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https://www.readbyqxmd.com/read/28635333/molecular-biomarkers-to-guide-precision-medicine-in-localized-prostate-cancer
#1
Minke Smits, Niven Mehra, Michiel Sedelaar, Winald Gerritsen, Jack A Schalken
Major advances through tumor profiling technologies, that include next-generation sequencing, epigenetic, proteomic and transcriptomic methods, have been made in primary prostate cancer, providing novel biomarkers that may guide precision medicine in the near future. Areas covered: The authors provided an overview of novel molecular biomarkers in tissue, blood and urine that may be used as clinical tools to assess prognosis, improve selection criteria for active surveillance programs, and detect disease relapse early in localized prostate cancer...
June 21, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28634552/inherited-paediatric-motor-neuron-disorders-beyond-spinal-muscular-atrophy
#2
REVIEW
Hooi Ling Teoh, Kate Carey, Hugo Sampaio, David Mowat, Tony Roscioli, Michelle Farrar
Paediatric motor neuron diseases encompass a group of neurodegenerative diseases characterised by the onset of muscle weakness and atrophy before the age of 18 years, attributable to motor neuron loss across various neuronal networks in the brain and spinal cord. While the genetic underpinnings are diverse, advances in next generation sequencing have transformed diagnostic paradigms. This has reinforced the clinical phenotyping and molecular genetic expertise required to navigate the complexities of such diagnoses...
2017: Neural Plasticity
https://www.readbyqxmd.com/read/28632965/frequent-col4-mutations-in-familial-microhematuria-accompanied-by-later-onset-alport-nephropathy-due-to-focal-segmental-glomerulosclerosis
#3
Louiza Papazachariou, Gregory Papagregoriou, Despina Hadjipanagi, Panagiota Demosthenous, Konstantinos Voskarides, Constantina Koutsofti, Kostas Stylianou, Petros Ioannou, Dimitris Xydakis, Ioannis Tzanakis, Antonia Papadaki, Nicolaos Kallivretakis, Nicolaos Nikolakakis, Garyfalia Perysinaki, Daniel P Gale, Athanasios Diamantopoulos, Pavlos Goudas, Dimitris Goumenos, Andreas Soloukides, Ioannis Boletis, Christina Melexopoulou, Eleni Georgaki, Elena Frysira, Fifi Komianou, Dimitrios Grekas, Christos Paliouras, Polichronis Alivanis, George Vergoulas, Alkis Pierides, Eugenios Daphnis, Constantinos Deltas
Familial microscopic hematuria (FMH) is associated with a genetically heterogeneous group of conditions including the collagen-IV nephropathies, the heritable C3/CFHR5 nephropathy and the glomerulopathy with fibronectin deposits. The clinical course varies widely, ranging from isolated benign familial hematuria to end-stage renal disease (ESRD) later in life. We investigated 24 families using Next Generation Sequencing (NGS) for five genes: COL4A3, COL4A4, COL4A5, CFHR5 and FN1. In 17 families (71%), we found 15 pathogenic mutations in COL4A3/A4/A5, nine of them novel...
June 20, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28631441/genetic-landscape-and-deregulated-pathways-in-b-cell-lymphoid-malignancies
#4
R Rosenquist, S Beà, M-Q Du, B Nadel, Q Pan-Hammarström
With the introduction of next-generation sequencing, the genetic landscape of the complex group of B-cell lymphoid malignancies has rapidly been unravelled in recent years. This has provided important information about recurrent genetic events and identified key pathways deregulated in each lymphoma subtype. In parallel, there has been intense search and development of novel types of targeted therapy that 'hit' central mechanisms in lymphoma pathobiology, such as BTK, PI3K or BCL2 inhibitors. In this review, we will outline the current view of the genetic landscape of selected entities: follicular lymphoma, diffuse large B-cell lymphoma, mantle cell lymphoma, chronic lymphocytic leukaemia and marginal zone lymphoma...
June 20, 2017: Journal of Internal Medicine
https://www.readbyqxmd.com/read/28630945/the-icr96-exon-cnv-validation-series-a-resource-for-orthogonal-assessment-of-exon-cnv-calling-in-ngs-data
#5
Shazia Mahamdallie, Elise Ruark, Shawn Yost, Emma Ramsay, Imran Uddin, Harriett Wylie, Anna Elliott, Ann Strydom, Anthony Renwick, Sheila Seal, Nazneen Rahman
Detection of deletions and duplications of whole exons (exon CNVs) is a key requirement of genetic testing. Accurate detection of this variant type has proved very challenging in targeted next-generation sequencing (NGS) data, particularly if only a single exon is involved. Many different NGS exon CNV calling methods have been developed over the last five years. Such methods are usually evaluated using simulated and/or in-house data due to a lack of publicly-available datasets with orthogonally generated results...
