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Next generation sequencing

Musaffe Tuna, Christopher I Amos
Approximately 18% of all human cancers have a viral etiology, and human papillomavirus (HPV) has been identified as one of the most prevalent viruses that plays causative role in nearly all cervical cancers and, in addition, in subset of head and neck, anal, penile and vulvar cancers. The recent introduction of next generation sequencing (NGS) and other 'omics' approaches have resulted in comprehensive knowledge on the pathogenesis of HPV-driven tumors. Specifically, these approaches have provided detailed information on genomic HPV integration sites, disrupted genes and pathways, and common and distinct genetic and epigenetic alterations in different human HPV-associated cancers...
October 23, 2016: Oncotarget
Francis B Panosyan, Rabi Tawil, David N Herrmann
INTRODUCTION: Episodic muscle weakness is the hallmark of a heterogeneous group of disorders known as periodic paralysis. A majority are due to single nucleotide mutations causing membrane depolarization. METHODS: We report 2 family members with chronic, slowly progressive, distal axonal neuropathy or Charcot-Marie-Tooth disease type 2 (CMT2) and episodic weakness resembling periodic paralysis. RESULTS: Next generation sequencing (NGS) identified a mitochondrial MT-ATP6 mutation m...
October 26, 2016: Muscle & Nerve
Tracy L Stockley, Amit M Oza, Hal K Berman, Natasha B Leighl, Jennifer J Knox, Frances A Shepherd, Eric X Chen, Monika K Krzyzanowska, Neesha Dhani, Anthony M Joshua, Ming-Sound Tsao, Stefano Serra, Blaise Clarke, Michael H Roehrl, Tong Zhang, Mahadeo A Sukhai, Nadia Califaretti, Mateya Trinkaus, Patricia Shaw, Theodorus van der Kwast, Lisa Wang, Carl Virtanen, Raymond H Kim, Albiruni R A Razak, Aaron R Hansen, Celeste Yu, Trevor J Pugh, Suzanne Kamel-Reid, Lillian L Siu, Philippe L Bedard
BACKGROUND: The clinical utility of molecular profiling of tumor tissue to guide treatment of patients with advanced solid tumors is unknown. Our objectives were to evaluate the frequency of genomic alterations, clinical "actionability" of somatic variants, enrollment in mutation-targeted or other clinical trials, and outcome of molecular profiling for advanced solid tumor patients at the Princess Margaret Cancer Centre (PM). METHODS: Patients with advanced solid tumors aged ≥18 years, good performance status, and archival tumor tissue available were prospectively consented...
October 25, 2016: Genome Medicine
André E R Soares, Ben J Novak, James Haile, Tim H Heupink, Jon Fjeldså, M Thomas P Gilbert, Hendrik Poinar, George M Church, Beth Shapiro
BACKGROUND: Pigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the nature and timing of the group's evolutionary radiation remains poorly resolved, despite recent advances in DNA sequencing and assembly and the growing database of pigeon mitochondrial genomes. One challenge has been to generate comparative data from the large number of extinct pigeon lineages, some of which are morphologically unique and therefore difficult to place in a phylogenetic context...
October 26, 2016: BMC Evolutionary Biology
Meiling Jin, Yuansheng Xie, Zhiqiang Chen, Yujie Liao, Zuoxiang Li, Panpan Hu, Yan Qi, Zhiwei Yin, Qinggang Li, Ping Fu, Xiangmei Chen
Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disorder mainly caused by mutation in PKD1/PKD2. However, ethnic differences in mutations, the association between mutation genotype/clinical phenotype, and the clinical applicable value of mutation detection are poorly understood. We made systematically analysis of Chinese ADPKD patients based on a next-generation sequencing platform. Among 148 ADPKD patients enrolled, 108 mutations were detected in 127 patients (85.8%)...
