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whole genome sequencing AND lung cancer

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https://www.readbyqxmd.com/read/29110840/immunohistochemical-and-genetic-characteristics-of-lung-cancer-mimicking-organizing-pneumonia
#1
Tomohiro Ichikawa, Koichi Saruwatari, Sachiyo Mimaki, Masato Sugano, Keiju Aokage, Motohiro Kojima, Tomoyuki Hishida, Satoshi Fujii, Junji Yoshida, Takeshi Kuwata, Atsushi Ochiai, Kenji Suzuki, Masahiro Tsuboi, Koichi Goto, Katsuya Tsuchihara, Genichiro Ishii
INTRODUCTION: Lung cancer mimicking organizing pneumonia (LCOP) is a novel radiological entity of lung adenocarcinoma that could be misdiagnosed as inflammatory lesions. However, the characteristic biological and genetic features of LCOP are not fully clarified. MATERIALS AND METHODS: We used thin-section CT images to select cases of (LCOP) among surgically resected lung adenocarcinoma patients. We compared the clinicopathological characteristics and the immunophenotypes of LCOP (n=44) and other lepidic-predominant adenocarcinomas (non-LCOP, n=56)...
November 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/29054765/characterization-of-germline-mutations-in-familial-lung-cancer-from-the-chinese-population
#2
Madiha Kanwal, Xiao-Jie Ding, Zhans-Han Ma, Lian-Wei Li, Ping Wang, Ying Chen, Yun-Chao Huang, Yi Cao
Compared with numerous studies of somatic mutations using sporadic lung cancer, the research into germline mutations using familial lung cancer (FLC) is limited. In the present study, we used FLC samples obtained from the Chinese population in highly air-polluted regions to screen for novel germline mutations in lung cancer. Through a whole genome sequencing (WGS) analysis of the nine subjects (four lung cancer patients and five normal family members of FLC), we obtained a whole genome dataset of DNA alterations in FLC samples...
October 17, 2017: Gene
https://www.readbyqxmd.com/read/29045549/emerging-treatment-paradigms-in-brain-metastasis-in-non-small-cell-lung-cancer-an-overview-of-the-current-landscape-and-challenges-ahead
#3
D Ulahannan, J Khalifa, C Faivre-Finn, S M Lee
Advances in the last decade in genomic profiling and the identification of druggable targets amenable to biological agents, has transformed the management and survival of a subgroup of patients with brain metastasis in non-small cell lung cancer. In parallel, clinicians have re-evaluated the role of whole brain radiotherapy in selected patients with brain metastases to reduce neurocognitive toxicity. Continual progress in this understudied field is required: optimisation of the sequence of schedules for therapies in patients with brain metastases of differing genomic profiles, focusing on new strategies to overcome mechanisms of biological resistance and increasing drug penetrability into the central nervous system...
October 17, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29039585/identification-of-genome-variations-in-patients-with-lung-adenocarcinoma-using-whole-genome-re%C3%A2-sequencing
#4
Guiyuan Li, Yunqing Mei, Fan Yang, Shengming Yi, Lemin Wang
Lung adenocarcinoma is one of the types of non‑small cell lung carcinoma, which tends to be treated with surgical therapy rather than radiation therapy. It occurs in smokers and non‑smokers, and is the most common form of lung cancer among non‑smokers and women. Gene rearrangements, including ALK, ROS1 and RET, and gene mutations, including epidermal growth factor receptor (EGFR), HER2, Kristen rat sarcoma viral oncogene homolog, BRAF, phosphoinositide‑3‑kinase, catalytic, α polypeptide and MET, have been identified in lung adenocarcinoma, which enable targeted therapy in lung adenocarcinoma, for example erlotinib, gefitinib and afatinib, which are EGFR inhibitors...
December 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29028887/identification-of-cancer-driver-genes-in-focal-genomic-aberrations-from-whole-exome-sequencing-data
#5
Ho Jang, Hyunju Lee
Summary: Whole-exome sequencing (WES) data have been used for identifying copy number aberrations in cancer cells. Nonetheless, the use of WES is still challenging for identification of focal aberrant regions in multiple samples that may contain cancer driver genes. In this study, we developed a wavelet-based method for identifying focal genomic aberrant regions in the WES data from cancer cells (WIFA-X). When we applied WIFA-X to glioblastoma multiforme and lung adenocarcinoma datasets, WIFA-X outperformed other approaches on identifying cancer driver genes...
