Structured Review

Roche gs amplicon variant analyzer
Variants of the three Pneumocystis jirovecii target DNA regions observed in our collection of samples by ultra-deep pyrosequencing (UDPS) . Analysis of all 31 samples led to the identification of seven variants for the internal transcribed spacer two region (ITS2), two for the partial dihydrofolate reductase gene (DHFR), and six for the mitochondrial ribosomal RNA large subunit gene (mtLSU), with respect to reference sequences (GenBank Accession number: JQ365725 , AF090368 , and JX499143 , respectively). Of note, for ITS2, the numbering corresponds to the ITS2 region and not to that of the whole <t>amplicon.</t> For the ITS2 target, three polymorphic bases at positions 66, 161, and 163 of the ITS2 region resulted in the observation of seven variants: TTG, TTA, ATA, AAA, AAG, ATG, and ATC. For the DHFR gene, two polymorphic bases at positions 192 and 218 of the amplicon resulted in the observation of only three variants. For the mtLSU target, two polymorphic bases at positions 84 and 247 of the amplicon resulted in the observation of six variants: AG (WT), TT, AT, CC, CT, and TC. Dots indicate bases identical to the reference sequence. Polymorphic bases are shown in color. The size of the consensus base (sequence Logo) is proportional to the proportion of sequences polymorphic at the corresponding position. WT, wild-type sequence corresponding to the reference sequence; MT, mutated sequence corresponding to polymorphic variants.
Gs Amplicon Variant Analyzer, supplied by Roche, used in various techniques. Bioz Stars score: 91/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/gs amplicon variant analyzer/product/Roche
Average 91 stars, based on 39 article reviews
Price from $9.99 to $1999.99
gs amplicon variant analyzer - by Bioz Stars, 2020-07
91/100 stars

Images

1) Product Images from "Diversity of Pneumocystis jirovecii during Infection Revealed by Ultra-Deep Pyrosequencing"

Article Title: Diversity of Pneumocystis jirovecii during Infection Revealed by Ultra-Deep Pyrosequencing

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2016.00733

Variants of the three Pneumocystis jirovecii target DNA regions observed in our collection of samples by ultra-deep pyrosequencing (UDPS) . Analysis of all 31 samples led to the identification of seven variants for the internal transcribed spacer two region (ITS2), two for the partial dihydrofolate reductase gene (DHFR), and six for the mitochondrial ribosomal RNA large subunit gene (mtLSU), with respect to reference sequences (GenBank Accession number: JQ365725 , AF090368 , and JX499143 , respectively). Of note, for ITS2, the numbering corresponds to the ITS2 region and not to that of the whole amplicon. For the ITS2 target, three polymorphic bases at positions 66, 161, and 163 of the ITS2 region resulted in the observation of seven variants: TTG, TTA, ATA, AAA, AAG, ATG, and ATC. For the DHFR gene, two polymorphic bases at positions 192 and 218 of the amplicon resulted in the observation of only three variants. For the mtLSU target, two polymorphic bases at positions 84 and 247 of the amplicon resulted in the observation of six variants: AG (WT), TT, AT, CC, CT, and TC. Dots indicate bases identical to the reference sequence. Polymorphic bases are shown in color. The size of the consensus base (sequence Logo) is proportional to the proportion of sequences polymorphic at the corresponding position. WT, wild-type sequence corresponding to the reference sequence; MT, mutated sequence corresponding to polymorphic variants.
Figure Legend Snippet: Variants of the three Pneumocystis jirovecii target DNA regions observed in our collection of samples by ultra-deep pyrosequencing (UDPS) . Analysis of all 31 samples led to the identification of seven variants for the internal transcribed spacer two region (ITS2), two for the partial dihydrofolate reductase gene (DHFR), and six for the mitochondrial ribosomal RNA large subunit gene (mtLSU), with respect to reference sequences (GenBank Accession number: JQ365725 , AF090368 , and JX499143 , respectively). Of note, for ITS2, the numbering corresponds to the ITS2 region and not to that of the whole amplicon. For the ITS2 target, three polymorphic bases at positions 66, 161, and 163 of the ITS2 region resulted in the observation of seven variants: TTG, TTA, ATA, AAA, AAG, ATG, and ATC. For the DHFR gene, two polymorphic bases at positions 192 and 218 of the amplicon resulted in the observation of only three variants. For the mtLSU target, two polymorphic bases at positions 84 and 247 of the amplicon resulted in the observation of six variants: AG (WT), TT, AT, CC, CT, and TC. Dots indicate bases identical to the reference sequence. Polymorphic bases are shown in color. The size of the consensus base (sequence Logo) is proportional to the proportion of sequences polymorphic at the corresponding position. WT, wild-type sequence corresponding to the reference sequence; MT, mutated sequence corresponding to polymorphic variants.

