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cfDNA NGS

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https://www.readbyqxmd.com/read/29305293/beyond-screening-for-chromosomal-abnormalities-advances-in-non-invasive-diagnosis-of-single-gene-disorders-and-fetal-exome-sequencing
#1
REVIEW
Jane Hayward, Lyn S Chitty
Emerging genomic technologies, largely based around next generation sequencing (NGS), are offering new promise for safer prenatal genetic diagnosis. These innovative approaches will improve screening for fetal aneuploidy, allow definitive non-invasive prenatal diagnosis (NIPD) of single gene disorders at an early gestational stage without the need for invasive testing, and improve our ability to detect monogenic disorders as the aetiology of fetal abnormalities. This presents clinicians and scientists with novel challenges as well as opportunities...
January 2, 2018: Seminars in Fetal & Neonatal Medicine
https://www.readbyqxmd.com/read/29277949/development-and-clinical-validation-of-a-circulating-tumor-dna-test-for-the-identification-of-clinically-actionable-mutations-in-non-small-cell-lung-cancer
#2
Liping Liu, Han Liu, Di Shao, Zu Liu, Jingjing Wang, Qiuhua Deng, Hailing Tang, Haihong Yang, Yalei Zhang, Yuan Qiu, Fei Cui, Meihua Tan, Pan Zhang, Zhilong Li, Jilong Liu, Wenhua Liang, Yuying Wang, Zhiyu Peng, Jian Wang, Huanming Yang, Mao Mao, Karsten Kristiansen, Mingzhi Ye, Jianxing He
Molecular analysis of potentially actionable mutations has become routine practice in oncological pathology. However, testing a wide range of oncogenes and mutations can be technically challenging because of limitations associated with tumor biopsy. Circulating tumor DNA (ctDNA) is a potential tool for the noninvasive profiling of tumors. In this study, we developed a next-generation sequencing (NGS)-based test for the detection of clinically relevant mutations in ctDNA and evaluated the feasibility of using this ctDNA NGS-based assay as an alternative to tissue genotyping...
December 26, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29216356/improved-egfr-mutation-detection-using-combined-exosomal-rna-and-circulating-tumor-dna-in-nsclc-patient-plasma
#3
A K Krug, D Enderle, C Karlovich, T Priewasser, S Bentink, A Spiel, K Brinkmann, J Emenegger, D G Grimm, E Castellanos-Rizaldos, J W Goldman, L V Sequist, J-C Soria, D R Camidge, S M Gadgeel, H A Wakelee, M Raponi, M Noerholm, J Skog
Background: A major limitation of circulating tumor DNA (ctDNA) for somatic mutation detection has been the low level of ctDNA found in a subset of cancer patients. We investigated whether using a combined isolation of exosomal RNA (exoRNA) and cell-free DNA (cfDNA) could improve blood-based liquid biopsy for EGFR mutation detection in NSCLC patients. Patients and methods: Matched pretreatment tumor and plasma were collected from 84 patients enrolled in TIGER-X (NCT01526928), a Ph1/2 study of rociletinib in mutant EGFR NSCLC patients...
December 5, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29184677/cell-free-dna-analysis-by-sire%C3%A2-next-generation-sequencing-panel-in-non-small-cell-lung-cancer-patients-focus-on-basal-setting
#4
Pasquale Pisapia, Francesco Pepe, Riccardo Smeraglio, Maria Russo, Danilo Rocco, Roberta Sgariglia, Mariantonia Nacchio, Caterina De Luca, Elena Vigliar, Claudio Bellevicine, Giancarlo Troncone, Umberto Malapelle
Background: Non small cell lung cancer (NSCLC) is diagnosed in most cases on small tissue samples, such as cytological preparations and histological biopsies; these limited tissue specimens may be not always sufficient for testing epidermal growth factor receptor (EGFR) mutations and other relevant predictive biomarkers. Cell-free DNA (cfDNA) can be used as a surrogate for EGFR mutational testing, whenever tissue is unavailable. However, the detection of gene mutations on cfDNA is challenging; in fact, the extremely low concentration of circulating tumor DNA requires the implementation of highly sensitive and validated next generation techniques...
October 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29172773/an-update-on-liquid-biopsy-analysis-for-diagnostic-and-monitoring-applications-in-non-small-cell-lung-cancer
#5
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...
