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Cecily P Vaughn, José Luis Costa, Harriet E Feilotter, Rosella Petraroli, Varun Bagai, Anna Maria Rachiglio, Federica Zito Marino, Bastiaan Tops, Henriette M Kurth, Kazuko Sakai, Andrea Mafficini, Roy R L Bastien, Anne Reiman, Delphine Le Corre, Alexander Boag, Susan Crocker, Michel Bihl, Astrid Hirschmann, Aldo Scarpa, José Carlos Machado, Hélène Blons, Orla Sheils, Kelli Bramlett, Marjolijn J L Ligtenberg, Ian A Cree, Nicola Normanno, Kazuto Nishio, Pierre Laurent-Puig
BACKGROUND: Gene fusion events resulting from chromosomal rearrangements play an important role in initiation of lung adenocarcinoma. The recent association of four oncogenic driver genes, ALK, ROS1, RET, and NTRK1, as lung tumor predictive biomarkers has increased the need for development of up-to-date technologies for detection of these biomarkers in limited amounts of material. METHODS: We describe here a multi-institutional study using the Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel to interrogate previously characterized lung tumor samples...
August 16, 2018: BMC Cancer
Ahn R Lee, Yu Gan, Yuxin Tang, Xuesen Dong
BACKGROUND: Prostate adenocarcinoma (AdPC) cells can undergo lineage switching to neuroendocrine cells and develop into therapy-resistant neuroendocrine prostate cancer (NEPC). While genomic/epigenetic alterations are shown to induce neuroendocrine differentiation via an intermediate stem-like state, RNA splicing factor SRRM4 can transform AdPC cells into NEPC xenografts through a direct neuroendocrine transdifferentiation mechanism. Whether SRRM4 can also regulate a stem-cell gene network for NEPC development remains unclear...
August 10, 2018: EBioMedicine
Lisett Contreras, Ruben I Calderon, Armando Varela-Ramirez, Hong-Yu Zhang, Yuan Quan, Umashankar Das, Jonathan R Dimmock, Rachid Skouta, Renato J Aguilera
PURPOSE: Previously, compounds containing a piperidone structure have been shown to be highly cytotoxic to cancer cells. Recently, we found that the piperidone compound P2 exhibits a potent anti-neoplastic activity against human breast cancer-derived cells. Here, we aimed to evaluate two piperidone compounds, P1 and P2, for their potential anti-neoplastic activity against human leukemia/lymphoma-derived cells. METHODS: Cytotoxicity and apoptosis induction were evaluated using MTS, annexin V-FITC/PI and mitochondrial membrane potential polychromatic assays to confirm the mode of action of the piperidone compounds...
August 7, 2018: Cellular Oncology (Dordrecht)
Young Saing Kim, Kyung Kim, Ghee-Young Kwon, Su Jin Lee, Se Hoon Park
BACKGROUND: Recent studies suggest that FGFR3 is a potential therapeutic target in urothelial carcinoma (UC). The purpose of this study was to evaluate the rates and types of FGFR3 aberrations in patients with muscle-invasive UC who received radical resection. METHODS: We analyzed surgical tumor samples from 74 UC patients who had received radical cystectomy (n = 40) or ureteronephrectomy (n = 34). Ion AmpliSeq Cancer Hotspot Panel v2 and nCounter Copy Number Variation Assay were used to detect FGFR3 aberrations...
July 31, 2018: BMC Urology
Vania Pereira, Antonio Longobardi, Claus Børsting
Massively parallel sequencing offers a fast and cost-effective method for sequencing of the whole mtDNA genome. The Precision ID mtDNA Whole Genome Panel amplifies the entire mtDNA genome in two multiplex PCRs with 81 primer sets using the Ion AmpliSeq™ technology. In this study, the performance of the panel was evaluated by testing different amplification methods (two-in-one or conservative), the number of PCR cycles (21, 23, and 25), and different reaction volumes (recommended volume or half-volume). Furthermore, a dilution series, controlled mtDNA mixtures, and casework samples were also sequenced...
