keyword
MENU ▼
Read by QxMD icon Read
search

whole genome sequencing AND lung cancer

keyword
https://www.readbyqxmd.com/read/28396363/genomic-and-molecular-screenings-identify-different-mechanisms-for-acquired-resistance-to-met-inhibitors-in-lung-cancer-cells
#1
Pol Gimenez-Xavier, Eva Pros, Ester Bonastre, Sebastian Moran, Ana Aza, Osvaldo Graña, Gonzalo Gómez-López, Sophia Derdak, Marc Dabad, Anna Esteve-Codina, Jose R Hernandez Mora, Diana Salinas-Chaparro, Manel Esteller, David Pisano, Montse Sanchez-Cespedes
The development of resistance to tyrosine kinase inhibitors (TKIs) limits the long-term efficacy of cancer treatments involving them. We aimed to understand the mechanisms that underlie acquired resistance (AR) to MET inhibitors in lung cancer. EBC1 cells, which have MET amplification and are sensitive to TKIs against MET, were used to generate multiple clones with AR to a MET-TKI. Whole-exome sequencing, RNA sequencing and global DNA methylation analysis were used to scrutinize the genetic and molecular characteristics of the resistant cells...
April 10, 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/28393575/using-circulating-cell-free-dna-to-monitor-personalized-cancer-therapy
#2
Michael Oellerich, Ekkehard Schütz, Julia Beck, Philipp Kanzow, Piers N Plowman, Glen J Weiss, Philip D Walson
High-quality genomic analysis is critical for personalized pharmacotherapy in patients with cancer. Tumor-specific genomic alterations can be identified in cell-free DNA (cfDNA) from patient blood samples and can complement biopsies for real-time molecular monitoring of treatment, detection of recurrence, and tracking resistance. cfDNA can be especially useful when tumor tissue is unavailable or insufficient for testing. For blood-based genomic profiling, next-generation sequencing (NGS) and droplet digital PCR (ddPCR) have been successfully applied...
April 10, 2017: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/28381877/the-genomic-dynamics-during-progression-of-lung-adenocarcinomas
#3
Bin Yang, Longhai Luo, Wen Luo, Yong Zhou, Chao Yang, Teng Xiong, Xiangchun Li, Xuan Meng, Lin Li, Xiaopin Zhang, Zhe Wang, Zhixin Wang
Intra-tumor heterogeneity is a big barrier to precision medicine. To explore the underlying clonal diversity in lung adenocarcinomas, we selected nine individuals with whole-genome sequencing data from primary and matched metastatic tumors as a cohort for study. Similar global pattern of arm-level copy number changes and large variations of somatic single-nucleotide variant between the primary and metastasis are observed in the majority of cases. Importantly, we found breakage-fusion-bridge (BFB) cycles acting as an important mechanism for underlying cancer gene amplification, such as amplification of CDK4, CDKN3 and FGFR1 in early stage...
April 6, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28327965/carbon-dating-cancer-defining-the-chronology-of-metastatic-progression-in-colorectal-cancer
#4
H Lote, I Spiteri, L Ermini, A Vatsiou, A Roy, A McDonald, N Maka, M Balsitis, N Bose, M Simbolo, A Mafficini, A Lampis, J C Hahne, F Trevisani, Z Eltahir, G Mentrasti, C Findlay, Eaj Kalkman, M Punta, B Werner, S Lise, A Aktipis, C Maley, M Greaves, C Braconi, J White, M Fassan, A Scarpa, A Sottoriva, N Valeri
Background: HASH(0x37d60f0) Patients often ask oncologists how long a cancer has been present before causing symptoms or spreading to other organs. The evolutionary trajectory of cancers can be defined using phylogenetic approaches but lack of chronological references makes dating the exact onset of tumours very challenging. Patients and Methods: HASH(0x386b138) Here we describe the case of a colorectal cancer patient presenting with synchronous lung metastasis and metachronous thyroid, chest wall and urinary tract metastases over the course of five years...
February 23, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28302866/genomic-profiling-of-patient-derived-xenografts-for-lung-cancer-identifies-b2m-inactivation-impairing-immunorecognition
#5
Carolina Pereira, Pol Gimenez-Xavier, Eva Pros, Maria J Pajares, Massimo Moro, Antonio Gomez, Alejandro Navarro, Enric Condom, Sebastian Moran, Gonzalo Gomez-Lopez, Osvaldo Graña, Miriam Rubio-Camarillo, Alex Martinez-Martí, Jun Yokota, Julian Carretero, Jose M Galbis, Ernest Nadal, David Pisano, Gabriella Sozzi, Enriqueta Felip, Luis M Montuenga, Luca Roz, Alberto Villanueva, Montse Sanchez-Cespedes
Purpose: We aimed to maximize the performance of detecting genetic alterations in lung cancer using high-throughput sequencing for patient-derived xenografts (PDXs).Experimental Design: We undertook an integrated RNA and whole-exome sequencing of 14 PDXs. We focused on the genetic and functional analysis of β2-microglobulin (B2M), a component of the HLA class-I complex.Results: We identified alterations in genes involved in various functions, such as B2M involved in immunosurveillance. We extended the mutational analysis of B2M to about 230 lung cancers...
