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https://www.readbyqxmd.com/read/28231327/functionally-focused-algorithmic-analysis-of-high-resolution-microarray-cgh-genomic-landscapes-demonstrates-comparable-genomic-copy-number-aberrations-in-msi-and-mss-sporadic-colorectal-cancer
#1
Hamad Ali, Milad S Bitar, Ashraf Al Madhoun, Makia Marafie, Fahd Al-Mulla
Array-based comparative genomic hybridization (aCGH) emerged as a powerful technology for studying copy number variations at higher resolution in many cancers including colorectal cancer. However, the lack of standardized systematic protocols including bioinformatic algorithms to obtain and analyze genomic data resulted in significant variation in the reported copy number aberration (CNA) data. Here, we present genomic aCGH data obtained using highly stringent and functionally relevant statistical algorithms from 116 well-defined microsatellites instable (MSI) and microsatellite stable (MSS) colorectal cancers...
2017: PloS One
https://www.readbyqxmd.com/read/28231257/targeted-sequencing-identifies-a-novel-sh2d1a-pathogenic-variant-in-a-chinese-family-carrier-screening-and-prenatal-genetic-testing
#2
Jun-Yu Zhang, Song-Chang Chen, Yi-Yao Chen, Shu-Yuan Li, Lan-Lan Zhang, Ying-Hua Shen, Chun-Xin Chang, Yu-Qian Xiang, He-Feng Huang, Chen-Ming Xu
X-linked lymphoproliferative disease type 1 (XLP1) is a rare primary immunodeficiency characterized by a clinical triad consisting of severe EBV-induced hemophagocytic lymphohistiocytosis, B-cell lymphoma, and dysgammaglobulinemia. Mutations in SH2D1A gene have been revealed as the cause of XLP1. In this study, a pregnant woman with recurrence history of birthing immunodeficiency was screened for pathogenic variant because the proband sample was unavailable. We aimed to clarify the genetic diagnosis and provide prenatal testing for the family...
2017: PloS One
https://www.readbyqxmd.com/read/28230599/a-targeted-next-generation-genetic-sequencing-study-on-tetralogy-of-fallot-combined-with-cleft-lip-and-palate
#3
Lin Liu, Haisong Bu, Yifeng Yang, Zhiping Tan, Fei Zhang, Shijun Hu, Tianli Zhao
BACKGROUND: Congenital heart disease (CHD), plus cleft lip and palate (CLP) are currently the most common types of structural malformation in infants. Many genes have been investigated for their involvement in CHD with CLP. Targeted next-generation sequencing can analyze large amounts of genetic information rapidly, and thus address this question. METHODS: The authors designed a targeted, next-generation sequencing gene panel for 455 genes previously implicated in CHD or CLP...
February 22, 2017: Journal of Craniofacial Surgery
https://www.readbyqxmd.com/read/28230530/developing-a-multi-component-immune-model-for-evaluating-the-risk-of-respiratory-illness-in-athletes
#4
Maree Gleeson, David B Pyne, Lisa J Elkington, Sharron T Hall, John R Attia, Christopher Oldmeadow, Lisa G Wood, Robin Callister
Clinical and laboratory identification of the underlying risk of respiratory illness in athletes has proved problematic. The aim of this study was to determine whether clinical data, combined with immune responses to standardised exercise protocols and genetic cytokine polymorphism status, could identify the risk of respiratory illness (symptoms) in a cohort of highly-trained athletes. Male endurance athletes (n=16; VO2max 66.5 ± 5.1 mL.kg-1.min-1) underwent a clinical evaluation of known risk factors by a physician and comprehensive laboratory analysis of immune responses both at rest and after two cycling ergometer tests: 60 min at 65% VO2max (LONG); and 6 x 3 min intervals at 90% VO2max (INTENSE)...
