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https://www.readbyqxmd.com/read/29457878/genetic-determinants-of-heart-failure-facts-and-numbers
#1
EDITORIAL
Frauke S Czepluch, Bernd Wollnik, Gerd Hasenfuß
The relevance of gene mutations leading to heart diseases and hence heart failure has become evident. The risk for and the course of heart failure depends on genomic variants and mutations underlying the so-called genetic predisposition. Genetic contribution to heart failure is highly heterogenous and complex. For any patient with a likely inherited heart failure syndrome, genetic counselling is recommended and important. In the last few years, novel sequencing technologies (named next-generation sequencing - NGS) have dramatically improved the availability of molecular testing, the efficiency of genetic analyses, and moreover reduced the cost for genetic testing...
February 19, 2018: ESC Heart Failure
https://www.readbyqxmd.com/read/29456477/dual-diagnosis-of-ellis-van-creveld-syndrome-and-hearing-loss-in-a-consanguineous-family
#2
Barbara Vona, Reza Maroofian, Geetu Mendiratta, Matthew Croken, Siwu Peng, Xiaoqian Ye, Jamileh Rezazadeh, Paulina Bahena, Caroline Lekszas, Thomas Haaf, Lisa Edelmann, Lisong Shi
Multilocus analysis of rare or genetically heterogeneous diseases is a distinct advantage of next-generation sequencing (NGS) over conventional single-gene investigations. Recent studies have begun to uncover an under-recognized prevalence of dual molecular diagnoses in patients with a "blended" phenotype that is the result of 2 clinical diagnoses involving 2 separate genetic loci. This blended phenotype could be mistakenly interpreted as a novel clinical extension of a single-gene disorder. In this study, we ascertained a proband from a large consanguineous Iranian family who manifests postlingual, progressive, moderate hearing loss in addition to suspected Ellis-van Creveld syndrome phenotype...
December 2017: Molecular Syndromology
https://www.readbyqxmd.com/read/29455155/newly-designed-11-gene-panel-reveals-first-case-of-hereditary-amyloidosis-captured-by-massive-parallel-sequencing
#3
Zuzana Chyra Kufova, Tereza Sevcikova, Jaroslav Januska, Petr Vojta, Arpad Boday, Pavla Vanickova, Jana Filipova, Katerina Growkova, Tomas Jelinek, Marian Hajduch, Roman Hajek
AIMS: Amyloidosis is caused by deposition of abnormal protein fibrils, leading to damage of organ function. Hereditary amyloidosis represents a monogenic disease caused by germline mutations in 11 amyloidogenic precursor protein genes. One of the important but non-specific symptoms of amyloidosis is hypertrophic cardiomyopathy. Diagnostics of hereditary amyloidosis is complicated and the real cause can remain overlooked. We aimed to design hereditary amyloidosis gene panel and to introduce new next-generation sequencing (NGS) approach to investigate hereditary amyloidosis in a cohort of patients with hypertrophic cardiomyopathy of unknown significance...
February 17, 2018: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/29454370/isolation-of-a-novel-rhabdovirus-from-an-insectivorous-bat-pipistrellus-kuhlii-in-italy
#4
Davide Lelli, Alice Prosperi, Ana Moreno, Chiara Chiapponi, Anna Maria Gibellini, Paola De Benedictis, Stefania Leopardi, Enrica Sozzi, Antonio Lavazza
BACKGROUND: Rhabdoviridae is one of the most ecologically diverse families of RNA viruses which can infect a wide range of vertebrates and invertebrates. Bats, among mammals, are pointed to harbor a significantly higher proportion of unknown or emerging viruses with zoonotic potential. Herein, we report the isolation of a novel rhabdovirus, detected in the framework of a virological survey on bats implemented in North Italy. METHODS: Virus isolation and identification were performed on samples of 635 bats by using cell cultures, negative staining electron microscopy and PCRs for different viruses...
