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Next generation sequencing AND lung cancer

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https://www.readbyqxmd.com/read/28088513/an-immunogram-for-the-cancer-immunity-cycle-towards-personalized-immunotherapy-of-lung-cancer
#1
Takahiro Karasaki, Kazuhiro Nagayama, Hideki Kuwano, Jun-Ichi Nitadori, Masaaki Sato, Masaki Anraku, Akihiro Hosoi, Hirokazu Matsushita, Yasuyuki Morishita, Kosuke Kashiwabara, Masaki Takazawa, Osamu Ohara, Kazuhiro Kakimi, Jun Nakajima
INTRODUCTION: The interaction of immune cells and cancer cells shapes the immunosuppressive tumor microenvironment. For successful cancer immunotherapy, comprehensive knowledge of anti-tumor immunity as a dynamic spacio-temporal process is required for each individual patient. To this end, we developed an immunogram for the cancer-immunity cycle using next-generation sequencing. METHODS: Whole-exome sequencing and RNA-Seq was performed in 20 non-small cell lung cancer patients (12 adenocarcinoma, 7 squamous cell carcinoma, and 1 large cell neuroendocrine carcinoma)...
January 11, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28088511/brief-report-egfr-l858m-l861q-cis-mutations-confer-selective-sensitivity-to-afatinib
#2
Jamie A Saxon, Lynette M Sholl, Pasi A Jänne
INTRODUCTION: Tyrosine kinase inhibitors (TKIs) have been developed to treat patients with epidermal growth factor receptor (EGFR)-mutant lung cancers. However, the therapeutic efficacy of TKIs in patients with uncommon EGFR mutations remains unclear. METHODS: Next-generation sequencing was performed on a patient's lung adenocarcinoma tumor sample, revealing rare combined in cis (on the same allele) EGFR mutations. Stable Ba/F3 and NIH-3T3 cell lines harboring the mutations were established to investigate the effect of first, second, and third generation EGFR TKIs on cell proliferation by MTS assay and EGFR phosphorylation by Western blotting...
January 11, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28065930/rapid-changes-in-circulating-tumor-dna-in-serially-sampled-plasma-during-treatment-of-breast-cancer-a-case-report
#3
Hiroshi Nakagomi, Yosuke Hirotsu, Kenji Amemiya, Haruka Nakada, Masayuki Inoue, Hitoshi Mochizuki, Toshio Oyama, Masao Omata
BACKGROUND The analysis of circulating tumor DNA (ctDNA) is expected to be a modality to determine the status of cancer in real time. This case indicated utilities and issues in measuring the ctDNA in cancer patients. CASE REPORT A 45-year-old woman with metastatic breast cancer was treated with bevacizumab and paclitaxel. The lung metastases were decreased but the meningitis carcinoma developed rapidly and she died. During the treatment with bevacizumab and paclitaxel, blood samples were taken serially and ctDNA was analyzed using a next-generation sequencer...
January 9, 2017: American Journal of Case Reports
https://www.readbyqxmd.com/read/28028034/rapamycin-insensitive-companion-of-mtor-rictor-amplification-defines-a-subset-of-advanced-gastric-cancer-and-is-sensitive-to-azd2014-mediated-mtorc1-2-inhibition
#4
S T Kim, S Y Kim, S J Klempner, J Yoon, N Kim, S Ahn, H Bang, K-M Kim, W Park, S H Park, J O Park, Y S Park, H Y Lim, S H Lee, K Park, W K Kang, J Lee
PURPOSE: Targeting oncogenic genomic aberrations is an established therapeutic strategy in multiple tumor types. Molecular classification has uncovered a number of novel targets, and rapamycin-insensitive companion of mTOR (RICTOR) amplification has been identified in lung cancer. Further investigation assessing the therapeutic potential of RICTOR amplification as a novel target across advanced cancers is needed. PATIENTS AND METHODS: Tumor samples from 640 patients with metastatic solid tumors, primarily gastrointestinal and lung cancers were prospectively subjected to a next-generation sequencing (NGS) assay to identify molecular targets...
December 27, 2016: Annals of Oncology: Official Journal of the European Society for Medical Oncology
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
#5
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/28000891/expression-of-mir%C3%A2-26a-exhibits-a-negative-correlation-with-hmga1-and-regulates-cancer-progression-by-targeting-hmga1-in-lung-adenocarcinoma-cells
#6
Noboru Sekimoto, Ayako Suzuki, Yutaka Suzuki, Sumio Sugano
Lung cancer is the most common cause of cancer‑associated mortality worldwide, and the number of cases is increasing annually. Several studies have shown that microRNAs (miRNAs) control proliferation, differentiation, and apoptosis in various cell types, and increasing evidence indicates the presence of aberrant miRNA expression profiles and unique miRNA signaling pathways in several types of cancer. The present study aimed to identify miRNAs, which correlated specifically with the progression of lung cancer through the analysis of 57,100 transcripts and 1,341 small RNA expression profiles in 26 lung adenocarcinoma cell lines using next‑generation sequencing...
