keyword
MENU ▼
Read by QxMD icon Read
search

copy number variation AND lung cancer

keyword
https://www.readbyqxmd.com/read/29748005/genomic-alterations-of-plasma-cell-free-dnas-in-small-cell-lung-cancer-and-their-clinical-relevance
#1
Meijun Du, Jonathan Thompson, Hannah Fisher, Peng Zhang, Chiang-Ching Huang, Liang Wang
OBJECTIVES: To identify genomic variations in cell-free DNA (cfDNA) and evaluate their clinical utility in small cell lung cancer (SCLC). MATERIALS AND METHODS: We performed whole genome sequencing using plasma cfDNAs derived from 24 SCLC patients for copy number variation (CNV) analysis, and targeted sequencing using 17 pairs of plasma cfDNA and their matched gDNA for mutation analysis. We defined somatic mutations by comparing cfDNA to its matched gDNA with 5% variant alleles as the cutoff for mutation calls...
June 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/29720381/whole-exome-and-transcriptome-analyses-integrated-with-microenvironmental-immune-signatures-of-lung-squamous-cell-carcinoma
#2
Jeong-Sun Seo, Ji Won Lee, Ahreum Kim, Jong-Yeon Shin, Yoo Jin Jung, Sae Bom Lee, Yoon Ho Kim, Samina Park, Hyun Joo Lee, In-Kyu Park, Chang Hyun Kang, Ji-Young Yun, Jihye Kim, Young T Kim
The immune microenvironment in lung squamous cell carcinoma (LUSC) is not well understood, with interactions between the host immune system and the tumor, as well as the molecular pathogenesis of LUSC, awaiting better characterization. To date, no molecularly targeted agents have been developed for LUSC treatment. Identification of predictive and prognostic biomarkers for LUSC could help optimize therapy decisions. We sequenced whole exomes and RNA from 101 tumors and matched noncancer control Korean samples...
May 2, 2018: Cancer Immunology Research
https://www.readbyqxmd.com/read/29704571/detection-of-egfr-variants-in-plasma-a-multilaboratory-comparison-of-the-cobas-egfr-mutation-test-v2-in-europe
#3
Cleo Keppens, John F Palma, Partha M Das, Sidney Scudder, Wei Wen, Nicola Normanno, J Han Van Krieken, Alessandra Sacco, Francesca Fenizia, David Gonzalez de Castro, Selma Hönigschnabl, Izidor Kern, Fernando Lopez-Rios, Maria D Lozano, Antonio Marchetti, Philippe Halfon, Ed Schuuring, Ulrike Setinek, Boe Sorensen, Phillipe Taniere, Markus Tiemann, Hana Vosmikova, Elisabeth M C Dequeker
Molecular testing of EGFR is required to predict the response likelihood to targeted therapy in non-small-cell lung cancer. Analysis of circulating tumor DNA in plasma may complement limitations of tumor tissue. This study evaluated the interlaboratory performance and reproducibility of the cobas EGFR Mutation Test v2 to detect EGFR variants in plasma. Fourteen laboratories received two identical panels of 27 single-blinded plasma samples. Samples were wild-type or spiked with plasmid DNA to contain seven common EGFR variants at six predefined concentrations from 50 to 5000 copies per mL...
April 25, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29667179/characteristics-of-genomic-alterations-of-lung-adenocarcinoma-in-young-never-smokers
#4
Wenxin Luo, Panwen Tian, Yue Wang, Heng Xu, Lu Chen, Chao Tang, Yang Shu, Shouyue Zhang, Zhoufeng Wang, Jun Zhang, Li Zhang, Lili Jiang, Lunxu Liu, Guowei Che, Chenglin Guo, Hong Zhang, Jiali Wang, Weimin Li
Non-small cell lung cancer (NSCLC) has been recognized as a highly heterogeneous disease with phenotypic and genotypic diversity in each subgroup. While never-smoker patients with NSCLC have been well studied through next generation sequencing, we have yet to recognize the potentially unique molecular features of young never-smoker patients with NSCLC. In this study, we conducted whole genome sequencing (WGS) to characterize the genomic alterations of 36 never-smoker Chinese patients, who were diagnosed with lung adenocarcinoma (LUAD) at 45 years or younger...