March 16, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28290769/sequencing-brain-metastases-and-opportunities-for-targeted-therapies
#6
Ugonma N Chukwueke, Priscilla K Brastianos
CNS metastases have long been recognized as a common and late complication of systemic malignancies. They represent the most common tumor of the brain. As outcomes and overall survival improve with better tolerated and more durable responses from therapies for systemic cancers, the incidence and prevalence of brain metastases is likely to increase. Among the most common systemic cancers leading to brain metastases include lung, melanoma, breast (triple-negative histology) and renal cell cancers. To date, there has been infrequent involvement of gastrointestinal and gynecologic malignancies; however, this may also change, reflecting improvement in overall survival and therapeutic regimens...
March 14, 2017: Pharmacogenomics
https://www.readbyqxmd.com/read/28263317/identification-of-methylation-haplotype-blocks-aids-in-deconvolution-of-heterogeneous-tissue-samples-and-tumor-tissue-of-origin-mapping-from-plasma-dna
#7
Shicheng Guo, Dinh Diep, Nongluk Plongthongkum, Ho-Lim Fung, Kang Zhang, Kun Zhang
Adjacent CpG sites in mammalian genomes can be co-methylated owing to the processivity of methyltransferases or demethylases, yet discordant methylation patterns have also been observed, which are related to stochastic or uncoordinated molecular processes. We focused on a systematic search and investigation of regions in the full human genome that show highly coordinated methylation. We defined 147,888 blocks of tightly coupled CpG sites, called methylation haplotype blocks, after analysis of 61 whole-genome bisulfite sequencing data sets and validation with 101 reduced-representation bisulfite sequencing data sets and 637 methylation array data sets...
April 2017: Nature Genetics
https://www.readbyqxmd.com/read/28185561/optimized-pipeline-of-mutect-and-gatk-tools-to-improve-the-detection-of-somatic-single-nucleotide-polymorphisms-in-whole-exome-sequencing-data
#8
Ítalo Faria do Valle, Enrico Giampieri, Giorgia Simonetti, Antonella Padella, Marco Manfrini, Anna Ferrari, Cristina Papayannidis, Isabella Zironi, Marianna Garonzi, Simona Bernardi, Massimo Delledonne, Giovanni Martinelli, Daniel Remondini, Gastone Castellani
BACKGROUND: Detecting somatic mutations in whole exome sequencing data of cancer samples has become a popular approach for profiling cancer development, progression and chemotherapy resistance. Several studies have proposed software packages, filters and parametrizations. However, many research groups reported low concordance among different methods. We aimed to develop a pipeline which detects a wide range of single nucleotide mutations with high validation rates. We combined two standard tools - Genome Analysis Toolkit (GATK) and MuTect - to create the GATK-LODN method...
November 8, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28125075/assigning-clinical-meaning-to-somatic-and-germ-line-whole-exome-sequencing-data-in-a-prospective-cancer-precision-medicine-study
#9
Arezou A Ghazani, Nelly M Oliver, Joseph P St Pierre, Andrea Garofalo, Irene R Rainville, Elaine Hiller, Daniel J Treacy, Vanesa Rojas-Rudilla, Sam Wood, Elizabeth Bair, Michael Parello, Franklin Huang, Marios Giannakis, Frederick H Wilson, Elizabeth H Stover, Steven M Corsello, Tom Nguyen, Huma Q Rana, Alanna J Church, Carol Lowenstein, Carrie Cibulskis, Ali Amin-Mansour, Jennifer Heng, Lauren Brais, Abigail Santos, Patrick Bauer, Amanda Waldron, Peter Lo, Megan Gorman, Christine A Lydon, Marisa Welch, Philip McNamara, Stacey Gabriel, Lynette M Sholl, Neal I Lindeman, Judy E Garber, Steven Joffe, Eliezer M Van Allen, Stacy W Gray, Pasi A Ja Nne, Levi A Garraway, Nikhil Wagle
PURPOSE: Implementing cancer precision medicine in the clinic requires assessing the therapeutic relevance of genomic alterations. A main challenge is the systematic interpretation of whole-exome sequencing (WES) data for clinical care. METHODS: One hundred sixty-five adults with metastatic colorectal and lung adenocarcinomas were prospectively enrolled in the CanSeq study. WES was performed on DNA extracted from formalin-fixed paraffin-embedded tumor biopsy samples and matched blood samples...
