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Cancer Next Generation Sequencing

Pascale Tomasini, Celine Mascaux, Kevin Jao, Catherine Labbe, Suzanne Kamel-Reid, Tracy Stockley, David M Hwang, Natasha B Leighl, Geoffrey Liu, Penelope A Bradbury, Melania Pintilie, Ming-Sound Tsao, Frances A Shepherd
BACKGROUND: KRAS and TP53 are common mutations in non-small-cell lung cancer (NSCLC). The Lung Adjuvant Cisplatin Evaluation Biological Program group found adjuvant chemotherapy to be deleterious in patients with coexisting KRAS/TP53 mutations. PATIENTS AND METHODS: To validate these results, patients with NSCLC tested for KRAS and TP53 mutations and receiving chemotherapy for any stage NSCLC were selected. Mutation status was analyzed using next generation sequencing (Illumina) or multiplex recurrent mutation detection (MassARRAY, Agena Biosciences) assays, and was correlated with clinical and demographic data...
December 19, 2018: Clinical Lung Cancer
Zhen Wu, Zhen Yang, Chun Sun Li, Wei Zhao, Zhi Xin Liang, Yu Dai, Qiang Zhu, Kai Ling Miao, Dong Hua Cui, Liang An Chen
Liquid biopsy has provided an efficient way for detection of gene alterations in advanced non-small-cell lung cancer (NSCLC). However, the correlation between systematic determination of somatic genomic alterations in liquid biopsy and tumor biopsy still remained unclear, and the concordance rate between cell-free DNA (cfDNA) and matched tumor tissue DNA needs to be increased. A prospective study was performed to detect differences in genetic profiles of cfDNA in sputum, plasma, urine, and tumor tissue from 50 advanced NSCLC patients in parallel by the same next-generation sequencing (NGS) platform...
February 14, 2019: Cancer Medicine
Yasmin Aghajan, Denise M Malicki, Michael L Levy, John Ross Crawford
Paediatric high-grade gliomas, including glioblastoma and anaplastic astrocytoma, make up 8%-12% of paediatric central nervous system tumours 1 and have poor prognosis, with 2-year survival less than 30% 2 and overall survival less than 10%. The only known prognostic factors in this population include extent of resection and tumour histological grade. We present the case of a 9-year-old boy with disseminated anaplastic astrocytoma treated with subtotal resection, craniospinal radiation and temozolomide, with 8-year survival despite metastatic disease at presentation and subtotal resection...
February 13, 2019: BMJ Case Reports
Z Pavelka, K Zitterbart, H Nosková, V Bajčiová, O Slabý, J Štěrba
BACKGROUND: Individuals with constitutional mismatch repair-deficiency syndrome (CMMR-D) are characterised by early occurrence of colon cancer, haematological malignancies, and brain tumors (malignant gliomas, high-grade gliomas) in childhood, adolescence, and early adulthood. High mutational tumor burden is typical of glioblastoma in CMMR-D patients and could be a reason why this type of glioblastoma responds well to immunotherapies, including those that employ checkpoint inhibitors...
2019: Klinická Onkologie: Casopis Ceské a Slovenské Onkologické Spolecnosti
Samantha X Y Wang, Bing M Zhang, Heather A Wakelee, Michael Z Koontz, MingGui Pan, Maximilian Diehn, Christian A Kunder, Joel W Neal
The mesenchymal-to-epithelial transition (MET) gene is altered and becomes a driver mutation in up to 5% of non-small-cell lung cancer (NSCLC). We report our institutional experience treating patients with MET exon 14 skipping (METex14) mutations, including responses to the MET inhibitors crizotinib and cabozantinib. We identified cases of NSCLC with METex14 mutations using an institutionally developed or commercial next-generation sequencing assay. We assessed patient and disease characteristics by retrospective chart review...