February 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/27994651/massive-parallel-sequencing-and-digital-gene-expression-analysis-reveals-potential-mechanisms-to-overcome-therapy-resistance-in-pulmonary-neuroendocrine-tumors
#7
Robert Fred Henry Walter, Claudia Vollbrecht, Daniel Christoph, Robert Werner, Jan Schmeller, Elena Flom, Georgia Trakada, Aggeliki Rapti, Vasilis Adamidis, Wolfgang Hohenforst-Schmidt, Jens Kollmeier, Thomas Mairinger, Jeremias Wohlschlaeger, Paul Zarogoulidis, Konstantinos Porpodis, Kurt Werner Schmidt, Fabian Dominik Mairinger
Background: Lung cancer is the leading cause of cancer-related deaths worldwide. 25% show neuroendocrine differentiation (typical/atypical carcinoids, large-/small-cell neuroendocrine carcinomas). Carcinoids present with long survival rates, but metastatic carcinoids correlate with decreased survival and are commonly insensitive to standard chemotherapy or radiation. Therefore, novel therapeutic strategies are urgently needed. Material and methods: 70 representative tumor specimens were used for next-generation sequencing analysis of 14 genes related to therapy response...
2016: Journal of Cancer
https://www.readbyqxmd.com/read/27987594/characterization-of-microbiome-in-bronchoalveolar-lavage-fluid-of-patients-with-lung-cancer-comparing-with-benign-mass-like-lesions
#8
Sang Hoon Lee, Ji Yeon Sung, Dongeun Yong, Jongsik Chun, Song Yee Kim, Joo Han Song, Kyung Soo Chung, Eun Young Kim, Ji Ye Jung, Young Ae Kang, Young Sam Kim, Se Kyu Kim, Joon Chang, Moo Suk Park
OBJECTIVES: Disruption in the stability of respiratory microbiota is known to be associated with many chronic respiratory diseases. However, only few studies have examined microbiomes in lung cancer. Therefore, we characterized and compared the microbiomes of patients with lung cancer and those with benign mass-like lesions. MATERIALS AND METHODS: Bronchoalveolar fluid was collected prospectively to evaluate lung masses in patients who had undergone bronchoscopies from May to September 2015...
December 2016: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/27974690/benefit-of-sunitinib-in-the-treatment-of-pulmonary-primitive-neuroectodermal-tumors-a-case-report-and-literature-review
#9
Chunhui Zhang, Jingchun Zhang, Guangyu Wang, Jiajia Xu, Yanlin Li, Qing Guo, Tongsen Zheng, Yanqiao Zhang
Primitive neuroectodermal tumor (PNET) is a highly aggressive small round celltumor but is extremely rare in the lung. Next-generation sequencing (NGS) has led to breakthroughs for genetic analyses and personalizedmedicine approaches for cancer treatment.We report the case of a 30-year-old woman with an advanced pulmonary PNET treated with multiple chemotherapeutic regimens, and achieved a partial response (PR) as a best response. However, there was a disease progression after these treatment regimens.The NGS revealed the presence of a copy number loss (CNL) of Von Hippel-Lindau (VHL), CDKN2A/B and TP53 genes...
December 10, 2016: Oncotarget
https://www.readbyqxmd.com/read/27926526/use-of-capture-based-next-generation-sequencing-to-detect-alk-fusion-in-plasma-cell-free-dna-of-patients-with-non-small-cell-lung-cancer
#10
Shaohua Cui, Wei Zhang, Liwen Xiong, Feng Pan, Yanjie Niu, Tianqing Chu, Huimin Wang, Yizhuo Zhao, Liyan Jiang
Capture-based next-generation sequencing (NGS) is a potentially useful diagnostic method to measure tumor tissue DNA in blood as it can identify concordant mutations between cell-free DNA (cfDNA) and primary tumor DNA in lung cancer patients. In this study, the sensitivity, specificity and accuracy of capture-based NGS for detecting ALK fusion in plasma cfDNA was assessed. 24 patients with tissue ALK-positivity and 15 who did not harbor ALK fusion were enrolled. 13 ALK-positive samples were identified by capture-based NGS among the 24 samples with tissue ALK-positivity...
