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Michael J Pishvaian, R Joseph Bender, Lynn M Matrisian, Lola Rahib, Andrew Hendifar, William A Hoos, Sam Mikhail, Vincent Chung, Vincent Picozzi, Craig Heartwell, Kimberly Mason, Katelyn Varieur, Metasebia Aberra, Subha Madhavan, Emanuel Petricoin, Jonathan R Brody
Recent improvements in next-generation sequencing (NGS) technology have enabled detection of biomarkers in cell-free DNA in blood and may ultimately replace invasive tissue biopsies. However, a better understanding of the performance of blood-based NGS assays is needed prior to routine clinical use. As part of an IRB-approved molecular profiling registry trial of pancreatic ductal adenocarcinoma (PDA) patients, we facilitated blood-based NGS testing of 34 patients from multiple community-based and high-volume academic oncology practices...
November 8, 2016: Oncotarget
Umberto Malapelle, Pasquale Pisapia, Danilo Rocco, Riccardo Smeraglio, Maria di Spirito, Claudio Bellevicine, Giancarlo Troncone
The advent of genomic based personalized medicine has led to multiple advances in the molecular characterization of many tumor types, such as non-small cell lung cancer (NSCLC). NSCLC is diagnosed in most cases on small tissue samples that may be not always sufficient for EGFR mutational assessment to select patients for first and second generations' tyrosine kinase inhibitors (TKIs) therapy. In patients without tissue availability at presentation, the analysis of cell free DNA (cfDNA) derived from liquid biopsy samples, in particular from plasma, represent an established alternative to provide EGFR mutational testing for treatment decision making...
October 2016: Translational Lung Cancer Research
Catherine W Bennett, Guy Berchem, Yeoun Jin Kim, Victoria El-Khoury
Personalized medicine has emerged as the future of cancer care to ensure that patients receive individualized treatment specific to their needs. In order to provide such care, molecular techniques that enable oncologists to diagnose, treat, and monitor tumors are necessary. In the field of lung cancer, cell free DNA (cfDNA) shows great potential as a less invasive liquid biopsy technique, and next-generation sequencing (NGS) is a promising tool for analysis of tumor mutations. In this review, we outline the evolution of cfDNA and NGS and discuss the progress of using them in a clinical setting for patients with lung cancer...
August 30, 2016: Oncotarget
Tatsuo Ohira, Kazuko Sakai, Jun Matsubayashi, Naohiro Kajiwara, Masatoshi Kakihana, Masaru Hagiwara, Masaaki Hibi, Koichi Yoshida, Junichi Maeda, Keishi Ohtani, Toshitaka Nagao, Kazuto Nishio, Norihiko Ikeda
Next-generation sequencing (NGS) and digital polymerase chain reaction (PCR) technologies allow analysis of the mutational profile of circulating cell-free DNA (cfDNA) in individuals with advanced lung cancer. We have now evaluated the feasibility of cfDNA sequencing for mutation detection in patients with non-small cell lung cancer (NSCLC) at earlier stages. A total of 150 matched tumor and serum samples were collected from NSCLC patients at stages IA-IIIA. Amplicon sequencing with DNA extracted from tumor tissue detected frequent mutations in EGFR (37% of patients), TP53 (39%), and KRAS (10%), consistent with previous findings...
August 30, 2016: Cancer Science
Jacqueline A Shaw, David S Guttery, Allison Hills, Daniel Fernandez-Garcia, Karen Page, Brenda M Rosales, Kate S Goddard, Robert K Hastings, Jinli Luo, Olivia Ogle, Laura Woodley, Simak Ali, Justin Stebbing, R Charles Coombes
PURPOSE: The purpose of this study was to directly compare mutation profiles in multiple single CTCs and cfDNA isolated from the same blood samples taken from patients with metastaic breast cancer (MBC). We aimed to determine whether cell-free DNA would reflect the heterogeneity observed in 40 single CTCs. EXPERIMENTAL DESIGN: CTCs were enumerated by Cellsearch. CTC count was compared with the quantity of matched cfDNA and serum CA15-3 and alkaline phosphatase (ALP) in 112 patients with metastatic breast cancer...