October 26, 2016: Scientific Reports
Yoichi Iwafuchi, Tetsuo Morioka, Yuko Oyama, Kandai Nozu, Kazumoto Iijima, Ichiei Narita
Many types of inherited renal diseases have ocular features that occasionally support a diagnosis. The following study describes an unusual example of a 40-year-old woman with granular corneal dystrophy type II complicated by renal involvement. These two conditions may coincidentally coexist; however, there are some reports that demonstrate an association between renal involvement and granular corneal dystrophy type II. Granular corneal dystrophy type II is caused by a mutation in the transforming growth factor-β-induced (TGFBI) gene...
September 2016: Case Reports in Nephrology and Dialysis
Daniel Wai-Hung Ho, Regina Cheuk-Lam Lo, Lo-Kong Chan, Irene Oi-Lin Ng
The pathogenesis of hepatocellular carcinoma (HCC) is a multistep process involving the progressive accumulation of molecular alterations pinpointing different molecular and cellular events. The next-generation sequencing technology is facilitating the global and systematic evaluation of molecular landscapes in HCC. There is emerging evidence supporting the importance of cancer metabolism and tumor microenvironment in providing a favorable and supportive niche to expedite HCC development. Moreover, recent studies have identified distinct surface markers of cancer stem cell (CSC) in HCC, and they also put forward the profound involvement of altered signaling pathways and epigenetic modifications in CSCs, in addition to the concomitant drug resistance and metastasis...
October 2016: Liver Cancer
Joon Ha Lee, In-Woo Kim, Mi-Ae Kim, Mi-Young Ahn, Eun-Young Yun, Jae Sam Hwang
In a previous study, we analyzed the transcriptome of Scolopendra subspinipes mutilans using next generation sequencing technology and identified several antimicrobial peptide candidates. One of peptides, scolopendrasin V, was selected based on the physicochemical properties of antimicrobial peptides using a bioinformatics strategy. In this study, we assessed the antimicrobial activities of scolopendrasin V by using radial diffusion assay and colony count assay. We also investigated the mode of action of scolopendrasin V using flow cytometry...
October 25, 2016: Journal of Microbiology and Biotechnology
Filippo Pietrantonio, Claudio Vernieri, Giulia Siravegna, Alessia Mennitto, Rosa Berenato, Federica Perrone, Annunziata Gloghini, Elena Tamborini, Sara Lonardi, Federica Morano, Benedetta Picciani, Adele Busico, Chiara C Volpi, Antonia Martinetti, Francesca Battaglin, Ilaria Bossi, Alessio Pellegrinelli, Massimo Milione, Chiara Cremolini, Maria Di Bartolomeo, Alberto Bardelli, Filippo de Braud
Purpose Even if RAS-BRAF wild-type and HER2/MET negative mCRC patients frequently respond to anti-EGFR monoclonal antibodies, acquired resistance almost invariably occurs. Mechanisms of resistance to EGFR blockade include the emergence of KRAS, NRAS and EGFR extracellular domain mutations as well as HER2/MET alterations. However, these findings derive from retrospective studies that analyzed one single resistance mechanism at a time; moreover, it is still unclear how molecular heterogeneity affects clonal evolution in patients...
October 25, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Yohsuke Yagi, Takuya Ohkubo, Hideya Kawaji, Akira Machida, Haruka Miyata, Saori Goda, Sugata Roy, Yoshihide Hayashizaki, Harukazu Suzuki, Takanori Yokota
MicroRNAs (miRNAs), particularly those found in human body fluids, have been suggested as potential biomarkers. Among various body fluids, the cerebrospinal fluid (CSF) shows promise as a profiling target for diagnosis and monitoring of neurological diseases. However, relevant genome-scale studies are limited and no studies have profiled exosomal miRNAs in CSF. Therefore, we conducted a next-generation sequencing-based genome-wide survey of small RNAs in the exosomal and non-exosomal (supernatant) fractions of healthy human CSF as well as serum in each donor...