February 17, 2018: Virology Journal
https://www.readbyqxmd.com/read/29453415/erlin1-mutations-cause-teenage-onset-slowly-progressive-als-in-a-large-turkish-pedigree
#5
Ceren Tunca, Fulya Akçimen, Cemre Coşkun, Aslı Gündoğdu-Eken, Cemile Kocoglu, Betül Çevik, Can Ebru Bekircan-Kurt, Ersin Tan, A Nazlı Başak
Amyotrophic lateral sclerosis (ALS) is a late-onset motor neuron disease with mostly dominant inheritance and a life expectancy of 2-5 years; however, a quite common occurrence of atypical forms of the disease, due to recessive inheritance, has become evident with the use of NGS technologies. In this paper, we describe a family with close consanguinity for at least four generations, suffering from a slowly progressive form of ALS. Spastic walking is observed since teenage years, while bulbar symptoms start much later, at the fifth or sixth decade of life...
February 16, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29452859/evaluation-of-liquid-biopsies-for-detection-of-emerging-mutated-genes-in-metastatic-colorectal-cancer
#6
Hiroyasu Furuki, Takeshi Yamada, Goro Takahashi, Takuma Iwai, Michihiro Koizumi, Seiichi Shinji, Yasuyuki Yokoyama, Kohki Takeda, Nobuhiko Taniai, Eiji Uchida
BACKGROUND: Detection of gene mutations is important for planning molecular targeted therapy. Although most gene mutations are concordant between primary colon cancers and their liver metastases, new mutations can emerge in metastases. The liquid biopsy is a newly developed, gene analytic method to detect mutations in metastatic tumors. In this prospective study, we evaluated the applicability of liquid biopsies in the detection of mutations in primary and metastatic tumors. METHODS: We included 22 patients with liver metastases from colorectal cancer and extracted DNA from primary colorectal tumors, metastatic liver tumors, and peripheral blood (liquid biopsy)...
February 2, 2018: European Journal of Surgical Oncology
https://www.readbyqxmd.com/read/29451897/selective-identification-of-somatic-mutations-in-pancreatic-cancer-cells-through-a-combination-of-next-generation-sequencing-of-plasma-dna-using-molecular-barcodes-and-a-bioinformatic-variant-filter
#7
Yoji Kukita, Kazuyoshi Ohkawa, Ryoji Takada, Hiroyuki Uehara, Kazuhiro Katayama, Kikuya Kato
The accuracy of next-generation sequencing (NGS) for detecting tumor-specific mutations in plasma DNA is hindered by errors introduced during PCR/sequencing, base substitutions caused by DNA damage, and pre-existing mutations in normal cells that are present at a low frequency. Here, we performed NGS of genes related to pancreatic cancer (comprising 2.8 kb of genomic DNA) in plasma DNA (average 4.5 ng) using molecular barcodes. The average number of sequenced molecules was 900, and the sequencing depth per molecule was 100 or more...
2018: PloS One
https://www.readbyqxmd.com/read/29449843/insights-into-the-structural-basis-of-antibody-affinity-maturation-from-next-generation-sequencing
#8
REVIEW
Arjun K Mishra, Roy A Mariuzza
Affinity maturation is the process whereby the immune system generates antibodies of higher affinities during a response to antigen. It is unique in being the only evolutionary mechanism known to operate on a molecule in an organism's own body. Deciphering the structural mechanisms through which somatic mutations in antibody genes increase affinity is critical to understanding the evolution of immune repertoires. Next-generation sequencing (NGS) has allowed the reconstruction of antibody clonal lineages in response to viral pathogens, such as HIV-1, which was not possible in earlier studies of affinity maturation...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29449000/an-immunohistochemical-and-molecular-analysis-of-papillary-proliferation-of-the-endometrium
#9
Colin J R Stewart, Susan Bigby, Tino Giardina, Fabienne Grieu-Iacopetta, Benhur Amanuel
Papillary proliferations of the endometrium (PPEs) are uncommon lesions that are often associated with endometrial polyps. PPEs occasionally precede or co-exist with atypical endometrial hyperplasia or adenocarcinoma, but their pathogenesis and relationship to endometrial neoplasia is uncertain. In the present study 11 PPEs, including eight benign papillary proliferations (BPPs) and three complex papillary hyperplasias (CPHs) were examined immunohistochemically for expression of PAX2, BAF250a, p16, β-catenin and DNA mismatch repair (MMR) proteins...