April 18, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29650813/-the-cutting-edge-of-sarcoma-genomics
#5
Katsuhito Takahashi
Sarcoma is well-known rare cancer with few therapeutic options. Recent comprehensive genomic analyses of adult soft tissue sarcoma revealed few somatic mutations and massive copy number variations(CNVs)by the specific chromosomes. Those features are quite different from the genomics of carcinoma such as lung and colon cancers in which driver and passenger mutations play a central role in the pathogenesis. Furthermore, it has been demonstrated that substantial population of sarcoma patients has pathological germline variants of cancer predisposition genes...
April 2018: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/29599906/dynamic-changes-during-the-treatment-of-pancreatic-cancer
#6
Robert A Wolff, Andrea Wang-Gillam, Hector Alvarez, Hervé Tiriac, Dannielle Engle, Shurong Hou, Abigail F Groff, Anthony San Lucas, Vincent Bernard, Kelvin Allenson, Jonathan Castillo, Dong Kim, Feven Mulu, Jonathan Huang, Bret Stephens, Ignacio I Wistuba, Matthew Katz, Gauri Varadhachary, YoungKyu Park, James Hicks, Arul Chinnaiyan, Louis Scampavia, Timothy Spicer, Chiara Gerhardinger, Anirban Maitra, David Tuveson, John Rinn, Gregory Lizee, Cassian Yee, Arnold J Levine
This manuscript follows a single patient with pancreatic adenocarcinoma for a five year period, detailing the clinical record, pathology, the dynamic evolution of molecular and cellular alterations as well as the responses to treatments with chemotherapies, targeted therapies and immunotherapies. DNA and RNA samples from biopsies and blood identified a dynamic set of changes in allelic imbalances and copy number variations in response to therapies. Organoid cultures established from biopsies over time were employed for extensive drug testing to determine if this approach was feasible for treatments...
March 13, 2018: Oncotarget
https://www.readbyqxmd.com/read/29588350/the-circular-rna-circprkci-promotes-tumor-growth-in-lung-adenocarcinoma
#7
Mantang Qiu, Wenjia Xia, Rui Chen, Siwei Wang, Youtao Xu, Zhifei Ma, Weizhang Xu, Erbao Zhang, Jie Wang, Tian Fang, Jingwen Hu, Gaochao Dong, Rong Yin, Jun Wang, Lin Xu
Somatic copy-number variations (CNV) may drive cancer progression through both coding and noncoding transcripts. However, noncoding transcripts resulting from CNV are largely unknown, especially for circular RNAs. By integrating bioinformatics analyses of alerted circRNAs and focal CNV in lung adenocarcinoma (LAC), we identify a proto-oncogenic circular RNA (circPRKCI) from the 3q26.2 amplicon, one of the most frequent genomic aberrations in multiple cancers. circPRKCI was overexpressed in LAC tissues, in part due to amplification of the 3q26...
March 27, 2018: Cancer Research
https://www.readbyqxmd.com/read/29555576/aberrant-high-expression-level-of-morc2-is-a-common-character-in-multiple-cancers
#8
Ding Qian-Shan, Zhang Li, Wang Bi-Cheng, Zeng Zhi, Zou Xian-Qiong, Cao Peng-Bo, M S Zhou Guang-Ming, Tang Meng, Wu Lu, B S Wu Lian-Lian, Yu Hong-Gang, Guo Yong, Zhou Fu-Xiang
Microrchidia 2 (MORC2) plays important roles in DNA damage repair and lipogenesis, but the clinical and functional role of MORC2 in cancer remains largely unexplored. In this study, we showed that MORC2 was widely expressed in human tissues while significantly up-regulated in most cancer types employing immunohistochemical staining and analysis of mRNA expression profile of more than 2000 human tissue samples from 15 different organs (lung, prostate, liver, breast, brain, stomach, colon/rectum, pancreas, ovary, endometrium, skin, nasopharynx, kidney, oesophagus and bladder)...
March 16, 2018: Human Pathology
https://www.readbyqxmd.com/read/29511269/patient-derived-conditionally-reprogrammed-cells-maintain-intra-tumor-genetic-heterogeneity
#9
Bruna R S Correa, Joanna Hu, Luiz O F Penalva, Richard Schlegel, David L Rimm, Pedro A F Galante, Seema Agarwal
Preclinical in vitro models provide an essential tool to study cancer cell biology as well as aid in translational research, including drug target identification and drug discovery efforts. For any model to be clinically relevant, it needs to recapitulate the biology and cell heterogeneity of the primary tumor. We recently developed and described a conditional reprogramming (CR) cell technology that addresses many of these needs and avoids the deficiencies of most current cancer cell lines, which are usually clonal in origin...
