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https://www.readbyqxmd.com/read/28531552/the-role-of-next-generation-sequencing-in-infection-prevention-in-human-parainfluenza-virus-3-infections-in-immunocompromised-patients
#1
Atul Kothari, Mary J Burgess, Juan Carlos Rico Crescencio, Joshua L Kennedy, Jesse L Denson, Kurt C Schwalm, Ashley N Stoner, John C Kincaid, Faith E Davies, Darrell L Dinwiddie
BACKGROUND: Respiratory viral infections are a significant problem in patients with hematologic malignancies. We report a cluster of HPIV 3 infections in our myeloma patients, and describe the utility of next generation sequencing (NGS) to identify transmission linkages which can assist in infection prevention. OBJECTIVES: To evaluate the utility of NGS to track respiratory viral infection outbreaks and delineate between community acquired and nosocomial infections in our cancer units...
May 12, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28529949/microrna-expression-varies-according-to-glucose-tolerance-measurement-platform-and-biological-source
#2
S Dias, S Hemmings, C Muller, J Louw, C Pheiffer
Dysregulated microRNA (miRNA) expression is observed during type 2 diabetes (T2D), although the consistency of miRNA expression across measurement platform and biological source is uncertain. Here we report miRNA profiling in the whole blood and serum of South African women with different levels of glucose tolerance, using next generation sequencing (NGS) and quantitative real time PCR (qRT-PCR). Whole blood-derived miRNAs from women with newly diagnosed T2D (n = 4), impaired glucose tolerance (IGT) (n = 4), and normal glucose tolerance (NGT) (n = 4) were subjected to NGS, whereafter transcript levels of selected miRNAs were quantified in the whole blood and serum of these women using qRT-PCR...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28529628/cross-platform-comparison-of-four-leading-technologies-for-detecting-egfr-mutations-in-circulating-tumor-dna-from-non-small-cell-lung-carcinoma-patient-plasma
#3
Ting Xu, Xiaozheng Kang, Xiaofang You, Liang Dai, Dequan Tian, Wanpu Yan, Yongbo Yang, Hongchao Xiong, Zhen Liang, Grace Q Zhao, Shengrong Lin, Ke-Neng Chen, Guobing Xu
Analysis of circulating tumor DNA (ctDNA) is emerging as a powerful tool for guiding targeted therapy and monitoring tumor evolution in patients with non-small cell lung cancer (NSCLC), especially when representative tissue biopsies are not available. Here, we have compared the ability of four leading technology platforms to detect epidermal growth factor receptor (EGFR) mutations (L858R, exon 19 deletion, T790M and G719X) in ctDNA from NSCLC patients. Two amplification refractory mutation systems (cobas-ARMS and ADx-ARMS), a droplet digital polymerase chain reaction (ddPCR) and a next-generation sequencing (Firefly NGS) platform were included in the comparison...
2017: Theranostics
https://www.readbyqxmd.com/read/28528510/immunogenomics-using-genomics-to-personalize-cancer-immunotherapy
#4
Rance C Siniard, Shuko Harada
While the use of genomic data has the potential to revolutionize patient care, there is still much work to be done with regard to the transformation of host-tumor interactions into favorable clinical outcomes for our patients. High-throughput technologies, such as next-generation sequencing (NGS), have rapidly advanced our understanding of oncology, and we are learning that most tumors do not simply possess consistently mutated genes that are responsible for tumorigenesis, facilitating the need for personalized cancer therapy...
May 20, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28527899/egfr-mutation-analysis-for-prospective-patient-selection-in-two-phase-ii-registration-studies-of-osimertinib
#5
Suzanne Jenkins, James Chih-Hsin Yang, Pasi A Jänne, Kenneth S Thress, Karen Yu, Rachel Hodge, Susie Weston, Simon Dearden, Sabina Patel, Mireille Cantarini, Frances A Shepherd
INTRODUCTION: Osimertinib is an oral, CNS active, epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) for the treatment of EGFR T790M-positive advanced non-small cell lung cancer (NSCLC). Here we evaluate EGFR mutation frequencies in two Phase II studies of osimertinib (AURA extension and AURA2). METHODS: Patients with EGFR mutation-positive advanced NSCLC provided tumor samples following progression on their latest line of therapy for mandatory central T790M testing for study selection criteria...
