method coupling amplicon based gene capture  (Roche)


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    Roche method coupling amplicon based gene capture
    Patient 3 (no. 3017) mutation detection. ( a ) A screenshot from the GS <t>Amplicon</t> Variant Analyzer software showing the COL4A4 missense sequence variant c.5044C > T (p.Arg1682Trp). The upper panel corresponds to a histogram indicating the percentage
    Method Coupling Amplicon Based Gene Capture, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 11795 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/method coupling amplicon based gene capture/product/Roche
    Average 85 stars, based on 11795 article reviews
    Price from $9.99 to $1999.99
    method coupling amplicon based gene capture - by Bioz Stars, 2020-09
    85/100 stars

    Images

    1) Product Images from "Advances in Alport syndrome diagnosis using next-generation sequencing"

    Article Title: Advances in Alport syndrome diagnosis using next-generation sequencing

    Journal: European Journal of Human Genetics

    doi: 10.1038/ejhg.2011.164

    Patient 3 (no. 3017) mutation detection. ( a ) A screenshot from the GS Amplicon Variant Analyzer software showing the COL4A4 missense sequence variant c.5044C > T (p.Arg1682Trp). The upper panel corresponds to a histogram indicating the percentage
    Figure Legend Snippet: Patient 3 (no. 3017) mutation detection. ( a ) A screenshot from the GS Amplicon Variant Analyzer software showing the COL4A4 missense sequence variant c.5044C > T (p.Arg1682Trp). The upper panel corresponds to a histogram indicating the percentage

    Techniques Used: Mutagenesis, Amplification, Variant Assay, Software, Sequencing

    Patient 2 (no. 2740) mutation detection. ( a ) A screenshot from the GS Amplicon Variant Analyzer software showing the COL4A3 missense sequence variant c.3440C > T (p.Ser1147Phe). The upper panel corresponds to a histogram indicating the percentage
    Figure Legend Snippet: Patient 2 (no. 2740) mutation detection. ( a ) A screenshot from the GS Amplicon Variant Analyzer software showing the COL4A3 missense sequence variant c.3440C > T (p.Ser1147Phe). The upper panel corresponds to a histogram indicating the percentage

    Techniques Used: Mutagenesis, Amplification, Variant Assay, Software, Sequencing

    2) Product Images from "SNP assay to detect the 'Hyuuga' red-brown lesion resistance gene for Asian soybean rust"

    Article Title: SNP assay to detect the 'Hyuuga' red-brown lesion resistance gene for Asian soybean rust

    Journal: TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik

    doi: 10.1007/s00122-010-1368-8

    Graphical genotypes of representative RSLs from Benning × Hyuuga in the Rpp ?(Hyuuga) region on chromosome Gm06 . LT indicates the type of lesion, Tan is the susceptible reaction and RB is the resistant reaction. STS70887, STS70891, STS70919, and STS70923 previously identified by Hyten et al. ( 2009 ) were located at nucleotide 43746435, 43786392, 44086038, and 44118117 on Gm06 , respectively
    Figure Legend Snippet: Graphical genotypes of representative RSLs from Benning × Hyuuga in the Rpp ?(Hyuuga) region on chromosome Gm06 . LT indicates the type of lesion, Tan is the susceptible reaction and RB is the resistant reaction. STS70887, STS70891, STS70919, and STS70923 previously identified by Hyten et al. ( 2009 ) were located at nucleotide 43746435, 43786392, 44086038, and 44118117 on Gm06 , respectively

    Techniques Used:

    Graphical genotypes of representative RILs from Dillon × Hyuuga in the Rpp ?(Hyuuga) region on chromosome Gm06 . LT indicates the type of lesion, Tan is the susceptible reaction and RB is the resistant reaction
    Figure Legend Snippet: Graphical genotypes of representative RILs from Dillon × Hyuuga in the Rpp ?(Hyuuga) region on chromosome Gm06 . LT indicates the type of lesion, Tan is the susceptible reaction and RB is the resistant reaction