February 12, 2019: Anti-cancer Drugs
Jerzy Lasota, Artur Kowalik, Anna Felisiak-Golabek, Sebastian Zięba, Piotr Waloszczyk, Marek Masiuk, Jaroslaw Wejman, Justyna Szumilo, Markku Miettinen
Primary malignant melanoma of esophagus is very rare, and its clinicopathologic and genetic features have not been extensively investigated. In this study, 20 tumors from 14 male and 6 female patients (40-79 years old) were evaluated. Dysphagia, chest pain, and weight loss were frequent symptoms. Thirteen melanomas, including two with multiple lesions, involved the distal third of esophagus. The median tumor diameter was 6 cm. Epithelioid morphology, moderate atypia, and pigmentation were typical findings...
February 13, 2019: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
Mansour Alsaleem, Michael S Toss, Chitra Joseph, Mohammed Aleskandarany, Sasagu Kurozumi, Ibrahim Alshankyty, Angela Ogden, Padmashree C G Rida, Ian O Ellis, Ritu Aneja, Andrew R Green, Nigel P Mongan, Emad A Rakha
E-cadherin is a tumor suppressor gene in invasive lobular breast cancer. However, a proportion of high-grade ductal carcinoma shows reduced/loss of E-cadherin. In this study, we assessed the underlying mechanisms and molecular implications of E-cadherin loss in invasive ductal carcinoma. This study used large, well-characterized cohorts of early-stage breast cancer-evaluated E-cadherin expression via various platforms including immunohistochemistry, microarray analysis using Illumina HT-12 v3, copy number analysis using Affymetrix SNP 6...
February 13, 2019: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
Nahyeon Kang, Su Yeon Choi, Bit Na Kim, Chang Dong Yeo, Chan Kwon Park, Young Kyoon Kim, Tae-Jung Kim, Seong-Beom Lee, Sug Hyung Lee, Jong Y Park, Mi Sun Park, Hyeon Woo Yim, Seung Joon Kim
BACKGROUND: A hypoxic microenvironment leads to an increase in the invasiveness and the metastatic potential of cancer cells within tumors via the epithelial-mesenchymal transition (EMT) and cancer stemness acquisition. However, hypoxia-induced changes in the expression and function of candidate stem cell markers and their possible molecular mechanism is still not understood. METHODS: Lung cell lines were analyzed in normoxic or hypoxic conditions. For screening among the stem cell markers, a transcriptome analysis using next-generation sequencing was performed...
February 13, 2019: BMC Cancer
Ryan Barrett, Cynthia L Neben, Anjali D Zimmer, Gilad Mishne, Wendy McKennon, Alicia Y Zhou, Jeremy Ginsberg
Next generation sequencing multi-gene panels have greatly improved the diagnostic yield and cost effectiveness of genetic testing and are rapidly being integrated into the clinic for hereditary cancer risk. With this technology comes a dramatic increase in the volume, type and complexity of data. This invaluable data though is too often buried or inaccessible to researchers, especially to those without strong analytical or programming skills. To effectively share comprehensive, integrated genotypic-phenotypic data, we built Color Data, a publicly available, cloud-based database that supports broad access and data literacy...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Takashi Yoshida, Tatsuya Yamaguchi, Shinya Maekawa, Shinichi Takano, Toru Kuno, Keisuke Tanaka, Fumihiko Iwamoto, Yuya Tsukui, Shoji Kobayashi, Yukiko Asakawa, Hiroko Shindo, Mitsuharu Fukasawa, Yasuhiro Nakayama, Taisuke Inoue, Tomoyoshi Uetake, Masahiko Ohtaka, Tadashi Sato, Kunio Mochizuki, Nobuyuki Enomoto
BACKGROUND AND AIMS: The recent advancement of next-generation sequencing (NGS) has enabled the identification of cancer-related somatic aberrations in advanced gastric cancer. However, these remain unclear in early gastric cancers, especially in intramucosal gastric cancers. PATIENTS AND METHODS: Thirty-one well-differentiated (tub1) intramucosal gastric cancers obtained by endoscopic submucosal dissection (ESD) from 29 patients were analyzed. After precise collection of tumors and non-tumors from formalin-fixed paraffin-embedded tissues using laser-captured microdissection (LCM), target sequencing analysis of 50 cancer-related genes was performed using an Ion-Proton sequencer...