May 17, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28526965/complete-sequence-and-genomic-annotation-of-carrot-torradovirus-1
#6
Zuriñe Rozado-Aguirre, Ian Adams, Adrian Fox, Matthew Dickinson, Neil Boonham
Carrot torradovirus 1 (CaTV1) is a new member of the genus Torradovirus within the family Secoviridae. CaTV1 genome sequences were obtained from a previous next-generation sequencing (NGS) study and were compared to other members and tentative new members of the genus. The virus has a bipartite genome, and RACE was used to amplify and sequence each end of RNA1 and RNA2. As a result, RNA1 and RNA2 are estimated to contain 6944 and 4995 nucleotides, respectively, with RNA1 encoding the proteins involved in virus replication, and RNA2 encoding the encapsidation and movement proteins...
May 19, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28526081/comprehensive-detection-of-germline-variants-by-msk-impact-a-clinical-diagnostic-platform-for-solid-tumor-molecular-oncology-and-concurrent-cancer-predisposition-testing
#7
Donavan T Cheng, Meera Prasad, Yvonne Chekaluk, Ryma Benayed, Justyna Sadowska, Ahmet Zehir, Aijazuddin Syed, Yan Elsa Wang, Joshua Somar, Yirong Li, Zarina Yelskaya, Donna Wong, Mark E Robson, Kenneth Offit, Michael F Berger, Khedoudja Nafa, Marc Ladanyi, Liying Zhang
BACKGROUND: The growing number of Next Generation Sequencing (NGS) tests is transforming the routine clinical diagnosis of hereditary cancers. Identifying whether a cancer is the result of an underlying disease-causing mutation in a cancer predisposition gene is not only diagnostic for a cancer predisposition syndrome, but also has significant clinical implications in the clinical management of patients and their families. METHODS: Here, we evaluated the performance of MSK-IMPACT (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets) in detecting genetic alterations in 76 genes implicated in cancer predisposition syndromes...
May 19, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28525389/biological-and-clinical-evidence-for-somatic-mutations-in-brca1-and-brca2-as-predictive-markers-for-olaparib-response-in-high-grade-serous-ovarian-cancers-in-the-maintenance-setting
#8
Brian A Dougherty, Zhongwu Lai, Darren R Hodgson, Maria C M Orr, Matthew Hawryluk, James Sun, Roman Yelensky, Stuart K Spencer, Jane D Robertson, Tony W Ho, Anitra Fielding, Jonathan A Ledermann, J Carl Barrett
To gain a better understanding of the role of somatic mutations in olaparib response, next-generation sequencing (NGS) of BRCA1 and BRCA2 was performed as part of a planned retrospective analysis of tumors from a randomized, double-blind, Phase II trial (Study 19; D0810C00019; NCT00753545) in 265 patients with platinum-sensitive high-grade serous ovarian cancer. BRCA1/2 loss-of-function mutations were found in 55% (114/209) of tumors, were mutually exclusive, and demonstrated high concordance with Sanger-sequenced germline mutations in matched blood samples, confirming the accuracy (97%) of tumor BRCA1/2 NGS testing...
May 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28524737/utilizing-next-generation-sequencing-in-the-management-of-multiple-myeloma
#9
Marta Lionetti, Antonino Neri
Multiple myeloma (MM) is a bone marrow plasma cell malignancy characterized by wide clinical presentation and heterogeneous genetic background. Despite the recent advances in patient outcome, new markers are needed for improving risk prediction and choice of a more appropriate therapy. In this perspective, the genetic makeup of MM cells is being better characterized by means of next-generation sequencing (NGS) technologies. Areas covered: The authors discuss how the application of NGS has improved our knowledge of MM biology by discovering its mutational landscape, identifying the operating mutational processes, and revealing the clonal composition of tumors and the dynamics of its evolution; and how this can have important clinical implications in terms of prognostication, therapeutic choices, and response assessment...
