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whole genome sequencing AND lung cancer

Garrett Jenkinson, Jordi Abante, Andrew P Feinberg, John Goutsias
BACKGROUND: DNA methylation is a stable form of epigenetic memory used by cells to control gene expression. Whole genome bisulfite sequencing (WGBS) has emerged as a gold-standard experimental technique for studying DNA methylation by producing high resolution genome-wide methylation profiles. Statistical modeling and analysis is employed to computationally extract and quantify information from these profiles in an effort to identify regions of the genome that demonstrate crucial or aberrant epigenetic behavior...
March 7, 2018: BMC Bioinformatics
Shoko Nakasone, Sachiyo Mimaki, Tomohiro Ichikawa, Keiju Aokage, Tomohiro Miyoshi, Masato Sugano, Motohiro Kojima, Satoshi Fujii, Takeshi Kuwata, Atsushi Ochiai, Masahiro Tsuboi, Koichi Goto, Katsuya Tsuchihara, Genichiro Ishii
PURPOSE: Podoplanin-positive cancer-associated fibroblasts (CAFs) play an essential role in tumor progression. However, it is still unclear whether specific genomic alterations of cancer cells are required to recruit podoplanin-positive CAFs. The aim of this study was to investigate the relationship between the mutation status of lung adenocarcinoma cells and the presence of podoplanin-positive CAFs. METHODS: Ninety-seven lung adenocarcinomas for which whole exome sequencing data were available were enrolled...
March 6, 2018: Journal of Cancer Research and Clinical Oncology
Nicolas Albin, Anne Mc Leer, Linda Sakhri
In recent years, high-throughput sequencing techniques have been developed for cancerology and many clinical trials are currently structured around biomarkers that can guide specific treatment choices. This approach is characteristic of precision medicine, which is actually a concept initiated several decades ago with, for example, retinoic acid in promyelocytic leukemia. This paper will review the different types of molecular alterations and « -omics » biological analyses, bioinformatics tools, coupled drug/biomarkers already validated, the ethical issues of whole genomic sequencing of an individual as part of an inclusion in a clinical trial and finally the first results of precision medicine trials...
February 28, 2018: Bulletin du Cancer
Alberto Ferrarini, Claudio Forcato, Genny Buson, Paola Tononi, Valentina Del Monaco, Mario Terracciano, Chiara Bolognesi, Francesca Fontana, Gianni Medoro, Rui Neves, Birte Möhlendick, Karim Rihawi, Andrea Ardizzoni, Semini Sumanasuriya, Penny Flohr, Maryou Lambros, Johann de Bono, Nikolas H Stoecklein, Nicolò Manaresi
Chromosomal instability and associated chromosomal aberrations are hallmarks of cancer and play a critical role in disease progression and development of resistance to drugs. Single-cell genome analysis has gained interest in latest years as a source of biomarkers for targeted-therapy selection and drug resistance, and several methods have been developed to amplify the genomic DNA and to produce libraries suitable for Whole Genome Sequencing (WGS). However, most protocols require several enzymatic and cleanup steps, thus increasing the complexity and length of protocols, while robustness and speed are key factors for clinical applications...
2018: PloS One
Benjamin J Drapkin, Julie George, Camilla L Christensen, Mari Mino-Kenudson, Ruben Dries, Tilak Sundaresan, Sarah Phat, David T Myers, Jun Zhong, Peter Igo, Mehlika H Hazar-Rethinam, Joseph A LiCausi, Maria Gomez-Caraballo, Marina Kem, Kandarp N Jani, Roxana Azimi, Nima Abedpour, Roopika Menon, Sotirios Lakis, Rebecca S Heist, Reinhard Büttner, Stefan Haas, Lecia V Sequist, Alice T Shaw, Kwok-Kin Wong, Aaron N Hata, Mehmet Toner, Shyamala Maheswaran, Daniel A Haber, Martin Peifer, Nicholas Dyson, Roman K Thomas, Anna F Farago
Small cell lung cancer (SCLC) patient-derived xenografts (PDXs) can be generated from biopsies or circulating tumor cells (CTCs), though scarcity of tissue and low efficiency of tumor growth have previously limited these approaches. Applying an established clinical-translational pipeline for tissue collection and an automated microfluidic platform for CTC-enrichment, we generated 17 biopsy-derived PDXs and 17 CTC-derived PDXs in a two-year timeframe, at 89% and 38% efficiency, respectively. Whole exome sequencing showed that somatic alterations are stably maintained between patient tumors and PDXs...
