multiple imaging parameters with genomic data, a new direction in medical research has emerged...
November 2, 2017: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/29093617/detection-of-kras-g12d-in-colorectal-cancer-stool-by-droplet-digital-pcr
#10
Susana Olmedillas-López, Dennis César Lévano-Linares, Carmen Laura Aúz Alexandre, Luz Vega-Clemente, Edurne León Sánchez, Alejandro Villagrasa, Jaime Ruíz-Tovar, Mariano García-Arranz, Damián García-Olmo
AIM: To assess KRAS G12D mutation detection by droplet digital PCR (ddPCR) in stool-derived DNA from colorectal cancer (CRC) patients. METHODS: In this study, tumor tissue and stool samples were collected from 70 patients with stage I-IV CRC diagnosed by preoperative biopsy. KRAS mutational status was determined by pyrosequencing analysis of DNA obtained from formalin-fixed paraffin-embedded (FFPE) tumor tissues. The KRAS G12D mutation was then analyzed by ddPCR in FFPE tumors and stool-derived DNA from patients with this point mutation...
October 21, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29090842/different-egfr-gene-mutations-in-two-patients-with-synchronous-multiple-lung-cancers-a-case-report
#11
Hiroki Sakai, Hisashi Saji, Hiroyuki Kimura, Masataka Tsuda, Yoichi Wakiyama, Tomoyuki Miyazawa, Hideki Marushima, Koji Kojima, Masahiro Hoshikawa, Masayuki Takagi, Haruhiko Nakamura
Routine clinical and pathological evaluations to determine the relationship between different lesions are often not completely conclusive. Interestingly, detailed genetic analysis of tumor samples may provide important additional information and identify second primary lung cancers. In the present study, we report cases of two synchronous lung adenocarcinomas composed of two distinct pathological subtypes with different EGFR gene mutations: a homozygous deletion in exon 19 of the papillary adenocarcinoma subtype and a point mutation of L858R in exon 21 of the tubular adenocarcinoma...
November 1, 2017: Thoracic Cancer
https://www.readbyqxmd.com/read/29078173/very-early-response-of-circulating-tumour-derived-dna-in-plasma-predicts-efficacy-of-nivolumab-treatment-in-patients-with-non-small-cell-lung-cancer
#12
Yuki Iijima, Yosuke Hirotsu, Kenji Amemiya, Yoshihiko Ooka, Hitoshi Mochizuki, Toshio Oyama, Takahiro Nakagomi, Yoshinori Uchida, Yoichi Kobayashi, Toshiharu Tsutsui, Yumiko Kakizaki, Taichiro Goto, Yoshihiro Miyashita, Masao Omata
INTRODUCTION: Immunotherapy has become a treatment option for lung cancer. The utility of nivolumab as second-line treatment for non-small cell lung cancer has been proven, but predictive biomarkers influencing its efficacy remain unknown. METHODS: This study involved 14 patients who were treated with nivolumab from February 1 to September 30, 2016. The early response of the level of circulating tumour DNA (ctDNA) after starting nivolumab was evaluated to ascertain whether it could predict treatment outcome...
October 24, 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/29057258/therapeutic-approaches-and-role-of-ncrnas-in-cardiovascular-disorders-and-insulin-resistance
#13
REVIEW
Kalupahana Irushi Pamodya Liyanage, Gamage Upeksha Ganegoda
Diseases resulting from alterations in gene expressions through mutations in the genes or through changes in the gene expression regulation could be identified through the analysis of RNA expressions. ncRNAs play a significant role in regulation of the gene expression by controlling the expression levels of the coding RNAs and other cellular processes. Discoveries have shown that the human genome is encoded with sequences responsible for the transcription of thousands of ncRNAs. Even though the studies conducted on ncRNAs are still at initial stages, facts established so far display biomarkers that confirm their relationship with certain diseases such as cancers, cardiovascular diseases, and insulin resistance...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29056275/current-and-future-applications-of-novel-immunotherapies-in-urological-oncology-a-critical-review-of-the-literature
#14
REVIEW
Berna C Özdemir, Arlene O Siefker-Radtke, Matthew T Campbell, Sumit K Subudhi
CONTEXT: Immunotherapies promote anticancer responses with varying levels of success based on the tumor type. OBJECTIVE: In this narrative review article, we searched the literature regarding immunotherapies in genitourinary malignancies to define the state of the field, explore future applications of immune checkpoint inhibitors, cytokines, vaccines, and cellular therapies in urological oncology and evaluate possible strategies to improve the selection of patients who might benefit from such approaches...
October 19, 2017: European Urology Focus
https://www.readbyqxmd.com/read/29051489/genomic-landscape-associated-with-potential-response-to-anti-ctla-4-treatment-in-cancers
#15
Chan-Young Ock, Jun-Eul Hwang, Bhumsuk Keam, Sang-Bae Kim, Jae-Jun Shim, Hee-Jin Jang, Sarang Park, Bo Hwa Sohn, Minse Cha, Jaffer A Ajani, Scott Kopetz, Keun-Wook Lee, Tae Min Kim, Dae Seog Heo, Ju-Seog Lee
Immunotherapy has emerged as a promising anti-cancer treatment, however, little is known about the genetic characteristics that dictate response to immunotherapy. We develop a transcriptional predictor of immunotherapy response and assess its prediction in genomic data from ~10,000 human tissues across 30 different cancer types to estimate the potential response to immunotherapy. The integrative analysis reveals two distinct tumor types: the mutator type is positively associated with potential response to immunotherapy, whereas the chromosome-instable type is negatively associated with it...
