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https://www.readbyqxmd.com/read/28454199/-genetic-diagnostics-for-cardiomyopathies
#1
Frauke Czepluch, Bernd Wollnik, Gerd Hasenfuß
Cardiomyopathies often have a genetic etiology. New genetic diagnostic strategies based on next generation sequencing (NGS)-approaches will continuously increase our knowledge about the genetic basis of cardiomyopathies within the following years. Diagnostics and therapy of rare, genetically-induced cardiac diseases increasingly require special cardiac and genetic knowledge. Interestingly, mutations in the same gene or even identical gene mutations can be associated with different cardiomyopathy phenotypes and can exhibit incomplete penetrance or variable expressivity...
May 2017: Deutsche Medizinische Wochenschrift
https://www.readbyqxmd.com/read/28454001/bacterial-community-shift-and-improved-performance-induced-by-in-situ-preparing-dual-graphene-modified-bioelectrode-in-microbial-fuel-cell
#2
Junfeng Chen, Yongyou Hu, Lihua Zhang, Wantang Huang, Jian Sun
Dual graphene modified bioelectrode (D-GM-BE) was prepared by in situ microbial-induced reduction of graphene oxide (GO) and polarity reversion in microbial fuel cell (MFC). Next Generation Sequencing technology was used to elucidate bacterial community shift in response to improved performance in D-GM-BE MFC. The results indicated an increase in the relative ratio of Proteobacteria, but a decrease of Firmicutes was observed in graphene modified bioanode (GM-BA); increase of Proteobacteria and Firmicutes were observed in graphene modified biocathode (GM-BC)...
April 17, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28453842/a-cluster-of-fatal-tick-borne-encephalitis-virus-infection-in-organ-transplant-setting
#3
Dariusz Lipowski, Marta Popiel, Karol Perlejewski, Shota Nakamura, Iwona Bukowska-Osko, Ewa Rzadkiewicz, Tomasz Dzieciatkowski, Anna Milecka, Wojciech Wenski, Michal Ciszek, Alicja Debska-Slizien, Ewa Ignacak, Kamila Caraballo Cortes, Agnieszka Pawelczyk, Andrzej Horban, Marek Radkowski, Tomasz Laskus
Background.: Tick-borne encephalitis virus (TBEV) infection has become a major health problem in Europe and is currently a common cause of viral brain infection in many countries. Encephalitis in transplant recipients, althrough rare, is becoming a recognized complication. Our study provides the first description of transmission of TBEV through transplantation of solid organs. Methods.: Three patients who received solid organ transplants from a single donor (2 received kidney, and 1 received liver) developed encephalitis 17-49 days after transplantation and subsequently died...
March 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28453743/targeted-next-generation-sequencing-of-pediatric-neuro-oncology-patients-improves-diagnosis-identifies-pathogenic-germline-mutations-and-directs-targeted-therapy
#4
Cassie N Kline, Nancy M Joseph, James P Grenert, Jessica van Ziffle, Eric Talevich, Courtney Onodera, Mariam Aboian, Soonmee Cha, David R Raleigh, Steve Braunstein, Joseph Torkildson, David Samuel, Michelle Bloomer, Alejandra G de Alba Campomanes, Anuradha Banerjee, Nicholas Butowski, Corey Raffel, Tarik Tihan, Andrew W Bollen, Joanna J Phillips, W Michael Korn, Iwei Yeh, Boris C Bastian, Nalin Gupta, Sabine Mueller, Arie Perry, Theodore Nicolaides, David A Solomon
Background.: Molecular profiling is revolutionizing cancer diagnostics and leading to personalized therapeutic approaches. Herein we describe our clinical experience performing targeted sequencing for 31 pediatric neuro-oncology patients. Methods.: We sequenced 510 cancer-associated genes from tumor and peripheral blood to identify germline and somatic mutations, structural variants, and copy number changes. Results.: Genomic profiling was performed on 31 patients with tumors including 11 high-grade gliomas, 8 medulloblastomas, 6 low-grade gliomas, 1 embryonal tumor with multilayered rosettes, 1 pineoblastoma, 1 uveal ganglioneuroma, 1 choroid plexus carcinoma, 1 chordoma, and 1 high-grade neuroepithelial tumor...
