Applications of Second Generation Sequencing Technologies in Complex Disorders

2011 ◽  
pp. 321-343 ◽  
Author(s):  
Mònica Bayés ◽  
Simon Heath ◽  
Ivo Glynne Gut
Keyword(s):  
Second Generation ◽  
Complex Disorders ◽  
Sequencing Technologies ◽  
Second Generation Sequencing ◽  
Generation Sequencing

scholarly journals NucMerge: Genome assembly quality improvement assisted by alternative assemblies and paired-end Illumina reads

2018 ◽  
Author(s):  
Ksenia Khelik ◽  
Alexander Johan Nederbragt ◽  
Geir Kjetil Sandve ◽  
Torbjørn Rognes
Keyword(s):  
Genome Assembly ◽  
Second Generation ◽  
Sequencing Technologies ◽  
Assembly Accuracy ◽  
Alternative Approach ◽  
Second Generation Sequencing ◽  
Genome Assemblies ◽  
And Inversion ◽  
Generation Sequencing ◽  
Genome Projects

AbstractBackgroundIn spite of the major breakthroughs in the second-generation sequencing technologies and the developments of a plethora of assemblers over the last ten years, the resulting genome assemblies may still be fragmented and contain errors. It is typical in genome projects with second-generation reads involved to run multiple assemblers with different parameters and choose the best assembly. However, such an approach is always a trade-off between the strengths and weaknesses of the assemblies. To exploit the advantages of different assemblers, an alternative approach that combines the best parts of several assemblies into one may be applied. The existing tools based on such an approach assist in elongation of assembly fragments and/or improvement of assembly accuracy. Though there has been progress with such a strategy, there is still room for improvement of the existing tools.ResultsWe present NucMerge, a tool for improving genome assembly accuracy by incorporating information derived from an alternative assembly and paired-end Illumina reads from the same genome. The tool corrects insertion, deletion, substitution, and inversion errors and locates different inter- and intra-chromosomal rearrangement errors. NucMerge was compared to two existing alternatives, namely Metassembler and GAM-NGS.ConclusionsThe benchmarking results show that NucMerge has generally better performance than the other tools tested, providing accuracy improvement of more assemblies. NucMerge is freely available at https://github.com/uio-bmi/NucMerge under the MPL license.

scholarly journals Evaluating approaches to find exon chains based on long reads

2016 ◽  
Author(s):  
Anna Kuosmanen ◽  
Veli Mäkinen
Keyword(s):  
Second Generation ◽  
Simulated Data ◽  
Error Rates ◽  
Third Generation ◽  
Sequencing Technologies ◽  
Third Generation Sequencing ◽  
Long Reads ◽  
Long Read ◽  
Second Generation Sequencing ◽  
Generation Sequencing

AbstractMotivationTranscript prediction can be modelled as a graph problem where exons are modelled as nodes and reads spanning two or more exons are modelled as exon chains. PacBio third-generation sequencing technology produces significantly longer reads than earlier second-generation sequencing technologies, which gives valuable information about longer exon chains in a graph. However, with the high error rates of third-generation sequencing, aligning long reads correctly around the splice sites is a challenging task. Incorrect alignments lead to spurious nodes and arcs in the graph, which in turn lead to incorrect transcript predictions.ResultsWe survey several approaches to find the exon chains corresponding to long reads in a splicing graph, and experimentally study the performance of these methods using simulated data to allow for sensitivity / precision analysis. Our experiments show that short reads from second-generation sequencing can be used to significantly improve exon chain correctness either by error-correcting the long reads before splicing graph creation, or by using them to create a splicing graph on which the long read alignments are then projected. We also study the memory and time consumption of various modules, and show that accurate exon chains lead to significantly increased transcript prediction accuracy.AvailabilityThe simulated data and in-house scripts used for this article are available at http://cs.helsinki.fi/u/aekuosma/exon_chain_evaluation_publish.tar.gz.

scholarly journals High-throughput DNA sequencing technologies for water and wastewater analysis

2019 ◽  
Vol 102 (4) ◽  
pp. 351-376
Author(s):  
Alexander WY Chan ◽  
James Naphtali ◽  
Herb E Schellhorn
Keyword(s):  
High Throughput ◽  
Second Generation ◽  
Water Quality Monitoring ◽  
Fecal Coliforms ◽  
Sequencing Technologies ◽  
Second Generation Sequencing ◽  
High Throughput Dna Sequencing ◽  
Water And Wastewater ◽  
Metagenome Sequencing ◽  
Generation Sequencing