Techniques Used: Amplification, Sequencing

2) Product Images from "Evaluation of Persistence of Resistant Variants with Ultra-Deep Pyrosequencing in Chronic Hepatitis C Patients Treated with Telaprevir"

Article Title: Evaluation of Persistence of Resistant Variants with Ultra-Deep Pyrosequencing in Chronic Hepatitis C Patients Treated with Telaprevir

Journal: PLoS ONE

doi: 10.1371/journal.pone.0041191

Prevalence of TVR resistance mutations at baseline and long-term follow-up. The percentage of resistant variants in the viral population at baseline (B) and at long-term follow-up time point (F) is depicted for each patient. For display purposes, only the segment from 95–100% is displayed; the portion of the viral population from 0–95% for all patients is WT. For comparison, viral population composition at the EOT time point is provided in Table 1 . Note that amplification of amplicon NS3-I for UDPS failed for patients 9 and 10 (B, F). Furthermore UDPS of both fragments (NS3-I, NS3-II) failed for patient 6 (B, F).
Figure Legend Snippet: Prevalence of TVR resistance mutations at baseline and long-term follow-up. The percentage of resistant variants in the viral population at baseline (B) and at long-term follow-up time point (F) is depicted for each patient. For display purposes, only the segment from 95–100% is displayed; the portion of the viral population from 0–95% for all patients is WT. For comparison, viral population composition at the EOT time point is provided in Table 1 . Note that amplification of amplicon NS3-I for UDPS failed for patients 9 and 10 (B, F). Furthermore UDPS of both fragments (NS3-I, NS3-II) failed for patient 6 (B, F).

Techniques Used: Amplification

3) Product Images from "RNA cytosine methylation analysis by bisulfite sequencing"

Article Title: RNA cytosine methylation analysis by bisulfite sequencing

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkn954

In vivo RNA bisulfite sequencing of tRNA Asp from total RNA (1 μg) after various deamination times. Five clones were sequenced for each time point and deamination rates (DR) were calculated based on the number of all cytosines (minus known m5C residues at positions C38 and C48). Black boxes indicate methylated cytosine residues, white boxes indicate unmethylated cytosine residues. Each PCR amplicon queried 17 cytosines in tRNA Asp (C = 17). Numbers below boxes indicate the cytosine positions in the primary RNA sequence.
Figure Legend Snippet: In vivo RNA bisulfite sequencing of tRNA Asp from total RNA (1 μg) after various deamination times. Five clones were sequenced for each time point and deamination rates (DR) were calculated based on the number of all cytosines (minus known m5C residues at positions C38 and C48). Black boxes indicate methylated cytosine residues, white boxes indicate unmethylated cytosine residues. Each PCR amplicon queried 17 cytosines in tRNA Asp (C = 17). Numbers below boxes indicate the cytosine positions in the primary RNA sequence.