December 1, 2016: Oncotarget
https://www.readbyqxmd.com/read/27912825/next-generation-sequencing-of-lung-cancers-lessons-learned-and-future-directions
#11
REVIEW
Siddhartha Devarakonda, Ashiq Masood, Ramaswamy Govindan
Targeted therapies and immune checkpoint inhibitors have significantly improved outcomes in a sizable fraction of patients with metastatic non-small cell lung cancer. Nevertheless, a majority of patients with lung cancer continue to have poor outcomes. The ability to comprehensively characterize the genomic alterations in various subtypes of lung cancer has the potential to transform cancer care by facilitating the identification of novel treatment strategies. The objective of this review is to summarize key findings from recent studies that have sequenced a large number of lung cancer samples and discuss the diagnostic, prognostic, and therapeutic relevance of these findings...
February 2017: Hematology/oncology Clinics of North America
https://www.readbyqxmd.com/read/27900322/patterns-of-transposable-element-expression-and-insertion-in-cancer
#12
Evan A Clayton, Lu Wang, Lavanya Rishishwar, Jianrong Wang, John F McDonald, I King Jordan
Human transposable element (TE) activity in somatic tissues causes mutations that can contribute to tumorigenesis. Indeed, TE insertion mutations have been implicated in the etiology of a number of different cancer types. Nevertheless, the full extent of somatic TE activity, along with its relationship to tumorigenesis, have yet to be fully explored. Recent developments in bioinformatics software make it possible to analyze TE expression levels and TE insertional activity directly from transcriptome (RNA-seq) and whole genome (DNA-seq) next-generation sequence data...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27899957/next-generation-sequencing-in-nsclc-and-melanoma-patients-a-cost-and-budget-impact-analysis
#13
Rosa A van Amerongen, Valesca P Retèl, Veerle Mh Coupé, Petra M Nederlof, Maartje J Vogel, Wim H van Harten
Next-generation sequencing (NGS) has reached the molecular diagnostic laboratories. Although the NGS technology aims to improve the effectiveness of therapies by selecting the most promising therapy, concerns are that NGS testing is expensive and that the 'benefits' are not yet in relation to these costs. In this study, we give an estimation of the costs and an institutional and national budget impact of various types of NGS tests in non-small-cell lung cancer (NSCLC) and melanoma patients within The Netherlands...
2016: Ecancermedicalscience
https://www.readbyqxmd.com/read/27899772/-lung-cancer
#14
Kazushi Yoshida, Takashi Kono
Personalized lung cancer therapy has progressed by targeting several oncogenic aberrations that drive lung carcinogenesis. Recent advances in gene analysis technologies, including next-generation sequencing that yields large amounts of genomic data, have greatly contributed to this progress. In addition, immune checkpoint blockade therapy has become available in Japan, and extensive searches for biomarkers predictive of therapeutic response have been carried out. "Clinical sequencing" which analyzes aberrations in a set of therapy-related genes in patient cancer specimens, has been actively conducted in Japan and other countries...
November 2016: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/27889782/molecular-pathology-a-requirement-for-precision-medicine-in-cancer
#15
Manfred Dietel
The increasing importance of targeting drugs and check-point inhibitors in the treatment of several tumor entities (breast, colon, lung, malignant melanoma, lymphoma, etc.) and the necessity of a companion diagnostic (HER2, (pan)RAS, EGFR, ALK, BRAF, ROS1, MET, PD-L1, etc.) is leading to new challenges for surgical pathology. Since almost all the biomarkers to be specifically detected are tissue based, a precise and reliable diagnostic is absolutely crucial. To meet this challenge surgical pathology has adapted a number of molecular methods (semi-quantitative immunohistochemistry, fluorescence in situ hybridization, PCR and its multiple variants, (pyro/Sanger) sequencing, next generation sequencing (amplicon, whole exome, whole genome), DNA arrays, methylation analyses, etc...