Conventional microbiological water monitoring uses culture-dependent techniques to screen indicator microbial species such as Escherichia coli and fecal coliforms. With high-throughput, second-generation sequencing technologies becoming less expensive, water quality monitoring programs can now leverage the massively parallel nature of second-generation sequencing technologies for batch sample processing to simultaneously obtain compositional and functional information of culturable and as yet uncultured microbial organisms. This review provides an introduction to the technical capabilities and considerations necessary for the use of second-generation sequencing technologies, specifically 16S rDNA amplicon and whole-metagenome sequencing, to investigate the composition and functional potential of microbiomes found in water and wastewater systems.

scholarly journals Precision Medication of Tacrolimus Based on the Genotype by Using Second-generation Sequencing

2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Yumeng Li
Keyword(s):  
Organ Transplantation ◽  
Second Generation ◽  
Low Cost ◽  
Single Nucleotide ◽  
Factors Affecting ◽  
Key Enzyme ◽  
Second Generation Sequencing ◽  
Degree Level ◽  
Generation Sequencing ◽  
Related Mortality

Organ transplantation has become a powerful strategy for the treatment of malignant diseases. Nevertheless, graft rejection is one of the main factors affecting graft survival after organ transplantation. Under this circumstance, the transplant-related mortality still keeps up. This invention includes the precise medication guidance of Tacrolimus (FK506) inapplicable population, against the side-effects of this drug. This invention, based on second-generation sequencing, has the advantages of relatively low cost and high sequencing throughput. During the design process, we collect the data of single nucleotide polymorphism (SNP) concerning the adverse drug reactions of Tacrolimus. Then we filter and summarize fifteen SNPs basing on importance degree (level >key enzyme>race). Thenceforth, after the process of analyzing the raw extract by operating BWA, Picard-tools, GATK, and Perl, we annotate SNPs by Annovar. Through this innovation, people can obtain further feedback on drugs that targets different genes in order to achieve the purpose of precision medication and minimizing the risks of misusing Tacrolimus.

scholarly journals A case report of the differential diagnosis of Cellulosimicrobium cellulans-infected endocarditis combined with intracranial infection by conventional blood culture and second-generation sequencing

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Huifang Zhang ◽  
Chunyan He ◽  
Rui Tian ◽  
Ruilan Wang
Keyword(s):  
Second Generation ◽  
Human Infection ◽  
Sequencing Data ◽  
Case Presentation ◽  
Intracranial Infection ◽  
Cellulosimicrobium Cellulans ◽  
Two Samples ◽  
Second Generation Sequencing ◽  
Generation Sequencing

Abstract Background Cellulosimicrobium cellulans is a gram-positive filamentous bacterium found primarily in soil and sewage that rarely causes human infection, especially in previously healthy adults, but when it does, it often indicates a poor prognosis. Case presentation We report a case of endocarditis and intracranial infection caused by C. cellulans in a 52-year-old woman with normal immune function and no implants in vivo. The patient started with a febrile headache that progressed to impaired consciousness after 20 days, and she finally died after treatment with vancomycin combined with rifampicin. C. cellulans was isolated from her blood cultures for 3 consecutive days after her admission; however, there was only evidence of C. cellulans sequences for two samples in the second-generation sequencing data generated from her peripheral blood, which were ignored by the technicians. No C. cellulans bands were detected in her cerebrospinal fluid by second-generation sequencing. Conclusions Second-generation sequencing seems to have limitations for certain specific strains of bacteria.

scholarly journals Second Generation Sequencing of the Mesothelioma Tumor Genome

PLoS ONE ◽  
2010 ◽  
Vol 5 (5) ◽  
pp. e10612 ◽  
Author(s):  
Raphael Bueno ◽  
Assunta De Rienzo ◽  
Lingsheng Dong ◽  
Gavin J. Gordon ◽  
Colin F. Hercus ◽  
...  
Keyword(s):  
Second Generation ◽  
Second Generation Sequencing ◽  
Tumor Genome ◽  
Generation Sequencing

Advances in understanding cancer genomes through second-generation sequencing

2010 ◽  
Vol 11 (10) ◽  
pp. 685-696 ◽  
Author(s):  
Matthew Meyerson ◽  
Stacey Gabriel ◽  
Gad Getz
Keyword(s):  
Second Generation ◽  
Cancer Genomes ◽  
Second Generation Sequencing ◽  
Generation Sequencing
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