July 30, 2018: Electrophoresis
Siti Syazani Suhaimi, Nurul-Syakima Ab Mutalib, Sheau S Khor, Reena Rahayu Md Zain, Saiful Effendi Syafruddin, Nadiah Abu, Ahmad Zailani Hatta Mohd Dali, Rahman Jamal
Endometrioid endometrial cancer (EEC) is the commonest form of endometrial cancer and can be divided into estrogen receptor (ER) positive and negative subtypes. The mutational profiles of EEC have been shown to aid in tailoring treatment; however, little is known about the differences between the gene mutation profiles between these two subtypes. This study aims to investigate the gene mutation profile in ER positive and negative EEC, and to further elucidate the role of WHSC1 mutations in this cancer. EEC and normal endometrial tissues were obtained from 29 patients and subjected to next-generation sequencing (NGS) using Ion Ampliseq Comprehensive Cancer PanelTM targeting 409 cancer related...
2018: Frontiers in Pharmacology
Julie A Vendrell, Paul Vilquin, Marion Larrieux, Charles Van Goethem, Jérôme Solassol
The recent deployment of next-generation sequencing approaches in routine laboratory analysis has considerably modified the landscape of BRCA1 and BRCA2 germline alteration detection in patients with a high risk of developing breast and/or ovarian cancer. Several commercial multiplex amplicon-based panels and bioinformatics solutions are currently available. In this study, we evaluated the combinations of several BRCA testing assays and bioinformatics solutions for the identification of single nucleotide variants, insertion/deletion variants (indels), and copy number variations (CNVs)...
July 25, 2018: Journal of Molecular Diagnostics: JMD
I Eguren-Santamaria, R Sanchez-Bayona, A Patiño-Garcia, Ignacio Gil-Bazo, J M Lopez-Picazo
BACKGROUND: The differential diagnosis between multiple primary lung cancer (MPLC) and advanced lung cancer has traditionally relied on conventional radiology and pathology. However, the outcomes of traditional diagnostic workup are often limited, and staging is uncertain. Increasing evidence suggests that next-generation sequencing (NGS) techniques offer the possibility of comparing multiple tumors on a genomic level. OBJECTIVES: The objective of this study is to assess the clinical impact utility of targeted sequencing in patients presenting with multiple synchronous or metachronous lung tumors...
August 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
Konstantinos Linos, Laura J Tafe
BACKGROUND: Isocitrate dehydrogenase 1 (IDH1) is a metabolic enzyme that converts isocitrate to α-ketoglutarate. IDH1 mutations are associated with the accumulation of the oncometabolite D-2-hydroxyglutarate, which acts as an epigenetic modifier, and the development of multiple malignancies. METHODS: From May 2013 - June 2017, 252 melanoma samples from 214 patients with advanced or distant metastatic disease were tested for somatic mutations with the 50 gene AmpliSeq v2 Cancer Hotspot Panel...
July 12, 2018: Histopathology
Sebastian Zięba, Artur Kowalik, Kamil Zalewski, Natalia Rusetska, Krzysztof Goryca, Agata Piaścik, Marcin Misiek, Elwira Bakuła-Zalewska, Janusz Kopczyński, Kamil Kowalski, Jakub Radziszewski, Mariusz Bidziński, Stanisław Góźdź, Magdalena Kowalewska
BACKGROUND: Vulvar squamous cell carcinoma (VSCC) constitutes over 90% of vulvar cancer. Its pathogenesis can follow two different pathways; high risk human papillomavirus (hrHPV)-dependent and HPV-independent. Due to the rarity of VSCC, molecular mechanisms underlying VSCC development remain largely unknown. The study aimed to identify pathogenic mutations implicated in the two pathways of VSCC development. METHODS: Using next generation sequencing, 81 VSCC tumors, 52 hrHPV(+) and 29 hrHPV(-), were screened for hotspot mutations in 50 genes covered by the Ion AmpliSeq Cancer Hotspot Panel v2 Kit (Thermo Fisher Scientific)...
July 3, 2018: Gynecologic Oncology
Benjamin Gollasch, Oskar Wischnewski, Birgit Rudolph, Yoland-Marie Anistan, Friedrich C Luft, Maik Gollasch
We present a 42-year-old man with a BMI of 32, who was referred because of proteinuria and decreased renal function. We were impressed by his markedly muscular physique. A renal biopsy was performed, which showed focal segmental glomerular sclerosis (FSGS). Is this patient merely an obese person with FSGS or is something else going on here? We performed extensive clinical and laboratory examinations, genetic testing, and anthropometric data monitoring over time. We transferred our methodology for routine FSGS mutation screening (Sanger sequencing) to the Ion Torrent PGM platform with a new custom-targeted NGS gene panel (Ion Ampliseq FSGS panel) and tested the performance of the system in two cohorts of patients with FSGS...
