2, 12 January 2016 | PLOS ONE, Vol. Arens, P. Tebas, and F.D. Massive parallel sequencing DNA sequencing Illumina RNA-Seq, cancer cell of globular pathogen, electronics, electronic Device, cancer Cell Of Globular Pathogen png; Personal Genome Diagnostics, Inc. Molecular Laboratories DNA sequencing Genomics, diagnostic laboratory, food, citrus, orange png ; Diagenode s.a. DOI identifier: 10.1002/humu.21415. Domingues, Structural descriptors of gp120 V3 loop for the prediction of HIV-1coreceptor usage, HIV entry: new insights and implications for patient management. Massive parallel resequencing is proving to be especially useful for identifying gene variants in viruses of infected patients [Wang et al., 2007]. 90, No. 6, 21 May 2014 | Frontiers in Plant Science, Vol. Crambe abyssinica, A Massively Parallel Pipeline to Clone DNA Variants and Examine Molecular Phenotypes of Human Disease Mutations, DNA Storage under High Temperature Conditions Does Not Affect Performance in Human Leukocyte Antigen Genotyping via Next-Generation Sequencing (DNA Integrity Maintained in Extreme Conditions), Retroviral Vectors for Analysis of Viral Mutagenesis and Recombination, Similar Prevalence of Low-Abundance Drug-Resistant Variants in Treatment-Naive Patients with Genotype 1a and 1b Hepatitis C Virus Infections as Determined by Ultradeep Pyrosequencing, Validation of an Oligonucleotide Ligation Assay for Quantification of Human Immunodeficiency Virus Type 1 Drug-Resistant Mutants by Use of Massively Parallel Sequencing, The Human Fetal Glial Cell Line SVG p12 Contains Infectious BK Polyomavirus, TP53 Mutation Analysis in Clinical Practice: Lessons From Chronic Lymphocytic Leukemia, Comparison of ultra-deep versus Sanger sequencing detection of minority mutations on the HIV-1 drug resistance interpretations after virological failure, Analysis of plant microbe interactions in the era of next generation sequencing technologies, Inference with viral quasispecies diversity indices: clonal and NGS approaches, Residual Viremia in an RT-SHIV Rhesus Macaque HAART Model Marked by the Presence of a Predominant Plasma Clone and a Lack of Viral Evolution. America 94: 277-282. Solanum lycopersicum and Solanum habrochaites (f. typicum) accession PI127826 emit a variety of sesquiterpenes. As an example, we observed a nonneglectable peak of small fragments upon DNA LabChip (Agilent Technologies, Santa Clara, CA, USA) analysis of a sample that had undergone PCR amplification of the HIV-1 V3 region. For example, monitoring HIV-1 drug resistance has become increasingly important for guiding treatment, especially for patients failing antiretroviral therapy (6,7). Location: Petrénsalen, Nobels väg 12b, KI, Solna. 45. 5, 2 January 2014 | Bioinformatics, Vol. Mitsuya, Y., V. Varghese, C. Wang, T.F. For example, for the development of a sensitive HIV-1 resistance test for the region of the reverse transcriptase gene that covers amino acids 59–190, an in-house database of aligned Sanger sequences from 266,781 samples was interrogated to achieve a good primer design. The power of the new sequencing technologies and their utility for variant detection derive from the ability to sequence single molecules in massive amounts. Unfortunately, correction for these errors is not possible by means of the current Roche Applied Science analysis software. Conflict of Interests. White squares, variants frequencies <1%; black squares, variant frequencies >1%. 454 Sequencing used a large-scale parallel pyrosequencing system capable of sequencing roughly 400-600 megabases of DNA per 10-hour run on the Genome Sequencer FLX with GS FLX Titanium series reagents. If this occurs at a low frequency, it remains unnoticed after quality check of the amplicon, and sequencing of this amplicon will lead to the erroneously reporting of a deletion in those reads passing the breakpoint (Figure 2). Department: Inst för mikrobiologi, tumör- och cellbiologi / Dept of Microbiology, Tumor and Cell Biology. Academy of Sciences of the United States of. In conclusion, in addition to cell lines, SMARCA4 is biallelically inactivated in a significant proportion of lung primary tumors, thereby constituting one of the most important genes contributing to the development of this type of cancer. The development of massively parallel sequencing (MPS) technologies heralded an era in which molecular diagnostics for multigenic disorders becomes reality. 