2017: Exercise Immunology Review
https://www.readbyqxmd.com/read/28229982/circulating-free-dna-mutation-associated-with-response-of-targeted-therapy-in-human-epidermal-growth-factor-receptor-2-positive-metastatic-breast-cancer
#5
Qing Ye, Fan Qi, Li Bian, Shao-Hua Zhang, Tao Wang, Ze-Fei Jiang
BACKGROUND: The addition of anti-human epidermal growth factor receptor 2 (HER2)-targeted drugs, such as trastuzumab, lapatinib, and trastuzumab emtansine (T-DM1), to chemotherapy significantly improved prognosis of HER2-positive breast cancer patients. However, it was confused that metastatic patients vary in the response of targeted drug. Therefore, methods of accurately predicting drug response were really needed. To overcome the spatial and temporal limitations of biopsies, we aimed to develop a more sensitive and less invasive method of detecting mutations associated with anti-HER2 therapeutic response through circulating-free DNA (cfDNA)...
2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28228113/validation-of-an-ngs-mutation-detection-panel-for-melanoma
#6
Anne Reiman, Hugh Kikuchi, Daniela Scocchia, Peter Smith, Yee Wah Tsang, David Snead, Ian A Cree
BACKGROUND: Knowledge of the genotype of melanoma is important to guide patient management. Identification of mutations in BRAF and c-KIT lead directly to targeted treatment, but it is also helpful to know if there are driver oncogene mutations in NRAS, GNAQ or GNA11 as these patients may benefit from alternative strategies such as immunotherapy. METHODS: While polymerase chain reaction (PCR) methods are often used to detect BRAF mutations, next generation sequencing (NGS) is able to determine all of the necessary information on several genes at once, with potential advantages in turnaround time...
February 22, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28226773/biclustering-strategies-for-genetic-marker-selection-in-gynecologic-tumor-cell-lines
#7
A Alevyzaki, S Sfakianakis, E S Bei, E Obermayr, R Zeillinger, D Fotiadis, M Zervakis, A Alevyzaki, S Sfakianakis, E S Bei, E Obermayr, R Zeillinger, D Fotiadis, M Zervakis, R Zeillinger, D Fotiadis, E S Bei, S Sfakianakis, M Zervakis, A Alevyzaki, E Obermayr
Over the past few decades great interest has been focused on cell lines derived from tumors, because of their usability as models to understand the biology of cancer. At the same time, advanced technologies such as DNA-microarrays have been broadly used to study the expression level of thousands of genes in primary tumors or cancer cell lines in a single experiment. Results from microarray analysis approaches have provided valuable insights into the underlying biology and proven useful for tumor classification, prognostication and prediction...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28224992/diagnostic-exome-sequencing-in-266-dutch-patients-with-visual-impairment
#8
Lonneke Haer-Wigman, Wendy Ag van Zelst-Stams, Rolph Pfundt, L Ingeborgh van den Born, Caroline Cw Klaver, Joke Bgm Verheij, Carel B Hoyng, Martijn H Breuning, Camiel Jf Boon, Anneke J Kievit, Virginie Jm Verhoeven, Jan Wr Pott, Suzanne Ceh Sallevelt, Johanna M van Hagen, Astrid S Plomp, Hester Y Kroes, Stefan H Lelieveld, Jayne Y Hehir-Kwa, Steven Castelein, Marcel Nelen, Hans Scheffer, Dorien Lugtenberg, Frans Pm Cremers, Lies Hoefsloot, Helger G Yntema
Inherited eye disorders have a large clinical and genetic heterogeneity, which makes genetic diagnosis cumbersome. An exome-sequencing approach was developed in which data analysis was divided into two steps: the vision gene panel and exome analysis. In the vision gene panel analysis, variants in genes known to cause inherited eye disorders were assessed for pathogenicity. If no causative variants were detected and when the patient consented, the entire exome data was analyzed. A total of 266 Dutch patients with different types of inherited eye disorders, including inherited retinal dystrophies, cataract, developmental eye disorders and optic atrophy, were investigated...
