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https://www.readbyqxmd.com/read/28224495/hidden-markov-models-in-bioinformatics-snv-inference-from-next-generation-sequence
#1
Jiawen Bian, Xiaobo Zhou
The rapid development of next generation sequencing (NGS) technology provides a novel avenue for genomic exploration and research. Hidden Markov models (HMMs) have wide applications in pattern recognition as well as Bioinformatics such as transcription factor binding sites and cis-regulatory modules detection. An application of HMM is introduced in this chapter with the in-deep developing of NGS. Single nucleotide variants (SNVs) inferred from NGS are expected to reveal gene mutations in cancer. However, NGS has lower sequence coverage and poor SNV detection capability in the regulatory regions of the genome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28224054/variant-profiling-of-evolving-prokaryotic-populations
#2
Markus Zojer, Lisa N Schuster, Frederik Schulz, Alexander Pfundner, Matthias Horn, Thomas Rattei
Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes...
2017: PeerJ
https://www.readbyqxmd.com/read/28223462/fallacy-of-the-unique-genome-sequence-diversity-within-single-helicobacter-pylori-strains
#3
Jenny L Draper, Lori M Hansen, David L Bernick, Samar Abedrabbo, Jason G Underwood, Nguyet Kong, Bihua C Huang, Allison M Weis, Bart C Weimer, Arnoud H M van Vliet, Nader Pourmand, Jay V Solnick, Kevin Karplus, Karen M Ottemann
Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its parent PMSS1 to assess intra- and intergenomic variability. Using high sequence coverage depth and experimental validation, we detected extensive genome plasticity within these H. pylori isolates, including movement of the transposable element IS607, large and small inversions, multiple single nucleotide polymorphisms, and variation in cagA copy number...
February 21, 2017: MBio
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
#4
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 18, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28222698/atgc-transcriptomics-a-web-based-application-to-integrate-explore-and-analyze-de-novo-transcriptomic-data
#5
Sergio Gonzalez, Bernardo Clavijo, Máximo Rivarola, Patricio Moreno, Paula Fernandez, Joaquín Dopazo, Norma Paniego
BACKGROUND: In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for evaluating differential gene expression by digital measurements. The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis...
February 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28222336/a-two-step-approach-for-sequencing-spliceosome-related-genes-as-a-complementary-diagnostic-assay-in-mds-patients-with-ringed-sideroblasts
#6
Kamila Janusz, Mónica Del Rey, María Abáigar, Rosa Collado, David Ivars, María Hernández-Sánchez, Alberto Valiente, Cristina Robledo, Rocío Benito, María Díez-Campelo, Fernando Ramos, Alexander Kohlmann, Consuelo Del Cañizo, Jesús María Hernández-Rivas
Our study aimed to analyze the presence of mutations in SF3B1 and other spliceosome-related genes in myelodysplastic syndromes with ringed sideroblasts (MDS-RS) by combining conventional Sanger and next-generation sequencing (NGS) methods, and to determine the feasibility of this approach in a clinical setting. 122 bone marrow samples from MDS-RS patients were studied. Initially, exons 14 and 15 of the SF3B1 gene were analyzed by Sanger sequencing. Secondly, they were studied by NGS covering besides SF3B1, SRSF2, U2AF1 and ZRSR2 genes...
February 4, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28222155/glm-based-optimization-of-ngs-data-analysis-a-case-study-of-roche-454-ion-torrent-pgm-and-illumina-nextseq-sequencing-data
#7
Sarah Sandmann, Aniek O de Graaf, Bert A van der Reijden, Joop H Jansen, Martin Dugas
BACKGROUND: There are various next-generation sequencing techniques, all of them striving to replace Sanger sequencing as the gold standard. However, false positive calls of single nucleotide variants and especially indels are a widely known problem of basically all sequencing platforms. METHODS: We considered three common next-generation sequencers-Roche 454, Ion Torrent PGM and Illumina NextSeq-and applied standard as well as optimized variant calling pipelines...
2017: PloS One
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
#8
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/28215547/next-generation-sequencing-analysis-of-twelve-known-causative-genes-in-congenital-hypothyroidism
#9
Xin Fan, Chunyun Fu, Yiping Shen, Chuan Li, Shiyu Luo, Qifei Li, Jingsi Luo, Jiasun Su, Shujie Zhang, Xuyun Hu, Rongyu Chen, Xuefan Gu, Shaoke Chen
BACKGROUND: Gene variants have been reported to be associated with congenital hypothyroidism (CH), the purpose of this study was to analyze the mutation spectrum and prevalence of 12 known causative genes (TSHR, PAX8, NKX2.1, NKX2.5, FOXE1, DUOX2, TG, TPO, GLIS3, NIS, SLC26A4 and DEHAL1) in CH in China. METHODS: Peripheral venous blood samples were collected from the patients. Genomic DNA was extracted from peripheral blood leukocytes. All exons and their exon-intron boundary sequences of the 12 known CH associated genes in 66 CH patients were screened by next-generation sequencing (NGS)...