    Techniques Used:

    3) Product Images from "Distinctive types of postzygotic single-nucleotide mosaicisms in healthy individuals revealed by genome-wide profiling of multiple organs"

    Article Title: Distinctive types of postzygotic single-nucleotide mosaicisms in healthy individuals revealed by genome-wide profiling of multiple organs

    Journal: PLoS Genetics

    doi: 10.1371/journal.pgen.1007395

    Distinct genomic characteristics between embryonic and clonal expansion pSNMs. (A-C) Mutation spectrums in NpG and non-NpG sites for embryonic pSNMs (A), clonal expansion pSNMs in BBLD1005’s liver (B), and clonal expansion pSNMs in BBL11121’s breast (C). Mutation rate was normalized by the total number of sites in the human genome. For embryonic pSNMs, CpG sites showed significantly higher rate of C > T mutations than non-CpG sites. (D) Varied DNA replication timing of the two pSNMs types. The grey line denotes the genomic average. Embryonic pSNMs were enriched in early-replicating regions, whereas clonal expansion pSNMs were enriched in late-replicating regions. (E-G) Proportion of pSNMs locating in open or closed chromatin regions in the HepG2 (E), HMEC (F), and K562 (G) cell-lines. Significantly higher proportions of embryonic pSNMs were observed in transcribed chromatin regions of all three cell types.
    Figure Legend Snippet: Distinct genomic characteristics between embryonic and clonal expansion pSNMs. (A-C) Mutation spectrums in NpG and non-NpG sites for embryonic pSNMs (A), clonal expansion pSNMs in BBLD1005’s liver (B), and clonal expansion pSNMs in BBL11121’s breast (C). Mutation rate was normalized by the total number of sites in the human genome. For embryonic pSNMs, CpG sites showed significantly higher rate of C > T mutations than non-CpG sites. (D) Varied DNA replication timing of the two pSNMs types. The grey line denotes the genomic average. Embryonic pSNMs were enriched in early-replicating regions, whereas clonal expansion pSNMs were enriched in late-replicating regions. (E-G) Proportion of pSNMs locating in open or closed chromatin regions in the HepG2 (E), HMEC (F), and K562 (G) cell-lines. Significantly higher proportions of embryonic pSNMs were observed in transcribed chromatin regions of all three cell types.

    Techniques Used: Mutagenesis

    Identification and validation of pSNMs in 27 organ samples obtained from five individuals. (A) Genomic landscape of the validated pSNMs. Circos plots from outer to inner represent individuals BBL1100C, BBL11121, BBLC1013, BBLD1005, and BBLD1010, respectively. The Y axis denotes the average minor allele fraction across pSNM-carrying organs of each donor. (B) Correlation of the allele fractions estimated by whole-genome sequencing and targeted ultra-deep resequencing (PASM) of the validated sites. The shape, color, and size of the dots represent the donor and organ type carrying the pSNMs and the site-specific depth of whole-genome sequencing.
    Figure Legend Snippet: Identification and validation of pSNMs in 27 organ samples obtained from five individuals. (A) Genomic landscape of the validated pSNMs. Circos plots from outer to inner represent individuals BBL1100C, BBL11121, BBLC1013, BBLD1005, and BBLD1010, respectively. The Y axis denotes the average minor allele fraction across pSNM-carrying organs of each donor. (B) Correlation of the allele fractions estimated by whole-genome sequencing and targeted ultra-deep resequencing (PASM) of the validated sites. The shape, color, and size of the dots represent the donor and organ type carrying the pSNMs and the site-specific depth of whole-genome sequencing.