February 22, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28224639/rigid-spine-syndrome-associated-with-sensory-motor-axonal-neuropathy-resembling-charcot-marie-tooth-disease-is-characteristic-of-bag3-gene-mutations-even-without-cardiac-involvement
#9
Jean-Baptiste Noury, Thierry Maisonobe, Pascale Richard, Valérie Delague, Edoardo Malfatti, Tanya Stojkovic
INTRODUCTION: BAG3 (Bcl-2 associated athanogene-3) mutations have been described in rare cases of rapidly progressive myofibrillar myopathies. Symptoms begin in the first decade with axial involvement and contractures and are associated with cardiac and respiratory impairment in the second decade. Axonal neuropathy has been documented, but usually not as a key clinical feature. METHODS: We report a 24-year-old woman with severe rigid spine syndrome and sensory-motor neuropathy resembling Charcot-Marie-Tooth disease (CMT)...
February 22, 2017: Muscle & Nerve
https://www.readbyqxmd.com/read/28223711/identification-of-novel-cancer-therapeutic-targets-using-a-designed-and-pooled-shrna-library-screen
#10
David Oliver, Hao Ji, Piaomu Liu, Alexander Gasparian, Ellen Gardiner, Samuel Lee, Adrian Zenteno, Lillian O Perinskaya, Mengqian Chen, Phillip Buckhaults, Eugenia Broude, Michael D Wyatt, Homayoun Valafar, Edsel Peña, Michael Shtutman
Targeted cancer therapeutics aim to exploit tumor-specific, genetic vulnerabilities specifically affecting neoplastic cells without similarly affecting normal cells. Here we performed sequencing-based screening of an shRNA library on a panel of cancer cells of different origins as well as normal cells. The shRNA library was designed to target a subset of genes previously identified using a whole genome screening approach. This focused shRNA library was infected into cells followed by analysis of enrichment and depletion of the shRNAs over the course of cell proliferation...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28223188/next-generation-sequencing-unravels-homozygous-mutation-in-glucose-6-phosphate-isomerase-gpic-1040g-a-p-arg347his-causing-hemolysis-in-an-indian-infant
#11
Manu Jamwal, Anu Aggarwal, Anirban Das, Arindam Maitra, Prashant Sharma, Shekhar Krishnan, Neeraj Arora, Deepak Bansal, Reena Das
INTRODUCTION: Inherited anemias diagnostic workup requires a step-wise algorithm. Causal genes implicated in congenital hemolytic anemia are numerous, making a gene-by-gene approach by Sanger sequencing time consuming, expensive and labour intensive. Targeted resequencing can be of great use in explaining these cases. METHODOLOGY: Six months female presented with neonatal jaundice and negative family history. Clinical and laboratory evidences were suggestive of hemolytic anemia...
February 20, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28222567/immune-biomarkers-for-the-diagnosis-of-mild-traumatic-brain-injury
#12
Ashley B Petrone, Valerie Gionis, Richard Giersch, Taura L Barr
BACKGROUND: In 2010, there were approximately 2.2 million emergency room visits associated with traumatic brain injury (TBI), with 80 percent diagnosed as mild TBI or concussion. In addition, there are a large number of TBIs, especially mild TBIs, which go either unreported by patients or initially undiagnosed by clinicians. Our team has previously identified a panel of immune-related genes that can diagnose ischemic stroke at triage, and due to shared pathophysiological mechanisms of TBI and stroke, we hypothesized that this panel of genes may also be utilized for the diagnosis of TBI...