Techniques Used: In Vivo, Methylation Sequencing, Clone Assay, Methylation, Polymerase Chain Reaction, Amplification, Sequencing

Establishment of RNA bisulfite sequencing. ( A ) Schematic diagram of the bisulfite conversion reaction. C, cytidine; CS cytidine sulfonate; US, uridine sulfonate; U, uridine. ( B ) Outline of the basic strategy to analyze tRNA for m5C methylation. Bisulfite-treated tRNAs are reverse transcribed using a tRNA 3′-sequence-specific stem–loop primer, amplified with primers binding only to deaminated sequences at the 5′ end, followed by standard cloning and sequencing. ( C ) As an example, in vitro transcribed tRNA Asp served as template for cDNA synthesis. RT, reverse transcriptase; arrow, tRNA amplicon. ( D ) Increasing deamination times lead to degradation of tRNA Asp . Equal amounts of cellular RNA (1 μg) were subjected to deamination for the time indicated, followed by cDNA synthesis and PCR amplification. ( E ) Dilution series of total RNA subjected to bisulfite treatment, followed by cDNA synthesis and PCR amplification of tRNA Asp . Ten nanograms of cellular RNA are sufficient to amplify bisulfite-treated tRNA Asp (32 amplification cycles). Arrow, tRNA amplicon; open arrowhead, aberrant PCR amplicon.
Figure Legend Snippet: Establishment of RNA bisulfite sequencing. ( A ) Schematic diagram of the bisulfite conversion reaction. C, cytidine; CS cytidine sulfonate; US, uridine sulfonate; U, uridine. ( B ) Outline of the basic strategy to analyze tRNA for m5C methylation. Bisulfite-treated tRNAs are reverse transcribed using a tRNA 3′-sequence-specific stem–loop primer, amplified with primers binding only to deaminated sequences at the 5′ end, followed by standard cloning and sequencing. ( C ) As an example, in vitro transcribed tRNA Asp served as template for cDNA synthesis. RT, reverse transcriptase; arrow, tRNA amplicon. ( D ) Increasing deamination times lead to degradation of tRNA Asp . Equal amounts of cellular RNA (1 μg) were subjected to deamination for the time indicated, followed by cDNA synthesis and PCR amplification. ( E ) Dilution series of total RNA subjected to bisulfite treatment, followed by cDNA synthesis and PCR amplification of tRNA Asp . Ten nanograms of cellular RNA are sufficient to amplify bisulfite-treated tRNA Asp (32 amplification cycles). Arrow, tRNA amplicon; open arrowhead, aberrant PCR amplicon.

Techniques Used: Methylation Sequencing, Methylation, Sequencing, Amplification, Binding Assay, Clone Assay, In Vitro, Polymerase Chain Reaction

Related Articles

Amplification:

Article Title: Evaluation of Persistence of Resistant Variants with Ultra-Deep Pyrosequencing in Chronic Hepatitis C Patients Treated with Telaprevir
Article Snippet: .. The presence of variants at amino acid positions 36, 54, 155 and 156 was analyzed using the GS Amplicon Variant Analyzer (AVA) software version 2.0.01 from Roche. .. The AVA software performs quality control, trims primer derived sequences, maps the reads against a reference sequence and calculates the frequency of variants at designated positions.

Article Title: Deep Sequencing Reveals Highly Complex Dynamics of Human Cytomegalovirus Genotypes in Transplant Patients over Time ▿
Article Snippet: .. GS Amplicon Variant Analyzer (AVA) version 2.0.01 software from Roche was used to analyze the ultradeep-sequencing data based on multiple alignments to the reference sequences, performed with the total number of amplicon sequence reads. .. The AVA software was used to automatically scan for and quantify the well-defined genotype sequences.

Article Title: Ultradeep Pyrosequencing of Hepatitis C Virus Hypervariable Region 1 in Quasispecies Analysis
Article Snippet: .. Retained sequences of 179 bp were visualized using GS Amplicon Variant Analyzer (Roche). .. Subsequently, primer sequences were trimmed from the target sequence and reads of 138 bp were aligned to the reference sequence for genotype 1b HCV (GenBank accession number AJ406073) and translated to amino acid sequences by (Molecular Evolutionary Genetics Analysis) MEGA, version 5.0 ( http://www.megasoftware.net/ ) [ ].