    Techniques Used: Sequencing

    Two types of pSNMs revealed by inter- and intra-organ profiles. (A) Minor allele fractions between different categories of pSNM. The organ-shared pSNMs demonstrated significantly higher allele fractions than the organ-unique pSNMs. (B) Number of pSNMs carried in different organ samples. Red and blue bars denote the organ-shared and organ-unique pSNMs, respectively. An excess of organ-unique pSNMs was observed in the breast sample of BBL11121 and the liver sample of BBLD1005. (C-D) Heatmap of minor allele fractions for pSNMs carried in multiple organ samples of BBLD1005 (C) and BBL11121 (D). Blood samples of two unrelated individuals (ACC1 and ACC4) served as negative controls. The color intensity of each tile represents allele fractions estimated by targeted ultra-depth resequencing. Gray tiles denote sites without sufficient read depth (
    Figure Legend Snippet: Two types of pSNMs revealed by inter- and intra-organ profiles. (A) Minor allele fractions between different categories of pSNM. The organ-shared pSNMs demonstrated significantly higher allele fractions than the organ-unique pSNMs. (B) Number of pSNMs carried in different organ samples. Red and blue bars denote the organ-shared and organ-unique pSNMs, respectively. An excess of organ-unique pSNMs was observed in the breast sample of BBL11121 and the liver sample of BBLD1005. (C-D) Heatmap of minor allele fractions for pSNMs carried in multiple organ samples of BBLD1005 (C) and BBL11121 (D). Blood samples of two unrelated individuals (ACC1 and ACC4) served as negative controls. The color intensity of each tile represents allele fractions estimated by targeted ultra-depth resequencing. Gray tiles denote sites without sufficient read depth (

    Techniques Used:

    4) Product Images from "Universal heteroplasmy of human mitochondrial DNA"

    Article Title: Universal heteroplasmy of human mitochondrial DNA

    Journal: Human Molecular Genetics

    doi: 10.1093/hmg/dds435

    Resolution of ultra-deep sequencing-by-synthesis assay. Demonstration of very low levels of noise in negative controls after quality-control filtering for poly-mononucleotide tracts and bidirectional validation of variants. An amplicon was produced from cloned DNA for each mtDNA amplicon ( MT-HV2, MT-CO3 ) along with an autosomal amplicon ( BRCA2 ) and a clone. All negative controls showed minimal numbers of base positions with any variants, and none at > 0.2% heteroplasmy level, with no inherent differences between the different DNA templates.
    Figure Legend Snippet: Resolution of ultra-deep sequencing-by-synthesis assay. Demonstration of very low levels of noise in negative controls after quality-control filtering for poly-mononucleotide tracts and bidirectional validation of variants. An amplicon was produced from cloned DNA for each mtDNA amplicon ( MT-HV2, MT-CO3 ) along with an autosomal amplicon ( BRCA2 ) and a clone. All negative controls showed minimal numbers of base positions with any variants, and none at > 0.2% heteroplasmy level, with no inherent differences between the different DNA templates.

    Techniques Used: Sequencing, Amplification, Produced, Clone Assay

    Very low-level heteroplasmic mtDNA variance was detected by ultra-deep amplicon resequencing. ( A ) Comparison of variants detected in the skeletal muscle (skm) DNA within the MT-HV2 amplicon in different patient groups shows no difference between healthy control ( n = 7) and OPA1 ( n = 8) subjects, but a significant excess of variance at all heteroplasmy levels in POLG subjects ( n = 8). ( B ) Comparison of variants detected in the blood DNA in healthy control ( n = 7), POLG ( n = 4) and OPA1 ( n = 7) subjects shows that variants are present, but less common than in the skeletal muscle DNA with the absence of higher level variants ( > 2% heteroplasmy) and no difference between patient groups.
    Figure Legend Snippet: Very low-level heteroplasmic mtDNA variance was detected by ultra-deep amplicon resequencing. ( A ) Comparison of variants detected in the skeletal muscle (skm) DNA within the MT-HV2 amplicon in different patient groups shows no difference between healthy control ( n = 7) and OPA1 ( n = 8) subjects, but a significant excess of variance at all heteroplasmy levels in POLG subjects ( n = 8). ( B ) Comparison of variants detected in the blood DNA in healthy control ( n = 7), POLG ( n = 4) and OPA1 ( n = 7) subjects shows that variants are present, but less common than in the skeletal muscle DNA with the absence of higher level variants ( > 2% heteroplasmy) and no difference between patient groups.

