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https://www.readbyqxmd.com/read/28431466/next-generation-sequencing-reveals-one-novel-missense-mutation-in-col1a2-gene-in-an-iranian-family-with-osteogenesis-imperfecta
#1
Farah Talebi, Farideh Ghanbari Mardasi, Mohammadi Asl Javad, Bavarsad Amir Hooshang, Salehi Kambo Masoumeh
BAckground: Osteogenesis imperfecta (OI) is a clinically and genetically heterogeneous disorder characterized by bone loss and bone fragility. The aim of this study was to investigate the variants of three genes involved in the pathogenesis of OI. Methods: Molecular genetic analyses were performed for COL1A1, COL1A2, and CRTAP genes in an Iranian family with OI. The DNA samples were analyzed by next-generation sequencing (NGS) gene panel and Sanger sequencing. Results: Five different variants were identified in COL1A1 and COL1A2, including two variants in COL1A1 and three variants in COL1A2...
April 22, 2017: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/28431395/correlation-of-genomic-alterations-assessed-by-next-generation-sequencing-ngs-of-tumor-tissue-dna-and-circulating-tumor-dna-ctdna-in-metastatic-renal-cell-carcinoma-mrcc-potential-clinical-implications
#2
Andrew W Hahn, David M Gill, Benjamin Maughan, Archana Agarwal, Lubina Arjyal, Sumati Gupta, Jessica Streeter, Erin Bailey, Sumanta K Pal, Neeraj Agarwal
INTRODUCTION: Tumor tissue and circulating tumor DNA (ctDNA) next-generation sequencing (NGS) testing are frequently performed to detect genomic alterations (GAs) to help guide treatment in metastatic renal cell carcinoma (mRCC), especially after progression on standard systemic therapy. Our objective was to assess if GAs detected by ctDNA NGS are different from those detected by tumor tissue NGS, specifically in patients with mRCC, and if these platforms are interchangeable or complimentary...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28430325/identification-of-a-disease-causing-mutation-in-a-chinese-patient-with-retinitis-pigmentosa-by-targeted-next-generation-sequencing
#3
Jianping Xiao, Xueqin Guo, Yong Wang, Mingkun Shao, Xiaoming Wei, Lique Du, Long Li, Yan Sun, Yun Yang
PURPOSE: To identify disease-causing mutations in a Chinese patient with retinitis pigmentosa (RP). METHODS: A detailed clinical examination was performed on the proband. Targeted next-generation sequencing (NGS) combined with bioinformatics analysis was performed on the proband to detect candidate disease-causing mutations. Sanger sequencing was performed on all subjects to confirm the candidate mutations and assess cosegregation within the family. RESULTS: Clinical examinations of the proband showed typical characteristics of RP...
April 14, 2017: European Journal of Ophthalmology
https://www.readbyqxmd.com/read/28428977/19th-workshop-of-the-international-stroke-genetics-consortium-april-28-29-2016-boston-massachusetts-usa-2016-001-mri-defined-cerebrovascular-genomics-the-charge-consortium
#4
S Debette, Y Saba, D Vojinovic, X Jian, H Adams, G Chauhan, M Sargurupremraj, S Kaffashian, J Ding, J C Bis, P Nyquist, K Mather, C Van Duijn, L J Launer, M A Ikram, H Schmidt, W T Longstreth, M Fornage, S Seshadri
The CHARGE consortium is an investigator-initiated collaboration to facilitate meta-analyses of genome-wide association studies (GWAS) and genomic analyses based on next generation sequencing (NGS), among multiple large and well-phenotyped population-based cohort studies around the world (http://www.chargeconsortium.com). Within the neuro-CHARGE working group, we are presenting an update of ongoing genomic studies on MRI-markers of cerebrovascular disease. Large population-based studies have shown that the burden of cerebrovascular disease extends far beyond that of clinical stroke...
March 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28428317/complete-nucleotide-sequence-of-an-isolate-of-grapevine-satellite-virus-and-evidence-for-the-presence-of-multimeric-forms-in-an-infected-grapevine
#5
T Candresse, A Marais, S Theil, C Faure, T Lacombe, J M Boursiquot
The complete nucleotide sequence of an isolate of grapevine satellite virus (GV-Sat) was determined by next-generation sequencing (NGS) and compared with the single available complete sequence. The NGS data unexpectedly provided evidence for the existence of multimeric forms of GV-Sat, which were experimentally confirmed, allowing the redefinition of GV-Sat genomic ends.