March 6, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29492964/interaction-analysis-between-germline-susceptibility-loci-and-somatic-alterations-in-lung-cancer
#10
Yuzhuo Wang, Cheng Wang, Jiahui Zhang, Meng Zhu, Xu Zhang, Zhihua Li, Juncheng Dai, Hongxia Ma, Zhibin Hu, Guangfu Jin, Hongbing Shen
Emerging evidence indicates that germline variations may interact with somatic events in carcinogenesis. However, the germline-somatic interaction in lung cancer remains largely unknown. We investigated whether lung cancer driver genes (CDGs) were more likely to locate within cancer susceptibility regions. Pathway analysis was performed to identify common pathways underlying CDGs and cancer susceptibility genes (CSGs). Next, we analyzed the associations between lung cancer risk SNPs and somatic alterations, including mutations and copy number alterations, in the level of genes, pathways, and overall burden of alterations...
March 1, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29489023/kras-mutation-is-predictive-of-outcome-in-patients-with-pulmonary-sarcomatoid-carcinoma
#11
Mitra Mehrad, Somak Roy, William A LaFramboise, Patti Petrosko, Caitlyn Miller, Pimpin Incharoen, Sanja Dacic
AIMS: Pulmonary sarcomatoid carcinoma (PSC) is a poorly differentiated non-small-cell lung carcinoma (NSCLC) with aggressive behaviour. This study aimed to evaluate the prognostic clinicopathological and genetic characteristics of PSCs. METHODS AND RESULTS: Fifty-three cases of surgically treated PSCs were selected, 23 of which were subjected to mutation and copy number variation analysis using the 50-gene Ion AmpliSeq Cancer Panel. The majority of the patients were male (32 of 53, 60...
February 28, 2018: Histopathology
https://www.readbyqxmd.com/read/29473341/expression-and-copy-number-gains-of-the-ret-gene-in-631-early-and-mid-stage-non-small-cell-lung-cancer-cases
#12
Ling Tan, Yerong Hu, Yongguang Tao, Bin Wang, Jun Xiao, Zhenjie Tang, Ting Lu, Hao Tang
BACKGROUND: To identify whether RET is a potential target for NSCLC treatment, we examined the status of the RET gene in 631 early and mid stage NSCLC cases from south central China. METHODS: RET expression was identified by Western blot. RET-positive expression samples were verified by immunohistochemistry. RET gene mutation, copy number variation, and rearrangement were analyzed by DNA Sanger sequencing, TaqMan copy number assays, and reverse transcription-PCR...
April 2018: Thoracic Cancer
https://www.readbyqxmd.com/read/29416799/correlation-among-genetic-variations-of-c-met-in-chinese-patients-with-non-small-cell-lung-cancer
#13
Jianchun Duan, Xiaodan Yang, Jun Zhao, Minglei Zhuo, Zhijie Wang, Tongtong An, Hua Bai, Jie Wang
Background: The purpose of our research was to determine the correlation of amplification, protein expression and somatic mutation of c-MET in IIIb-IV stage NSCLC (Non-small cell lung cancer). We also explored correlation of c-MET variation with clinical outcome. Results: c-MET expression was observed in 28.6% (56/196) cases, and among those 13.8% (27/196) were shown to be FISH positive. Only 2.67% patients in this study carried the c-MET mutation. Cases with c-MET FISH positive were all IHC positive ,but in IHC positive cases, only half were FISH positive...