February 16, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28214514/detecting-circulating-tumor-dna-in-renal-cancer-an-open-challenge
#10
Claudia Corrò, Tomas Hejhal, Cédric Poyet, Tullio Sulser, Thomas Hermanns, Thomas Winder, Gerald Prager, Peter J Wild, Ian Frew, Holger Moch, Markus Rechsteiner
BACKGROUND: Detection of circulating tumor DNA (ctDNA) in blood of cancer patients is regarded as an important step towards personalized medicine and treatment monitoring. In the present study, we investigated the clinical applicability of ctDNA as liquid biopsy in renal cancer. METHODS: ctDNA in serum and plasma samples derived from ccRCC and colon cancer patients as well as ctDNA isolated from RCC xenografts with known VHL mutation status was investigated using next generation sequencing (NGS)...
February 15, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28212557/using-high-sensitivity-sequencing-for-the-detection-of-mutations-in-btk-and-plc%C3%AE-2-genes-in-cellular-and-cell-free-dna-and-correlation-with-progression-in-patients-treated-with-btk-inhibitors
#11
Adam Albitar, Wanlong Ma, Ivan DeDios, Jeffrey Estella, Inhye Ahn, Mohammed Farooqui, Adrian Wiestner, Maher Albitar
Patients with chronic lymphocytic leukemia (CLL) that develop resistance to Bruton tyrosine kinase (BTK) inhibitors are typically positive for mutations in BTK or phospholipase c gamma 2 (PLCγ2). We developed a high sensitivity (HS) assay utilizing wild-type blocking polymerase chain reaction achieved via bridged and locked nucleic acids. We used this high sensitivity assay in combination with Sanger sequencing and next generation sequencing (NGS) and tested cellular DNA and cell-free DNA (cfDNA) from patients with CLL treated with the BTK inhibitor, ibrutinib...
February 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28212394/de-novo-transcriptome-analysis-and-microsatellite-marker-development-for-population-genetic-study-of-a-serious-insect-pest-rhopalosiphum-padi-l-hemiptera-aphididae
#12
Xinle Duan, Kang Wang, Sha Su, Ruizheng Tian, Yuting Li, Maohua Chen
The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. In this study, we used transcriptome information obtained by RNA-Seq to develop polymorphic microsatellites for investigating population genetics in this species. The transcriptome of R. padi was sequenced on an Illumina HiSeq 2000 platform...
2017: PloS One
https://www.readbyqxmd.com/read/28212382/de-novo-assembly-of-the-sea-trout-salmo-trutta-m-trutta-skin-transcriptome-to-identify-putative-genes-involved-in-the-immune-response-and-epidermal-mucus-secretion
#13
Magdalena Malachowicz, Roman Wenne, Artur Burzynski
In fish, the skin is a multifunctional organ and the first barrier against pathogens. Salmonids differ in their susceptibility to microorganisms due to varied skin morphology and gene expression patterns. The brown trout is a salmonid species with important commercial and ecological value in Europe. However, there is a lack of knowledge regarding the genes involved in the immune response and mucus secretion in the skin of this fish. Thus, we characterized the skin transcriptome of anadromous brown trout using next-generation sequencing (NGS)...
2017: PloS One
https://www.readbyqxmd.com/read/28212287/big-data-analytics-for-genomic-medicine
#14
REVIEW
Karen Y He, Dongliang Ge, Max M He
Genomic medicine attempts to build individualized strategies for diagnostic or therapeutic decision-making by utilizing patients' genomic information. Big Data analytics uncovers hidden patterns, unknown correlations, and other insights through examining large-scale various data sets. While integration and manipulation of diverse genomic data and comprehensive electronic health records (EHRs) on a Big Data infrastructure exhibit challenges, they also provide a feasible opportunity to develop an efficient and effective approach to identify clinically actionable genetic variants for individualized diagnosis and therapy...