September 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28950338/successful-targeting-of-the-nrg1-pathway-indicates-novel-treatment-strategy-for-metastatic-cancer
#6
M R Jones, H Lim, Y Shen, E Pleasance, C Ch'ng, C Reisle, S Leelakumari, C Zhao, S Yip, J Ho, E Zhong, T Ng, D Ionescu, D F Schaeffer, A J Mungall, K L Mungall, Y Zhao, R A Moore, Y Ma, S Chia, C Ho, D J Renouf, K Gelmon, S J M Jones, M A Marra, J Laskin
Background: NRG1 fusion-positive lung cancers have emerged as potentially actionable events in lung cancer but clinical support is currently limited and no evidence of efficacy of this approach in cancers beyond lung has been shown. Patients and Methods: Here we describe two patients with advanced cancers refractory to standard therapies. Patient 1 had lung adenocarcinoma and patient 2 cholangiocarcinoma. Whole-genome and transcriptome sequencing were carried out for these cases with select findings validated by fluorescence in situ hybridization...
September 18, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28894165/evolution-analysis-of-heterogeneous-non-small-cell-lung-carcinoma-by-ultra-deep-sequencing-of-the-mitochondrial-genome
#7
Wafa Amer, Csaba Toth, Erik Vassella, Jeannine Meinrath, Ulrike Koitzsch, Anne Arens, Jia Huang, Hannah Eischeid, Alexander Adam, Reinhard Buettner, Andreas Scheel, Stephan C Schaefer, Margarete Odenthal
Accurate assessment of tumour heterogeneity is an important issue that influences prognosis and therapeutic decision in molecular pathology. Due to the shortage of protective histones and a limited DNA repair capacity, the mitochondrial (mt)-genome undergoes high variability during tumour development. Therefore, screening of mt-genome represents a useful molecular tool for assessing precise cell lineages and tracking tumour history. Here, we describe a highly specific and robust multiplex PCR-based ultra-deep sequencing technology for analysis of the whole mt-genome (wmt-seq) on low quality-DNA from formalin-fixed paraffin-embedded tissues...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28862803/patient-and-cell-type-specific-heterogeneity-of-metformin-response
#8
Michael K Asiedu, Matthew Barron, Marie Christine Aubry, Dennis A Wigle
Most FDA approved drugs are not equally effective in all patients, suggesting that identification of biomarkers to predict responders to a chemoprevention agent will be needed to stratify patients and achieve maximum benefit. The goal of this study was to investigate both patient-specific and cell-context-specific heterogeneity of metformin response, using fibroblast cell lines and induced pluripotent stem cells differentiated into lung epithelial lineages. We performed cell survival analysis, transcriptome and whole exome sequencing analysis on both patient-derived cell lines and cancer cell lines to assess differential metformin response and identify response genes...
September 1, 2017: Basic & Clinical Pharmacology & Toxicology
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
#9
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/28819847/negative-enrichment-and-isolation-of-circulating-tumor-cells-for-whole-genome-amplification
#10
Nisha Kanwar, Susan J Done
Circulating tumor cells (CTCs) are a rare population of cells found in the peripheral blood of patients with many types of cancer such as breast, prostate, colon, and lung cancers. Higher numbers of these cells in blood are associated with a poorer prognosis of patients. Genomic profiling of CTCs would help characterize markers specific for the identification of these cells in blood, and also define genomic alterations that give these cells a metastatic advantage over other cells in the primary tumor. Here, we describe an immunomagnetic method to enrich CTCs from the blood of patients with breast cancer, followed by single-cell laser capture microdissection to isolate single CTCs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28759038/high-depth-high-accuracy-microsatellite-genotyping-enables-precision-lung-cancer-risk-classification
#11
K R Velmurugan, R T Varghese, N C Fonville, H R Garner
There remains a large discrepancy between the known genetic contributions to cancer and that which can be explained by genomic variants, both inherited and somatic. Recently, understudied repetitive DNA regions called microsatellites have been identified as genetic risk markers for a number of diseases including various cancers (breast, ovarian and brain). In this study, we demonstrate an integrated process for identifying and further evaluating microsatellite-based risk markers for lung cancer using data from the cancer genome atlas and the 1000 genomes project...
July 31, 2017: Oncogene
https://www.readbyqxmd.com/read/28668385/driving-to-cancer-on-a-four-lane-expressway
#12
Lorenzo Galluzzi, Ilio Vitale
Recent findings from a prospective clinical study involving multiregion whole-exome sequencing suggest that driver mutations in cancer-relevant genes including EGFR and TP53 are often clonal and precede whole-genome duplication events in early lung carcinogenesis. This paves an expressway to extensive subclonal diversification, elevated intratumoral heterogeneity, and dismal disease outcome.