2, 27 January 2014 | PLoS ONE, Vol. Our work ow was rstvalidatedinapanelof patientspreviouslySanger sequenced. Nonspecific binding of one of the primers either within, up or downstream of the region of interest, will lead to shorter or larger amplicons as compared with the intended region. International Journal of Gynecological Pathology. This preprocessing tool identifies large gaps by pairwise alignment of each read to the reference, using a small gap extension penalty. … The Amplicon Variant Analyzer software, used for the alignment of reads and the variant calling, automatically corrects for this type of errors by trimming the reads (Figure 1A). Practical Tools to Implement Massive Parallel Pyrosequencing of PCR Products in Next Generation Molecular Diagnostics Kim De Leeneer1*, Joachim De Schrijver3, Lieven Clement4, Machteld Baetens1, Steve Lefever1, Sarah De Keulenaer2, Wim Van Criekinge2,3, Dieter Deforce2,5, Filip Van Nieuwerburgh2,5, Sofie Bekaert2, Filip Pattyn1, Bram De Wilde1, Paul Coucke1,2, Jo Vandesompele1,2, … Wegner KM (2009) Massive parallel MHC genotyping: titanium that shines. Massive parallel pyrosequencing of the trichome transcriptomes resulted in 195,377 reads from cDNA derived from S. lycopersicum and 182,386 reads from S. habrochaites accession PI127826, both with an average length of 80 nucleotides. View Article Google Scholar 9. Pfister, and R. Kaiser, Prevalence of minor variants of HIV strains at reverse transcriptase position 103 in therapy-naive patients and their impact on the virological failure, Hoffmann, C., N. Minkah, J. Leipzig, G. Wang, M.Q. 454 Life Sciences-Wikipedia. The aim of this study was to implement the massively parallel sequencing technology for diagnostic applications. The specificity of DNA amplification during PCR is determined by the ratio of the primers’ capability and affinity to recognize and bind the intended target DNA sequence as compared with nontarget DNA sequences. Further processing of this sample in the 454 workflow and subsequent data analysis (n = 10,687 reads) revealed that 37% (n = 3951) of the reads were derived from primer dimers. In case such solution is not possible because of a variable target region without proximity of a conserved nucleotide stretch, the mixing of different primers or the use of degenerate nucleotides could be an alternative. SRY mutation analysis by next generation (deep) sequencing in a cohort of chromosomal Disorders of Sex Development (DSD) patients with a mosaic karyotype. ow using massive parallel pyrosequencing in a bench top GS Junior sequencer together with homopolymer scanning to screen for muta-tions in the BRCA and BRCA genes. Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats. using Roche-454 massive parallel pyrosequencing tech-nology. Eshleman, Improved detection of human immunodeficiency virus type 1 variants by analysis of replicate amplification reactions: relevance to studies of human immunodeficiency virus type 1 vertical transmission. Bacheler S.M.S. Landry, K. Dieckhaus, M.I. A consensus sequence was established to perform subtype assignment, phylogenetic analysis, and recombination recombination Subject Category: Miscellaneous This thesis deals with the extended diagnosis of KIT and PDGFRA positive gastrointestinal stromal tumors (GIST) using molecular methods, like sequencing by Sanger or the so called next generation sequencing (NGS), a massive parallel sequencing technology (MPS). Trimming of the reads at the breakpoint or splitting the read in two separate reads (before and after the breakpoint) might be envisaged during analysis, however this strategy is impaired as the exact position of the breakpoint is uncertain. 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