January 26, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28115307/fast-isolation-and-ex-vivo-culture-of-circulating-tumor-cells-from-the-peripheral-blood-of-lung-cancer-patients
#10
Wu Wenjun, Wang Zhihua, Wang Zhuo, Deng Yuliang, Shi Qihui
Circulating tumor cells (CTCs) are free tumor cells shed from tumor site and enter into blood circulation. CTCs represent a reliable source of tumor cells for the molecular characteristics of the original tumor. However, the extraordinary rarity of CTCs makes the subsequent molecular and functional analysis technically challenging. Here, we describe a one-step microfludics-based immunomagnetic isolation method to isolate CTCs directly from the whole blood of lung adenocarcinoma patients. This method avoids harsh sample preparation and enrichment steps, and therefore preserves the viability (>90%) of CTCs during the in vitro isolation...
January 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28114404/transcriptome-sequencing-reveals-key-pathways-and-genes-associated-with-cisplatin-resistance-in-lung-adenocarcinoma-a549-cells
#11
Yani Fang, Cheng Zhang, Tong Wu, Qi Wang, Jinhui Liu, Penggao Dai
Acquired resistance to cisplatin-based chemotherapy frequently occurs in patients with non-small cell lung cancer, and the underlying molecular mechanisms are not well understood. The aim of this study was to investigate whether a distinct gene expression pattern is associated with acquired resistance to cisplatin in human lung adenocarcinoma. Whole-transcriptome sequencing was performed to compare the genome-wide gene expression patterns of the human lung adenocarcinoma A549 cisplatin-resistant cell line A549/DDP with those of its progenitor cell line A549...
2017: PloS One
https://www.readbyqxmd.com/read/28089356/insertions-and-deletions-target-lineage-defining-genes-in-human-cancers
#12
Marcin Imielinski, Guangwu Guo, Matthew Meyerson
Certain cell types function as factories, secreting large quantities of one or more proteins that are central to the physiology of the respective organ. Examples include surfactant proteins in lung alveoli, albumin in liver parenchyma, and lipase in the stomach lining. Whole-genome sequencing analysis of lung adenocarcinomas revealed noncoding somatic mutational hotspots near VMP1/MIR21 and indel hotspots in surfactant protein genes (SFTPA1, SFTPB, and SFTPC). Extrapolation to other solid cancers demonstrated highly recurrent and tumor-type-specific indel hotspots targeting the noncoding regions of highly expressed genes defining certain secretory cellular lineages: albumin (ALB) in liver carcinoma, gastric lipase (LIPF) in stomach carcinoma, and thyroglobulin (TG) in thyroid carcinoma...
January 26, 2017: Cell
https://www.readbyqxmd.com/read/28046008/cell-free-dna-provides-a-good-representation-of-the-tumor-genome-despite-its-biased-fragmentation-patterns
#13
Xiangyuan Ma, Liangjun Zhu, Xue Wu, Hua Bao, Xiaonan Wang, Zhili Chang, Yang W Shao, Zhenxin Wang
Cell-free DNA (cfDNA) is short, extracellular, fragmented double-stranded DNA found in plasma. Plasma of patients with solid tumor has been found to show significantly increased quantities of cfDNA. Although currently poorly understood, the mechanism of cfDNA generation is speculated to be a product of genomic DNA fragmentation during cellular apoptosis and necrosis. Sequencing of cfDNA with tumor origin has identified tumor biomarkers, elucidating molecular pathology and assisting in accurate diagnosis. In this study, we performed whole-genome sequencing ofcfDNA samples with matching tumor and whole blood samples from five patients diagnosed with stage IV gastric or lung cancer...
2017: PloS One
https://www.readbyqxmd.com/read/28009993/characterization-of-rna-editome-in-primary-and-metastatic-lung-adenocarcinomas
#14
Lihua Peng, Leo J Lee, Heng Xiong, Hong Su, Junhua Rao, Dakai Xiao, Jianxing He, Kui Wu, Dongbing Liu
RNA editing results in post-transcriptional modification and could potentially contribute to carcinogenesis. However, RNA editing in advanced lung adenocarcinomas has not yet been studied. Based on whole genome and transcriptome sequencing data, we identified 1,071,296 RNA editing events from matched normal, primary and metastatic samples contributed by 24 lung adenocarcinoma patients, with 91.3% A-to-G editing on average, and found significantly more RNA editing sites in tumors than in normal samples. To investigate cancer relevant editing events, we detected 67,851 hyper-editing sites in primary and 50,480 hyper-editing sites in metastatic samples...