January 5, 2018: Oncotarget
https://www.readbyqxmd.com/read/29346604/unique-genetic-profiles-from-cerebrospinal-fluid-cell-free-dna-in-leptomeningeal-metastases-of-egfr-mutant-non-small-cell-lung-cancer-a-new-medium-of-liquid-biopsy
#14
Y S Li, B Y Jiang, J J Yang, X C Zhang, Z Zhang, J Y Ye, W Z Zhong, H Y Tu, H J Chen, Z Wang, C R Xu, B C Wang, H J Du, S Chuai, H Han-Zhang, J Su, Q Zhou, X N Yang, W B Guo, H H Yan, Y H Liu, L X Yan, B Huang, M M Zheng, Y L Wu
Background: Leptomeningeal metastases (LM) are more frequent in non-small-cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) mutations. Due to limited access to leptomeningeal lesions, the purpose of this study was to explore the potential role of cerebrospinal fluid (CSF) as a source of liquid biopsy in patients with LM. Patients and methods: Primary tumor, CSF, and plasma in NSCLC with LM were tested by next-generation sequencing. In total, 45 patients with suspected LM underwent lumbar puncture, and those with EGFR mutations diagnosed with LM were enrolled...
April 1, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29322935/classifying-cancer-genome-aberrations-by-their-mutually-exclusive-effects-on-transcription
#15
Jonathan B Dayton, Stephen R Piccolo
BACKGROUND: Malignant tumors are typically caused by a conglomeration of genomic aberrations-including point mutations, small insertions, small deletions, and large copy-number variations. In some cases, specific chemotherapies and targeted drug treatments are effective against tumors that harbor certain genomic aberrations. However, predictive aberrations (biomarkers) have not been identified for many tumor types and treatments. One way to address this problem is to examine the downstream, transcriptional effects of genomic aberrations and to identify characteristic patterns...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29178066/mitochondrial-dna-in-lung-cancer
#16
Fangming Liu, David E Sanin, Xiangdong Wang
Mitochondrial DNA (mtDNA) variations are increasingly discovered and expected to be potential biomarkers to monitor severity, duration, stage, response to therapy, and prognosis in patients with lung cancer. The present article illustrates alterations of mtDNA in lung cancer, including alterations of mtDNA copy number and sequence mutations, as well as their possible mechanisms for carcinogenesis and development of lung cancer. The clear and comprehensive relationships between mtDNA variations and lung cancer are to be further confirmed to benefit effective strategies for lung cancer diagnosis and therapy...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29054765/characterization-of-germline-mutations-in-familial-lung-cancer-from-the-chinese-population
#17
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...
January 30, 2018: Gene
https://www.readbyqxmd.com/read/29039585/identification-of-genome-variations-in-patients-with-lung-adenocarcinoma-using-whole-genome-re%C3%A2-sequencing
#18
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/28960030/gab2-amplification-in-squamous-cell-lung-cancer-of-non-smokers
#19
Yu Rang Park, Soo Hyeon Bae, Wonjun Ji, Eul Ju Seo, Jae Cheol Lee, Hyeong Ryul Kim, Se Jin Jang, Chang Min Choi
Lung squamous cell cancer (SCC) is typically found in smokers and has a very low incidence in non-smokers, indicating differences in the tumor biology of lung SCC in smokers and non-smokers. However, the specific mutations that drive tumor growth in non-smokers have not been identified. To identify mutations in lung SCC of non-smokers, we performed a genetic analysis using arrays comparative genomic hybridization (ArrayCGH). We analyzed 19 patients with lung SCC who underwent surgical treatment between April 2005 and April 2015...
November 2017: Journal of Korean Medical Science
https://www.readbyqxmd.com/read/28947568/discrimination-of-germline-egfr-t790m-mutations-in-plasma-cell-free-dna-allows-study-of-prevalence-across-31-414-cancer-patients
#20
Yuebi Hu, Ryan S Alden, Justin I Odegaard, Stephen R Fairclough, Ruthia Chen, Jennifer Heng, Nora Feeney, Rebecca J Nagy, Jayshree Shah, Bryan Ulrich, Martin Gutierrez, Richard B Lanman, Judy E Garber, Cloud P Paweletz, Geoffrey R Oxnard
Purpose: Plasma cell-free DNA (cfDNA) analysis is increasingly used clinically for cancer genotyping, but may lead to incidental identification of germline-risk alleles. We studied EGFR T790M mutations in non-small cell lung cancer (NSCLC) toward the aim of discriminating germline and cancer-derived variants within cfDNA. Experimental Design: Patients with EGFR -mutant NSCLC, some with known germline EGFR T790M, underwent plasma genotyping. Separately, deidentified genomic data and buffy coat specimens from a clinical plasma next-generation sequencing (NGS) laboratory were reviewed and tested...
December 1, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
keyword
keyword
67433
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"