October 22, 2016: Neuroscience Letters
Virginie Gaget, Angela Keulen, Melody Lau, Paul Monis, Justin D Brookes
AIMS: Benthic cyanobacteria produce toxic and odorous compounds similar to their planktonic counterparts, challenging the quality of drinking water supplies. The biofilm that benthic algae and other micro-organisms produce is a complex and protective matrix. Monitoring to determine the abundance and identification of cyanobacteria therefore relies on molecular techniques, with the choice of DNA isolation technique critical. This study investigated which DNA extraction method is optimal for DNA recovery in order to guarantee the best DNA yield for PCR-based analysis of benthic cyanobacteria...
October 25, 2016: Journal of Applied Microbiology
Qingping Zhang, Jiarui Li, Ying Zhao, Xinhua Bao, Liping Wei, Jiaping Wang
To investigate the genetic characteristics and clinical features of a cohort of Chinese patients with early-onset epileptic encephalopathies (EOEEs). Targeted next-generation sequencing (NGS), focusing on 17 genes, was performed on 175 Chinese patients with EOEEs to screen gene mutations. The mutation rate was 32% (56/175). All mutations were de novo and heterozygous, including 41 novel and 15 reported mutations. Patients with cyclin-dependent kinase-like 5 (CDKL5) gene mutation accounted for the largest proportion-13...
October 25, 2016: Clinical Genetics
Jia-Ze Tan, Yuan Man, Fei Xiao
BACKGROUND: Congenital myasthenic syndromes are a group of rare disorders that are clinically and genetically heterogeneous and caused by mutations in the genes encoding proteins of the neuromuscular junction. Here, we described a Chinese family that presented with phenotypes of classic slow-channel congenital myasthenic syndrome (SCCMS). METHODS: Clinical characteristics and electrophysiological features of three patients from a Chinese family were examined, and next-generation sequencing followed by direct sequencing was carried out...
2016: Chinese Medical Journal
Marie Eliade, Jeremy Skrzypski, Amandine Baurand, Caroline Jacquot, Geoffrey Bertolone, Catherine Loustalot, Charles Coutant, France Guy, Pierre Fumoleau, Yannis Duffourd, Laurent Arnould, Alexandra Delignette, Marie-Martine Padéano, Côme Lepage, Géraldine Raichon-Patru, Axelle Boudrant, Marie-Christine Bône-Lépinoy, Anne-Laure Villing, Aurélie Charpin, Karine Peignaux, Sandy Chevrier, Frédérique Vegran, François Ghiringhelli, Romain Boidot, Nicolas Sevenet, Sarab Lizard, Laurence Faivre
Until recently, the molecular diagnosis of hereditary breast and ovarian cancer (HBOC) was mostly based on BRCA1/2 testing. Next generation sequencing and the recent discovery of new genes involved in HBOC now permit the transfer of genomic capture targeting multiple candidate genes from research to clinical use. However, the implications for the management of patients and their families have not been extensively studied, in particular since some of these genes are not well-established cancer predisposing genes...
October 15, 2016: Oncotarget
Yung-Mei Chao, You-Lin Tain, Steve Leu, Kay L H Wu, Wei-Chia Lee, Julie Y H Chan
Excessive fructose intake is related to a high prevalence of metabolic syndrome, while little attention has been paid to the impact of maternal high-fructose (HF) intake on the development of metabolic syndrome and organ-specific transcriptome alterations in the offspring. We utilized RNA next-generation sequencing (NGS) technology to analyze the transcriptome expression in four organs (kidney, brain, heart, and urinary bladder) from 1-day, 3-week, and 3-month-old male offspring exposed to maternal HF diet...
October 25, 2016: Sheng Li Xue Bao: [Acta Physiologica Sinica]
Sara J Bowne, Lori S Sullivan, Dianna K Wheaton, Kirsten G Locke, Kaylie D Jones, Daniel C Koboldt, Robert S Fulton, Richard K Wilson, Susan H Blanton, David G Birch, Stephen P Daiger
PURPOSE: To identify the underlying cause of disease in a large family with North Carolina macular dystrophy (NCMD). METHODS: A large four-generation family (RFS355) with an autosomal dominant form of NCMD was ascertained. Family members underwent comprehensive visual function evaluations. Blood or saliva from six affected family members and three unaffected spouses was collected and DNA tested for linkage to the MCDR1 locus on chromosome 6q12. Three affected family members and two unaffected spouses underwent whole exome sequencing (WES) and subsequently, custom capture of the linkage region followed by next-generation sequencing (NGS)...