Article Title: RNA cytosine methylation analysis by bisulfite sequencing
Article Snippet: .. Deep-sequencing data were analyzed for sequence specific cytosine content using the GS Amplicon Variant Analyzer (Roche). .. Establishment of RNA bisulfite sequencing Recently, the cytosine-5 methyltransferase Dnmt2 has been shown to catalyze the methylation of tRNAAsp at position C38 in various organisms, including Drosophila melanogaster ( ).

Article Title: CBFB-MYH11 hypomethylation signature and PBX3 differential methylation revealed by targeted bisulfite sequencing in patients with acute myeloid leukemia
Article Snippet: .. Data from 454 pyrosequencing were aligned to a reference in GS Amplicon Variant Analyzer (AVA) (Roche) software and DNA methylation levels were assessed using the web-based software BISMA [ ]. ..

Article Title: Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use
Article Snippet: .. The sequences of the V3 env regions were first processed using GS Amplicon Variant Analyzer (AVA) software (Roche). .. Illumina deep sequencing of the HIV-1 V3 env region The samples were prepared for sequencing on Illumina MiSeq at the genomic platform of Toulouse ( http://get.genotoul.fr/ ).

Article Title: Diversity of Pneumocystis jirovecii during Infection Revealed by Ultra-Deep Pyrosequencing
Article Snippet: .. After a 10-h run, total reads were analyzed with GS amplicon variant analyzer (AVA) software (Roche), filtered and assigned, by demultiplexing, to the correct patient sample on the basis of MID correspondence. .. Analysis of UDPS data AVA software (Roche) also aligned the generated sequence reads with the chosen reference sequence (JQ365725 for 5.8S-ITS2-28S, AF090368 for DHFR, JX499143 for mtLSU) and identified the proportion of polymorphism for each variable position in the sequences amplified.

Article Title: ALK Kinase Domain Mutations in Primary Anaplastic Large Cell Lymphoma: Consequences on NPM-ALK Activity and Sensitivity to Tyrosine Kinase Inhibitors
Article Snippet: .. Sequence alignments and variant detection was performed using GS Amplicon Variant Analyzer (AVA) 2.7 (Roche Applied Science), in combination with a blast-based pipeline for low frequent large INDELs detection (CRIBI Genomics, University of Padova, Padova, Italy). .. AVA software filters were set to display sequence variances represented even by a single read, using human NPM-ALK kinase mRNA sequence (GenBank U04946.1) for reference.

DNA Methylation Assay:

Article Title: CBFB-MYH11 hypomethylation signature and PBX3 differential methylation revealed by targeted bisulfite sequencing in patients with acute myeloid leukemia
Article Snippet: .. Data from 454 pyrosequencing were aligned to a reference in GS Amplicon Variant Analyzer (AVA) (Roche) software and DNA methylation levels were assessed using the web-based software BISMA [ ]. ..

Sequencing:

Article Title: Deep Sequencing Reveals Highly Complex Dynamics of Human Cytomegalovirus Genotypes in Transplant Patients over Time ▿
Article Snippet: .. GS Amplicon Variant Analyzer (AVA) version 2.0.01 software from Roche was used to analyze the ultradeep-sequencing data based on multiple alignments to the reference sequences, performed with the total number of amplicon sequence reads. .. The AVA software was used to automatically scan for and quantify the well-defined genotype sequences.

Article Title: RNA cytosine methylation analysis by bisulfite sequencing
Article Snippet: .. Deep-sequencing data were analyzed for sequence specific cytosine content using the GS Amplicon Variant Analyzer (Roche). .. Establishment of RNA bisulfite sequencing Recently, the cytosine-5 methyltransferase Dnmt2 has been shown to catalyze the methylation of tRNAAsp at position C38 in various organisms, including Drosophila melanogaster ( ).

Article Title: ALK Kinase Domain Mutations in Primary Anaplastic Large Cell Lymphoma: Consequences on NPM-ALK Activity and Sensitivity to Tyrosine Kinase Inhibitors
Article Snippet: .. Sequence alignments and variant detection was performed using GS Amplicon Variant Analyzer (AVA) 2.7 (Roche Applied Science), in combination with a blast-based pipeline for low frequent large INDELs detection (CRIBI Genomics, University of Padova, Padova, Italy). .. AVA software filters were set to display sequence variances represented even by a single read, using human NPM-ALK kinase mRNA sequence (GenBank U04946.1) for reference.