February 12, 2018: Pathology
https://www.readbyqxmd.com/read/29444661/rna-qc-chain-comprehensive-and-fast-quality-control-for-rna-seq-data
#10
Qian Zhou, Xiaoquan Su, Gongchao Jing, Songlin Chen, Kang Ning
BACKGROUND: RNA-Seq has become one of the most widely used applications based on next-generation sequencing technology. However, raw RNA-Seq data may have quality issues, which can significantly distort analytical results and lead to erroneous conclusions. Therefore, the raw data must be subjected to vigorous quality control (QC) procedures before downstream analysis. Currently, an accurate and complete QC of RNA-Seq data requires of a suite of different QC tools used consecutively, which is inefficient in terms of usability, running time, file usage, and interpretability of the results...
February 14, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29444253/hiv-1-genotypic-resistance-testing-using-the-vela-automated-next-generation-sequencing-platform
#11
Stéphanie Raymond, Florence Nicot, Romain Carcenac, Caroline Lefebvre, Nicolas Jeanne, Karine Saune, Pierre Delobel, Jacques Izopet
Objectives: To evaluate the diagnostic performance of the Vela next-generation sequencing (NGS) system in conjunction with the Sentosa SQ HIV Genotyping Assay for genotyping HIV-1. Methods: Plasma RNA was extracted and templates prepared with the Sentosa SX instrument before sequencing the HIV-1 polymerase on the Sentosa SQ301 Sequencer (PGM IonTorrent). The Vela NGS System was compared with direct sequencing and the 454 GS-FLX (Roche) and MiSeq (Illumina) systems for genotypic resistance testing on clinical samples...
February 12, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29444237/compression-of-genomic-sequencing-reads-via-hash-based-reordering-algorithm-and-analysis
#12
Shubham Chandak, Kedar Tatwawadi, Tsachy Weissman, Inanc Birol
Motivation: New Generation Sequencing (NGS) technologies for genome sequencing produce large amounts of short genomic reads per experiment, which are highly redundant and compressible. However, general-purpose compressors are unable to exploit this redundancy due to the special structure present in the data. Results: We present a new algorithm for compressing reads both with and without preserving the read order. In both cases, it achieves 1.4×-2× compression gain over state-of-the-art read compression tools for datasets containing as many as 3 billion Illumina reads...
February 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29443391/human-papillomavirus-genome-integration-in-squamous-carcinogenesis-what-have-next-generation-sequencing-studies-taught-us
#13
REVIEW
Ian J Groves, Nicholas Coleman
Human papillomavirus (HPV) infection is associated with ~5% of all human cancers, including a range of squamous cell carcinomas (SCCs). Persistent infection by high-risk HPVs (HRHPVs) is associated with the integration of virus genomes (which are usually stably maintained as extrachromosomal episomes) into host chromosomes. Although HRHPV integration rates differ across human sites of infection, this process appears to be an integral event in HPV-associated neoplastic progression, leading to deregulation of virus oncogene expression, host gene expression modulation and further genomic instability...
February 14, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29442617/assembly-of-highly-repetitive-genomes-using-short-reads-the-genome-of-discrete-typing-unit-iii-trypanosoma-cruzi-strain-231
#14
Rodrigo P Baptista, Joao Luis Reis-Cunha, Jeremy D DeBarry, Egler Chiari, Jessica C Kissinger, Daniella C Bartholomeu, Andrea M Macedo
Next-generation sequencing (NGS) methods are low-cost high-throughput technologies that produce thousands to millions of sequence reads. Despite the high number of raw sequence reads, their short length, relative to Sanger, PacBio or Nanopore reads, complicates the assembly of genomic repeats. Many genome tools are available, but the assembly of highly repetitive genome sequences using only NGS short reads remains challenging. Genome assembly of organisms responsible for important neglected diseases such as Trypanosoma cruzi, the aetiological agent of Chagas disease, is known to be challenging because of their repetitive nature...
February 14, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29441694/presynaptic-congenital-myasthenic-syndrome-with-altered-synaptic-vesicle-homeostasis-linked-to-compound-heterozygous-sequence-variants-in-rph3a
#15
Ricardo A Maselli, Jessica Vázquez, Leah Schrumpf, Juan Arredondo, Marian Lara, Jonathan B Strober, Peter Pytel, Robert L Wollmann, Michael Ferns
BACKGROUND: Monogenic defects of synaptic vesicle (SV) homeostasis have been implicated in many neurologic diseases, including autism, epilepsy, and movement disorders. In addition, abnormal vesicle exocytosis has been associated with several endocrine dysfunctions. METHODS: We report an 11 year old girl with learning disabilities, tremors, ataxia, transient hyperglycemia, and muscle fatigability responsive to albuterol sulfate. Failure of neuromuscular transmission was confirmed by single fiber electromyography...