June 28, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28646744/systematic-biobanking-novel-imaging-techniques-and-advanced-molecular-analysis-for-precise-tumor-diagnosis-and-therapy-the-polish-mobit-project
#13
Jacek Niklinski, Adam Kretowski, Marcin Moniuszko, Joanna Reszec, Anna Michalska-Falkowska, Magdalena Niemira, Michal Ciborowski, Radoslaw Charkiewicz, Dorota Jurgilewicz, Miroslaw Kozlowski, Rodryg Ramlau, Cezary Piwkowski, Miroslaw Kwasniewski, Monika Kaczmarek, Andrzej Ciereszko, Tomasz Wasniewski, Robert Mroz, Wojciech Naumnik, Ewa Sierko, Magdalena Paczkowska, Joanna Kisluk, Anetta Sulewska, Adam Cybulski, Zenon Mariak, Boguslaw Kedra, Jacek Szamatowicz, Paweł Kurzawa, Lukasz Minarowski, Angelika Edyta Charkiewicz, Barbara Mroczko, Jolanta Malyszko, Christian Manegold, Lothar Pilz, Heike Allgayer, Mohammed L Abba, Hartmut Juhl, Frauke Koch
Personalized and precision medicine is gaining recognition due to the limitations by standard diagnosis and treatment; many areas of medicine, from cancer to psychiatry, are moving towards tailored and individualized treatment for patients based on their clinical characteristics and genetic signatures as well as novel imaging techniques. Advances in whole genome sequencing have led to identification of genes involved in a variety of diseases. Moreover, biomarkers indicating severity of disease or susceptibility to treatment are increasingly being characterized...
September 2017: Advances in Medical Sciences
https://www.readbyqxmd.com/read/28618934/identification-of-curcumin-inhibited-extracellular-matrix-receptors-in-non-small-cell-lung-cancer-a549-cells-by-rna-sequencing
#14
Huiping Li, Hongjin Wu, Hongfang Zhang, Ying Li, Shuang Li, Qiang Hou, Shixiu Wu, Shuan-Ying Yang
Curcumin is a potent anti-cancer drug in several types of human cancers. Despite of several preclinical and clinical studies of curcumin, the precise mechanism of curcumin in cancer prevention has remained unclear. In our study, we for the first time investigated whole transcriptome alteration in A549 non-small cell lung cancer (NSCLC) cell lines after treatment with curcumin using RNA sequencing. We found that lots of genes and signaling pathways were significantly altered after curcumin treatment in A549 cells...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28608921/whole-exome-sequencing-reveals-critical-genes-underlying-metastasis-in-oesophageal-squamous-cell-carcinoma
#15
Wei Dai, Josephine Mun Yee Ko, Sheyne Sta Ana Choi, Zhouyou Yu, Luwen Ning, Hong Zheng, Vinod Gopalan, Kin Tak Chan, Nikki Pui-Yue Lee, Kwok Wah Chan, Simon Ying-Kit Law, Alfred King-Yin Lam, Maria Li Lung
Oesophageal squamous cell carcinoma (ESCC) is one of the most lethal cancers, owing to a high frequency of metastasis. However, little is known about the genomic landscape of metastatic ESCC. To identify the genetic alterations that underlie ESCC metastasis, whole-exome sequencing was performed for 41 primary tumours and 15 lymph nodes (LNs) with metastatic ESCCs. Eleven cases included matched primary tumours, synchronous LN metastases, and non-neoplastic mucosa. Approximately 50-76% of the mutations identified in primary tumours appeared in the synchronous LN metastases...
August 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28557978/prevalence-of-somatic-mitochondrial-mutations-and-spatial-distribution-of-mitochondria-in-non-small-cell-lung-cancer
#16
Daniel Kazdal, Alexander Harms, Volker Endris, Roland Penzel, Mark Kriegsmann, Florian Eichhorn, Thomas Muley, Albrecht Stenzinger, Nicole Pfarr, Wilko Weichert, Arne Warth
BACKGROUND: Mitochondria are considered relevant players in many tumour entities and first data indicate beneficial effects of mitochondria-targeted antioxidants in both cancer prevention and anticancer therapies. To further dissect the potential roles of mitochondria in NSCLC we comprehensively analysed somatic mitochondrial mutations, determined the spatial distribution of mitochondrial DNA within complete tumour sections and investigated the mitochondrial load in a large-scale approach...