Antiviral Assay:

Article Title: Evaluation of Persistence of Resistant Variants with Ultra-Deep Pyrosequencing in Chronic Hepatitis C Patients Treated with Telaprevir
Article Snippet: .. The presence of variants at amino acid positions 36, 54, 155 and 156 was analyzed using the GS Amplicon Variant Analyzer (AVA) software version 2.0.01 from Roche. .. The AVA software performs quality control, trims primer derived sequences, maps the reads against a reference sequence and calculates the frequency of variants at designated positions.

Article Title: Deep Sequencing Reveals Highly Complex Dynamics of Human Cytomegalovirus Genotypes in Transplant Patients over Time ▿
Article Snippet: .. GS Amplicon Variant Analyzer (AVA) version 2.0.01 software from Roche was used to analyze the ultradeep-sequencing data based on multiple alignments to the reference sequences, performed with the total number of amplicon sequence reads. .. The AVA software was used to automatically scan for and quantify the well-defined genotype sequences.

Article Title: CBFB-MYH11 hypomethylation signature and PBX3 differential methylation revealed by targeted bisulfite sequencing in patients with acute myeloid leukemia
Article Snippet: .. Data from 454 pyrosequencing were aligned to a reference in GS Amplicon Variant Analyzer (AVA) (Roche) software and DNA methylation levels were assessed using the web-based software BISMA [ ]. ..

Article Title: Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use
Article Snippet: .. The sequences of the V3 env regions were first processed using GS Amplicon Variant Analyzer (AVA) software (Roche). .. Illumina deep sequencing of the HIV-1 V3 env region The samples were prepared for sequencing on Illumina MiSeq at the genomic platform of Toulouse ( http://get.genotoul.fr/ ).

Article Title: Diversity of Pneumocystis jirovecii during Infection Revealed by Ultra-Deep Pyrosequencing
Article Snippet: .. After a 10-h run, total reads were analyzed with GS amplicon variant analyzer (AVA) software (Roche), filtered and assigned, by demultiplexing, to the correct patient sample on the basis of MID correspondence. .. Analysis of UDPS data AVA software (Roche) also aligned the generated sequence reads with the chosen reference sequence (JQ365725 for 5.8S-ITS2-28S, AF090368 for DHFR, JX499143 for mtLSU) and identified the proportion of polymorphism for each variable position in the sequences amplified.

Article Title: ALK Kinase Domain Mutations in Primary Anaplastic Large Cell Lymphoma: Consequences on NPM-ALK Activity and Sensitivity to Tyrosine Kinase Inhibitors
Article Snippet: .. Sequence alignments and variant detection was performed using GS Amplicon Variant Analyzer (AVA) 2.7 (Roche Applied Science), in combination with a blast-based pipeline for low frequent large INDELs detection (CRIBI Genomics, University of Padova, Padova, Italy). .. AVA software filters were set to display sequence variances represented even by a single read, using human NPM-ALK kinase mRNA sequence (GenBank U04946.1) for reference.

Variant Assay:

Article Title: Evaluation of Persistence of Resistant Variants with Ultra-Deep Pyrosequencing in Chronic Hepatitis C Patients Treated with Telaprevir
Article Snippet: .. The presence of variants at amino acid positions 36, 54, 155 and 156 was analyzed using the GS Amplicon Variant Analyzer (AVA) software version 2.0.01 from Roche. .. The AVA software performs quality control, trims primer derived sequences, maps the reads against a reference sequence and calculates the frequency of variants at designated positions.

Article Title: Deep Sequencing Reveals Highly Complex Dynamics of Human Cytomegalovirus Genotypes in Transplant Patients over Time ▿
Article Snippet: .. GS Amplicon Variant Analyzer (AVA) version 2.0.01 software from Roche was used to analyze the ultradeep-sequencing data based on multiple alignments to the reference sequences, performed with the total number of amplicon sequence reads. .. The AVA software was used to automatically scan for and quantify the well-defined genotype sequences.