February 10, 2017: NeuroRehabilitation
https://www.readbyqxmd.com/read/28222413/a-new-tr%C3%AE-mutation-in-resistance-to-thyroid-hormone-syndrome
#13
Corina Neamţu, Claudiu Ţupea, Diana Păun, Anca Hoisescu, Adina Ghemigian, Samuel Refetoff, Chutintorn Sriphrapradang
Thyroid hormones (TH) exert their actions by binding nuclear receptors alpha (TRα1) and beta (TRß1 and TRß2). Resistance to thyroid hormone (RTH) is a clinical syndrome with various clinical manifestations, its hallmark being decreased tissue sensitivity to the action of thyroid hormones. We report the case of a family harbouring a novel TRß mutation. Sequencing of the TRβ gene revealed a single nucleotide substitution-C to G in codon 340: glutamine was replaced by glutamic acid. The clinical picture and biochemical and hormonal panel showed significant differences within the family, despite their sharing the same mutation...
October 2016: Hormones: International Journal of Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28221917/escherichia-coli-o157-h7-strains-isolated-from-high-event-period-beef-contamination-have-strong-biofilm-forming-ability-and-low-sanitizer-susceptibility-which-are-associated-with-high-po157-plasmid-copy-number
#14
Rong Wang, Brandon E Luedtke, Joseph M Bosilevac, John W Schmidt, Norasak Kalchayanand, Terrance M Arthur
In the meat industry, a high-event period (HEP) is defined as a time period when beef processing establishments experience an increased occurrence of product contamination by Escherichia coli O157:H7. Our previous studies suggested that bacterial biofilm formation and sanitizer resistance might contribute to HEPs. We conducted the present study to further characterize E. coli O157:H7 strains isolated during HEPs for their potential to cause contamination and to investigate the genetic basis for their strong biofilm-forming ability and high sanitizer resistance...
November 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28221346/synthesis-of-ent-be-43547a1-reveals-a-potent-hypoxia-selective-anticancer-agent-and-uncovers-the-biosynthetic-origin-of-the-apd-cld-natural-products
#15
Nikolaj L Villadsen, Kristian M Jacobsen, Ulrik B Keiding, Esben T Weibel, Bjørn Christiansen, Thomas Vosegaard, Morten Bjerring, Frank Jensen, Mogens Johannsen, Thomas Tørring, Thomas B Poulsen
Tumour hypoxia is speculated to be a key driver of therapeutic resistance and metastatic dissemination. Consequently, the discovery of new potent agents that selectively target the hypoxic cell population may reveal new and untapped antitumour mechanisms. Here we demonstrate that the BE-43547 subclass of the APD-CLD (amidopentadienoate-containing cyclolipodepsipeptides) natural products possesses highly hypoxia-selective growth-inhibitory activity against pancreatic cancer cells. To enable this discovery, we have developed the first synthesis of the BE-43547-macrocyclic scaffold in 16 steps (longest linear sequence), which also allowed access to the full panel of relative stereoisomers and ultimately to the assignment of stereochemical configuration...