February 26, 2018: Cancer Discovery
Hashim M Aljohani, Mohamed Aittaleb, John M Furgason, Peter Amaya, Ayham Deeb, Jeffery J Chalmers, El Mustapha Bahassi
Approximately 90% of all cancer deaths arise from the metastatic spread of primary tumours. Of all the processes involved in carcinogenesis, local invasion and the formation of metastases are clinically the most relevant, but they are the least well understood at the molecular level. As a barrier to metastasis, cells normally undergo an apoptotic process known as 'anoikis', in circulation. The recent technological advances in the isolation and characterisation of rare circulating tumour cells (CTCs) will allow a better understanding of anoikis resistance...
February 21, 2018: Mutagenesis
So Hyeon Bak, Hyunjin Park, Ho Yun Lee, Youngwook Kim, Hyung-Lae Kim, Sin-Ho Jung, Hyeseung Kim, Jonghoon Kim, Keunchil Park
Imaging features can be useful for identifying distinct genomic differences and have predictive power for certain phenotypes attributed to genomic mutations. We aimed to identify predictive imaging biomarkers that underpin genomic alterations and clinical outcomes in lung squamous cell carcinoma (SQCC) using a radiomics approach. In 57 patients with lung SQCC who underwent preoperative computed tomography (CT) and whole-exome DNA sequencing, 63 quantitative imaging features were extracted from CT and 73 clinicoradiological features including imaging features were classified into 8 categories: clinical, global, histogram-based, lung cancer-specific, shape, local, regional, and emphysema...
February 19, 2018: Scientific Reports
Olga Vera, Carlos Rodriguez-Antolin, Javier de Castro, Florian A Karreth, Thomas A Sellers, Inmaculada Ibañez de Caceres
Long noncoding RNAs (lncRNAs) are critical regulators of cell biology whose alteration can lead to the development of diseases such as cancer. The potential role of lncRNAs and their epigenetic regulation in response to platinum treatment are largely unknown. We analyzed four paired cisplatin-sensitive/resistant non-small cell lung cancer and ovarian cancer cell lines. The epigenetic landscape of overlapping and cis-acting lncRNAs was determined by combining human microarray data on 30,586 lncRNAs and 20,109 protein coding mRNAs with whole-genome bisulfite sequencing...
February 13, 2018: Epigenetics: Official Journal of the DNA Methylation Society
Min He, Shanshan Liu, Sachith Gallolu Kankanamalage, Mark D Borromeo, Luc Girard, Adi F Gazdar, John D Minna, Jane E Johnson, Melanie H Cobb
Small cell lung cancer (SCLC) is an aggressive neuroendocrine carcinoma, designated as a recalcitrant cancer by the National Cancer Institute, in urgent need of new rational therapeutic targets. Previous studies have determined that the basic helix-loop-helix transcription factor achaete-scute homolog 1 (ASCL1) is essential for the survival and progression of a fraction of pulmonary neuroendocrine cancer cells, which include both SCLC and a subset of non-SCLC. Previously, to understand how ASCL1 initiates tumorigenesis in pulmonary neuroendocrine cancer and identify the transcriptional targets of ASCL1, whole-genome RNA-sequencing analysis combined with chromatin immunoprecipitation-sequencing was performed with a series of lung cancer cell lines...
February 1, 2018: Translational Oncology
Loic Verlingue, Antoine Hollebecque, Ludovic Lacroix, Sophie Postel-Vinay, Andrea Varga, Yolla El Dakdouki, Capucine Baldini, Rastilav Balheda, Anas Gazzah, Jean-Marie Michot, Aurélien Marabelle, Olivier Mir, Monica Arnedos, Etienne Rouleau, Eric Solary, Thierry De Baere, Eric Angevin, Jean-Pierre Armand, Stefan Michiels, Fabrice André, Eric Deutsch, Jean-Yves Scoazec, Jean-Charles Soria, Christophe Massard
INTRODUCTION: Therapeutic inhibition of the human epidermal receptor 3 (ERBB3, HER3) has been challenged by the low frequency of ERBB3 somatic alterations across cancer types. We have evaluated the clinical utility to use available inhibitors of the HER family in the context of ERBB3 mutations. PATIENTS AND METHODS: In this study, we have selected patients with somatic ERBB3 alterations detected in their tumours from the molecular screening programs running at our institution...