April 20, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28428148/plasma-ctdna-analysis-for-detection-of-the-egfr-t790m-mutation-in-patients-with-advanced-non-small-cell-lung-cancer
#6
Suzanne Jenkins, James C-H Yang, Suresh S Ramalingam, Karen Yu, Sabina Patel, Susie Weston, Rachel Hodge, Mireille Cantarini, Pasi A Jänne, Tetsuya Mitsudomi, Glenwood D Goss
INTRODUCTION: Tumor biopsies for detecting epidermal growth factor receptor mutations (EGFRm) in advanced non-small cell lung cancer (NSCLC) are invasive, costly and not always feasible for patients with late-stage disease. The clinical utility of the cobas(®) EGFR Mutation Test v2 with plasma samples from patients with NSCLC at disease progression following previous EGFR-tyrosine kinase inhibitor (TKI) therapy was investigated to determine osimertinib treatment eligibility. METHODS: Matched tumor tissue and plasma samples from patients screened for AURA extension and AURA2 phase II studies were tested for EGFRm using tissue- and plasma-based cobas(®) EGFR Mutation Tests v2...
April 17, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28427807/targeted-next-generation-sequencing-in-patients-with-myotonia-congenita
#7
Valentina Ferradini, Marco Cassone, Sara Nuovo, Ilaria Bagni, Rosaria D'Apice, Annalisa Botta, Giuseppe Novelli, Federica Sangiuolo
INTRODUCTION: Myotonia Congenita (MC) is a nondystrophic skeletal muscle disease characterized by muscle stiffness, weakness, delayed skeletal relaxation and hypertrophic muscle. The disease can be inherited as dominant or recessive. More than 130 mutations in CLCN1 gene have been identified. MATERIALS AND METHODS: We analyzed the entire coding region and exon-intron boundaries of the CLCN1 gene in 40 MC patients. Samples already Sanger-sequenced were successively evaluated by Next Generation Sequencing (NGS), on Ion Torrent PGM...
April 17, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28424887/a-metagenomics-study-for-the-identification-of-respiratory-viruses-in-mixed-clinical-specimens-an-application-of-the-iterative-mapping-approach
#8
Yu-Nong Gong, Shu-Li Yang, Guang-Wu Chen, Yu-Wen Chen, Yhu-Chering Huang, Hsiao-Chen Ning, Kuo-Chien Tsao
Metagenomic approaches to detect viral genomes and variants in clinical samples have various challenges, including low viral titers and bacterial and human genome contamination. To address these limitations, we examined a next-generation sequencing (NGS) and iterative mapping approach for virus detection in clinical samples. We analyzed 40 clinical specimens from hospitalized children diagnosed with acute bronchiolitis, croup, or respiratory tract infections in which virus identification by viral culture or polymerase chain reaction (PCR) was unsuccessful...
April 19, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28424865/immunostaining-for-hu-c-d-and-cd56-is-useful-for-a-definitive-histopathological-diagnosis-of-congenital-and-acquired-isolated-hypoganglionosis
#9
Koichiro Yoshimaru, Tomoaki Taguchi, Satoshi Obata, Junkichi Takemoto, Yoshiaki Takahashi, Tsuyoshi Iwanaka, Yusuke Yanagi, Masaaki Kuda, Kina Miyoshi, Toshiharu Matsuura, Yoshiaki Kinoshita, Takako Yoshioka, Atsuko Nakazawa, Yoshinao Oda
Isolated hypoganglionosis (IHG) has been proposed as a distinct entity with two subtypes: congenital IHG (CIHG) and acquired IHG (AIHG). However, due to the rarity of the disease and the lack of defining histological criteria, the concept of IHG is not widely accepted. We studied paraffin-embedded intestinal specimens from 79 patients diagnosed with Hirschsprung's disease (HD) (n = 49), CIHG (n = 25), and AIHG (n = 5) collected between January 1996 and December 2015. Histopathological diagnosis of HD, CIHG, and AIHG was confirmed by hematoxylin and eosin staining and immunohistochemical staining using Hu C/D and CD56...