2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28629604/novel-fkrp-mutations-in-a-japanese-mdc1c-sibship-clinically-diagnosed-with-fukuyama-congenital-muscular-dystrophy
#6
Mieko Yoshioka, Kazuhiro Kobayashi, Tatsushi Toda
INTRODUCTION: Fukuyama congenital muscular dystrophy (FCMD), caused by fukutin mutations, is the most common form of Japanese CMD. We followed a Japanese CMD sibship without fukutin mutation, and herein identified new FKRP mutations causing MDC1C rarely reported in Oriental countries. PATIENTS: Two affected siblings, individuals 1 (I-1, male) and 2 (I-2, female), were born uneventfully to unaffected, non-consanguineous parents. Severe hypotonia was soon apparent and serum CK levels were elevated: I-1: 1025 IU/L (normal range <130 IU/L) and I-2: 5350 IU/L...
June 16, 2017: Brain & Development
https://www.readbyqxmd.com/read/28629316/a-multiplex-primer-design-algorithm-for-target-amplification-of-continuous-genomic-regions
#7
Ahmet Rasit Ozturk, Tolga Can
BACKGROUND: Targeted Next Generation Sequencing (NGS) assays are cost-efficient and reliable alternatives to Sanger sequencing. For sequencing of very large set of genes, the target enrichment approach is suitable. However, for smaller genomic regions, the target amplification method is more efficient than both the target enrichment method and Sanger sequencing. The major difficulty of the target amplification method is the preparation of amplicons, regarding required time, equipment, and labor...
June 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28628911/a-carasil-patient-from-americas-with-novel-mutation-and-atypical-features-case-presentation-and-literature-review
#8
Muhammad Ibrahimi, Hiroaki Nozaki, Angelica Lee, Osamu Onodera, Raymond Reichwein, Matthew Wicklund, Mohammad El-Ghanem
OBJECTIVE: Reporting a novel mutation in the HTRA1 gene in a CARASIL patient from Americas. METHODS: Clinical presentation and neuroimaging were consistent with CARASIL. HTRA1 DNA sequencing was performed using advanced ("next generation") sequencing technology. The results revealed a homozygous missense mutation as c.616G>A (p.Gly206Arg) in the HTRA1 gene. RESULTS: A 24-year-old man with a history of chronic back pain presented with recurrent ischemic strokes...
June 21, 2017: Cerebrovascular Diseases
https://www.readbyqxmd.com/read/28626224/reference-standards-for-next-generation-sequencing
#9
REVIEW
Simon A Hardwick, Ira W Deveson, Tim R Mercer
Next-generation sequencing (NGS) provides a broad investigation of the genome, and it is being readily applied for the diagnosis of disease-associated genetic features. However, the interpretation of NGS data remains challenging owing to the size and complexity of the genome and the technical errors that are introduced during sample preparation, sequencing and analysis. These errors can be understood and mitigated through the use of reference standards - well-characterized genetic materials or synthetic spike-in controls that help to calibrate NGS measurements and to evaluate diagnostic performance...
June 19, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28625771/comparison-of-plasma-to-tissue-dna-mutations-in-surgical-patients-with-non-small-cell-lung-cancer
#10
Kezhong Chen, Jingbo Zhang, Tian Guan, Fan Yang, Feng Lou, Wei Chen, Mingyu Zhao, Jay Zhang, Siyi Chen, Jun Wang
OBJECTIVE: Noninvasive liquid biopsies of circulating tumor DNA (ctDNA) can be used to assess non-small cell lung cancer (NSCLC), but previous work focused on patients with advanced-stage cancer. Thus, we evaluated the feasibility and their potential clinical application of circulating tumor DNA approached for surgical patients with NSCLC. METHOD: Consecutive patients with suspected lung cancer who underwent curative-intent lung resection were enrolled prospectively in this study...