January 27, 2018: European Journal of Cancer
Elaine C Maggi, Silvia Gravina, Haiying Cheng, Bilal Piperdi, Ziqiang Yuan, Xiao Dong, Steven K Libutti, Jan Vijg, Cristina Montagna
The goal of this study was to develop a method for whole genome cell-free DNA (cfDNA) methylation analysis in humans and mice with the ultimate goal to facilitate the identification of tumor derived DNA methylation changes in the blood. Plasma or serum from patients with pancreatic neuroendocrine tumors or lung cancer, and plasma from a murine model of pancreatic adenocarcinoma was used to develop a protocol for cfDNA isolation, library preparation and whole-genome bisulfite sequencing of ultra low quantities of cfDNA, including tumor-specific DNA...
2018: Frontiers in Genetics
Lei Liu, Yanquan Zhang, Chi Chun Wong, Jingwan Zhang, Yujuan Dong, Xiangchun Li, Wei Kang, Francis Kl Chan, Joseph Jy Sung, Jun Yu
Gene amplification is a hallmark of cancer and is frequently observed in colorectal cancer (CRC). Previous whole-genome sequencing of CRC clinical specimens identified amplification of Ring finger protein 6 (RNF6), a RING-domain E3 ubiquitin ligase. In this study, we show that RNF6 is upregulated in 73.5% (147/200) of CRC patients, and was positively associated with RNF6 gene amplification. Further, RNF6 expression and its gene amplification were independent prognostic factors for poor outcome of CRC patients...
January 26, 2018: Cancer Research
Timothy O'Donnell, Elizabeth L Christie, Arun Ahuja, Jacqueline Buros, B Arman Aksoy, David D L Bowtell, Alexandra Snyder, Jeff Hammerbacher
BACKGROUND: Patients with highly mutated tumors, such as melanoma or smoking-related lung cancer, have higher rates of response to immune checkpoint blockade therapy, perhaps due to increased neoantigen expression. Many chemotherapies including platinum compounds are known to be mutagenic, but the impact of standard treatment protocols on mutational burden and resulting neoantigen expression in most human cancers is unknown. METHODS: We sought to quantify the effect of chemotherapy treatment on computationally predicted neoantigen expression for high grade serous ovarian carcinoma patients enrolled in the Australian Ovarian Cancer Study...
January 22, 2018: BMC Cancer
Michael K Asiedu, Charles F Thomas, Jie Dong, Sandra C Schulte Tomaszek, Prasidda Khadka, Zhifu Sun, Farhad Kosari, Jin Jen, Julian R Molina, George Vasmatzis, Rui Kuang, Marie Christine Aubry, Ping Yang, Dennis A Wigle
PURPOSE: Pulmonary carcinoid tumors account for up to 5% of all lung malignancies in adults, comprise 30% of all carcinoid malignancies, and are defined histologically as typical carcinoid (TC) and atypical carcinoid (AC) tumors. The role of specific genomic alterations in the pathogenesis of pulmonary carcinoid tumors remains poorly understood. We sought to identify genomic alterations and pathways that are deregulated in these tumors to find novel therapeutic targets for pulmonary carcinoid tumors...
January 19, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Hira Rizvi, Francisco Sanchez-Vega, Konnor La, Walid Chatila, Philip Jonsson, Darragh Halpenny, Andrew Plodkowski, Niamh Long, Jennifer L Sauter, Natasha Rekhtman, Travis Hollmann, Kurt A Schalper, Justin F Gainor, Ronglai Shen, Ai Ni, Kathryn C Arbour, Taha Merghoub, Jedd Wolchok, Alexandra Snyder, Jamie E Chaft, Mark G Kris, Charles M Rudin, Nicholas D Socci, Michael F Berger, Barry S Taylor, Ahmet Zehir, David B Solit, Maria E Arcila, Marc Ladanyi, Gregory J Riely, Nikolaus Schultz, Matthew D Hellmann
Purpose Treatment of advanced non-small-cell lung cancer with immune checkpoint inhibitors (ICIs) is characterized by durable responses and improved survival in a subset of patients. Clinically available tools to optimize use of ICIs and understand the molecular determinants of response are needed. Targeted next-generation sequencing (NGS) is increasingly routine, but its role in identifying predictors of response to ICIs is not known. Methods Detailed clinical annotation and response data were collected for patients with advanced non-small-cell lung cancer treated with anti-programmed death-1 or anti-programmed death-ligand 1 [anti-programmed cell death (PD)-1] therapy and profiled by targeted NGS (MSK-IMPACT; n = 240)...