April 19, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28424669/inferring-microbial-interactions-in-the-gut-of-the-hong-kong-whipping-frog-polypedates-megacephalus-and-a-validation-using-probiotics
#10
Francis Cheng-Hsuan Weng, Grace Tzun-Wen Shaw, Chieh-Yin Weng, Yi-Ju Yang, Daryi Wang
The concerted activity of intestinal microbes is crucial to the health and development of their host organisms. Investigation of microbial interactions in the gut should deepen our understanding of how these micro-ecosystems function. Due to advances in Next Generation Sequencing (NGS) technologies, various bioinformatic strategies have been proposed to investigate these microbial interactions. However, due to the complexity of the intestinal microbial community and difficulties in monitoring their interactions, at present there is a gap between the theory and biological application...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28424161/response-and-progression-on-midostaurin-in-advanced-systemic-mastocytosis-kit-d816v-and-other-molecular-markers
#11
Mohamad Jawhar, Juliana Schwaab, Nicole Naumann, Hans-Peter Horny, Karl Sotlar, Torsten Haferlach, Georgia Metzgeroth, Alice Fabarius, Peter Valent, Wolf-Karsten Hofmann, Nicholas C P Cross, Manja Meggendorfer, Andreas Reiter
In advanced systemic mastocytosis (advSM), disease evolution is often triggered by activating KIT mutations (D816V in >80% of cases) and by additional mutations, e.g. in SRSF2, ASXL1 and/or RUNX1 (S/A/R(pos), >60% of cases). In a recently reported phase-II-study, midostaurin, a multikinase/KIT inhibitor, demonstrated an overall response rate (ORR) of 60% in advSM but biomarkers predictive of response are lacking. We evaluated the impact of molecular markers (KIT D816V, S/A/R(pos)) at baseline and during follow-up in 38 midostaurin-treated advSM patients...
April 19, 2017: Blood
https://www.readbyqxmd.com/read/28423598/next-generation-mapping-reveals-novel-large-genomic-rearrangements-in-prostate-cancer
#12
Weerachai Jaratlerdsiri, Eva K F Chan, Desiree C Petersen, Claire Yang, Peter I Croucher, M S Riana Bornman, Palak Sheth, Vanessa M Hayes
Complex genomic rearrangements are common molecular events driving prostate carcinogenesis. Clinical significance, however, has yet to be fully elucidated. Detecting the full range and subtypes of large structural variants (SVs), greater than one kilobase in length, is challenging using clinically feasible next generation sequencing (NGS) technologies. Next generation mapping (NGM) is a new technology that allows for the interrogation of megabase length DNA molecules outside the detection range of single-base resolution NGS...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423545/hobnail-variant-of-papillary-thyroid-carcinoma-molecular-profiling-and-comparison-to-classical-papillary-thyroid-carcinoma-poorly-differentiated-thyroid-carcinoma-and-anaplastic-thyroid-carcinoma
#13
Lianghong Teng, Wanglong Deng, Junliang Lu, Jing Zhang, Xinyu Ren, Huanli Duan, Shannon Chuai, Feidie Duan, Wei Gao, Tao Lu, Huanwen Wu, Zhiyong Liang
BACKGROUND: As a rare but aggressive papillary thyroid carcinoma (PTC) variant, the genetic changes of hobnail variant of PTC (HVPTC) are still unclear. RESULTS: The prevalence of HVPTC was 1.69% (18/1062) of all PTC diagnosed in our cohort. 73 samples from 55 patients (17 HVPTC, 26 CPTC, 7 PDTC and 5 ATC) were successfully analyzed using targeted NGS with an 18-gene panel. Thirty-seven mutation variant types were identified among 11 genes. BRAF V600E mutation was the most common mutation, which is present in almost all HVPTC samples (16/17, 94%), most CPTC samples (20/26, 77%), and none of the ATC and PDTC samples...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423512/kinase-analysis-of-penile-squamous-cell-carcinoma-on-multiple-platforms-to-identify-potential-therapeutic-targets
#14
Eddy S Yang, Christopher D Willey, Amitkumar Mehta, Michael R Crowley, David K Crossman, Dongquan Chen, Joshua C Anderson, Gurudatta Naik, Deborah L Della Manna, Tiffiny S Cooper, Guru Sonpavde
Penile squamous cell carcinoma (PSCC) is an orphan malignancy with poorly understood biology and suboptimal systemic therapy. Given that kinases may be drivers and readily actionable, we performed comprehensive multiplatform analysis of kinases in PSCC tumor and normal tissue. Fresh frozen tumors were collected from 11 patients with PSCC. After macrodissection to demarcate tumor from normal tissue, the samples underwent multiplatform analysis of kinases. Next Generation Sequencing (NGS) of 517 kinase genes was performed using Agilent Kinome capture and run on the Illumina MiSeq at PE150bp...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423363/multiple-gene-panel-analysis-in-a-case-series-of-255-women-with-hereditary-breast-and-ovarian-cancer
#15
Gianluca Tedaldi, Michela Tebaldi, Valentina Zampiga, Rita Danesi, Valentina Arcangeli, Mila Ravegnani, Ilaria Cangini, Francesca Pirini, Elisabetta Petracci, Andrea Rocca, Fabio Falcini, Dino Amadori, Daniele Calistri
As new genes predisposing to breast (BC) and ovarian cancer (OC) are constantly emerging, the use of panels of genes analyzed by Next-Generation Sequencing (NGS) is increasing in clinical diagnostics. The identification of a large number of new germline mutations allows for deeper knowledge of cancer predisposition, although raising many questions about patient management.BC and OC patients recruited by our counseling service between 2012-2015 were included in this study. DNA was extracted from peripheral blood and a panel of 94 genes involved in hereditary tumors was analyzed by NGS...