February 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28211474/dissection-of-genomic-features-and-variations-of-three-pathotypes-of-puccinia-striiformis-through-whole-genome-sequencing
#15
Kanti Kiran, Hukam C Rawal, Himanshu Dubey, R Jaswal, Subhash C Bhardwaj, P Prasad, Dharam Pal, B N Devanna, Tilak R Sharma
Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici, is one of the important diseases of wheat. We used NGS technologies to generate a draft genome sequence of two highly virulent (46S 119 and 31) and a least virulent (K) pathotypes of P. striiformis from the Indian subcontinent. We generated ~24,000-32,000 sequence contigs (N50;7.4-9.2 kb), which accounted for ~86X-105X sequence depth coverage with an estimated genome size of these pathotypes ranging from 66.2-70.2 Mb. A genome-wide analysis revealed that pathotype 46S 119 might be highly evolved among the three pathotypes in terms of year of detection and prevalence...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211206/variable-familial-exudative-vitreoretinopathy-in-a-family-harbouring-variants-in-both-fzd4-and-tspan12
#16
Patrik Schatz, Arif O Khan
PURPOSE: To report a family affected by familial exudative vitreoretinopathy (FEVR) in which more severe disease phenotypes segregated with digenic rather than monogenic variants in FEVR-related genes. METHODS: Phenotype was documented with high-resolution imaging of retinal structure and wide-field fundus photography. Next-generation sequencing (NGS) of known genes involved in FEVR was performed. RESULTS: Three affected individuals within a family with FEVR presented with variable disease severity...
February 16, 2017: Acta Ophthalmologica
https://www.readbyqxmd.com/read/28208788/next-generation%C3%A2-sequencing-based%C3%A2-ribomethseq%C3%A2-protocol%C3%A2-for%C3%A2-analysis%C3%A2-of%C3%A2-trna%C3%A2-2-o-methylation
#17
Virginie Marchand, Florian Pichot, Kathrin Thüring, Lilia Ayadi, Isabel Freund, Alexander Dalpke, Mark Helm, Yuri Motorin
Analysis of RNA modifications by traditional physico-chemical approaches is labor  intensive,  requires  substantial  amounts  of  input  material  and  only  allows  site-by-site  measurements.  The  recent  development  of  qualitative  and  quantitative  approaches  based  on   next-generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA  species.  The  Illumina  sequencing-based  RiboMethSeq  protocol  was  initially  developed  and  successfully applied for mapping of ribosomal RNA (rRNA) 2'-O-methylations...
February 9, 2017: Biomolecules
https://www.readbyqxmd.com/read/28202952/imputation-approach-for-deducing-a-complete-mitogenome-sequence-from-low-depth-coverage-next-generation-sequencing-data-application-to-ancient-remains-from-the-moon-pyramid-mexico
#18
Fuzuki Mizuno, Masahiko Kumagai, Kunihiko Kurosaki, Michiko Hayashi, Saburo Sugiyama, Shintaroh Ueda, Li Wang
It is considered that more than 15 depths of coverage are necessary for next-generation sequencing (NGS) data to obtain reliable complete nucleotide sequences of the mitogenome. However, it is difficult to satisfy this requirement for all nucleotide positions because of problems obtaining a uniform depth of coverage for poorly preserved materials. Thus, we propose an imputation approach that allows a complete mitogenome sequence to be deduced from low-depth-coverage NGS data. We used different types of mitogenome data files as panels for imputation: a worldwide panel comprising all the major haplogroups, a worldwide panel comprising sequences belonging to the estimated haplogroup alone, a panel comprising sequences from the population most closely related to an individual under investigation, and a panel comprising sequences belonging to the estimated haplogroup from the population most closely related to an individual under investigation...
February 16, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28201993/structure-and-variation-of-crispr-and-crispr-flanking-regions-in-deleted-direct-repeat-region-mycobacterium-tuberculosis-complex-strains
#19
Paul Jeffrey Freidlin, Israel Nissan, Anna Luria, Drora Goldblatt, Lana Schaffer, Hasia Kaidar-Shwartz, Daniel Chemtob, Zeev Dveyrin, Steven Robert Head, Efrat Rorman
BACKGROUND: CRISPR and CRISPR-flanking genomic regions are important for molecular epidemiology of Mycobacterium tuberculosis complex (MTBC) strains, and potentially for adaptive immunity to phage and plasmid DNA, and endogenous roles in the bacterium. Genotyping in the Israel National Mycobacterium Reference Center Tel-Aviv of over 1500 MTBC strains from 2008-2013 showed three strains with validated negative 43-spacer spoligotypes, that is, with putatively deleted direct repeat regions (deleted-DR/CRISPR regions)...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28199989/presence-of-cancer-associated-mutations-in-exhaled-breath-condensates-of-healthy-individuals-by-next-generation-sequencing
#20
Omar Youssef, Aija Knuuttila, Päivi Piirilä, Tom Böhling, Virinder Sarhadi, Sakari Knuutila
Exhaled breath condensate (EBC) is a non-invasive source that can be used for studying different genetic alterations occurring in lung tissue. However, the low yield of DNA available from EBC has hampered the more detailed mutation analysis by conventional methods. We applied the more sensitive amplicon-based next generation sequencing (NGS) to identify cancer related mutations in DNA isolated from EBC. In order to apply any method for the purpose of mutation screening in cancer patients, it is important to clarify the incidence of these mutations in healthy individuals...
February 9, 2017: Oncotarget
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