March 1, 2018: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
Aditya Deshpande, Wenhua Lang, Tina McDowell, Smruthy Sivakumar, Jiexin Zhang, Jing Wang, F Anthony San Lucas, Jerry Fowler, Humam Kadara, Paul Scheet
BACKGROUND: 'Next-generation' (NGS) sequencing has wide application in medical genetics, including the detection of somatic variation in cancer. The Ion Torrent-based (IONT) platform is among NGS technologies employed in clinical, research and diagnostic settings. However, identifying mutations from IONT deep sequencing with high confidence has remained a challenge. We compared various computational variant-calling methods to derive a variant identification pipeline that may improve the molecular diagnostic and research utility of IONT...
January 4, 2018: BMC Bioinformatics
Jenny Nyqvist, Fredrik Persson, Toshima Z Parris, Khalil Helou, Elisabeth Kenne Sarenmalm, Zakaria Einbeigi, Åke Borg, Per Karlsson, Anikó Kovács
The number of patients with multiple primary malignancies has been increasing steadily in recent years. In the present study, we describe a unique case of an 81-year-old woman with 5 metachronous and synchronous primary malignant neoplasms. The patient was first diagnosed with an endometrium adenocarcinoma in 1997 and a colon adenocarcinoma in 2002. Eleven years after her colon surgery, in 2013, the patient presented with 3 other primary malignancies within a 4-month time span: an invasive malignant melanoma on the lower leg, an invasive mucinous breast carcinoma in the right breast, and a pleomorphic spindle cell sarcoma on the left upper arm...
September 2017: Case Reports in Oncology
Sneh Lata, Maddalena Marasa, Yifu Li, David A Fasel, Emily Groopman, Vaidehi Jobanputra, Hila Rasouly, Adele Mitrotti, Rik Westland, Miguel Verbitsky, Jordan Nestor, Lindsey M Slater, Vivette D'Agati, Marcin Zaniew, Anna Materna-Kiryluk, Francesca Lugani, Gianluca Caridi, Luca Rampoldi, Aditya Mattoo, Chad A Newton, Maya K Rao, Jai Radhakrishnan, Wooin Ahn, Pietro A Canetta, Andrew S Bomback, Gerald B Appel, Corinne Antignac, Glen S Markowitz, Christine K Garcia, Krzysztof Kiryluk, Simone Sanna-Cherchi, Ali G Gharavi
Background: The utility of whole-exome sequencing (WES) for the diagnosis and management of adult-onset constitutional disorders has not been adequately studied. Genetic diagnostics may be advantageous in adults with chronic kidney disease (CKD), in whom the cause of kidney failure often remains unknown. Objective: To study the diagnostic utility of WES in a selected referral population of adults with CKD. Design: Observational cohort. Setting: A major academic medical center...
January 16, 2018: Annals of Internal Medicine
Liwei Qu, Bo Zhou, Guizhen Wang, Guangbiao Zhou
Lung squamous cell carcinoma (LUSC) causes approximately 400 000 deaths each year worldwide. The occurrence of LUSC is attributed to exposure to cigarette smoke, which induces the development of numerous genomic abnormalities. However, few studies have investigated the genomic variations that occur only in normal tissues that have been similarly exposed to tobacco smoke as tumor tissues. In this study, we sequenced the whole genomes of three normal lung tissue samples and their paired adjacent squamous cell carcinomas...
November 28, 2017: Frontiers of Medicine
Clara Mayo-de-Las-Casas, Mónica Garzón Ibáñez, Núria Jordana-Ariza, Beatriz García-Peláez, Ariadna Balada-Bel, Sergio Villatoro, Umberto Malapelle, Niki Karachaliou, Giancarlo Troncone, Rafael Rosell, Miguel Angel Molina-Vila
Collection of tumor samples is not always feasible in non-small cell lung cancer (NSCLC) patients, and circulating free DNA (cfDNA) extracted from blood represents a viable alternative. Different sensitive platforms have been developed for genetic cfDNA testing, some of which are already in clinical use. However, several difficulties remain, particularly the lack of standardization of these methodologies. Areas covered: Here, the authors present a review of the literature to update the applicability of cfDNA for diagnosis and monitoring of NSCLC patients...
January 2018: Expert Review of Molecular Diagnostics
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