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Cell free tumour DNA

Elena Trujillo-Arribas, Hada C Macher, Pilar Jiménez-Arriscado, Fernando de la Portilla, Patrocinio Molinero, Juan M Guerrero, Amalia Rubio
Genomic characterization of cell-free circulating tumour DNA (ctDNA) may offer an opportunity to assess clonal dynamics throughout the course of a patient's illness. The existence of KRAS driver mutations in colon cancer patients is determinant to decide their treatment and to predict their outcome. DNA is extracted automatically from 400 μL of serum using the MagNa Pure Compact with the Nucleic Acid Isolation Kit I. DNA amplification, COLD-PCR and HRM were performed in the same run in the Light Cycler 480...
2016: Advances in Experimental Medicine and Biology
Fiona Taylor, James Bradford, Penella J Woll, Dawn Teare, Angela Cox
Molecular profiling using low coverage whole genome sequencing of cell free DNA (cfDNA) represents a non-targeted approach to identify multiple somatic copy number alterations (SCNA) across different lung cancer subtypes. We aim to establish that SCNA can be detected in cfDNA of lung cancer cases.Standard protocols were followed to process matched cfDNA, formalin-fixed paraffin embedded (FFPE) tumour and lymphocyte DNA. Copy number profiles for cfDNA or FFPE DNA were normalised to profiles from matched lymphocyte DNA with the software CNAnorm...
2016: Advances in Experimental Medicine and Biology
Arancha Cebrián, Teresa Gómez Del Pulgar, Maria Jesús Fernández-Aceñero, Aurea Borrero-Palacios, Laura Del Puerto-Nevado, Javier Martínez-Useros, Juan Pablo Marín-Arango, Cristina Caramés, Ricardo Vega-Bravo, María Rodríguez-Remírez, Felix Manzarbeitia, Jesús García-Foncillas
AIM: Polo-like kinase 1 (Plk1) plays a key role in mitotic cell division and DNA damage repair. It has been observed that either up-regulated or down-regulated Plk1 could induce mitotic defects that results in aneuploidy and tumorigenesis, probably depending on the context. Few previous reports have associated Plk1 expression with prognosis and response to radiotherapy in rectal carcinomas. The aim of this study is to investigate the prognostic impact of Plk1 expression and its role in predicting response to neoadjuvant cheomoradiotherapy in rectal cancer...
September 22, 2016: Pathology, Research and Practice
Alex F Herrera, Haesook T Kim, Katherine A Kong, Malek Faham, Heather Sun, Aliyah R Sohani, Edwin P Alyea, Victoria E Carlton, Yi-Bin Chen, Corey S Cutler, Vincent T Ho, John Koreth, Chitra Kotwaliwale, Sarah Nikiforow, Jerome Ritz, Scott J Rodig, Robert J Soiffer, Joseph H Antin, Philippe Armand
Next-generation sequencing (NGS)-based circulating tumour DNA (ctDNA) detection is a promising monitoring tool for lymphoid malignancies. We evaluated whether the presence of ctDNA was associated with outcome after allogeneic haematopoietic stem cell transplantation (HSCT) in lymphoma patients. We studied 88 patients drawn from a phase 3 clinical trial of reduced-intensity conditioning HSCT in lymphoma. Conventional restaging and collection of peripheral blood samples occurred at pre-specified time points before and after HSCT and were assayed for ctDNA by sequencing of the immunoglobulin or T-cell receptor genes...
October 6, 2016: British Journal of Haematology
El-Mokadem Ismail, Kidd Thomas, Pratt Norman, Fleming Stewart, Nabi Ghulam
BACKGROUND: Genetic alterations on chromosome 9p, including inactivation of the tumour suppressor gene, CDKN2A, result in cellular proliferation and growth of tumours. Our aim was to use microsatellite analysis and fluorescence in situ hybridization (FISH) to characterise the architecture of this region. RESULTS: Seventy-five out of 77 clear cell renal cell cancers (tumour/normal pairs) were interpretable for LOH analysis on chromosome 9p (two tumours were excluded, as all five primers were uninformative)...
September 22, 2016: Oncotarget
Baolong Yan, Weiwei Sun, Lanzhu Yan, Liangliang Zhang, Yuan Zheng, Yuzhen Zeng, Huicong Huang, Shaohui Liang
Fork head box transcription factors subfamily O (FoxO) is regarded to be significant in cell-cycle control, cell differentiation, ageing, stress response, apoptosis, tumour formation and DNA damage repair. In the free-living nematode Caenorhabditis elegans, the FoxO transcription factor is encoded by Ce-daf-16, which is negatively regulated by insulin-like signaling (IIS) and involved in promoting dauer formation through bringing about its hundreds of downstream genes expression. In nematode parasites, orthologues of daf-16 from several species have been identified, with functions in rescue of dauer phenotypes determined in a surrogate system C...