May 24, 2017: Journal of Thoracic and Cardiovascular Surgery
https://www.readbyqxmd.com/read/28625653/most-t790m-mutations-are-present-on-the-same-egfr-allele-as-activating-mutations-in-patients-with-non-small-cell-lung-cancer
#11
Noriko Hidaka, Eiji Iwama, Naoki Kubo, Taishi Harada, Kohta Miyawaki, Kentaro Tanaka, Isamu Okamoto, Eishi Baba, Koichi Akashi, Hiroyuki Sasaki, Yoichi Nakanishi
OBJECTIVES: The T790M and C797S mutations of the epidermal growth factor receptor gene (EGFR) confer resistance to first- and third-generation EGFR tyrosine kinase inhibitors (TKIs), respectively, in patients with non-small cell lung cancer (NSCLC) harboring activating mutations of EGFR. C797S has been identified in cis or in trans with T790M in tumor specimens from patients who experienced treatment failure with first- and third-generation EGFR-TKIs. The allelic relation between T790M and activating mutations of EGFR has not been well characterized, however...
June 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/28625332/considerations-of-developing-an-ngs-assay-for-clinical-applications-in-precision-oncology-the-nci-match-ngs-assay-experience
#12
Chih-Jian Lih, Naoko Takebe
Next generation sequencing (NGS) technologies have been widely adapted in clinical oncology by utilizing the profiled genetic mutation information to select patients and to guide the choice of target therapy. To fulfill the regulatory compliance, development of an NGS assay that will be used in clinical trials requires an analytical validation to meet its intend clinical use. NCI-MATCH trial is the largest precision oncology basket trial which uses a single NGS assay (NCI-MATHC NGS assay) to screen the actionable mutations in 6000 patients, who have relapsed/refractory solid tumors and lymphomas after standard systemic treatment, and assigns matched treatment...
May 2017: Current Problems in Cancer
https://www.readbyqxmd.com/read/28624463/insights-from-genotype-phenotype-correlations-by-novel-speg-mutations-causing-centronuclear-myopathy
#13
Haicui Wang, Claudia Castiglioni, Ayşe Kaçar Bayram, Fabiana Fattori, Serdar Pekuz, Diego Araneda, Hüseyin Per, Ricardo Erazo, Hakan Gümüş, Suzan Zorludemir, Kerstin Becker, Ximena Ortega, Jorge Alfredo Bevilacqua, Enrico Bertini, Sebahattin Cirak
Centronuclear myopathies (CNM) are a clinically and genetically heterogeneous group of congenital myopathies, defined histologically by increased number of fibres with centrally located nuclei, and type I fibre predominance in muscle biopsy. Myotubular myopathy, the X-linked form of CNM caused by mutations in the phosphoinositide phosphatase MTM1, is histologically characteristic since muscle fibres resemble myotubes. Here we present two unrelated patients with CNM and typical myotubular fibres in the muscle biopsy caused by mutations in striated muscle preferentially expressed protein kinase (SPEG)...
May 24, 2017: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/28623888/ub-isap-a-streamlined-unix-pipeline-for-mining-unique-viral-vector-integration-sites-from-next-generation-sequencing-data
#14
Atul Kamboj, Claus V Hallwirth, Ian E Alexander, Geoffrey B McCowage, Belinda Kramer
BACKGROUND: The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration site identification is a key step in the genetic mapping of viral elements in mutagenesis screens that aim to elucidate gene function. RESULTS: We have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads...
June 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28621158/signaling-pathway-profiling-using-reverse-phase-protein-array-and-its-clinical-applications
#15
Mari Masuda, Tesshi Yamada
Increased accessibility to next-generation sequencing within the last decade has led to a paradigm shift in cancer treatment from one-size-fits-all medicine to precision medicine providing therapeutic strategies tailored to the requirements of individual patients. However, the effect of even the most successful agent yet tested is only transient, and durable efficacy has yet to be achieved. Genome- and transcriptome-based approaches cannot fully predict the diversity of protein expression patterns or post-translational modifications that directly contribute to cancer pathogenesis and physiology...