May 2018: Case Reports in Nephrology and Dialysis
Cham Han Lee, Soo Jeong Lee, Sung Ho Choi, Sei Hyun Ahn, Byung Ho Son, Jong Won Lee, Jong Han Yu, Nak-Jung Kwon, Woo Chung Lee, Kap-Seok Yang, Dong Hyoung Lee, Du Yeol Han, Mi So Choi, Pyeong-Soo Park, Hyun Kyung Lee, Myoung Shin Kim, Jinseon Lee, Byung Hee Jeon
Liquid biopsy using circulating tumor cells (CTCs) is a noninvasive and repeatable procedure, and is therefore useful for molecular assays. However, the rarity of CTCs remains a challenge. To overcome this issue, our group developed a novel technology for the isolation of CTCs on the basis of cell size difference. The present study isolated CTCs from patients with breast cancer using this method, and then used these cells for cancer gene panel analysis. Blood samples from eight patients with breast cancer were collected, and CTCs were enriched using size-based filtration...
July 2018: Oncology Letters
Mert Karakaya, Markus Storbeck, Eike A Strathmann, Andrea Delle Vedove, Irmgard Hölker, Janine Altmueller, Leyla Naghiyeva, Lea Schmitz-Steinkrüger, Katharina Vezyroglou, Susanne Motameny, Salem Alawbathani, Holger Thiele, Ayse Ipek Polat, Derya Okur, Reza Boostani, Ehsan Ghayoor Karimiani, Gilbert Wunderlich, Didem Ardicli, Haluk Topaloglu, Janbernd Kirschner, Bertold Schrank, Reza Maroofian, Olafur Magnusson, Uluc Yis, Peter Nürnberg, Raoul Heller, Brunhilde Wirth
Spinal muscular atrophies (SMAs) are a heterogeneous group of disorders characterized by muscular atrophy, weakness, and hypotonia due to suspected lower motor neuron degeneration (LMND). In a large cohort of 3,465 individuals suspected with SMA submitted for SMN1 testing to our routine diagnostic laboratory, 48.8% carried a homozygous SMN1 deletion, 2.8% a subtle mutation, and an SMN1 deletion, whereas 48.4% remained undiagnosed. Recently, several other genes implicated in SMA/LMND have been reported. Despite several efforts to establish a diagnostic algorithm for non-5q-SMA (SMA without deletion or point mutations in SMN1 [5q13...
June 2, 2018: Human Mutation
Antoine Legras, Anne Tallet, Audrey Didelot, Aurélie Cazes, Claire Danel, Angela Hin, Raphaël Borie, Bruno Crestani, Yves Castier, Patrick Bagan, Françoise Le Pimpec-Barthes, Marc Riquet, Hélène Blons, Pierre Mordant
Background: Unicentric mediastinal Castleman disease (CD) is a rare condition, poorly characterized due to the small number of cases and the absence of genomic study. We analyzed clinical, radiological, histological and genomic patterns associated with mediastinal CD in a substantial case series. Methods: We retrospectively reviewed cases of unicentric mediastinal CD managed in 2 French thoracic surgery departments between 1988 and 2012. Clinical, radiological, surgical and pathological data were recorded...
April 2018: Journal of Thoracic Disease
Audrey C Papp, Abul K Azad, Maciej Pietrzak, Amanda Williams, Samuel K Handelman, Robert P Igo, Catherine M Stein, Katherine Hartmann, Larry S Schlesinger, Wolfgang Sadee
Human alveolar macrophages (HAM) are primary bacterial niche and immune response cells during Mycobacterium tuberculosis (M.tb) infection, and human blood monocyte-derived macrophages (MDM) are a model for investigating M.tb-macrophage interactions. Here, we use a targeted RNA-Seq method to measure transcriptome-wide changes in RNA expression patterns of freshly obtained HAM (used within 6 h) and 6 day cultured MDM upon M.tb infection over time (2, 24 and 72 h), in both uninfected and infected cells from three donors each...