November 26, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/29163793/rapid-ultra-low-coverage-copy-number-profiling-of-cell-free-dna-as-a-precision-oncology-screening-strategy
#6
Daniel H Hovelson, Chia-Jen Liu, Yugang Wang, Qing Kang, James Henderson, Amy Gursky, Scott Brockman, Nithya Ramnath, John C Krauss, Moshe Talpaz, Malathi Kandarpa, Rashmi Chugh, Missy Tuck, Kirk Herman, Catherine S Grasso, Michael J Quist, Felix Y Feng, Christine Haakenson, John Langmore, Emmanuel Kamberov, Tim Tesmer, Hatim Husain, Robert J Lonigro, Dan Robinson, David C Smith, Ajjai S Alva, Maha H Hussain, Arul M Chinnaiyan, Muneesh Tewari, Ryan E Mills, Todd M Morgan, Scott A Tomlins
Current cell-free DNA (cfDNA) next generation sequencing (NGS) precision oncology workflows are typically limited to targeted and/or disease-specific applications. In advanced cancer, disease burden and cfDNA tumor content are often elevated, yielding unique precision oncology opportunities. We sought to demonstrate the utility of a pan-cancer, rapid, inexpensive, whole genome NGS of cfDNA approach (PRINCe) as a precision oncology screening strategy via ultra-low coverage (~0.01x) tumor content determination through genome-wide copy number alteration (CNA) profiling...
October 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137355/a-pilot-study-evaluating-concordance-between-blood-based-and-patient-matched-tumor-molecular-testing-within-pancreatic-cancer-patients-participating-in-the-know-your-tumor-kyt-initiative
#7
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...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29110843/frequency-and-clinical-impact-of-preoperative-circulating-tumor-cells-in-resectable-non-metastatic-lung-adenocarcinomas
#8
Nadia Dandachi, Verena Tiran, Joerg Lindenmann, Luka Brcic, Nicole Fink-Neuboeck, Karl Kashofer, Gudrun Absenger, Angelika Bezan, Richard J Cote, Ram Datar, Marija Balic
OBJECTIVES: Despite successful surgery, 30-50% of patients with resectable non-small cell lung cancer develop tumor recurrence within 5 years of surgery. MATERIALS AND METHODS: In this prospective study, we performed CTC enumerations in 40 patients with non-metastatic lung adenocarcinoma (NMLA) using a size-based microfilter. Additionally, cfDNA isolated from plasma was analyzed in 35 out of 40 patients. RESULTS: CTCs were identified in 15 out of 40 patients (37...
November 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/29051321/liquid-biopsies-using-plasma-exosomal-nucleic-acids-and-plasma-cell-free-dna-compared-with-clinical-outcomes-of-patients-with-advanced-cancers
#9
Lino Möhrmann, Helen J Huang, David S Hong, Apostolia M Tsimberidou, Siqing Fu, Sarina A Piha-Paul, Vivek Subbiah, Daniel D Karp, Aung Naing, Anne Krug, Daniel Enderle, Tina Priewasser, Mikkel Noerholm, Erez Eitan, Christine Coticchia, Georg Stoll, Lisa-Marie Jordan, Cathy Eng, E Scott Kopetz, Johan Skog, Funda Meric-Bernstam, Filip Janku
Purpose: Blood-based liquid biopsies offer easy access to genomic material for molecular diagnostics in cancer. Commonly used cell-free DNA (cfDNA) originates from dying cells. Exosomal nucleic acids (exoNAs) originate from living cells, which can better reflect underlying cancer biology.Experimental Design: Next-generation sequencing (NGS) was used to test exoNA, and droplet digital PCR (ddPCR) and BEAMing PCR were used to test cfDNA for BRAFV600, KRASG12/G13, and EGFRexon19del/L858R mutations in 43 patients with progressing advanced cancers...
October 19, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28973495/identification-of-mutations-in-cell-free-circulating-tumor-dna-in-adrenocortical-carcinoma-a-case-series
#10
Sara G Creemers, Esther Korpershoek, Peggy N Atmodimedjo, Winand N M Dinjens, Peter M van Koetsveld, Richard A Feelders, Leo J Hofland
Context: The disease course of adrenocortical carcinoma (ACC) patients is heterogeneous. A marker for prognosis and treatment response would facilitate choices for diagnosis and therapy. In other cancer types, circulating cell-free tumor DNA predicted tumor dynamics. Case Descriptions: The present pilot study included six patients. Next-generation sequencing (NGS) showed mutations in three ACC cases. From these patients, blood was drawn before (1 to 2 weeks) and after surgery and cell-free circulating DNA (cfDNA) was isolated...