June 16, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28620717/multiple-variants-in-families-with-amyotrophic-lateral-sclerosis-and-frontotemporal-dementia-related-to-c9orf72-repeat-expansion-further-observations-on-their-oligogenic-nature
#16
Maria Pia Giannoccaro, Anna Bartoletti-Stella, Silvia Piras, Annalisa Pession, Patrizia De Massis, Federico Oppi, Michelangelo Stanzani-Maserati, Elena Pasini, Simone Baiardi, Patrizia Avoni, Piero Parchi, Rocco Liguori, Sabina Capellari
The C9orf72 repeat expansion (RE) is one of the most frequent causative mutations of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). However, it is still unclear how the C9orf72 RE can lead to a heterogeneous phenotype. Several reports have shown the coexistence of mutations in multiple ALS/FTD causative genes in the same family, suggesting an oligogenic etiology for ALS and FTD. Our aim was to investigate this phenomenon in an Italian group of ALS/FTD pedigrees carrying the C9orf72 RE...
June 15, 2017: Journal of Neurology
https://www.readbyqxmd.com/read/28620608/a-path-to-implement-precision-child-health-cardiovascular-medicine
#17
REVIEW
Marlin Touma, Brian Reemtsen, Nancy Halnon, Juan Alejos, J Paul Finn, Stanley F Nelson, Yibin Wang
Congenital heart defects (CHDs) affect approximately 1% of live births and are a major source of childhood morbidity and mortality even in countries with advanced healthcare systems. Along with phenotypic heterogeneity, the underlying etiology of CHDs is multifactorial, involving genetic, epigenetic, and/or environmental contributors. Clear dissection of the underlying mechanism is a powerful step to establish individualized therapies. However, the majority of CHDs are yet to be clearly diagnosed for the underlying genetic and environmental factors, and even less with effective therapies...
2017: Frontiers in Cardiovascular Medicine
https://www.readbyqxmd.com/read/28618409/identification-of-8-novel-mutations-in-nephrogenesis-related-genes-in-chinese-han-patients-with-unilateral-renal-agenesis
#18
Hangdi Wu, Qian Xu, Jingyuan Xie, Jun Ma, Panpan Qiao, Wen Zhang, Haijin Yu, Weiming Wang, Ying Qian, Qianying Zhang, Yiqing Guo, Yonghua Tang, Xiao-Nong Chen, Zhaohui Wang, Nan Chen
BACKGROUND: Few genetic studies have focused on unilateral renal agenesis (URA), which is a disorder with insidious clinical manifestations and a tendency to result in renal failure. We aimed to detect pathogenic mutations in nephrogenesis-related genes, which were identified by a literature review conducted among a large cohort of Chinese Han patients with URA. METHODS: Totally, 86 unrelated URA patients were included. All URA patients were diagnosed by employing radiological methods...
June 16, 2017: American Journal of Nephrology
https://www.readbyqxmd.com/read/28618405/upregulation-of-circulating-mir-195-3p-in-heart-failure
#19
Xia He, Jun Ji, Tao Wang, Ming-Bang Wang, Xiao-Ling Chen
OBJECTIVES: Many circulating microRNAs (miRs) have been shown to have potential biomarker effects in cardiovascular disease. We studied the dysregulation of circulating miR-195-3p in patients with heart failure (HF) to elucidate its value as a potential biomarker for HF. METHODS: Eight ischemic HF (IHF) patients, 8 nonischemic HF patients (NIHF), and 8 healthy volunteers (matched by age and sex - normal controls [NCs]) were chosen for miR sequencing. The plasma RNA was extracted, and a small RNA library of HF was established and then sequenced using next-generation sequencing (NGS) technology...
June 16, 2017: Cardiology
https://www.readbyqxmd.com/read/28618399/rna-sequencing-investigation-identifies-an-effective-risk-score-generated-by-three-novel-lncrnas-for-the-survival-of-papillary-thyroid-cancer-patients
#20
Yi-Huan Luo, Liang Liang, Rong-Quan He, Dong-Yue Wen, Guo-Fei Deng, Hong Yang, Yun He, Wei Ma, Xiao-Yong Cai, Jun-Qiang Chen, Gang Chen
Scholars are striving to apply molecular biology involving long non-coding RNA (lncRNA) in the prognostication of papillary thyroid cancer (PTC). However, the clinical role of lncRNAs in the prognostic setting of PTC is still unclear. Herein, a comprehensive inquiry was performed to screen lncRNA expression profiling with 507 PTC patients from The Cancer Genome Atlas RNA-sequencing datasets. A total of 734 lncRNAs were detected to be aberrantly expressed, among which three novel lncRNAs including AC079630.2, CRNDE and CTD-2171N6...
May 26, 2017: Oncotarget
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