    Techniques Used: Amplification

    5) Product Images from "Universal heteroplasmy of human mitochondrial DNA"

    Article Title: Universal heteroplasmy of human mitochondrial DNA

    Journal: Human Molecular Genetics

    doi: 10.1093/hmg/dds435

    Resolution of ultra-deep sequencing-by-synthesis assay. Demonstration of very low levels of noise in negative controls after quality-control filtering for poly-mononucleotide tracts and bidirectional validation of variants. An amplicon was produced from cloned DNA for each mtDNA amplicon ( MT-HV2, MT-CO3 ) along with an autosomal amplicon ( BRCA2 ) and a clone. All negative controls showed minimal numbers of base positions with any variants, and none at > 0.2% heteroplasmy level, with no inherent differences between the different DNA templates.
    Figure Legend Snippet: Resolution of ultra-deep sequencing-by-synthesis assay. Demonstration of very low levels of noise in negative controls after quality-control filtering for poly-mononucleotide tracts and bidirectional validation of variants. An amplicon was produced from cloned DNA for each mtDNA amplicon ( MT-HV2, MT-CO3 ) along with an autosomal amplicon ( BRCA2 ) and a clone. All negative controls showed minimal numbers of base positions with any variants, and none at > 0.2% heteroplasmy level, with no inherent differences between the different DNA templates.

    Techniques Used: Sequencing, Amplification, Produced, Clone Assay

    Very low-level heteroplasmic mtDNA variance was detected by ultra-deep amplicon resequencing. ( A ) Comparison of variants detected in the skeletal muscle (skm) DNA within the MT-HV2 amplicon in different patient groups shows no difference between healthy control ( n = 7) and OPA1 ( n = 8) subjects, but a significant excess of variance at all heteroplasmy levels in POLG subjects ( n = 8). ( B ) Comparison of variants detected in the blood DNA in healthy control ( n = 7), POLG ( n = 4) and OPA1 ( n = 7) subjects shows that variants are present, but less common than in the skeletal muscle DNA with the absence of higher level variants ( > 2% heteroplasmy) and no difference between patient groups.
    Figure Legend Snippet: Very low-level heteroplasmic mtDNA variance was detected by ultra-deep amplicon resequencing. ( A ) Comparison of variants detected in the skeletal muscle (skm) DNA within the MT-HV2 amplicon in different patient groups shows no difference between healthy control ( n = 7) and OPA1 ( n = 8) subjects, but a significant excess of variance at all heteroplasmy levels in POLG subjects ( n = 8). ( B ) Comparison of variants detected in the blood DNA in healthy control ( n = 7), POLG ( n = 4) and OPA1 ( n = 7) subjects shows that variants are present, but less common than in the skeletal muscle DNA with the absence of higher level variants ( > 2% heteroplasmy) and no difference between patient groups.

    Techniques Used: Amplification

    6) Product Images from "Universal heteroplasmy of human mitochondrial DNA"

    Article Title: Universal heteroplasmy of human mitochondrial DNA

    Journal: Human Molecular Genetics

    doi: 10.1093/hmg/dds435

    Resolution of ultra-deep sequencing-by-synthesis assay. Demonstration of very low levels of noise in negative controls after quality-control filtering for poly-mononucleotide tracts and bidirectional validation of variants. An amplicon was produced from cloned DNA for each mtDNA amplicon ( MT-HV2, MT-CO3 ) along with an autosomal amplicon ( BRCA2 ) and a clone. All negative controls showed minimal numbers of base positions with any variants, and none at > 0.2% heteroplasmy level, with no inherent differences between the different DNA templates.
    Figure Legend Snippet: Resolution of ultra-deep sequencing-by-synthesis assay. Demonstration of very low levels of noise in negative controls after quality-control filtering for poly-mononucleotide tracts and bidirectional validation of variants. An amplicon was produced from cloned DNA for each mtDNA amplicon ( MT-HV2, MT-CO3 ) along with an autosomal amplicon ( BRCA2 ) and a clone. All negative controls showed minimal numbers of base positions with any variants, and none at > 0.2% heteroplasmy level, with no inherent differences between the different DNA templates.

