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Mutation analysis biomarkers cancer

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https://www.readbyqxmd.com/read/28104537/correlation-between-classic-driver-oncogene-mutations-in-egfr-alk-or-ros1-and-22c3-pd-l1-%C3%A2-50-expression-in-lung-adenocarcinoma
#1
Deepa Rangachari, Paul A VanderLaan, Meghan Shea, Xiuning Le, Mark S Huberman, Susumu S Kobayashi, Daniel B Costa
INTRODUCTION: Targeted somatic genomic analysis (EGFR, ALK and ROS1) and PD-L1 tumor proportion score (TPS) by immunohistochemistry (IHC) are used for selection of 1(st)-line therapies in advanced lung cancer; however, the frequency of overlap of these biomarkers in routine clinical practice is poorly reported. METHODS: We retrospectively probed the first 71 lung adenocarcinoma-patient pairs from our institution analyzed for PD-L1 IHC using the clone 22C3 pharmDx kit and evaluated co-occurrence of genomic aberrations along with clinical-pathologic characteristics...
January 16, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28101802/cold-pcr-technologies-in-the-area-of-personalized-medicine-methodology-and-applications
#2
REVIEW
Florence Mauger, Alexandre How-Kit, Jörg Tost
Somatic mutations bear great promise for use as biomarkers for personalized medicine, but are often present only in low abundance in biological material and are therefore difficult to detect. Many assays for mutation analysis in cancer-related genes (hotspots) have been developed to improve diagnosis, prognosis, prediction of drug resistance, and monitoring of the response to treatment. Two major approaches have been developed: mutation-specific amplification methods and methods that enrich and detect mutations without prior knowledge on the exact location and identity of the mutation...
January 18, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28101226/evaluation-of-plasma-microrna-levels-to-predict-insensitivity-of-patients-with-advanced-lung-adenocarcinomas-to-pemetrexed-and-platinum
#3
Jinghua Zhu, Yuhua Qi, Jianzhong Wu, Meiqi Shi, Jifeng Feng, Longbang Chen
Pemetrexed combined with platinum is a first-line therapy used to treat patients with advanced non-small cell lung cancer (NSCLC) that exhibit negative or unknown epidermal growth factor receptor (EGFR) mutational status or anaplastic lymphoma kinase (ALK) rearrangements. Lung adenocarcinoma (LAC) is the primary type of NSCLC. In order to prevent overtreatment, it is necessary to identify patients with LAC who may not benefit from certain chemotherapies. Patients recruited in the present study (n=129) were diagnosed with advanced LAC and received first-line pemetrexed and platinum-based chemotherapy...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28099251/utility-of-assessing-the-number-of-mutated-kras-cdkn2a-tp53-and-smad4-genes-using-a-targeted-deep-sequencing-assay-as-a-prognostic-biomarker-for-pancreatic-cancer
#4
Hideyuki Hayashi, Takashi Kohno, Hideki Ueno, Nobuyoshi Hiraoka, Shunsuke Kondo, Motonobu Saito, Yoko Shimada, Hitoshi Ichikawa, Mamoru Kato, Tatsuhiro Shibata, Chigusa Morizane, Yasunari Sakamoto, Kazuaki Shimada, Yoshito Komatsu, Naoya Sakamoto, Takuji Okusaka
OBJECTIVES: KRAS, CDKN2A, TP53, and SMAD4 have been recognized as major driver genes in pancreatic carcinogenesis. We examined somatic mutations in 50 cancer-related genes, including the four above-mentioned driver genes, to identify genomic biomarkers for predicting the outcome of patients with pancreatic cancer. METHODS: Genomic DNA was extracted from fresh-frozen specimens obtained from 100 patients with pancreatic cancer who had undergone a pancreatectomy with curative intent...
January 18, 2017: Pancreas
https://www.readbyqxmd.com/read/28098895/microrna-133b-is-regulated-by-tap63-while-no-gene-mutation-is-present-in-colorectal-cancer
#5
Yifei Chen, Yi Zhang, Jianhuai He, Ying Fu, Changwei Lin, Xiaorong Li
Downregulation of miR-133b has been reported in multiple types of malignancies including colorectal cancer (CRC). We previously confirmed that TAp63 actively translates microRNA-133b (miR-133b) transcripts. While the presence of miRNA mutations have frequently been described in CRC, most CRCs do not show any variation in the miR‑133b coding sequence. Therefore, it is important to elucidate the relationship between TAp63 and miR-133b, and identify other mediators of miR-133b downregulation in CRC. The expression of TAp63 was detected by RT-qPCR, western blotting, immunohistochemistry (IHC) and densitometric analysis using Image-Pro Plus 6...