February 11, 2019: Gastric Cancer
Mengxi Ge, Qiong Zhan, Zhenzhen Zhang, Xiaoyu Ji, Xinli Zhou, Ruofan Huang, Xiaohua Liang
BACKGROUND: The nucleic acid mutation status in intracranial metastasis is markedly significant clinically. The goal of the current study was to explore whether the tumor-associated mutations can be detected by different next-generation sequencing (NGS) pipelines in paired cerebrospinal fluid (CSF) and plasma samples from lung adenocarcinoma (LAC) patients with leptomeningeal metastases (LM). METHODS: Paired CSF cell free DNA (cfDNA), CSF cells, plasma and formalin-fixed and paraffin-embedded (FFPE) samples of primary tumors were collected from 29 LAC patients with LM to detect the mutations by different NGS pipelines...
February 12, 2019: BMC Cancer
Hui-Wen Tseng, Sung-Chou Li, Kuo-Wang Tsai
Melanoma is a highly aggressive cancer with high mortality in advanced stages.Metformin is an oral biguanide drug used for diabetes and has demonstrated positive effects oncancer prevention and treatment. Herein, we found that metformin significantly suppressedmelanoma cancer cell motility and growth through inducing cell cycle arrest at the G2/M phase andpromoting cell apoptosis. Using the next-generation sequencing approach, we identified threeupregulated microRNAs (miRNA; miR-192-5p, miR-584-3p, and miR-1246) in melanoma cellstreated with metformin...
February 11, 2019: Cancers
Sophia R Chaudhry, Michael A Tainsky
Molecular genetic testing provides the capability for personalized prediction, diagnosis, and pharmacological treatments of disease and disorders. Variant assessment of next-generation sequencing (NGS) is a crucial component of genetic testing for clinicians to counsel patients on risk and management. The iVariantGuide application is a dynamic Web-based application made for the tertiary analysis of NGS. Along with variant assessment, iVariantGuide provides a unique interactive pathway impact analysis of genetic variants, as well as a unique Gene Ontology (GO) analysis...
February 12, 2019: Current Protocols in Bioinformatics
Luke K Genutis, Jerneja Tomsic, Ralf Bundschuh, Pamela Brock, Michelle D Williams, Sameek Roychowdhury, Julie W Reeser, Wendy L Frankel, Mohammed Alsomali, Mark J Routbort, Russell R Broaddus, Paul E Wakely, John E Phay, Christopher J Walker, Albert de la Chapelle
BACKGROUND: Inactivation of DNA mismatch repair (MMR) and the resulting microsatellite instability (MSI) are frequently observed in endometrial, stomach and colorectal cancers as well as more rarely in other solid tumor types. The prevalence of MSI in thyroid cancer has not been explored in-depth, although recent studies utilizing data from large cancer sequencing efforts such as The Cancer Genome Atlas indicate MSI is absent or at least very rare in the most common and most well-studied histologic subtype, papillary carcinoma...
February 12, 2019: Thyroid: Official Journal of the American Thyroid Association
Tihana Ibrahimpasic, Ronald Ghossein, Jatin P Shah, Ian Ganly
BACKGROUND: Poorly differentiated thyroid cancer (PDTC) is a rare but clinically highly significant entity because it accounts for most fatalities from non-anaplastic follicular cell-derived thyroid cancer. Due to the relative rarity of the disease and heterogeneous diagnostic criteria, studies on PDTC have been limited. In light of the evolution of ultra deep next-generation sequencing (NGS) technologies and through correlation of clinico-pathological and genomic characteristics of PDTC, an improved understanding of the biology of PDTC has been facilitated...