May 1, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28453708/towards-a-global-cancer-knowledge-network-dissecting-the-current-international-cancer-genomic-sequencing-landscape
#5
D J Vis, J Lewin, R G Liao, M Mao, F Andre, R L Ward, F Calvo, B T Teh, A A Camargo, B M Knoppers, C L Sawyers, L F A Wessels, M Lawler, L L Siu, E Voest
Background: While next generation sequencing has enhanced our understanding of the biological basis of malignancy, current knowledge on global practices for sequencing cancer samples is limited. To address this deficiency, we developed a survey to provide a snapshot of current sequencing activities globally, identify barriers to data sharing and use this information to develop sustainable solutions for the cancer research community. Methods: A multi-item survey was conducted assessing demographics, clinical data collection, genomic platforms, privacy/ethics concerns, funding sources and data sharing barriers for sequencing initiatives globally...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28453696/epstein-barr-virus-associated-gastric-cancer-reveals-intratumoral-heterogeneity-of-pik3ca-mutations
#6
C Böger, S Krüger, H M Behrens, S Bock, J Haag, H Kalthoff, C Röcken
Background: Recent whole-genome sequencing identified four molecular subtypes of gastric cancer (GC), of which the subgroup of Epstein-Barr virus-associated GC (EBVaGC) showed a significant enrichment of PIK3CA mutations. We here aimed to validate independently the enrichment of PIK3CA mutations in EBVaGC of a Central European GC cohort, to correlate EBV status with clinico-pathological patient characteristics and to test for a major issue of GC, intratumoral heterogeneity. Patients and methods: In a first step, 484 GCs were screened for EBV and PIK3CA hot spot mutations of exon 9/20 using EBER in situ hybridization and pyrosequencing, respectively...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28453677/afs-identification-and-quantification-of-species-composition-by-metagenomic-sequencing
#7
Yongchao Liu, Fabian Ripp, Rene Koeppel, Hanno Schmidt, Sören Lukas Hellmann, Mathias Weber, Christopher Felix Krombholz, Bertil Schmidt, Thomas Hankeln
Summary: DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453527/altered-nucleocytoplasmic-proteome-and-transcriptome-distributions-in-an-in-vitro-model-of-amyotrophic-lateral-sclerosis
#8
Jee-Eun Kim, Yoon Ho Hong, Jin Young Kim, Gye Sun Jeon, Jung Hee Jung, Byung-Nam Yoon, Sung-Yeon Son, Kwang-Woo Lee, Jong-Il Kim, Jung-Joon Sung
Aberrant nucleocytoplasmic localization of proteins has been implicated in many neurodegenerative diseases. Evidence suggests that cytoplasmic mislocalization of nuclear proteins such as transactive response DNA-binding protein 43 (TDP-43) and fused in sarcoma (FUS) may be associated with neurotoxicity in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration. This study investigated the changes in nucleocytoplasmic distributions of the proteome and transcriptome in an in vitro model of ALS...
2017: PloS One
https://www.readbyqxmd.com/read/28453362/a-novel-mutation-in-the-dominantly-inherited-topors-gene-supports-haploinsufficiency-as-the-mechanism-of-retinitis-pigmentosa
#9
Marta Latasiewicz, Anna Paola Salvetti, Robert E MacLaren
BACKGROUND: Inherited retinal degenerations are a major cause of untreatable blindness in the younger age group. Recent advances in gene therapy using adeno-associated viral (AAV) vectors have raised the possibility of slowing or stopping retinal degenerations with gene replacement in cases of gene deficiency. MATERIALS AND METHODS: In this report, we present a family with autosomal dominant retinitis pigmentosa. A screen for common ADRP genes was performed with 105 genes targeted...