January 16, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28095868/pik3ca-mutations-are-common-in-lobular-carcinoma-in-situ-but-are-not-a-biomarker-of-progression
#6
Vandna Shah, Salpie Nowinski, Dina Levi, Irek Shinomiya, Narda Kebaier Ep Chaabouni, Cheryl Gillett, Anita Grigoriadis, Trevor A Graham, Rebecca Roylance, Michael A Simpson, Sarah E Pinder, Elinor J Sawyer
BACKGROUND: Lobular carcinoma in situ (LCIS) is a non-invasive breast lesion that is typically found incidentally on biopsy and is often associated with invasive lobular carcinoma (ILC). LCIS is considered by some to be a risk factor for future breast cancer rather than a true precursor lesion. The aim of this study was to identify genetic changes that could be used as biomarkers of progression of LCIS to invasive disease using cases of pure LCIS and comparing their genetic profiles to LCIS which presented contemporaneously with associated ILC, on the hypothesis that the latter represents LCIS that has already progressed...
January 17, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28095352/the-relationship-of-rel-proto-oncogene-to-pathobiology-and-chemoresistance-in-follicular-and-transformed-follicular-lymphoma
#7
Xiaozhou Hu, Esra Baytak, Jinnan Li, Burcu Akman, Kaan Okay, Genfu Hu, Anna Scuto, Wenyan Zhang, Can Küçük
Follicular lymphoma (FL) is a common type of indolent lymphoma that occasionally transforms to more aggressive B-cell lymphomas. These transformed follicular lymphomas (tFL) are often associated with chemoresistance whose mechanisms are currently unknown. REL, a proto-oncogene located on frequently amplified 2p16.1-p15 locus, promotes tumorigenesis in many cancer types through deregulation of the NF-κB pathway; however, its role in FL pathobiology or chemoresistance has not been addressed. Here, we evaluated REL gene copy number by q-PCR on FFPE FL tumor samples, and observed REL amplification in 30...
January 9, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28089283/myc-amplification-as-a-predictive-factor-of-complete-pathologic-response-to-docetaxel-based-neoadjuvant-chemotherapy-for-breast-cancer
#8
Cynthia Brito Lins Pereira, Mariana Ferreira Leal, Eliana Saul Furquim Werneck Abdelhay, Sâmia Demachki, Paulo Pimentel Assumpção, Mirian Carvalho de Souza, Caroline Aquino Moreira-Nunes, Adriana Michiko da Silva Tanaka, Marília Cardoso Smith, Rommel Rodríguez Burbano
BACKGROUND: Neoadjuvant chemotherapy is a standard treatment for stage II and III breast cancer. The identification of biomarkers that may help in the prediction of response to neoadjuvant therapies is necessary for a more precise definition of the best drug or drug combination to induce a better response. MATERIAL AND METHODS: We assessed the role of Ki67, hormone receptors expression, HER2, MYC genes and their protein status, and KRAS codon 12 mutations as predictor factors of pathologic response to anthracycline-cyclophosphamide (AC) followed by taxane docetaxel (T) neoadjuvant chemotherapy (AC+T regimen) in 51 patients with invasive ductal breast cancer...
December 24, 2016: Clinical Breast Cancer
https://www.readbyqxmd.com/read/28077799/kras-and-tp53-mutations-in-inflammatory-bowel-disease-associated-colorectal-cancer-a-meta-analysis
#9
Lijun Du, John J Kim, Jinhua Shen, Binrui Chen, Ning Dai
Although KRAS and TP53 mutations are common in both inflammatory bowel disease-associated colorectal cancer (IBD-CRC) and sporadic colorectal cancer (S-CRC), molecular events leading to carcinogenesis may be different. Previous studies comparing the frequency of KRAS and TP53 mutations in IBD-CRC and S-CRC were inconsistent. We performed a meta-analysis to compare the presence of KRAS and TP53 mutations among patients with IBD-CRC, S-CRC, and IBD without dysplasia. A total of 19 publications (482 patients with IBD-CRC, 4,222 with S-CRC, 281 with IBD without dysplasia) met the study inclusion criteria...
January 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28077296/extracellular-vesicle-communication-pathways-as-regulatory-targets-of-oncogenic-transformation
#10
REVIEW
Dongsic Choi, Tae Hoon Lee, Cristiana Spinelli, Shilpa Chennakrishnaiah, Esterina D'Asti, Janusz Rak
Pathogenesis of human cancers bridges intracellular oncogenic driver events and their impact on intercellular communication. Among multiple mediators of this 'pathological connectivity' the role of extracellular vesicles (EVs) and their subsets (exosomes, ectosomes, oncosomes) is of particular interest for several reasons. The release of EVs from cancer cells represents a unique mechanism of regulated expulsion of bioactive molecules, a process that also mediates cell-to-cell transfer of lipids, proteins, and nucleic acids...