    Techniques Used: Sequencing, Amplification, Produced, Clone Assay

    Very low-level heteroplasmic mtDNA variance was detected by ultra-deep amplicon resequencing. ( A ) Comparison of variants detected in the skeletal muscle (skm) DNA within the MT-HV2 amplicon in different patient groups shows no difference between healthy control ( n = 7) and OPA1 ( n = 8) subjects, but a significant excess of variance at all heteroplasmy levels in POLG subjects ( n = 8). ( B ) Comparison of variants detected in the blood DNA in healthy control ( n = 7), POLG ( n = 4) and OPA1 ( n = 7) subjects shows that variants are present, but less common than in the skeletal muscle DNA with the absence of higher level variants ( > 2% heteroplasmy) and no difference between patient groups.
    Figure Legend Snippet: Very low-level heteroplasmic mtDNA variance was detected by ultra-deep amplicon resequencing. ( A ) Comparison of variants detected in the skeletal muscle (skm) DNA within the MT-HV2 amplicon in different patient groups shows no difference between healthy control ( n = 7) and OPA1 ( n = 8) subjects, but a significant excess of variance at all heteroplasmy levels in POLG subjects ( n = 8). ( B ) Comparison of variants detected in the blood DNA in healthy control ( n = 7), POLG ( n = 4) and OPA1 ( n = 7) subjects shows that variants are present, but less common than in the skeletal muscle DNA with the absence of higher level variants ( > 2% heteroplasmy) and no difference between patient groups.

    Techniques Used: Amplification

    7) Product Images from "Next generation sequencing in sporadic retinoblastoma patients reveals somatic mosaicism"

    Article Title: Next generation sequencing in sporadic retinoblastoma patients reveals somatic mosaicism

    Journal: European Journal of Human Genetics

    doi: 10.1038/ejhg.2015.6

    Implications of detection of low-frequency mosaic variants in sporadic retinoblastoma patients. Screening of the RB1 gene performed by next generation sequencing in multiple tissues allows the detection of low-frequency mosaic variants (right), while
    Figure Legend Snippet: Implications of detection of low-frequency mosaic variants in sporadic retinoblastoma patients. Screening of the RB1 gene performed by next generation sequencing in multiple tissues allows the detection of low-frequency mosaic variants (right), while

    Techniques Used: Next-Generation Sequencing

    Related Articles

    Amplification:

    Article Title: The Human Fetal Glial Cell Line SVG p12 Contains Infectious BK Polyomavirus
    Article Snippet: .. Briefly, the combined libraries were amplified by emulsion PCR and the clonally amplified DNA molecules were enriched and purified using the Roche GS Junior Titanium emPCR kit according to the manufacturer's instructions. .. Finally, the enriched fragments were sequenced on the Roche GS Junior instrument, using the Roche GS Junior Titanium sequencing kit.

    Article Title: Advances in Alport syndrome diagnosis using next-generation sequencing
    Article Snippet: .. We used a method coupling amplicon based gene capture with resequencing on a 454 Roche platform (Genome Sequencer Junior System, Roche Applied Science, Mannheim, Germany) to identify mutations in three Alport patients, analysing all the three genes in a single experiment. ..

    Article Title: TLR7 dosage polymorphism shapes interferogenesis and HIV-1 acute viremia in women
    Article Snippet: .. The PCR products were amplified on capture beads in water-in-oil emulsion microreactors, and pyrosequencing was performed on a Roche 454 GS Junior system. .. The sequence reads were quantified with the GS amplicon variant analyzer (Roche).