June 22, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Maurice Phm Jansen, John Wm Martens, Jean Ca Helmijr, Corine M Beaufort, Ronald van Marion, Niels Mg Krol, Kim Monkhorst, Anita Mac Trapman-Jansen, Marion E Meijer-van Gelder, Marjolein Ja Weerts, Diana E Ramirez-Ardila, Hendrikus Jan Dubbink, John A Foekens, Stefan Sleijfer, Els Mjj Berns
The aim was to identify mutations in serum cell-free DNA (cfDNA) associated with disease progression on tamoxifen treatment in metastatic breast cancer (MBC). Sera available at start of therapy, during therapy and at disease progression were selected from 10 estrogen receptor (ER)-positive breast cancer patients. DNA from primary tumor and normal tissue and cfDNA from minute amounts of sera were analyzed by targeted next generation sequencing (NGS) of 45 genes (1,242 exons). At disease progression, stop-gain single nucleotide variants (SNVs) for CREBBP (1 patient) and SMAD4 (1 patient) and non-synonymous SNVs for AKAP9 (1 patient), PIK3CA (2 patients) and TP53 (2 patients) were found...
July 12, 2016: Oncotarget
L Sorber, K Zwaenepoel, V Deschoolmeester, P E Y Van Schil, J Van Meerbeeck, F Lardon, C Rolfo, P Pauwels
Lung cancer is the predominant cause of cancer-related mortality in the world. The majority of patients present with locally advanced or metastatic non-small-cell lung cancer (NSCLC). Treatment for NSCLC is evolving from the use of cytotoxic chemotherapy to personalized treatment based on molecular alterations. Unfortunately, the quality of the available tumor biopsy and/or cytology material is not always adequate to perform the necessary molecular testing, which has prompted the search for alternatives. This review examines the use of circulating cell-free nucleic acids (cfNA), consisting of both circulating cell-free (tumoral) DNA (cfDNA-ctDNA) and RNA (cfRNA), as a liquid biopsy in lung cancer...
May 4, 2016: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
Vincent Camus, Nasrin Sarafan-Vasseur, Elodie Bohers, Sydney Dubois, Sylvain Mareschal, Philippe Bertrand, Pierre-Julien Viailly, Philippe Ruminy, Catherine Maingonnat, Emilie Lemasle, Aspasia Stamatoullas, Jean-Michel Picquenot, Marie Cornic, Ludivine Beaussire, Christian Bastard, Thierry Frebourg, Hervé Tilly, Fabrice Jardin
Diffuse large B-cell lymphoma (DLBCL) is an aggressive and heterogeneous malignancy harboring frequent targetable activating somatic mutations. Emerging evidence suggests that circulating cell-free DNA (cfDNA) can be used to detect somatic variants in DLBCL using Next-Generation Sequencing (NGS) experiments. In this proof-of-concept study, we chose to develop simple and valuable digital PCR (dPCR) assays for the detection of recurrent exportin-1 (XPO1) E571K, EZH2 Y641N, and MYD88 L265P mutations in DLBCL patients, thereby identifying patients most likely to potentially benefit from targeted therapies...
September 2016: Leukemia & Lymphoma
M Jamal-Hanjani, G A Wilson, S Horswell, R Mitter, O Sakarya, T Constantin, R Salari, E Kirkizlar, S Sigurjonsson, R Pelham, S Kareht, B Zimmermann, C Swanton
BACKGROUND: The aim of this pilot study was to assess whether both ubiquitous and heterogeneous somatic mutations could be detected in cell-free DNA (cfDNA) from patients with early-stage non-small-cell lung cancer (NSCLC). PATIENTS AND METHODS: Three stage I and one stage II primary NSCLC tumors were subjected to multiregion whole-exome sequencing (WES) and validated with AmpliSeq. A subset of ubiquitous and heterogeneous single-nucleotide variants (SNVs) were chosen...