January 8, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28068936/retrospective-study-of-ras-pik3ca-braf-tumor-mutations-as-predictors-of-response-to-first-line-chemotherapy-with-bevacizumab-in-metastatic-colorectal-cancer-patients
#11
Izuma Nakayama, Eiji Shinozaki, Tomohiro Matsushima, Takeru Wakatsuki, Mariko Ogura, Takashi Ichimura, Masato Ozaka, Daisuke Takahari, Mitsukuni Suenaga, Keisho Chin, Nobuyuki Mizunuma, Kensei Yamaguchi
BACKGROUND: After analysis of minor RAS mutations (KRAS exon 3, 4/NRAS) in the FIRE-3 and PRIME studies, an expanded range of RAS mutations were established as a negative predictive marker for the efficacy of anti-EGFR antibody treatment. BRAF and PIK3CA mutations may be candidate biomarkers for anti-EGFR targeted therapies. However, it remains unknown whether RAS/PIK3CA/BRAF tumor mutations can predict the efficacy of bevacizumab in metastatic colorectal cancer. We assessed whether selection according to RAS/PIK3CA/BRAF mutational status could be beneficial for patients treated with bevacizumab as first-line treatment for metastatic colorectal cancer...
January 9, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28061489/the-influence-of-biomarker-mutations-and-systemic-treatment-on-cerebral-metastases-from-nsclc-treated-with-radiosurgery
#12
Min Ho Lee, Doo-Sik Kong, Ho Jun Seol, Do-Hyun Nam, Jung-Il Lee
OBJECTIVE: The purpose of this study was to analyze outcomes and identify prognostic factors in patients with cerebral metastases from non-small cell lung cancer (NSCLC) treated with gamma knife radiosurgery (GKS) particularly, focusing on associations of biomarkers and systemic treatments. METHODS: We retrospectively reviewed the medical records of 134 patients who underwent GKS for brain metastases due to NSCLC between January 2002 and December 2012. Representative biomarkers including epidermal growth factor receptor (EGFR) mutation, K-ras mutation, and anaplastic lymphoma kinase (ALK) mutation status were investigated...
January 1, 2017: Journal of Korean Neurosurgical Society
https://www.readbyqxmd.com/read/28058082/on-chip-wavelength-multiplexed-detection-of-cancer-dna-biomarkers-in-blood
#13
H Cai, M A Stott, D Ozcelik, J W Parks, A R Hawkins, H Schmidt
We have developed an optofluidic analysis system that processes biomolecular samples starting from whole blood and then analyzes and identifies multiple targets on a silicon-based molecular detection platform. We demonstrate blood filtration, sample extraction, target enrichment, and fluorescent labeling using programmable microfluidic circuits. We detect and identify multiple targets using a spectral multiplexing technique based on wavelength-dependent multi-spot excitation on an antiresonant reflecting optical waveguide chip...
November 2016: Biomicrofluidics
https://www.readbyqxmd.com/read/28056336/the-clinical-role-of-circulating-free-tumor-dna-in-gastrointestinal-malignancy
#14
REVIEW
Jessica A Howell, Shahid A Khan, Susanne Knapp, Mark R Thursz, Rohini Sharma
Circulating cell-free DNA (cfDNA) is DNA released from necrotic or apoptotic cells into the bloodstream. While both healthy cells and cancer cells release cfDNA, tumors are associated with higher levels of tumor-derived circulating cell-free DNA (ctDNA) detectable in blood. Absolute levels of ctDNA and its genetic mutations and epigenetic changes show promise as potentially useful biomarkers of tumor biology, progression, and response to therapy. Moreover, studies have demonstrated the discriminative accuracy of ctDNA levels for diagnosis of gastrointestinal cancer compared with benign inflammatory diseases...