March 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28220839/pten-status-is-a-crucial-determinant-of-the-functional-outcome-of-combined-mek-and-mtor-inhibition-in-cancer
#16
Michele Milella, Italia Falcone, Fabiana Conciatori, Silvia Matteoni, Andrea Sacconi, Teresa De Luca, Chiara Bazzichetto, Vincenzo Corbo, Michele Simbolo, Isabella Sperduti, Antonina Benfante, Anais Del Curatolo, Ursula Cesta Incani, Federico Malusa, Adriana Eramo, Giovanni Sette, Aldo Scarpa, Marina Konopleva, Michael Andreeff, James Andrew McCubrey, Giovanni Blandino, Matilde Todaro, Giorgio Stassi, Ruggero De Maria, Francesco Cognetti, Donatella Del Bufalo, Ludovica Ciuffreda
Combined MAPK/PI3K pathway inhibition represents an attractive, albeit toxic, therapeutic strategy in oncology. Since PTEN lies at the intersection of these two pathways, we investigated whether PTEN status determines the functional response to combined pathway inhibition. PTEN (gene, mRNA, and protein) status was extensively characterized in a panel of cancer cell lines and combined MEK/mTOR inhibition displayed highly synergistic pharmacologic interactions almost exclusively in PTEN-loss models. Genetic manipulation of PTEN status confirmed a mechanistic role for PTEN in determining the functional outcome of combined pathway blockade...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28220018/germline-variants-in-familial-pituitary-tumour-syndrome-genes-are-common-in-young-patients-and-families-with-additional-endocrine-tumours
#17
Sunita Mc De Sousa, Mark J McCabe, Kathy Wu, Tony Roscioli, Velimir Gayevskiy, Katelyn Brook, Lesley Rawlings, Hamish S Scott, Tanya J Thompson, Peter Earls, Anthony J Gill, Mark J Cowley, Marcel E Dinger, Ann I McCormack
Objective: Familial pituitary tumour syndromes (FPTS) account for 5% of pituitary adenomas. Multi-gene analysis via next generation sequencing (NGS) may unveil greater prevalence and inform clinical care. We aimed to identify germline variants in selected patients with pituitary adenomas using a targeted NGS panel. Design: We undertook a nation-wide cross-sectional study of patients with pituitary adenomas with onset ≤40 years of age and/or other personal/family history of endocrine neoplasia. A custom NGS panel was performed on germline DNA to interrogate eight FPTS genes...
February 20, 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/28219841/experimental-and-computational-surface-hydrophobicity-analysis-of-a-non-enveloped-virus-and-proteins
#18
Caryn L Heldt, Amna Zahid, K Saagar Vijayaragavan, Xue Mi
The physical characteristics of viruses needs to be understood in order to manipulate the interaction of viruses with host cells, as well as to create specific molecular recognition techniques to detect, purify, and remove viruses. Viruses are generally believed to be positively charged at physiological pH, but there are few other defining characteristics. Here, we have experimentally and computationally demonstrated that a non-enveloped virus is more hydrophobic than a panel of model proteins. Reverse-phase and hydrophobic interaction chromatography and ANS fluorescence determined the experimental hydrophobic strength of each entity...
February 13, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28217764/vpreb-serves-as-an-invariant-surrogate-antigen-for-selecting-immunoglobulin-antigen-binding-sites
#19
Mohamed Khass, Tessa Blackburn, Peter D Burrows, Mark R Walter, Emidio Capriotti, Harry W Schroeder
Developmental checkpoints eliminate B cells synthesizing defective immunoglobulin heavy (HC) and light (LC) chains. The first checkpoint tests for formation of a VpreB/λ5/µHC-containing preB-cell receptor (preBCR) and predicts whether µHCs will bind conventional LCs to form membrane IgM. VpreB and λ5 also create a sensing site that interacts with µHC antigen-binding region CDR-H3, but whether it plays a role in immunoglobulin repertoire selection and function is unknown. On a position-by-position basis, we analyzed the amino acid content of CDR-H3s from H chains cloned from living and apoptotic preB cells and from IgG:Antigen structures...
July 14, 2016: Science Immunology
https://www.readbyqxmd.com/read/28217227/cardiac-conduction-defects-and-brugada-syndrome-a-family-with-overlap-syndrome-carrying-a-nonsense-scn5a-mutation
#20
Hisaaki Aoki, Yoshihide Nakamura, Seiko Ohno, Takeru Makiyama, Minoru Horie
BACKGROUND: Phenotypes often differ even within family members carrying the same SCN5A mutation. We aimed to evaluate the genetic modifiers in a family with Brugada syndrome (BrS) and sick sinus syndrome (SSS) with an SCN5A mutation that causes the truncated alpha-subunit of cardiac Na channel protein. METHODS: To detect the genetic modifiers, we performed targeted panel sequencing of the coding region of 46 genes that are related to primary arrhythmia syndrome, by using a bench-top, next generation sequencer...
February 2017: Journal of Arrhythmia
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