Article Title: Ultradeep Pyrosequencing of Hepatitis C Virus Hypervariable Region 1 in Quasispecies Analysis
Article Snippet: .. Retained sequences of 179 bp were visualized using GS Amplicon Variant Analyzer (Roche). .. Subsequently, primer sequences were trimmed from the target sequence and reads of 138 bp were aligned to the reference sequence for genotype 1b HCV (GenBank accession number AJ406073) and translated to amino acid sequences by (Molecular Evolutionary Genetics Analysis) MEGA, version 5.0 ( http://www.megasoftware.net/ ) [ ].

Article Title: RNA cytosine methylation analysis by bisulfite sequencing
Article Snippet: .. Deep-sequencing data were analyzed for sequence specific cytosine content using the GS Amplicon Variant Analyzer (Roche). .. Establishment of RNA bisulfite sequencing Recently, the cytosine-5 methyltransferase Dnmt2 has been shown to catalyze the methylation of tRNAAsp at position C38 in various organisms, including Drosophila melanogaster ( ).

Article Title: CBFB-MYH11 hypomethylation signature and PBX3 differential methylation revealed by targeted bisulfite sequencing in patients with acute myeloid leukemia
Article Snippet: .. Data from 454 pyrosequencing were aligned to a reference in GS Amplicon Variant Analyzer (AVA) (Roche) software and DNA methylation levels were assessed using the web-based software BISMA [ ]. ..

Article Title: Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use
Article Snippet: .. The sequences of the V3 env regions were first processed using GS Amplicon Variant Analyzer (AVA) software (Roche). .. Illumina deep sequencing of the HIV-1 V3 env region The samples were prepared for sequencing on Illumina MiSeq at the genomic platform of Toulouse ( http://get.genotoul.fr/ ).

Article Title: Diversity of Pneumocystis jirovecii during Infection Revealed by Ultra-Deep Pyrosequencing
Article Snippet: .. After a 10-h run, total reads were analyzed with GS amplicon variant analyzer (AVA) software (Roche), filtered and assigned, by demultiplexing, to the correct patient sample on the basis of MID correspondence. .. Analysis of UDPS data AVA software (Roche) also aligned the generated sequence reads with the chosen reference sequence (JQ365725 for 5.8S-ITS2-28S, AF090368 for DHFR, JX499143 for mtLSU) and identified the proportion of polymorphism for each variable position in the sequences amplified.

Article Title: ALK Kinase Domain Mutations in Primary Anaplastic Large Cell Lymphoma: Consequences on NPM-ALK Activity and Sensitivity to Tyrosine Kinase Inhibitors
Article Snippet: .. Sequence alignments and variant detection was performed using GS Amplicon Variant Analyzer (AVA) 2.7 (Roche Applied Science), in combination with a blast-based pipeline for low frequent large INDELs detection (CRIBI Genomics, University of Padova, Padova, Italy). .. AVA software filters were set to display sequence variances represented even by a single read, using human NPM-ALK kinase mRNA sequence (GenBank U04946.1) for reference.

Software:

Article Title: Evaluation of Persistence of Resistant Variants with Ultra-Deep Pyrosequencing in Chronic Hepatitis C Patients Treated with Telaprevir
Article Snippet: .. The presence of variants at amino acid positions 36, 54, 155 and 156 was analyzed using the GS Amplicon Variant Analyzer (AVA) software version 2.0.01 from Roche. .. The AVA software performs quality control, trims primer derived sequences, maps the reads against a reference sequence and calculates the frequency of variants at designated positions.

Article Title: Deep Sequencing Reveals Highly Complex Dynamics of Human Cytomegalovirus Genotypes in Transplant Patients over Time ▿
Article Snippet: .. GS Amplicon Variant Analyzer (AVA) version 2.0.01 software from Roche was used to analyze the ultradeep-sequencing data based on multiple alignments to the reference sequences, performed with the total number of amplicon sequence reads. .. The AVA software was used to automatically scan for and quantify the well-defined genotype sequences.