October 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/29050365/mitochondrial-genome-variation-and-prostate-cancer-a-review-of-the-mutational-landscape-and-application-to-clinical-management
#16
REVIEW
Anton M F Kalsbeek, Eva K F Chan, Niall M Corcoran, Christopher M Hovens, Vanessa M Hayes
Prostate cancer is a genetic disease. While next generation sequencing has allowed for the emergence of molecular taxonomy, classification is restricted to the nuclear genome. Mutations within the maternally inherited mitochondrial genome are known to impact cancer pathogenesis, as a result of disturbances in energy metabolism and apoptosis. With a higher mutation rate, limited repair and increased copy number compared to the nuclear genome, the clinical relevance of mitochondrial DNA (mtDNA) variation requires deeper exploration...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050249/profiling-cancer-associated-genetic-alterations-and-molecular-classification-of-cancer-in-korean-gastric-cancer-patients
#17
Yoonjung Kim, Mee-Yon Cho, Juwon Kim, Sung Nam Kim, Seoung Chul Oh, Kyung-A Lee
Recently, the Cancer Genome Atlas (TCGA) Research Network and Asian Cancer Research Group provided a new classification of gastric cancer (GC) to aid the development of biomarkers for targeted therapy and predict prognosis. We studied associations between genetically aberrant profiles of cancer-related genes, environmental factors, and histopathological features in 107 paired gastric tumor-non-tumor tissue GC samples. 6.5% of our GC cases were classified as the EBV subtype, 17.8% as the MSI subtype, 43.0% as the CIN subtype, and 32...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050246/nrf2-regulated-metabolic-gene-signature-as-a-prognostic-biomarker-in-non-small-cell-lung-cancer
#18
Akhileshwar Namani, Qin Qin Cui, Yihe Wu, Hongyan Wang, Xiu Jun Wang, Xiuwen Tang
Mutations in Kelch-like ECH-associated protein 1 (KEAP1) cause the aberrant activation of nuclear factor erythroid-derived 2-like 2 (NRF2), which leads to oncogenesis and drug resistance in lung cancer cells. Our study was designed to identify the genes involved in lung cancer progression targeted by NRF2. A series of microarray experiments in normal and cancer cells, as well as in animal models, have revealed regulatory genes downstream of NRF2 that are involved in wide variety of pathways. Specifically, we carried out individual and combinatorial microarray analysis of KEAP1 overexpression and NRF2 siRNA-knockdown in a KEAP1 mutant-A549 non-small cell lung cancer (NSCLC) cell line...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29046514/protein-phosphatase-magnesium-dependent-1%C3%AE-ppm1d-expression-as-a-prognostic-marker-in-adult-supratentorial-diffuse-astrocytic-and-oligodenroglial-tumors
#19
Hui Jeong Jeong, Chang Gok Woo, Bora Lee, Shin Kwang Khang, Soo Jeong Nam, Jene Choi
Background: Protein phosphatase magnesium-dependent 1δ (PPM1D) is a p53-induced serine/threonine phosphatase, which is overexpressed in various human cancers. A recent study reported that the mutation in the PPM1D gene is associated with poor prognosis in brainstem gliomas. In this study, we evaluate the utility of PPM1D as a prognostic biomarker of adult supratentorial diffuse astrocytic and oligodenroglial tumors. Materials and Methods: To investigate PPM1D protein expression, mRNA expression, and copy number changes, immunohistochemistry, RNAscope in situ hybridization, and fluorescence in situ hybridization in 84 adult supratentorial diffuse gliomas were performed, respectively...
October 18, 2017: Journal of Pathology and Translational Medicine
https://www.readbyqxmd.com/read/29045505/surfaceome-profiling-enables-isolation-of-cancer-specific-exosomal-cargo-in-liquid-biopsies-from-pancreatic-cancer-patients
#20
J Castillo, V Bernard, F A San Lucas, K Allenson, M Capello, D U Kim, P Gascoyne, F C Mulu, B M Stephens, J Huang, H Wang, A A Momin, R O Jacamo, M Katz, R Wolff, M Javle, G Varadhachary, I I Wistuba, S Hanash, A Maitra, H Alvarez
Background: Detection of circulating tumor DNA (ctDNA) can be limited due to their relative scarcity in circulation, particularly while patients are actively undergoing therapy. Exosomes provide a vehicle through which cancer-specific material can be enriched from the compendium of circulating non-neoplastic tissue-derived nucleic acids. We performed a comprehensive profiling of the pancreatic ductal adenocarcinoma (PDAC) exosomal "surfaceome" in order to identify surface proteins that will render liquid biopsies amenable to cancer-derived exosome enrichment for downstream molecular profiling...
September 25, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
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