September 9, 2016: Acta Tropica
Joonil Jung, Joon Sang Lee, Mark A Dickson, Gary K Schwartz, Axel Le Cesne, Andrea Varga, Rastilav Bahleda, Andrew J Wagner, Edwin Choy, Maja J de Jonge, Madelyn Light, Steve Rowley, Sandrine Macé, James Watters
In tumours that harbour wild-type p53, p53 protein function is frequently disabled by the mouse double minute 2 protein (MDM2, or HDM2 in humans). Multiple HDM2 antagonists are currently in clinical development. Preclinical data indicate that TP53 mutations are a possible mechanism of acquired resistance to HDM2 inhibition; however, this resistance mechanism has not been reported in patients. Utilizing liquid biopsies, here we demonstrate that TP53 mutations appear in circulating cell-free DNA obtained from patients with de-differentiated liposarcoma being treated with an inhibitor of the HDM2-p53 interaction (SAR405838)...
2016: Nature Communications
Ruben T H M Larue, Lien Van De Voorde, Maaike Berbée, Wouter J C van Elmpt, Ludwig J Dubois, Kranthi M Panth, Sarah G J A Peeters, Ann Claessens, Wendy M J Schreurs, Marius Nap, Fabiënne A R M Warmerdam, Frans L G Erdkamp, Meindert N Sosef, Philippe Lambin
BACKGROUND: Neo-adjuvant chemoradiotherapy followed by surgery is the standard treatment with curative intent for oesophageal cancer patients, with 5-year overall survival rates up to 50 %. However, patients' quality of life is severely compromised by oesophagectomy, and eventually many patients die due to metastatic disease. Most solid tumours, including oesophageal cancer, contain hypoxic regions that are more resistant to chemoradiotherapy. The hypoxia-activated prodrug evofosfamide works as a DNA-alkylating agent under these hypoxic conditions, which directly kills hypoxic cancer cells and potentially minimizes resistance to conventional therapy...
2016: BMC Cancer
Can Kockan, Faraz Hach, Iman Sarrafi, Robert H Bell, Brian McConeghy, Kevin Beja, Anne Haegert, Alexander W Wyatt, Stanislav V Volik, Kim N Chi, Colin C Collins, S Cenk Sahinalp
MOTIVATION: Successful development and application of precision oncology approaches require robust elucidation of the genomic landscape of a patient's cancer and, ideally, the ability to monitor therapy-induced genomic changes in the tumour in an inexpensive and minimally invasive manner. Thanks to recent advances in sequencing technologies, "liquid biopsy", the sampling of patient's bodily fluids such as blood and urine, is considered as one of the most promising approaches to achieve this goal...
August 16, 2016: Bioinformatics
G Gremel, R J Lee, M R Girotti, A K Mandal, S Valpione, G Garner, M Ayub, S Wood, D G Rothwell, A Fusi, A Wallace, G Brady, C Dive, N Dhomen, P Lorigan, R Marais
BACKGROUND: The application of precision medicine in oncology requires in-depth characterisation of a patient's tumours and the dynamics of their responses to treatment. PATIENTS AND METHODS: We used next-generation sequencing of circulating cell-free DNA (cfDNA) to monitor the response of a KIT p.L576P-mutant metastatic vaginal mucosal melanoma to sequential targeted, immuno- and chemotherapy. RESULTS: Despite a KIT mutation, the response to imatinib was mixed...
October 2016: Annals of Oncology: Official Journal of the European Society for Medical Oncology
Ian A Cree
The importance of RAS mutation in carcinogenesis is established, and knowledge of an individual cancer's mutation status is important for optimal treatment. Areas covered: This paper is restricted to RAS testing in cancer, and highlights papers relevant to current practice. Expert commentary: Multiple laboratory methods are available for RAS gene analysis. PCR is commonly used to determine RAS status, providing a robust and inexpensive technology for clinical use. Next generation sequencing (NGS) platforms are changing the way in which mutation status is determined, though they require considerable expertise...
October 2016: Expert Review of Molecular Diagnostics
Ismail El-Mokadem, Alison Lim, Thomas Kidd, Katherine Garret, Norman Pratt, David Batty, Stewart Fleming, Ghulam Nabi
BACKGROUND: Long-term prognostic significance of loss of heterozygosity on chromosome 9p21 for localized renal cell carcinoma following surgery remains unreported. The study assessed the frequency of deletions of different loci of chromosome 9p along with immunohistochemical profile of proteins in surgically resected renal cancer tissue and correlated this with long-term outcomes. METHODS: DNA was extracted from renal tumours and corresponding normal kidney tissues in prospectively collected samples of 108 patients who underwent surgical resection for clinically localized disease between January 2001 and December 2005, providing a minimum of 9 years follow-up for each participant...