Article Title: CBFB-MYH11 hypomethylation signature and PBX3 differential methylation revealed by targeted bisulfite sequencing in patients with acute myeloid leukemia
Article Snippet: .. Data from 454 pyrosequencing were aligned to a reference in GS Amplicon Variant Analyzer (AVA) (Roche) software and DNA methylation levels were assessed using the web-based software BISMA [ ]. ..

Article Title: Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use
Article Snippet: .. The sequences of the V3 env regions were first processed using GS Amplicon Variant Analyzer (AVA) software (Roche). .. Illumina deep sequencing of the HIV-1 V3 env region The samples were prepared for sequencing on Illumina MiSeq at the genomic platform of Toulouse ( http://get.genotoul.fr/ ).

Article Title: Diversity of Pneumocystis jirovecii during Infection Revealed by Ultra-Deep Pyrosequencing
Article Snippet: .. After a 10-h run, total reads were analyzed with GS amplicon variant analyzer (AVA) software (Roche), filtered and assigned, by demultiplexing, to the correct patient sample on the basis of MID correspondence. .. Analysis of UDPS data AVA software (Roche) also aligned the generated sequence reads with the chosen reference sequence (JQ365725 for 5.8S-ITS2-28S, AF090368 for DHFR, JX499143 for mtLSU) and identified the proportion of polymorphism for each variable position in the sequences amplified.

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 91
    Roche gs amplicon variant analyzer
    Variants of the three Pneumocystis jirovecii target DNA regions observed in our collection of samples by ultra-deep pyrosequencing (UDPS) . Analysis of all 31 samples led to the identification of seven variants for the internal transcribed spacer two region (ITS2), two for the partial dihydrofolate reductase gene (DHFR), and six for the mitochondrial ribosomal RNA large subunit gene (mtLSU), with respect to reference sequences (GenBank Accession number: JQ365725 , AF090368 , and JX499143 , respectively). Of note, for ITS2, the numbering corresponds to the ITS2 region and not to that of the whole <t>amplicon.</t> For the ITS2 target, three polymorphic bases at positions 66, 161, and 163 of the ITS2 region resulted in the observation of seven variants: TTG, TTA, ATA, AAA, AAG, ATG, and ATC. For the DHFR gene, two polymorphic bases at positions 192 and 218 of the amplicon resulted in the observation of only three variants. For the mtLSU target, two polymorphic bases at positions 84 and 247 of the amplicon resulted in the observation of six variants: AG (WT), TT, AT, CC, CT, and TC. Dots indicate bases identical to the reference sequence. Polymorphic bases are shown in color. The size of the consensus base (sequence Logo) is proportional to the proportion of sequences polymorphic at the corresponding position. WT, wild-type sequence corresponding to the reference sequence; MT, mutated sequence corresponding to polymorphic variants.
    Gs Amplicon Variant Analyzer, supplied by Roche, used in various techniques. Bioz Stars score: 91/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/gs amplicon variant analyzer/product/Roche
    Average 91 stars, based on 39 article reviews
    Price from $9.99 to $1999.99
    gs amplicon variant analyzer - by Bioz Stars, 2020-07
    91/100 stars
      Buy from Supplier

    Image Search Results


    Variants of the three Pneumocystis jirovecii target DNA regions observed in our collection of samples by ultra-deep pyrosequencing (UDPS) . Analysis of all 31 samples led to the identification of seven variants for the internal transcribed spacer two region (ITS2), two for the partial dihydrofolate reductase gene (DHFR), and six for the mitochondrial ribosomal RNA large subunit gene (mtLSU), with respect to reference sequences (GenBank Accession number: JQ365725 , AF090368 , and JX499143 , respectively). Of note, for ITS2, the numbering corresponds to the ITS2 region and not to that of the whole amplicon. For the ITS2 target, three polymorphic bases at positions 66, 161, and 163 of the ITS2 region resulted in the observation of seven variants: TTG, TTA, ATA, AAA, AAG, ATG, and ATC. For the DHFR gene, two polymorphic bases at positions 192 and 218 of the amplicon resulted in the observation of only three variants. For the mtLSU target, two polymorphic bases at positions 84 and 247 of the amplicon resulted in the observation of six variants: AG (WT), TT, AT, CC, CT, and TC. Dots indicate bases identical to the reference sequence. Polymorphic bases are shown in color. The size of the consensus base (sequence Logo) is proportional to the proportion of sequences polymorphic at the corresponding position. WT, wild-type sequence corresponding to the reference sequence; MT, mutated sequence corresponding to polymorphic variants.