July 11, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28548104/genomic-analysis-of-oesophageal-squamous-cell-carcinoma-identifies-alcohol-drinking-related-mutation-signature-and-genomic-alterations
#17
Jiang Chang, Wenle Tan, Zhiqiang Ling, Ruibin Xi, Mingming Shao, Mengjie Chen, Yingying Luo, Yanjie Zhao, Yun Liu, Xiancong Huang, Yuchao Xia, Jinlin Hu, Joel S Parker, David Marron, Qionghua Cui, Linna Peng, Jiahui Chu, Hongmin Li, Zhongli Du, Yaling Han, Wen Tan, Zhihua Liu, Qimin Zhan, Yun Li, Weimin Mao, Chen Wu, Dongxin Lin
Approximately half of the world's 500,000 new oesophageal squamous-cell carcinoma (ESCC) cases each year occur in China. Here, we show whole-genome sequencing of DNA and RNA in 94 Chinese individuals with ESCC. We identify six mutational signatures (E1-E6), and Signature E4 is unique in ESCC linked to alcohol intake and genetic variants in alcohol-metabolizing enzymes. We discover significantly recurrent mutations in 20 protein-coding genes, 4 long non-coding RNAs and 10 untranslational regions. Functional analyses show six genes that have recurrent copy-number variants in three squamous-cell carcinomas (oesophageal, head and neck and lung) significantly promote cancer cell proliferation, migration and invasion...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28522810/integrative-analysis-of-genomic-sequencing-data-reveals-higher-prevalence-of-lrp1b-mutations-in-lung-adenocarcinoma-patients-with-copd
#18
Dakai Xiao, Fuqiang Li, Hui Pan, Han Liang, Kui Wu, Jianxing He
Both chronic Obstruction Pulmonary Disease (COPD) and lung cancer are leading causes of death globally. Although COPD and lung cancer coexist frequently, it is unknown whether lung cancer patients with COPD harbor distinct genomic characteristics compared to those without COPD. In this study, we retrospectively analyzed genomic sequencing data from 272 patients with lung adenocarcinoma (LUAD) and compared the genetic alterations in LUAD patients with and without COPD. Integrative analysis of whole-genome and exome sequencing data revealed that COPD and non-COPD groups showed high concordance in mutational burden and spectra...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28498782/clonal-history-and-genetic-predictors-of-transformation-into-small-cell-carcinomas-from-lung-adenocarcinomas
#19
June-Koo Lee, Junehawk Lee, Sehui Kim, Soyeon Kim, Jeonghwan Youk, Seongyeol Park, Yohan An, Bhumsuk Keam, Dong-Wan Kim, Dae Seog Heo, Young Tae Kim, Jin-Soo Kim, Se Hyun Kim, Jong Seok Lee, Se-Hoon Lee, Keunchil Park, Ja-Lok Ku, Yoon Kyung Jeon, Doo Hyun Chung, Peter J Park, Joon Kim, Tae Min Kim, Young Seok Ju
Purpose Histologic transformation of EGFR mutant lung adenocarcinoma (LADC) into small-cell lung cancer (SCLC) has been described as one of the major resistant mechanisms for epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs). However, the molecular pathogenesis is still unclear. Methods We investigated 21 patients with advanced EGFR-mutant LADCs that were transformed into EGFR TKI-resistant SCLCs. Among them, whole genome sequencing was applied for nine tumors acquired at various time points from four patients to reconstruct their clonal evolutionary history and to detect genetic predictors for small-cell transformation...
September 10, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28494184/current-status-of-research-and-treatment-for-non-small-cell-lung-cancer-in-never-smoking-females
#20
Shin Saito, Fernando Espinoza-Mercado, Hui Liu, Naohiro Sata, Xiaojiang Cui, Harmik J Soukiasian
Lung cancer is the leading cause of cancer-related deaths worldwide with over 1 million deaths each year. The overall prognosis of lung cancer patients remains unsatisfactory, with a 5-year overall survival rate of less than 15%. Although most lung cancers are a result of smoking, approximately 25% of lung cancer cases worldwide are not attributable to tobacco use. Notably, more than half of the lung cancer cases in women occur in non-smokers. Among non-small-cell lung cancer (NSCLC) cases, cigarette-smokers have a greater association with squamous cell carcinoma than adenocarcinoma, which is more common in non-smokers...
June 3, 2017: Cancer Biology & Therapy
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