    Titration:

    Article Title: Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species
    Article Snippet: .. Emulsion PCR, titration and the two quarter 454 pyrosequencing runs were done on a GS-FLX + and were performed following the manufacturer’s protocols for titanium series reagents (Roche Applied Science, Basel, Switzerland) by The Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Australia. .. The resulting libraries of sequences were filtered according to amplicon data processing pipeline in the manufacturer’s manual (Roche Applied Science Basel, Switzerland).

    Polymerase Chain Reaction:

    Article Title: Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species
    Article Snippet: .. Emulsion PCR, titration and the two quarter 454 pyrosequencing runs were done on a GS-FLX + and were performed following the manufacturer’s protocols for titanium series reagents (Roche Applied Science, Basel, Switzerland) by The Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Australia. .. The resulting libraries of sequences were filtered according to amplicon data processing pipeline in the manufacturer’s manual (Roche Applied Science Basel, Switzerland).

    Article Title: The Human Fetal Glial Cell Line SVG p12 Contains Infectious BK Polyomavirus
    Article Snippet: .. Briefly, the combined libraries were amplified by emulsion PCR and the clonally amplified DNA molecules were enriched and purified using the Roche GS Junior Titanium emPCR kit according to the manufacturer's instructions. .. Finally, the enriched fragments were sequenced on the Roche GS Junior instrument, using the Roche GS Junior Titanium sequencing kit.

    Article Title: More Than Meets the Eye: Associations of Vaginal Bacteria with Gram Stain Morphotypes Using Molecular Phylogenetic Analysis
    Article Snippet: .. Broad-range PCR and pyrosequencing of 16S rRNA gene amplicons We performed broad-range 16S-rRNA gene PCR with pyrosequencing using 454 Life Sciences FLX technology (Roche, Branford,CT) targeting the V3-V4 region of the 16S-rRNA gene [ ]. .. Sequence reads (426,602 reads) were classified using a phylogenetic placement tool pplacer [ ] and a curated reference set of key vaginal bacteria [ ].

    Article Title: TLR7 dosage polymorphism shapes interferogenesis and HIV-1 acute viremia in women
    Article Snippet: .. The PCR products were amplified on capture beads in water-in-oil emulsion microreactors, and pyrosequencing was performed on a Roche 454 GS Junior system. .. The sequence reads were quantified with the GS amplicon variant analyzer (Roche).

    Sequencing:

    Article Title: Distinctive types of postzygotic single-nucleotide mosaicisms in healthy individuals revealed by genome-wide profiling of multiple organs
    Article Snippet: .. Cancer panel sequencing of BBLD1005’s liver samples To screen for potential driver mutations related to the clonal expansion events in BBLD1005’s liver samples, we captured 1407 cancer-related genes from the liver #2 and #8 samples of BBLD1005 using a Roche SeqCap panel (Pleasanton, CA, USA) designed by Genecast Biotechnology (Beijing, China). .. The captured libraries were sequenced by Illumina Novaseq6000 (Illumina, San Diego, CA, USA) using 150-bp paired-end reads, with an average depth of ~2000X.

    Article Title: SNP assay to detect the 'Hyuuga' red-brown lesion resistance gene for Asian soybean rust
    Article Snippet: .. Chromosome Gm06 from 43 to 45 Mbp templates were obtained from the soybean genome sequence database ( http://www.phytozome.net/soybean ), and a total of 50 primers were designed from this genomic region with the LightCycler Probe Design software (Roche Applied Science, Indianapolis, IN, USA). .. All PCR primers were used to amplify genomic DNA of Dillon and Hyuuga.

    Purification:

    Article Title: The Human Fetal Glial Cell Line SVG p12 Contains Infectious BK Polyomavirus
    Article Snippet: .. Briefly, the combined libraries were amplified by emulsion PCR and the clonally amplified DNA molecules were enriched and purified using the Roche GS Junior Titanium emPCR kit according to the manufacturer's instructions. .. Finally, the enriched fragments were sequenced on the Roche GS Junior instrument, using the Roche GS Junior Titanium sequencing kit.