    Journal: Frontiers in Microbiology

    Article Title: Diversity of Pneumocystis jirovecii during Infection Revealed by Ultra-Deep Pyrosequencing

    doi: 10.3389/fmicb.2016.00733

    Figure Lengend Snippet: Variants of the three Pneumocystis jirovecii target DNA regions observed in our collection of samples by ultra-deep pyrosequencing (UDPS) . Analysis of all 31 samples led to the identification of seven variants for the internal transcribed spacer two region (ITS2), two for the partial dihydrofolate reductase gene (DHFR), and six for the mitochondrial ribosomal RNA large subunit gene (mtLSU), with respect to reference sequences (GenBank Accession number: JQ365725 , AF090368 , and JX499143 , respectively). Of note, for ITS2, the numbering corresponds to the ITS2 region and not to that of the whole amplicon. For the ITS2 target, three polymorphic bases at positions 66, 161, and 163 of the ITS2 region resulted in the observation of seven variants: TTG, TTA, ATA, AAA, AAG, ATG, and ATC. For the DHFR gene, two polymorphic bases at positions 192 and 218 of the amplicon resulted in the observation of only three variants. For the mtLSU target, two polymorphic bases at positions 84 and 247 of the amplicon resulted in the observation of six variants: AG (WT), TT, AT, CC, CT, and TC. Dots indicate bases identical to the reference sequence. Polymorphic bases are shown in color. The size of the consensus base (sequence Logo) is proportional to the proportion of sequences polymorphic at the corresponding position. WT, wild-type sequence corresponding to the reference sequence; MT, mutated sequence corresponding to polymorphic variants.

    Article Snippet: After a 10-h run, total reads were analyzed with GS amplicon variant analyzer (AVA) software (Roche), filtered and assigned, by demultiplexing, to the correct patient sample on the basis of MID correspondence.

    Techniques: Amplification, Sequencing

    Prevalence of TVR resistance mutations at baseline and long-term follow-up. The percentage of resistant variants in the viral population at baseline (B) and at long-term follow-up time point (F) is depicted for each patient. For display purposes, only the segment from 95–100% is displayed; the portion of the viral population from 0–95% for all patients is WT. For comparison, viral population composition at the EOT time point is provided in Table 1 . Note that amplification of amplicon NS3-I for UDPS failed for patients 9 and 10 (B, F). Furthermore UDPS of both fragments (NS3-I, NS3-II) failed for patient 6 (B, F).

    Journal: PLoS ONE

    Article Title: Evaluation of Persistence of Resistant Variants with Ultra-Deep Pyrosequencing in Chronic Hepatitis C Patients Treated with Telaprevir

    doi: 10.1371/journal.pone.0041191

    Figure Lengend Snippet: Prevalence of TVR resistance mutations at baseline and long-term follow-up. The percentage of resistant variants in the viral population at baseline (B) and at long-term follow-up time point (F) is depicted for each patient. For display purposes, only the segment from 95–100% is displayed; the portion of the viral population from 0–95% for all patients is WT. For comparison, viral population composition at the EOT time point is provided in Table 1 . Note that amplification of amplicon NS3-I for UDPS failed for patients 9 and 10 (B, F). Furthermore UDPS of both fragments (NS3-I, NS3-II) failed for patient 6 (B, F).

    Article Snippet: The presence of variants at amino acid positions 36, 54, 155 and 156 was analyzed using the GS Amplicon Variant Analyzer (AVA) software version 2.0.01 from Roche.

    Techniques: Amplification