April 28, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28449382/current-use-of-chromosomal-microarray-by-australian-paediatricians-and-implications-for-the-implementation-of-next-generation-sequencing
#10
Victoria McKay, Daryl Efron, Elizabeth E Palmer, Susan M White, Chris Pearson, Margie Danchin
AIM: Chromosomal microarray (CMA) is an important diagnostic test for children with multiple congenital anomalies or certain developmental behavioural problems suggestive of an underlying genetic diagnosis. However, there are medical and ethical complexities to its use and few Australian policies to guide practice. We aimed to describe the current practice of Australian paediatricians in relation to CMA testing. We hypothesised that there are knowledge gaps in their use of CMA. METHODS: Online survey completed between September 2015 and January 2016 by paediatricians in secondary care settings...
April 27, 2017: Journal of Paediatrics and Child Health
https://www.readbyqxmd.com/read/28449315/panelcn-mops-copy-number-detection-in-targeted-ngs-panel-data-for-clinical-diagnostics
#11
Gundula Povysil, Antigoni Tzika, Julia Vogt, Verena Haunschmid, Ludwine Messiaen, Johannes Zschocke, Günter Klambauer, Sepp Hochreiter, Katharina Wimmer
Targeted next-generation-sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy number variations (CNVs) in addition to single-nucleotide-variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control, incidental findings, and user-friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn...
April 27, 2017: Human Mutation
https://www.readbyqxmd.com/read/28449120/sigseeker-a-peak-calling-ensemble-approach-for-constructing-epigenetic-signatures
#12
Jens Lichtenberg, Laura Elnitski, David M Bodine
Motivation: Epigenetic data are invaluable when determining the regulatory programs governing a cell. Based on use of next-generation sequencing data for characterizing epigenetic marks and transcription factor binding, numerous peak-calling approaches have been developed to determine sites of genomic significance in these data. Such analyses can produce a large number of false positive predictions, suggesting that sites supported by multiple algorithms provide a stronger foundation for inferring and characterizing regulatory programs associated with the epigenetic data...
April 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28449108/poly-a-clickseq-click-chemistry-for-next-generation-3%C3%AE-end-sequencing-without-rna-enrichment-or-fragmentation
#13
Andrew Routh, Ping Ji, Elizabeth Jaworski, Zheng Xia, Wei Li, Eric J Wagner
The recent emergence of alternative polyadenylation (APA) as an engine driving transcriptomic diversity has stimulated the development of sequencing methodologies designed to assess genome-wide polyadenylation events. The goal of these approaches is to enrich, partition, capture and ultimately sequence poly(A) site junctions. However, these methods often require poly(A) enrichment, 3΄ linker ligation steps, and RNA fragmentation, which can necessitate higher levels of starting RNA, increase experimental error and potentially introduce bias...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449106/microbiomeanalyst-a-web-based-tool-for-comprehensive-statistical-visual-and-meta-analysis-of-microbiome-data
#14
Achal Dhariwal, Jasmine Chong, Salam Habib, Irah L King, Luis B Agellon, Jianguo Xia
The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational pipelines and robust protocols have been established to enable efficient raw data processing and annotation. The focus has shifted toward downstream statistical analysis and functional interpretation...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28448960/utility-of-genomic-analysis-in-differentiating-synchronous-and-metachronous-lung-adenocarcinomas-from-primary-adenocarcinomas-with-intrapulmonary-metastasis
#15
Jad Saab, Hamid Zia, Susan Mathew, Michael Kluk, Navneet Narula, Helen Fernandes
Distinguishing synchronous and metachronous primary lung adenocarcinomas from adenocarcinomas with intrapulmonary metastasis is essential for optimal patient management. In this study, multiple lung adenocarcinomas occurring in the same patient were evaluated using comprehensive histopathologic evaluation supplemented with molecular analysis. The cohort included 18 patients with a total of 52 lung adenocarcinomas. Eleven patients had a new diagnosis of multiple adenocarcinomas in the same lobe (n=5) or different lobe (n=6)...