February 12, 2019: Thyroid: Official Journal of the American Thyroid Association
Jian Wu, Wei Dai, Lin Wu, Weiwei Li, Xinyi Xia, Jinke Wang
Cell free DNA (cfDNA) in human plasma carries abundant information, which has therefore been the key sample for non-invasive prenatal testing (NIPT) and liquid biopsy. Especially by using the rapidly developed next-generation sequencing (NGS) techniques, the genetic and epigenetic information embedded in cfDNA has been effectively and extensively decoded. In this process, a key step is to construct the NGS library. Due to its high degradation, the single strand-based method was reported to be more qualified to construct the NGS library of cfDNA...
February 12, 2019: International Journal of Cancer. Journal International du Cancer
Zhicheng Huang, Zhiqiang Sun, Xueying Zhang, Kai Niu, Ying Wang, Jun Zheng, Hang Li, Ying Liu
PIEZO channels involve in wound sealing, cell  proliferation in many cell types. Recent study in lung cancer by using next generation sequencing analysis has indicated that PIEZOs' functions were implicated in LC development. However, the expression and role of PIEZO channels in non-small cell lung cancer (NSCLC) progression remain elusive. In current study, we investigated the gene expression and alteration frequency in human NSCLC tissue, accessed the prognostic roles of PIEZO channels in NSCLC patients, and further studied the effect of PIEZOs in NSCLC cells proliferation and tumor growth in vivo...
February 11, 2019: Bioscience Reports
Olga D'Almeida, Omar Mothar, Esther Apraku Bondzie, Yolande Lieumo, Laure Tagne, Sumeet Gupta, Thomas Volkert, Stuart Levine, Jean-Bosco Tagne
BACKGROUND: MicroRNAs are noncoding RNA molecules of ~ 22 nucleotides with diagnostic and therapeutic action [Curr Drug Targets, 2015. 16(12): p. 1381-403], affecting the expression of mRNAs involved in invasion, migration, and development [Oncotarget, 2015. 6(9): p. 6472-98, Cancer Manag Res, 2014. 6: p. 205-16]. miR-200c is part of the miR-200c/141 cluster on chromosome 12p13. Its mechanism of action when encapsulated is critical in lung cancer when patients express changes in miRNAs...
February 11, 2019: BMC Cancer
Guanggui Ding, Jian Wang, Peikun Ding, Yuxin Wen, Lin Yang
Patients with non-small cell lung cancer (NSCLC) harboring MET exon 14 skipping can benefit from crizotinib treatment. Currently, the main resistance mechanisms to crizotinib are MET D1228N and Y1230C mutations. We reported a case of a Chinese NSCLC patient with MET exon 14 skipping detected by targeted next-generation sequencing (NGS) achieved clinical and imaging remission after crizotinib treatment. Then, amplification of multiple genes such as erb-b2 receptor tyrosine kinase 2 (HER2) was detected when disease progressed, indicating novel resistance mechanisms to crizotinib...
February 11, 2019: Cancer Biology & Therapy
Maria Maddalena Simile, Paola Bagella, Gianpaolo Vidili, Angela Spanu, Roberto Manetti, Maria Antonietta Seddaiu, Sergio Babudieri, Giordano Madeddu, Pier Andrea Serra, Matteo Altana, Panagiotis Paliogiannis
Cholangiocarcinoma (CCA) is a highly-aggressive malignancy arising from the biliary tree, characterized by a steady increase in incidence globally and a high mortality rate. Most CCAs are diagnosed in the advanced and metastatic phases of the disease, due to the paucity of signs and symptoms in the early stages. This fact, along with the poor results of the local and systemic therapies currently employed, is responsible for the poor outcome of CCA patients and strongly supports the need for novel therapeutic agents and strategies...
February 8, 2019: Medicina
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