October 1, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28949453/somatic-mutation-detection-using-various-targeted-detection-assays-in-paired-samples-of-circulating-tumor-dna-primary-tumor-and-metastases-from-patients-undergoing-resection-of-colorectal-liver-metastases
#11
(no author information available yet)
Assessing circulating tumor DNA (ctDNA) is a promising method to evaluate somatic mutations from solid tumors in a minimally-invasive way. In a group of twelve metastatic colorectal cancer (mCRC) patients undergoing liver metastasectomy, from each patient DNA from cell-free DNA (cfDNA), the primary tumor, metastatic liver tissue, normal tumor-adjacent colon or liver tissue, and whole blood were obtained. Investigated was the feasibility of a targeted NGS approach to identify somatic mutations in ctDNA. This targeted NGS approach was also compared with NGS preceded by mutant allele enrichment using synchronous coefficient of drag alteration technology embodied in the OnTarget assay, and for selected mutations with digital PCR (dPCR)...
December 2016: Molecular Oncology
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
#12
Yuebi Hu, Ryan S Alden, Justin I Odegaard, Stephen R Fairclough, Ruthia Chen, Jennifer Heng, Nora Feeney, Rebecca 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...
September 25, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28905136/highly-sensitive-detection-of-esr1-mutations-in-cell-free-dna-from-patients-with-metastatic-breast-cancer-using-molecular-barcode-sequencing
#13
Nanae Masunaga, Naofumi Kagara, Daisuke Motooka, Shota Nakamura, Tomohiro Miyake, Tomonori Tanei, Yasuto Naoi, Masafumi Shimoda, Kenzo Shimazu, Seung Jin Kim, Shinzaburo Noguchi
PURPOSE: We aimed to develop a highly sensitive method to detect ESR1 mutations in cell-free DNA (cfDNA) using next-generation sequencing with molecular barcode (MB-NGS) targeting the hotspot segment (c.1600-1713). METHODS: The sensitivity of MB-NGS was tested using serially diluted ESR1 mutant DNA and then cfDNA samples from 34 patients with metastatic breast cancer were analyzed with MB-NGS. The results of MB-NGS were validated in comparison with conventional NGS and droplet digital PCR (ddPCR)...
September 13, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28723342/molecular-analysis-of-circulating-free-dna-from-lung-cancer-patients-in-routine-laboratory-practice-a-cross-platform-comparison-of-three-different-molecular-methods-for-mutation-detection
#14
Stephan Bartels, Sascha Persing, Britta Hasemeier, Elisa Schipper, Hans Kreipe, Ulrich Lehmann
Cell-free DNA (cfDNA), which is isolated from blood plasma, represents a noninvasive source for the detection of mutations conferring resistance against epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors in non-small-cell lung cancer patients. In advanced disease stages, performing regular biopsies is often not possible because of the general health condition of the patients. Furthermore, a biopsy of a single tumor lesion or metastasis may not reflect the heterogeneous genotype of the tumor and its metastases...
July 16, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28683468/correlation-between-circulating-mutant-dna-and-metabolic-tumour-burden-in-advanced-non-small-cell-lung-cancer-patients
#15
Anne Winther-Larsen, Christina Demuth, Joan Fledelius, Anne Tranberg Madsen, Karin Hjorthaug, Peter Meldgaard, Boe Sandahl Sorensen
BACKGROUND: Mutated circulating cell-free DNA (cfDNA) has been suggested as a surrogate marker of tumour burden and aggressiveness of disease. We examined the association between the level of plasma mutant cfDNA and metabolic tumour burden (MTB) measured by 18F-fluoro-D-glucose positron emission tomography/computed tomography (18F-FDG PET/CT). Furthermore, the presence of mutant cfDNA was correlated with patient survival. METHODS: Forty-six advanced non-small cell lung cancer (NSCLC) patients were included...
August 22, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28636991/non-invasive-detection-of-somatic-mutations-using-next-generation-sequencing-in-primary-central-nervous-system-lymphoma
#16
Maxime Fontanilles, Florent Marguet, Élodie Bohers, Pierre-Julien Viailly, Sydney Dubois, Philippe Bertrand, Vincent Camus, Sylvain Mareschal, Philippe Ruminy, Catherine Maingonnat, Stéphane Lepretre, Elena-Liana Veresezan, Stéphane Derrey, Hervé Tilly, Jean-Michel Picquenot, Annie Laquerrière, Fabrice Jardin
PURPOSE: Primary central nervous system lymphomas (PCNSL) have recurrent genomic alterations. The main objective of our study was to demonstrate that targeted sequencing of circulating cell-free DNA (cfDNA) released by PCNSL at the time of diagnosis could identify somatic mutations by next-generation sequencing (NGS). PATIENTS AND METHODS: PlasmacfDNA and matched tumor DNA (tDNA) from 25 PCNSL patients were sequenced using an Ion Torrent Personal Genome Machine (Life Technologies®)...