December 22, 2016: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/28048759/tu-a-207b-00-imaging-genomics-associations-and-biological-correlates-of-radiomics
#15
Yitan Zhu
With the growth of quantitative imaging and quantitative image analysis, image-based biomarkers (i.e. image-based phenotypes) are becoming potential descriptors in personalized medicine as well as in cancer discovery research. Genomic study measures molecular cancer status and provides abundant information about cancer development mechanism. There is a need to understand the relationship between the image-based cancer phenotypes (from radiomics) and the underlying molecular and genomic system. Imaging scientists and genomic scientists need to be able to speak the same language in this common era of Big Data...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047278/tu-a-207b-01-imaging-genomics-associations-and-biological-correlates-of-radiomics
#16
Y Zhu
With the growth of quantitative imaging and quantitative image analysis, image-based biomarkers (i.e. image-based phenotypes) are becoming potential descriptors in personalized medicine as well as in cancer discovery research. Genomic study measures molecular cancer status and provides abundant information about cancer development mechanism. There is a need to understand the relationship between the image-based cancer phenotypes (from radiomics) and the underlying molecular and genomic system. Imaging scientists and genomic scientists need to be able to speak the same language in this common era of Big Data...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28029662/guidance-to-rational-use-of-pharmaceuticals-in-gallbladder-sarcomatoid-carcinoma-using-patient-derived-cancer-cells-and-whole-exome-sequencing
#17
Feiling Feng, Qingbao Cheng, Liang Yang, Dadong Zhang, Shunlong Ji, Qiangzu Zhang, Yihui Lin, Fugen Li, Lei Xiong, Chen Liu, Xiaoqing Jiang
PURPOSE: Gallbladder sarcomatoid carcinoma is a rare cancer with no clinical standard treatment. With the rapid development of next generation sequencing, it has been able to provide reasonable treatment options for patients based on genetic variations. However, most cancer drugs are not approval for gallbladder sarcomatoid carcinoma indications. The correlation between drug response and a genetic variation needs to be further elucidated. EXPERIMENTAL DESIGN: Three patient-derived cells-JXQ-3D-001, JXQ-3D-002, and JXQ-3D-003, were derived from biopsy samples of one gallbladder sarcomatoid carcinoma patient with progression and have been characterized...
December 24, 2016: Oncotarget
https://www.readbyqxmd.com/read/28027313/base-position-error-rate-analysis-of-next-generation-sequencing-applied-to-circulating-tumor-dna-in-non-small-cell-lung-cancer-a-prospective-study
#18
Nicolas Pécuchet, Eleonora Zonta, Audrey Didelot, Pierre Combe, Constance Thibault, Laure Gibault, Camille Lours, Yves Rozenholc, Valérie Taly, Pierre Laurent-Puig, Hélène Blons, Elizabeth Fabre
BACKGROUND: Circulating tumor DNA (ctDNA) is an approved noninvasive biomarker to test for the presence of EGFR mutations at diagnosis or recurrence of lung cancer. However, studies evaluating ctDNA as a noninvasive "real-time" biomarker to provide prognostic and predictive information in treatment monitoring have given inconsistent results, mainly due to methodological differences. We have recently validated a next-generation sequencing (NGS) approach to detect ctDNA. Using this new approach, we evaluated the clinical usefulness of ctDNA monitoring in a prospective observational series of patients with non-small cell lung cancer (NSCLC)...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/28026870/vulvar-and-vaginal-melanoma-a-unique-subclass-of-mucosal-melanoma-based-on-a-comprehensive-molecular-analysis-of-51-cases-compared-with-2253-cases-of-nongynecologic-melanoma
#19
June Y Hou, Caitlin Baptiste, Radhika Bangalore Hombalegowda, Ana I Tergas, Rebecca Feldman, Nathaniel L Jones, Sudeshna Chatterjee-Paer, Ama Bus-Kwolfski, Jason D Wright, William M Burke
BACKGROUND: Optimal treatments for vulvar and vaginal melanomas (VVMs) have not been identified. Herein, the authors compare molecular profiles between VVM and nongynecologic melanoma (NGM) subtypes with the objective of identifying novel, targetable biomarkers. METHODS: In total, 2304 samples of malignant melanoma that were submitted to Caris Life Sciences between 2009 and 2015 were reviewed. In situ hybridization and immunohistochemistry were used to assess copy numbers and protein expression of selected genes...
December 27, 2016: Cancer
https://www.readbyqxmd.com/read/28025786/egfr-gene-amplification-and-kras-mutation-predict-response-to-combination-targeted-therapy-in-metastatic-colorectal-cancer
#20
Sajid A Khan, Zhaoshi Zeng, Jinru Shia, Philip B Paty
Genetic variability in KRAS and EGFR predicts response to cetuximab in irinotecan refractory colorectal cancer. Whether these markers or others remain predictive in combination biologic therapies including bevacizumab is unknown. We identified predictive biomarkers from patients with irinotecan refractory metastatic colorectal cancer treated with cetuximab plus bevacizumab. Patients who received cetuximab plus bevacizumab for irinotecan refractory colorectal cancer in either of two Phase II trials conducted were identified...
December 26, 2016: Pathology Oncology Research: POR
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