May 2016: Annals of Oncology: Official Journal of the European Society for Medical Oncology
Cécile Jovelet, Ecaterina Ileana, Marie-Cécile Le Deley, Nelly Motté, Silvia Rosellini, Alfredo Romero, Celine Lefebvre, Marion Pedrero, Noémie Pata-Merci, Nathalie Droin, Marc Deloger, Christophe Massard, Antoine Hollebecque, Charles Ferté, Amélie Boichard, Sophie Postel-Vinay, Maud Ngo-Camus, Thierry De Baere, Philippe Vielh, Jean-Yves Scoazec, Gilles Vassal, Alexander Eggermont, Fabrice André, Jean-Charles Soria, Ludovic Lacroix
PURPOSE: Liquid biopsies based on circulating cell-free DNA (cfDNA) analysis are described as surrogate samples for molecular analysis. We evaluated the concordance between tumor DNA (tDNA) and cfDNA analysis on a large cohort of patients with advanced or metastatic solid tumor, eligible for phase I trial and with good performance status, enrolled in MOSCATO 01 trial (clinical trial NCT01566019). EXPERIMENTAL DESIGN: Blood samples were collected at inclusion and cfDNA was extracted from plasma for 334 patients...
June 15, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Dominic G Rothwell, Nigel Smith, Daniel Morris, Hui Sun Leong, Yaoyong Li, Antoine Hollebecque, Mahmood Ayub, Louise Carter, Jenny Antonello, Lynsey Franklin, Crispin Miller, Fiona Blackhall, Caroline Dive, Ged Brady
Molecular information obtained from cancer patients' blood is an emerging and powerful research tool with immense potential as a companion diagnostic for patient stratification and monitoring. Blood, which can be sampled routinely, provides a means of inferring the current genetic status of patients' tumours via analysis of circulating tumour cells (CTCs) or circulating tumour DNA (ctDNA). However, accurate assessment of both CTCs and ctDNA requires all blood cells to be maintained intact until samples are processed...
April 2016: Molecular Oncology
Irene Vanni, Simona Coco, Anna Truini, Marta Rusmini, Maria Giovanna Dal Bello, Angela Alama, Barbara Banelli, Marco Mora, Erika Rijavec, Giulia Barletta, Carlo Genova, Federica Biello, Claudia Maggioni, Francesco Grossi
Next-generation sequencing (NGS) is a cost-effective technology capable of screening several genes simultaneously; however, its application in a clinical context requires an established workflow to acquire reliable sequencing results. Here, we report an optimized NGS workflow analyzing 22 lung cancer-related genes to sequence critical samples such as DNA from formalin-fixed paraffin-embedded (FFPE) blocks and circulating free DNA (cfDNA). Snap frozen and matched FFPE gDNA from 12 non-small cell lung cancer (NSCLC) patients, whose gDNA fragmentation status was previously evaluated using a multiplex PCR-based quality control, were successfully sequenced with Ion Torrent PGM™...
2015: International Journal of Molecular Sciences
Cloud P Paweletz, Adrian G Sacher, Chris K Raymond, Ryan S Alden, Allison O'Connell, Stacy L Mach, Yanan Kuang, Leena Gandhi, Paul Kirschmeier, Jessie M English, Lee P Lim, Pasi A Jänne, Geoffrey R Oxnard
PURPOSE: Tumor genotyping is a powerful tool for guiding non-small cell lung cancer (NSCLC) care; however, comprehensive tumor genotyping can be logistically cumbersome. To facilitate genotyping, we developed a next-generation sequencing (NGS) assay using a desktop sequencer to detect actionable mutations and rearrangements in cell-free plasma DNA (cfDNA). EXPERIMENTAL DESIGN: An NGS panel was developed targeting 11 driver oncogenes found in NSCLC. Targeted NGS was performed using a novel methodology that maximizes on-target reads, and minimizes artifact, and was validated on DNA dilutions derived from cell lines...
February 15, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Sho Kurihara, Yuka Ueda, Yoshiyuki Onitake, Taijiro Sueda, Emi Ohta, Nagisa Morihara, Shoko Hirano, Fumiko Irisuna, Eiso Hiyama
PURPOSE: Our aims are to determine circulating free DNA (cfDNA) in childhood solid tumor patients who underwent surgical intervention and to analyze any relationships with clinical parameters. METHODS: Fourty-four consenting children admitted with solid tumors between 2010 and 2014 were recruited. CfDNAs isolated from 0.5mL plasma obtained before and 1-30days after surgery were analyzed by next-generation sequencing (NGS: IonTorrent Cancer Hotspot panel) and by gene amplification analysis using a digital PCR (dPCR) platform...