February 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28007623/small-cell-lung-cancer-exhibits-frequent-inactivating-mutations-in-the-histone-methyltransferase-kmt2d-mll2-calgb-151111-alliance
#15
Arnaud Augert, Qing Zhang, Breanna Bates, Min Cui, Xiaofei Wang, Gary Wildey, Afshin Dowlati, David MacPherson
INTRODUCTION: SCLC is a lethal neuroendocrine tumor type that is highly prone to metastasis. There is an urgency to understand the mutated genes that promote SCLC, as there are no approved targeted therapies yet available. SCLC is rarely resected, limiting the number of samples available for genomic analyses of somatic mutations. METHODS: To identify potential driver mutations in human SCLC we sequenced the whole exomes of 18 primary SCLCs and seven cell lines along with matched normal controls...
April 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28003304/genomic-profiling-of-patient-derived-xenografts-for-lung-cancer-identifies-b2m-inactivation-impairing-immunorecognition
#16
Carolina Pereira, Pol Gimenez-Xavier, Eva Pros, Maria J Pajares, Massimo Moro, Antonio Gomez, Alejandro Navarro, Enric Condom, Sebastian Moran, Gonzalo Gómez-López, Osvaldo Graña, Miriam Rubio-Camarillo, Alex Martinez-Martí, Jun Yokota, Julian Carretero, Jose M Galbis, Ernest Nadal, David G Pisano, Gabriella Sozzi, Enriqueta Felip, Luis M Montuenga, Luca Roz, Alberto Villanueva, Montse Sanchez-Cespedes
PURPOSE: We aimed to maximize the performance of detecting genetic alterations in lung cancer (LC) using high-throughput sequencing for patient-derived xenografts (PDXs). EXPERIMENTAL DESIGN: We undertook an integrated RNA and whole-exome sequencing of 14 PDXs. We focused on the genetic and functional analysis of B2-microglobulin (B2M), a component of the HLA class-I complex. RESULTS: We identified alterations in genes involved in various functions, such as B2M involved in immunosurveillance...
December 21, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27993895/mutation-patterns-in-small-cell-and-non-small-cell-lung-cancer-patients-suggest-a-different-level-of-heterogeneity-between-primary-and-metastatic-tumors
#17
Ali Saber, T Jeroen N Hiltermann, Klaas Kok, M Martijn Terpstra, Kim de Lange, Wim Timens, Harry J M Groen, Anke van den Berg
Several studies have shown heterogeneity in lung cancer, with parallel existence of multiple subclones characterized by their own specific mutational landscape. The extent to which minor clones become dominant in distinct metastasis is not clear. The aim of our study was to gain insight in the evolution pattern of lung cancer by investigating genomic heterogeneity between primary tumor and its distant metastases. Whole exome sequencing (WES) was performed on 24 tumor and five normal samples of two small cell lung carcinoma (SCLC) and three non-SCLC (NSCLC) patients...
February 1, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/27923066/somatic-genomics-and-clinical-features-of-lung-adenocarcinoma-a-retrospective-study
#18
Jianxin Shi, Xing Hua, Bin Zhu, Sarangan Ravichandran, Mingyi Wang, Cu Nguyen, Seth A Brodie, Alessandro Palleschi, Marco Alloisio, Gianluca Pariscenti, Kristine Jones, Weiyin Zhou, Aaron J Bouk, Joseph Boland, Belynda Hicks, Adam Risch, Hunter Bennett, Brian T Luke, Lei Song, Jubao Duan, Pengyuan Liu, Takashi Kohno, Qingrong Chen, Daoud Meerzaman, Crystal Marconett, Ite Laird-Offringa, Ian Mills, Neil E Caporaso, Mitchell H Gail, Angela C Pesatori, Dario Consonni, Pier Alberto Bertazzi, Stephen J Chanock, Maria Teresa Landi
BACKGROUND: Lung adenocarcinoma (LUAD) is the most common histologic subtype of lung cancer and has a high risk of distant metastasis at every disease stage. We aimed to characterize the genomic landscape of LUAD and identify mutation signatures associated with tumor progression. METHODS AND FINDINGS: We performed an integrative genomic analysis, incorporating whole exome sequencing (WES), determination of DNA copy number and DNA methylation, and transcriptome sequencing for 101 LUAD samples from the Environment And Genetics in Lung cancer Etiology (EAGLE) study...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27900322/patterns-of-transposable-element-expression-and-insertion-in-cancer
#19
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
#20
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
keyword
keyword
66446
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"