April 24, 2017: Translational Oncology
https://www.readbyqxmd.com/read/28448897/a-performance-evaluation-of-nextera-xt-and-kapa-hyperplus-for-rapid-illumina-library-preparation-of-long-range-mitogenome-amplicons
#16
Joseph D Ring, Kimberly Sturk-Andreaggi, Michelle A Peck, Charla Marshall
Next-generation sequencing (NGS) facilitates the rapid and high-throughput generation of human mitochondrial genome (mitogenome) data to build population and reference databases for forensic comparisons. To this end, long-range amplification provides an effective method of target enrichment that is amenable to library preparation assays employing DNA fragmentation. This study compared the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA) and the KAPA HyperPlus Library Preparation Kit (Kapa Biosystems, Wilmington, MA) for enzymatic fragmentation and indexing of ∼8500bp mitogenome amplicons for Illumina sequencing...
April 5, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28448765/digital-assays-part-i-partitioning-statistics-and-digital-pcr
#17
Amar S Basu
A digital assay is one in which the sample is partitioned into many small containers such that each partition contains a discrete number of biological entities (0, 1, 2, 3, …). A powerful technique in the biologist's toolkit, digital assays bring a new level of precision in quantifying nucleic acids, measuring proteins and their enzymatic activity, and probing single-cell genotypes and phenotypes. Part I of this review begins with the benefits and Poisson statistics of partitioning, including sources of error...
April 1, 2017: SLAS Technology
https://www.readbyqxmd.com/read/28448556/a-highly-specific-and-sensitive-massive-parallel-sequencer-based-test-for-somatic-mutations-in-non-small-cell-lung-cancer
#18
Yoshiaki Inoue, Jun Shiihara, Hitoshi Miyazawa, Hiromitsu Ohta, Megumi Higo, Yoshiaki Nagai, Kunihiko Kobayashi, Yasuo Saijo, Masanori Tsuchida, Mitsuo Nakayama, Koichi Hagiwara
Molecular targeting therapy for non-small cell lung cancer (NSCLC) has clarified the importance of mutation testing when selecting treatment regimens. As a result, multiple-gene mutation tests are urgently needed. We developed a next-generation sequencer (NGS)-based, multi-gene test named the MINtS for investigating driver mutations in both cytological specimens and snap-frozen tissue samples. The MINtS was used to investigate the EGFR, KRAS, BRAF genes from DNA, and the ERBB2, and the ALK, ROS1, and RET fusion genes from RNA...
2017: PloS One
https://www.readbyqxmd.com/read/28448495/dysregulation-of-inf2-mediated-mitochondrial-fission-in-spop-mutated-prostate-cancer
#19
Xiaofeng Jin, Jie Wang, Kun Gao, Pingzhao Zhang, Longfang Yao, Yan Tang, Lisha Tang, Jian Ma, Jiantao Xiao, Enceng Zhang, Jie Zhu, Bin Zhang, Shi-Min Zhao, Yao Li, Shancheng Ren, Haojie Huang, Long Yu, Chenji Wang
Next-generation sequencing of the exome and genome of prostate cancers has identified numerous genetic alternations. SPOP (Speckle-type POZ Protein) was one of the most frequently mutated genes in primary prostate cancer, suggesting SPOP is a potential driver of prostate cancer development and progression. However, how SPOP mutations contribute to prostate cancer pathogenesis remains poorly understood. SPOP acts as an adaptor protein of the CUL3-RBX1 E3 ubiquitin ligase complex that generally recruits substrates for ubiquitination and subsequent degradation...
April 27, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28448473/transcriptomic-analysis-of-calcium-remodeling-in-colorectal-cancer
#20
Enrique Pérez-Riesgo, Lucía G Gutiérrez, Daniel Ubierna, Alberto Acedo, Mary P Moyer, Lucía Núñez, Carlos Villalobos
Colorectal cancer (CRC) cells undergo the remodeling of intracellular Ca(2+) homeostasis, which contributes to cancer hallmarks such as enhanced proliferation, invasion and survival. Ca(2+) remodeling includes critical changes in store-operated Ca(2+) entry (SOCE) and Ca(2+) store content. Some changes have been investigated at the molecular level. However, since nearly 100 genes are involved in intracellular Ca(2+) transport, a comprehensive view of Ca(2+) remodeling in CRC is lacking. We have used Next Generation Sequencing (NGS) to investigate differences in expression of 77 selected gene transcripts involved in intracellular Ca(2+) transport in CRC...
April 27, 2017: International Journal of Molecular Sciences
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