July 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28540249/liquid-biopsies-for-bladder-cancer
#17
EDITORIAL
Douglas G Ward, Richard T Bryan
The development of accurate urinary biomarkers for the non-invasive detection of urothelial bladder cancer (UBC) could transform patient pathways by reducing reliance on cystoscopy, and the identification of highly prognostic (or even predictive) biomarkers could better guide patient management. A number of approaches are being utilised to address these challenges in both urinary- and plasma-borne tumour DNA (tDNA), so-called "liquid biopsies". Next generation sequencing (NGS) and droplet digital PCR (ddPCR) allow detection of very low levels of such tDNA amongst a large excess of non-tumour DNA, the former permitting large mutation panels to be assessed and the latter potentially identifying ultrarare mutant alleles yet restricted for multiplexing...
April 2017: Translational Andrology and Urology
https://www.readbyqxmd.com/read/28536309/development-and-validation-of-an-ultradeep-next-generation-sequencing-assay-for-testing-of-plasma-cell-free-dna-from-patients-with-advanced-cancer
#18
Filip Janku, Shile Zhang, Jill Waters, Li Liu, Helen J Huang, Vivek Subbiah, David S Hong, Daniel D Karp, Siqing Fu, Xuyu Cai, Nishma M Ramzanali, Kiran Madwani, Goran Cabrilo, Debra L Andrews, Yue Zhao, Milind Javle, E Scott Kopetz, Rajyalakshmi Luthra, Hyunsung J Kim, Sante Gnerre, Ravi Vijaya Satya, Han-Yu Chuang, Kristina M Kruglyak, Jonathan Toung, Chen Zhao, Richard Shen, John V Heymach, Funda Meric-Bernstam, Gordon B Mills, Jian-Bing Fan, Neeraj S Salathia
Purpose: Tumor-derived cell-free DNA (cfDNA) in plasma can be used for molecular testing and provide an attractive alternative to tumor tissue. Commonly used PCR-based technologies can test for limited number of alterations at the time. Therefore, novel ultrasensitive technologies capable of testing for a broad spectrum of molecular alterations are needed to further personalized cancer therapy.Experimental Design: We developed a highly sensitive ultradeep next-generation sequencing (NGS) assay using reagents from TruSeqNano library preparation and NexteraRapid Capture target enrichment kits to generate plasma cfDNA sequencing libraries for mutational analysis in 61 cancer-related genes using common bioinformatics tools...
September 15, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28522829/somatic-tumor-mutations-detected-by-targeted-next-generation-sequencing-in-minute-amounts-of-serum-derived-cell-free-dna
#19
Marjolein J A Weerts, Ronald van Marion, Jean C A Helmijr, Corine M Beaufort, Niels M G Krol, Anita M A C Trapman-Jansen, Winand N M Dinjens, Stefan Sleijfer, Maurice P H M Jansen, John W M Martens
The use of blood-circulating cell-free DNA (cfDNA) as 'liquid-biopsy' is explored worldwide, with hopes for its potential in providing prognostic or predictive information in cancer treatment. In exploring cfDNA, valuable repositories are biobanks containing material collected over time, however these retrospective cohorts have restrictive resources. In this study, we aimed to detect tumor-specific mutations in only minute amounts of serum-derived cfDNA by using a targeted next generation sequencing (NGS) approach...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28511612/ngs-analysis-on-tumor-tissue-and-cfdna-for-genotype-directed-therapy-in-metastatic-nsclc-patients-between-hope-and-hype
#20
Alexander T Falk, Simon Heeke, Véronique Hofman, Virginie Lespinet, Camille Ribeyre, Olivier Bordone, Michel Poudenx, Josiane Otto, Georges Garnier, Olivier Castelnau, Joël Guigay, Sylvie Leroy, Charles-Hugo Marquette, Paul Hofman, Marius Ilié
The advent of genomic based precision medicine led to the implementation of biomarker testing in metastatic non-small cell lung cancer (NSCLC) patients. Next generation sequencing (NGS) has been recently implemented to routine diagnostic requirements in lung oncology. Areas covered: Two cases of patients with metastatic NSCLC for whom NGS analysis performed on both tumor and liquid biopsy has not improved the clinical course of their disease are reported. These cases illustrate the difficulty of the so-called 'personalized or precision' medicine in clinical routine practice for metastatic NSCLC...
August 2017: Expert Review of Anticancer Therapy
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