February 14, 2018: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/29440707/systematic-assessment-of-the-performance-of-whole-genome-amplification-for-snp-cnv-detection-and-%C3%AE-thalassemia-genotyping
#16
Fei He, Wanjun Zhou, Ren Cai, Tizhen Yan, Xiangmin Xu
In this study, we aimed to assess the performance of two whole-genome amplification methods, multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycle (MALBAC), for β-thalassemia genotyping and single-nucleotide polymorphism (SNP)/copy-number variant (CNV) detection using two DNA sequencing assays. We collected peripheral blood, cell lines, and discarded embryos, and carried out MALBAC and MDA on single-cell and five-cell samples. We detected and statistically analyzed differences in the amplification efficiency, positive predictive value, sensitivity, allele dropout (ADO) rate, SNPs, and CV values between the two methods...
February 13, 2018: Journal of Human Genetics
https://www.readbyqxmd.com/read/29440463/immune-activation-underlies-a-sustained-clinical-response-to-yttrium-90-radioembolisation-in-hepatocellular-carcinoma
#17
Valerie Chew, Yun Hua Lee, Lu Pan, Nurul J M Nasir, Chun Jye Lim, Camillus Chua, Liyun Lai, Sharifah Nur Hazirah, Tony Kiat Hon Lim, Brian K P Goh, Alexander Chung, Richard H G Lo, David Ng, Rene L F Filarca, Salvatore Albani, Pierce K H Chow
OBJECTIVES: Yttrium-90 (Y90)-radioembolisation (RE) significantly regresses locally advanced hepatocellular carcinoma and delays disease progression. The current study is designed to deeply interrogate the immunological impact of Y90-RE, which elicits a sustained therapeutic response. DESIGN: Time-of-flight mass cytometry and next-generation sequencing (NGS) were used to analyse the immune landscapes of tumour-infiltrating leucocytes (TILs), tumour tissues and peripheral blood mononuclear cells (PBMCs) at different time points before and after Y90-RE...
February 13, 2018: Gut
https://www.readbyqxmd.com/read/29439875/consensus-document-on-the-implementation-of-next-generation-sequencing-in-the-genetic-diagnosis-of-hereditary-cancer
#18
José Luis Soto, Ignacio Blanco, Orland Díez, Javier García Planells, Isabel Lorda, Gert Matthijs, Mercedes Robledo, Erika Souche, Conxi Lázaro
Genetic diagnosis of hereditary cancer syndromes offers the opportunity to establish more effective predictive and preventive measures for the patient and their families. The ultimate objective is to decrease cancer morbidity and mortality in high genetic risk families. Next Generation Sequencing (NGS) offers an important improvement in the efficiency of genetic diagnosis, allowing an increase in diagnostic yield with a substantial reduction in response times and economic costs. Consequently, the implementation of this new technology is a great opportunity for improvement in the clinical management of affected families...
February 10, 2018: Medicina Clínica
https://www.readbyqxmd.com/read/29439663/salp-a-new-single-stranded-dna-library-preparation-method-especially-useful-for-the-high-throughput-characterization-of-chromatin-openness-states
#19
Jian Wu, Wei Dai, Lin Wu, Jinke Wang
BACKGROUND: Next-generation sequencing (NGS) is fundamental to the current biological and biomedical research. Construction of sequencing library is a key step of NGS. Therefore, various library construction methods have been explored. However, the current methods are still limited by some shortcomings. RESULTS: This study developed a new NGS library construction method, Single strand Adaptor Library Preparation (SALP), by using a novel single strand adaptor (SSA)...
February 13, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29439048/genomic-sequence-of-a-swine-pasivirus-type-1-strain-identified-in-u-s-swine
#20
Baoqing Guo, Hanjun Kim, Ying Zheng, Huigang Shen, Roman M Pogranichniy, Kent J Schwartz, Ganwu Li, Kyoung-Jin Yoon
We report for the first time in the United States the identification of a swine pasivirus (SPaV) strain with a genomic sequence identity of less than 80% to other SPaVs reported in Europe and China, using a next-generation sequencing (NGS) technique in sow tissues collected from an animal study conducted in 2001, suggesting virus circulation in domestic swine.
February 8, 2018: Genome Announcements
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