May 19, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28524730/recent-advances-in-genetic-testing-for-familial-hypercholesterolemia
#10
Michael A Iacocca, Robert A Hegele
Familial hypercholesterolemia (FH) is a common genetic cause of premature coronary heart disease that is widely underdiagnosed and undertreated. To improve the identification of FH and initiate timely and appropriate treatment strategies, genetic testing is becoming increasingly offered worldwide as a central part of diagnosis. Areas covered: Recent advances have been propelled by an improved understanding of the genetic determinants of FH together with substantially reduced costs of appropriate screening strategies...
May 19, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28523199/de-novo-pten-mutation-in-a-young-boy-with-cutaneous-vasculitis
#11
Angela Mauro, Ebun Omoyinmi, Neil James Sebire, Angela Barnicoat, Paul Brogan
Phosphatase and tensin homolog (PTEN) is the protein encoded by the PTEN gene (10q23.3). PTEN mutations are related to a variety of rare diseases referred to collectively as PTEN hamartoma tumor syndromes (PHTS), which include Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome, Proteus Syndrome, and Proteus-like syndrome. These diseases are associated with an increased risk of malignancy and for this reason an accurate and early diagnosis is essential in order to institute cancer surveillance. PTEN is a regulator of growth and homeostasis in immune system cells, although there are limited data describing immune dysregulation caused by PTEN mutations...
2017: Case Reports in Pediatrics
https://www.readbyqxmd.com/read/28523154/survival-rate-and-prognostic-factors-of-surgically-resected-clinically-synchronous-multiple-primary-non-small-cell-lung-cancer-and-further-differentiation-from-intrapulmonary-metastasis
#12
Fei Xiao, Deruo Liu, Yongqing Guo, Bin Shi, Zhiyi Song, Yanchu Tian, Zhenrong Zhang, Chaoyang Liang
BACKGROUND: The diagnosis, staging, and therapeutic strategy for synchronous multiple primary non-small cell lung cancer (SMP-NSCLC) remain unclear. Distinguishing SMP-NSCLC from intrapulmonary metastasis is difficult but of great importance for selecting the surgical procedure and prognoses. METHODS: Fifty-two patients diagnosed with SMP-NSCLC according to the modified Martini-Melamed criteria in the thoracic surgery department of the China-Japan Friendship Hospital from November 2004 to December 2015 were enrolled in this retrospective study...
April 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28522829/somatic-tumor-mutations-detected-by-targeted-next-generation-sequencing-in-minute-amounts-of-serum-derived-cell-free-dna
#13
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/28521186/timely-diagnosis-of-sitosterolemia-by-next-generation-sequencing-in-two-children-with-severe-hypercholesterolemia
#14
Paola Sabrina Buonuomo, Lorenzo Iughetti, Livia Pisciotta, Claudio Rabacchi, Francesco Papadia, Patrizia Bruzzi, Albina Tummolo, Andrea Bartuli, Claudio Cortese, Stefano Bertolini, Sebastiano Calandra
BACKGROUND AND AIMS: Severe hypercholesterolemia associated or not with xanthomas in a child may suggest the diagnosis of homozygous autosomal dominant hypercholesterolemia (ADH), autosomal recessive hypercholesterolemia (ARH) or sitosterolemia, depending on the transmission of hypercholesterolemia in the patient's family. Sitosterolemia is a recessive disorder characterized by high plasma levels of cholesterol and plant sterols due to mutations in the ABCG5 or the ABCG8 gene, leading to a loss of function of the ATP-binding cassette (ABC) heterodimer transporter G5-G8...