2016: Molecular Vision
Jason Roszik, Lauren E Haydu, Kenneth R Hess, Junna Oba, Aron Y Joon, Alan E Siroy, Tatiana V Karpinets, Francesco C Stingo, Veera Baladandayuthapani, Michael T Tetzlaff, Jennifer A Wargo, Ken Chen, Marie-Andrée Forget, Cara L Haymaker, Jie Qing Chen, Funda Meric-Bernstam, Agda K Eterovic, Kenna R Shaw, Gordon B Mills, Jeffrey E Gershenwald, Laszlo G Radvanyi, Patrick Hwu, P Andrew Futreal, Don L Gibbons, Alexander J Lazar, Chantale Bernatchez, Michael A Davies, Scott E Woodman
BACKGROUND: While clinical outcomes following immunotherapy have shown an association with tumor mutation load using whole exome sequencing (WES), its clinical applicability is currently limited by cost and bioinformatics requirements. METHODS: We developed a method to accurately derive the predicted total mutation load (PTML) within individual tumors from a small set of genes that can be used in clinical next generation sequencing (NGS) panels. PTML was derived from the actual total mutation load (ATML) of 575 distinct melanoma and lung cancer samples and validated using independent melanoma (n = 312) and lung cancer (n = 217) cohorts...
October 25, 2016: BMC Medicine
Wenzao Li, Peng Zhou, Congmin Zhao, Yuping Zhang
Tuberous sclerosis complex (TSC), a multisystem genetic syndrome, often affects the central nervous system. The age of onset of TSC ranges from 0 to 15 years. The clinical features manifest as a combination of seizures, mental retardation, facial angiofibroma, renal angiomyolipoma, and cardiac rhabdomyoma. Most cases of TSC are caused by mutations of the TSC1 or TSC2 genes. We characterized a Chinese patient with a novel de novo mutation in the TSC2 gene associated with the TSC detected by next-generation sequencing...
October 25, 2016: Journal of Neurogenetics
Sinead Toomey, Stephen F Madden, Simon J Furney, Yue Fan, Mark McCormack, Carragh Stapleton, Mattia Cremona, Gianpiero L Cavalleri, Malgorzata Milewska, Naomi Elster, Aoife Carr, Joanna Fay, Elaine W Kay, Susan Kennedy, John Crown, William M Gallagher, Bryan T Hennessy, Alex J Eustace
BACKGROUND: Trastuzumab treatment for women with HER2-positive breast cancer (BC) resulted in the significant improvement of both relapse free survival (RFS) and overall survival (OS). However, many women who are classified as HER2-positive do not respond. Many studies have focused on the role of somatic mutations rather than germline polymorphisms in trastuzumab resistance. RESULTS: We completed an Agena MassArray screen of 10 ERBB-family single nucleotide polymorphisms (SNPs) in 194 adjuvant trastuzumab treated HER2-positive BC patients...
October 20, 2016: Oncotarget
Gráinne S Gorman, Patrick F Chinnery, Salvatore DiMauro, Michio Hirano, Yasutoshi Koga, Robert McFarland, Anu Suomalainen, David R Thorburn, Massimo Zeviani, Douglass M Turnbull
Mitochondrial diseases are a group of genetic disorders that are characterized by defects in oxidative phosphorylation and caused by mutations in genes in the nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) that encode structural mitochondrial proteins or proteins involved in mitochondrial function. Mitochondrial diseases are the most common group of inherited metabolic disorders and are among the most common forms of inherited neurological disorders. One of the challenges of mitochondrial diseases is the marked clinical variation seen in patients, which can delay diagnosis...
October 20, 2016: Nature Reviews. Disease Primers
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