2018: PloS One
Duarte Mendes Oliveira, Carmelo Laudanna, Simona Migliozzi, Pietro Zoppoli, Gianluca Santamaria, Katia Grillone, Laura Elia, Chiara Mignogna, Flavia Biamonte, Rosario Sacco, Francesco Corcione, Giuseppe Viglietto, Donatella Malanga, Antonia Rizzuto
The objective of this study was to investigate the mutational profiles of cancers arising in different colon segments. To this aim, we have analyzed 37 colon cancer samples by use of the Ion AmpliSeq™ Comprehensive Cancer Panel. Overall, we have found 307 mutated genes, most of which already implicated in the development of colon cancer. Among these, 15 genes were mutated in tumors originating in all six colon segments and were defined "common genes" (i.e. APC, PIK3CA, TP53) whereas 13 genes were preferentially mutated in tumors originating only in specific colon segments and were defined "site-associated genes" (i...
May 8, 2018: Oncotarget
Abeer E Mustafa, Tariq Faquih, Batoul Baz, Rana Kattan, Abdulelah Al-Issa, Asma I Tahir, Faiqa Imtiaz, Khushnooda Ramzan, Moeenaldeen Al-Sayed, Mohammed Alowain, Zuhair Al-Hassnan, Hamad Al-Zaidan, Mohamed Abouelhoda, Bashayer R Al-Mubarak, Nada A Al Tassan
Quick and accurate molecular testing is necessary for the better management of many inherited diseases. Recent technological advances in various next generation sequencing (NGS) platforms, such as target panel-based sequencing, has enabled comprehensive, quick, and precise interrogation of many genetic variations. As a result, these technologies have become a valuable tool for gene discovery and for clinical diagnostics. The AmpliSeq Inherited Disease Panel (IDP) consists of 328 genes underlying more than 700 inherited diseases...
May 22, 2018: Genes
Shari Javadiyan, Sionne E M Lucas, Dechen Wangmo, Meng Ngy, Kapila Edussuriya, Jamie E Craig, Adam Rudkin, Robert Casson, Dinesh Selva, Shiwani Sharma, Karen M Lower, James Meucke, Kathryn P Burdon
BACKGROUND: Pediatric cataract is an important cause of blindness and visual impairment in children. A large proportion of pediatric cataracts are inherited, and many genes have been described for this heterogeneous Mendelian disease. Surveys of schools for the blind in Bhutan, Cambodia, and Sri Lanka have identified many children with this condition and we aimed to identify the genetic causes of inherited cataract in these populations. METHODS: We screened, in parallel, 51 causative genes for inherited cataracts in 33 probands by Ampliseq enrichment and sequencing on an Ion Torrent PGM...
May 16, 2018: Molecular Genetics & Genomic Medicine
Nicky D'Haene, Quitterie Fontanges, Nancy De Nève, Oriane Blanchard, Barbara Melendez, Monique Delos, Marie-Françoise Dehou, Calliope Maris, Nathalie Nagy, Emmanuel Rousseau, Josse Vandenhove, André Gilles, Carine De Prez, Laurine Verset, Marie-Paule Van Craynest, Pieter Demetter, Jean-Luc Van Laethem, Isabelle Salmon, Marie Le Mercier
International guidelines made RAS (KRAS and NRAS) status a prerequisite for the use of anti-EGFR agents for metastatic colorectal cancer (CRC) patients. Daily, new data emerges on the theranostic and prognostic role of molecular biomarkers; this is a strong incentive for a validated, sensitive, and broadly available molecular screening test. Next-generation sequencing (NGS) has begun to supplant other technologies for genomic profiling. We report here our 2 years of clinical practice using NGS results to guide therapeutic decisions...
April 17, 2018: Oncotarget
Laura N Toth, Francine B de Abreu, Laura J Tafe
Isocitrate dehydrogenase 1 and 2 (IDH1/2) are important metabolic enzymes that convert isocitrate to α-ketoglutarate. IDH1/2 mutations are associated with the development of multiple malignancies. In this study, we examine the prevalence and features of non-small cell lung cancers (NSCLC) with IDH1/2 mutations. From May 2013 - March 2017, 800 lung cancer samples were successfully sequenced for somatic mutations on the Ion Torrent PGM with the 50 gene AmpliSeq Cancer Hotspot Panel v2 on the Ion Torrent PGM (318 chip)...
April 30, 2018: Human Pathology
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