2016: BMC Cancer
Federico Rojo, Abel González-Pérez, Jessica Furriol, Ma Jesús Nicolau, Jaime Ferrer, Octavio Burgués, MohammadA Sabbaghi, Irene González-Navarrete, Ion Cristobal, Laia Serrano, Sandra Zazo, Juan Madoz, Sonia Servitja, Ignasi Tusquets, Joan Albanell, Ana Lluch, Ana Rovira, Pilar Eroles
BACKGROUND: NF-κB signalling appears deregulated in breast tumours. The purpose of this study was to determine whether the non-canonical NF-κB pathway, is activated in oestrogen receptor positive (ER+) breast cancer, to identify any correlation between its activity and the clinico-pathological phenotype and to explore whether NF-κB2 and RelB subunits and/or any of their target genes might be used as a predictive marker. METHODS: Two independent cohorts of ER+ early breast cancer patients treated with adjuvant endocrine therapy were included in the study...
July 26, 2016: British Journal of Cancer
Puey Ling Chia, Hongdo Do, Adrienne Morey, Paul Mitchell, Alexander Dobrovic, Thomas John
AZD9291, a T790M specific epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI), has demonstrated impressive response rates in tumours harbouring the EGFR T790M resistance mutation. Emergence of resistance to AZD9291 has been shown to occur through several different mechanisms including the development of new mutations (e.g. C797S) in the EGFR tyrosine kinase domain. We studied two patients with paired tumour biopsies and blood samples pre- and post-progression on AZD9291 to explore possible resistance mechanisms...
August 2016: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
Y Ozluk, P Firat, G Yegen, J Hocaoglu, S Tas, D Yilmazbayhan
OBJECTIVE: Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) have shown benefits regarding progression-free and overall survival in patients whose tumours show EGFR mutations. Most patients' lung cancer is metastatic when detected. Small tissue samples and cytological materials are widely used in diagnosis. The aim of the present study was to compare the EGFR mutation analysis results between cytology, small biopsies and resections. METHODS: Archival material for EGFR testing was reviewed...
July 8, 2016: Cytopathology: Official Journal of the British Society for Clinical Cytology
Kjetil Søreide, Martin M Watson, Dordi Lea, Oddmund Nordgård, Jon Arne Søreide, Hanne R Hagland
BACKGROUND: More accurate predictive and prognostic biomarkers for patients with colorectal cancer (CRC) primaries or colorectal liver metastasis (CLM) are needed. Outside clinical trials, the translational integration of emerging pathways and novel techniques should facilitate exploration of biomarkers for improved staging and prognosis. METHODS: An observational study exploring predictive and prognostic biomarkers in a population-based, consecutive cohort of surgically treated colorectal cancers and resected colorectal liver metastases...
2016: Journal of Translational Medicine
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
Liam Masterson, David M Winder, Siolian L R Ball, Katie Vaughan, Martin Lehmann, Lars-Uwe Scholtz, Jane C Sterling, Holger H Sudhoff, Peter K C Goon
BACKGROUND: Human papillomavirus DNA detection in head and neck squamous cell carcinoma has been linked to improved patient prognosis. The main aims of the study was to test the hypotheses that HPV16 E6/E7 oncogene and p53 function within tumours were associated with the widely reported improved patient survival and prognosis in head and neck cancer. METHODS: HPV16 DNA, mRNA and p53 mRNA presence were analysed in a prospective study of 42 unselected HNSCC patients; correlating the data with patient age, tumour staging/grade, treatment response, disease recurrence and survival...
2016: BMC Cancer
Naoto Hadano, Yoshiaki Murakami, Kenichiro Uemura, Yasusi Hashimoto, Naru Kondo, Naoya Nakagawa, Taijiro Sueda, Eiso Hiyama
BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is frequently diagnosed at an advanced stage, leading to a poor prognosis. Therefore, interest in the development of non-invasive biomarkers for prognostic prediction has grown rapidly. Here, we assessed the clinical implications of v-Ki-ras2 kirsten rat sarcoma viral oncogene homolog (KRAS)-mutated circulating tumour DNA (ctDNA) as a useful surrogate biomarker in patients with resectable PDAC. METHODS: We used droplet digital polymerase chain reaction to detect rare mutant tumour-derived KRAS genes in plasma cell-free DNA (cfDNA) as ctDNA...
June 28, 2016: British Journal of Cancer
Michael S Lee, Elizabeth J McGuffey, Jeffrey S Morris, Ganiraju Manyam, Veerabahdran Baladandayuthapani, Wei Wei, Van K Morris, Michael J Overman, Dipen M Maru, Zhi-Qin Jiang, Stanley R Hamilton, Scott Kopetz
BACKGROUND: High EREG and AREG expression, and left-sided primary tumours are associated with superior efficacy of anti-epidermal growth factor receptor (EGFR) therapy in metastatic colorectal cancer (CRC), but a unifying explanation of these findings is lacking. METHODS: RNA-seq, gene expression arrays, and DNA methylation profiling were completed on 179 CRC tumours. Results were validated using independent The Cancer Genome Atlas data sets. An independent cohort of 198 KRAS wild-type metastatic CRC tumours was tested for CpG island methylator phenotype (CIMP) status, and progression-free survival (PFS) with the first anti-EGFR regimen was retrospectively determined...
June 14, 2016: British Journal of Cancer
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