2016: Oncology Research and Treatment
https://www.readbyqxmd.com/read/27875625/clinical-and-genetic-determinants-of-ovarian-metastases-from-colorectal-cancer
#16
Karuna Ganesh, Ronak H Shah, Efsevia Vakiani, Garrett M Nash, Hugh P Skottowe, Rona Yaeger, Andrea Cercek, Anne Lincoln, Christina Tran, Neil H Segal, Diane L Reidy, Anna Varghese, Andrew S Epstein, Yukio Sonoda, Dennis Chi, Jose Guillem, Larissa Temple, Philip Paty, Jaclyn Hechtman, Jinru Shia, Martin Weiser, Julio Garcia Aguilar, Nancy Kemeny, Michael F Berger, Leonard Saltz, Zsofia K Stadler
BACKGROUND: Ovarian metastases from colorectal cancer (OM-CRC) often are unresponsive to chemotherapy and are associated with poor survival. To the authors' knowledge, the clinicopathologic and genomic predictors of OM-CRC are poorly characterized and optimal clinical management remains unclear. METHODS: Women with a histopathological diagnosis of OM-CRC who were treated at Memorial Sloan Kettering Cancer Center from 1999 to 2015 were identified. Next-generation somatic mutation profiling (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets [MSK-IMPACT]) was performed on 38 OM-CRC cases, including 21 matched tumor pairs/trios...
November 22, 2016: Cancer
https://www.readbyqxmd.com/read/27866095/continuing-egfr-inhibition-beyond-progression-in-advanced-non-small-cell-lung-cancer
#17
REVIEW
Timothy A Yap, Aislinn Macklin-Doherty, Sanjay Popat
The majority of patients with epidermal growth factor receptor (EGFR) mutant non-small cell lung cancer (NSCLC) respond to first-line EGFR tyrosine kinase inhibitors (TKIs), but nearly all inevitably acquire resistance and develop disease progression. Conventional practice would be to switch treatments to second-line therapy. However, continuing TKIs beyond progression is becoming increasingly commonplace in patients with indolent, small volume asymptomatic growth, who may potentially continue to derive ongoing clinical benefit and to avoid a 'withdrawal tumour flare'...
January 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/27865871/clinical-impact-of-hybrid-capture-based-next-generation-sequencing-on-changes-in%C3%A2-treatment-decisions-in-lung-cancer
#18
Anna Belilovski Rozenblum, Maya Ilouze, Elizabeth Dudnik, Addie Dvir, Lior Soussan-Gutman, Smadar Geva, Nir Peled
INTRODUCTION: Targeted therapy significantly prolongs survival in lung adenocarcinoma. Current diagnostic guidelines include only EGFR and anaplastic lymphoma receptor tyrosine kinase gene (ALK) testing. Next-generation sequencing (NGS) reveals more actionable genomic alterations than do standard diagnostic methods. Data on the influence of hybrid capture (HC)-based NGS on treatment are limited, and we investigated its impact on treatment decisions and clinical outcomes. METHODS: This retrospective study included patients with advanced lung cancer on whom HC-based NGS was performed between November 2011 and October 2015...
November 16, 2016: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/27865624/w-alk-into-the-next-stage
#19
REVIEW
Gouji Toyokawa, Takashi Seto, Mitsuhiro Takenoyama, Yukito Ichinose
In 2007, the rearrangement of anaplastic lymphoma kinase (ALK) was identified to be associated with the pathogenesis of a subset of patients with non-small-cell lung cancer (NSCLC). Surprisingly, approximately 4 years after the discovery of ALK rearrangement in lung cancer, the first-in-class ALK inhibitor (ALKi), crizotinib, was approved for metastatic ALK-rearranged NSCLC by the US Food and Drug Administration. Subsequently, next-generation ALKis, such as alectinib and ceritinib, have been developed, and some of them have been applied in the clinical setting...
October 26, 2016: Clinical Lung Cancer
https://www.readbyqxmd.com/read/27863497/next-generation-sequencing-facilitates-detection-of-the-classic-e13-a20-eml4-alk-fusion-in-an-alk-fish-ihc-inconclusive-biopsy-of-a-stage-iv-lung-cancer-patient-a-case-report
#20
Anna-Lena Volckmar, Volker Endris, Farastuk Bozorgmehr, Clemens Lier, Carlota Porcel, Martina Kirchner, Jonas Leichsenring, Roland Penzel, Michael Thomas, Peter Schirmacher, Arne Warth, Albrecht Stenzinger
BACKGROUND: Inhibition of the oncogenic fusion-gene EML4-ALK is a current first-line approach for patients with stage IV non-small cell lung cancer. While FISH was established as the gold standard for identifying these patients, there is accumulating evidence that other methods of detection, i.e., immunohistochemistry and next-generation sequencing (NGS), exist that may be equally successful. However, the concordance of these methods is under investigation. CASE PRESENTATION: Adding to the current literature, we here report a 56 year old female never-smoker with stage IV lung adenocarcinoma whose biopsy was IHC and FISH inconclusive but positive in NGS...
November 18, 2016: Diagnostic Pathology
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