May 4, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28515723/different-somatic-hypermutation-levels-among-antibody-subclasses-disclosed-by-a-new-next-generation-sequencing-based-antibody-repertoire-analysis
#15
Kazutaka Kitaura, Hiroshi Yamashita, Hitomi Ayabe, Tadasu Shini, Takaji Matsutani, Ryuji Suzuki
A diverse antibody repertoire is primarily generated by the rearrangement of V, D, and J genes and subsequent somatic hypermutation (SHM). Class-switch recombination (CSR) produces various isotypes and subclasses with different functional properties. Although antibody isotypes and subclasses are considered to be produced by both direct and sequential CSR, it is still not fully understood how SHMs accumulate during the process in which antibody subclasses are generated. Here, we developed a new next-generation sequencing (NGS)-based antibody repertoire analysis capable of identifying all antibody isotype and subclass genes and used it to examine the peripheral blood mononuclear cells of 12 healthy individuals...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28512758/reporting-practices-for-unsolicited-and-secondary-findings-from-next-generation-sequencing-technologies-perspectives-of-laboratory-personnel
#16
Danya F Vears, Karine Sénécal, Pascal Borry
While next generation sequencing has enormous potential to identify genetic causes of disease, the nature of the technology means that it can also identify additional information about the individual receiving sequencing that is unrelated to the original rationale for testing. Reporting these unsolicited findings (UF) to clinicians, and subsequently to patients, could lead to potentially lifesaving interventions. Most international guidelines provide limited specific recommendations as to whether these UF should be reported...
May 16, 2017: Human Mutation
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
#17
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...
May 17, 2017: Expert Review of Anticancer Therapy
https://www.readbyqxmd.com/read/28511131/genetic-diversity-and-phylogenetic-analysis-of-the-orf5-gene-of-prrsv-from-central-china
#18
Liujun Zhang, Yan Feng, Darren P Martin, Jing Chen, Sixu Ma, Pingan Xia, Gaiping Zhang
To more fully understand the genetic diversity and molecular epidemiology of prevailing porcine reproductive and respiratory syndrome virus (PRRSV) in Henan province of China, 112 full-length ORF5 gene sequences, originating from Henan province between 2006 and 2015, were subjected to sequence variation and phylogenetic analysis. Phylogenetic analysis revealed that all Henan isolates belonged to the Type 2 genotype and could be further divided into three subgroups. Subgroup 1 and 2 viruses predominated in Henan and subgroup 2 overtook subgroup 1 as the most prevalent PRRSV between 2006 and 2015...
May 11, 2017: Research in Veterinary Science
https://www.readbyqxmd.com/read/28510119/genetic-epidemiology-of-titin-truncating-variants-in-the-etiology-of-dilated-cardiomyopathy
#19
REVIEW
Ali M Tabish, Valerio Azzimato, Aris Alexiadis, Byambajav Buyandelger, Ralph Knöll
Heart failure (HF) is a complex clinical syndrome defined by the inability of the heart to pump enough blood to meet the body's metabolic demands. Major causes of HF are cardiomyopathies (diseases of the myocardium associated with mechanical and/or electrical dysfunction), among which the most common form is dilated cardiomyopathy (DCM). DCM is defined by ventricular chamber enlargement and systolic dysfunction with normal left ventricular wall thickness, which leads to progressive HF. Over 60 genes are linked to the etiology of DCM...
May 5, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28509937/next-generation-sequencing-is-informing-phenotype-a-tp53-example
#20
R O'Shea, R Clarke, E Berkley, C Giffney, M Farrell, E O'Donovan, D J Gallagher
The increased availability of next generation sequencing (NGS) and multi gene panel testing has resulted in more frequent TP53 testing of families that do not meet classic testing criteria. We investigated testing criteria, family history and result outcome in a cohort of Irish probands undergoing TP53 full sequencing. All TP53 test requests processed through the national genetic testing laboratory between 2012 and 2014 were retrospectively reviewed. Personal and family cancer histories were collected, including tumour type and age at diagnosis, from two adult cancer genetic services in Ireland...
May 16, 2017: Familial Cancer
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