April 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423279/ngmcp-noble-gas-bound-half-sandwich-complexes-ng-he-rn-m-be-ba-cp-%C3%AE-5-c5h5
#16
Ranajit Saha, Sudip Pan, Pratim Kumar Chattaraj
Structures, bonding and stability half-sandwich complexes with general formula, NgMCp+ (Ng = He-Rn, M = Be-Ba, Cp = 5-C5H5) are analyzed through ab initio computation. MCp+ complexes possess remarkable Ng binding ability, particularly for M = Be and Mg. While for Ar-Rn bound analogues the bond dissociation energy in the former complex ranges within 17.5-28.0 kcal mol-1, it becomes 10.4-18.7 kcal mol-1 in the latter complex. In fact, BeCp+ is able to form strong bond with the two most inert elements, He and Ne...
April 19, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28420428/significant-heterogeneity-in-wolbachia-copy-number-within-and-between-populations-of-onchocerca-volvulus
#17
Samuel Armoo, Stephen R Doyle, Mike Y Osei-Atweneboana, Warwick N Grant
BACKGROUND: Wolbachia are intracellular bacteria found in arthropods and several filarial nematode species. The filarial Wolbachia have been proposed to be involved in the immunopathology associated with onchocerciasis. Higher Wolbachia-to-nematode ratios have been reported in the savannah-ecotype compared to the forest-ecotype, and have been interpreted as consistent with a correlation between Wolbachia density and disease severity. However, factors such as geographic stratification and ivermectin drug exposure can lead to significant genetic heterogeneity in the nematode host populations, so we investigated whether Wolbachia copy number variation is also associated with these underlying factors...
April 18, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28420126/novel-genetic-variants-associated-with-child-refractory-esophageal-stricture-with-food-allergy-by-exome-sequencing
#18
Min Yang, Min Xiong, Huan Chen, Lanlan Geng, Peiyu Chen, Jing Xie, Shui Qing Ye, Ding-You Li, Sitang Gong
BACKGROUND: Refractory esophageal stricture (RES) may be attributed to food allergy. Its etiology and pathogenesis are not fully understood. Identification of novel genetic variants associated with this disease by exome sequencing (exome-seq) may provide new mechanistic insights and new therapeutic targets. METHODS: To identify new and novel disease-associating variants, whole-exome sequencing was performed on an Illumina NGS platform in three children with RES as well as food allergy...
April 15, 2017: Nutrients
https://www.readbyqxmd.com/read/28419837/identification-and-molecular-cloning-of-novel-transcripts-of-the-human-kallikrein-related-peptidase-10-klk10-gene-using-next-generation-sequencing
#19
Panagiotis G Adamopoulos, Christos K Kontos, Andreas Scorilas
Kallikreins (KLKs) form the largest group of serine proteases in the human genome sharing many structural and functional characteristics. Multiple alternative transcripts have been reported for most human KLKs, while many of them have been found aberrantly expressed in various human malignancies, thus possessing significant prognostic or/and diagnostic value. Alternative splicing of cancer-related genes is a common cellular mechanism accounting for cancer cell transcriptome complexity, as it affects cell cycle control, proliferation, apoptosis, invasion, and metastasis...
April 15, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28419628/hla-hd-an-accurate-hla-typing-algorithm-for-next-generation-sequencing-data
#20
Shuji Kawaguchi, Koichiro Higasa, Masakazu Shimizu, Ryo Yamada, Fumihiko Matsuda
The accurate typing of HLA alleles is critical for a variety of medical applications, such as genomic studies of multifactorial diseases, including immune system and inflammation-related disorders, and donor selection in organ transplantation and regenerative medicine. Here we developed a new algorithm for determining HLA alleles using next-generation sequencing (NGS) results. The method consists of constructing an extensive dictionary of HLA alleles, precise mapping of the NGS reads, and calculating a score based on weighted read counts to select the most suitable pair of alleles...
April 16, 2017: Human Mutation
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