December 2015: Journal of Pediatric Surgery
Renee Stokowski, Eric Wang, Karen White, Annette Batey, Bo Jacobsson, Herb Brar, Madhumitha Balanarasimha, Desiree Hollemon, Andrew Sparks, Kypros Nicolaides, Thomas J Musci
OBJECTIVE: To evaluate the clinical performance of non-invasive prenatal testing for trisomy 21, 18, and 13 using targeted cell-free DNA (cfDNA) analysis. METHODS: Targeted cfDNA analysis using DANSR™ and FORTE™ with microarray quantitation was used to evaluate the risk of trisomy 21, 18, and 13 in blinded samples from 799 singleton, twin, natural, and IVF pregnancies. Subjects either had fetal chromosome evaluation by karyotype, FISH, QF-PCR, or karyotype for newborns with suspected aneuploidy at birth...
December 2015: Prenatal Diagnosis
Jean Sebastien Frenel, Suzanne Carreira, Jane Goodall, Desam Roda, Raquel Perez-Lopez, Nina Tunariu, Ruth Riisnaes, Susana Miranda, Ines Figueiredo, Daniel Nava-Rodrigues, Alan Smith, Christophe Leux, Isaac Garcia-Murillas, Roberta Ferraldeschi, David Lorente, Joaquin Mateo, Michael Ong, Timothy A Yap, Udai Banerji, Delila Gasi Tandefelt, Nick Turner, Gerhardt Attard, Johann S de Bono
PURPOSE: We evaluated whether next-generation sequencing (NGS) of circulating cell-free DNA (cfDNA) could be used for patient selection and as a tumor clone response biomarker in patients with advanced cancers participating in early-phase clinical trials of targeted drugs. EXPERIMENTAL DESIGN: Plasma samples from patients with known tumor mutations who completed at least two courses of investigational targeted therapy were collected monthly, until disease progression...
October 15, 2015: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
David S Guttery, Karen Page, Allison Hills, Laura Woodley, Stephanie D Marchese, Basma Rghebi, Robert K Hastings, Jinli Luo, J Howard Pringle, Justin Stebbing, R Charles Coombes, Simak Ali, Jacqueline A Shaw
BACKGROUND: Activating mutations in the estrogen receptor 1 (ESR1) gene are acquired on treatment and can drive resistance to endocrine therapy. Because of the spatial and temporal limitations of needle core biopsies, our goal was to develop a highly sensitive, less invasive method of detecting activating ESR1 mutations via circulating cell-free DNA (cfDNA) and tumor cells as a "liquid biopsy." METHODS: We developed a targeted 23-amplicon next-generation sequencing (NGS) panel for detection of hot-spot mutations in ESR1, phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA), tumor protein p53 (TP53), fibroblast growth factor receptor 1 (FGFR1), and fibroblast growth factor receptor 2 (FGFR2) in 48 patients with estrogen receptor-α-positive metastatic breast cancer who were receiving systemic therapy...
July 2015: Clinical Chemistry
Sébastien Couraud, Felipe Vaca-Paniagua, Stéphanie Villar, Javier Oliver, Tibor Schuster, Hélène Blanché, Nicolas Girard, Jean Trédaniel, Laurent Guilleminault, Radj Gervais, Nathalie Prim, Michel Vincent, Jacques Margery, Sébastien Larivé, Pascal Foucher, Bernard Duvert, Maxime Vallee, Florence Le Calvez-Kelm, James McKay, Pascale Missy, Franck Morin, Gérard Zalcman, Magali Olivier, Pierre-Jean Souquet
PURPOSE: Tumor somatic mutation analysis is part of the standard management of metastatic lung cancer. However, physicians often have to deal with small biopsies and consequently with challenging mutation testing. Circulating free DNA (cfDNA) is a promising tool for accessing the tumor genome as a liquid biopsy. Here, we evaluated next-generation sequencing (NGS) on cfDNA samples obtained from a consecutive series of patients for the screening of a range of clinically relevant mutations...
September 1, 2014: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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