    Software:

    Article Title: SNP assay to detect the 'Hyuuga' red-brown lesion resistance gene for Asian soybean rust
    Article Snippet: .. Chromosome Gm06 from 43 to 45 Mbp templates were obtained from the soybean genome sequence database ( http://www.phytozome.net/soybean ), and a total of 50 primers were designed from this genomic region with the LightCycler Probe Design software (Roche Applied Science, Indianapolis, IN, USA). .. All PCR primers were used to amplify genomic DNA of Dillon and Hyuuga.

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    Roche amplicon based resequencing
    Resolution of ultra-deep sequencing-by-synthesis assay. Demonstration of very low levels of noise in negative controls after quality-control filtering for poly-mononucleotide tracts and bidirectional validation of variants. An <t>amplicon</t> was produced from cloned DNA for each mtDNA amplicon ( MT-HV2, MT-CO3 ) along with an autosomal amplicon ( BRCA2 ) and a clone. All negative controls showed minimal numbers of base positions with any variants, and none at > 0.2% heteroplasmy level, with no inherent differences between the different DNA templates.
    Amplicon Based Resequencing, supplied by Roche, used in various techniques. Bioz Stars score: 88/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicon based resequencing/product/Roche
    Average 88 stars, based on 12 article reviews
    Price from $9.99 to $1999.99
    amplicon based resequencing - by Bioz Stars, 2020-09
    88/100 stars
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    Roche gs flx amplicon resequencing
    Resolution of ultra-deep sequencing-by-synthesis assay. Demonstration of very low levels of noise in negative controls after quality-control filtering for poly-mononucleotide tracts and bidirectional validation of variants. An <t>amplicon</t> was produced from cloned DNA for each mtDNA amplicon ( MT-HV2, MT-CO3 ) along with an autosomal amplicon ( BRCA2 ) and a clone. All negative controls showed minimal numbers of base positions with any variants, and none at > 0.2% heteroplasmy level, with no inherent differences between the different DNA templates.
    Gs Flx Amplicon Resequencing, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Resolution of ultra-deep sequencing-by-synthesis assay. Demonstration of very low levels of noise in negative controls after quality-control filtering for poly-mononucleotide tracts and bidirectional validation of variants. An amplicon was produced from cloned DNA for each mtDNA amplicon ( MT-HV2, MT-CO3 ) along with an autosomal amplicon ( BRCA2 ) and a clone. All negative controls showed minimal numbers of base positions with any variants, and none at > 0.2% heteroplasmy level, with no inherent differences between the different DNA templates.

    Journal: Human Molecular Genetics

    Article Title: Universal heteroplasmy of human mitochondrial DNA

    doi: 10.1093/hmg/dds435

    Figure Lengend Snippet: Resolution of ultra-deep sequencing-by-synthesis assay. Demonstration of very low levels of noise in negative controls after quality-control filtering for poly-mononucleotide tracts and bidirectional validation of variants. An amplicon was produced from cloned DNA for each mtDNA amplicon ( MT-HV2, MT-CO3 ) along with an autosomal amplicon ( BRCA2 ) and a clone. All negative controls showed minimal numbers of base positions with any variants, and none at > 0.2% heteroplasmy level, with no inherent differences between the different DNA templates.

    Article Snippet: We, therefore, sought to improve the depth of resolution for very low-frequency heteroplasmy by developing an amplicon-based resequencing method on the Roche 454 GS FLX platform.

    Techniques: Sequencing, Amplification, Produced, Clone Assay

    Very low-level heteroplasmic mtDNA variance was detected by ultra-deep amplicon resequencing. ( A ) Comparison of variants detected in the skeletal muscle (skm) DNA within the MT-HV2 amplicon in different patient groups shows no difference between healthy control ( n = 7) and OPA1 ( n = 8) subjects, but a significant excess of variance at all heteroplasmy levels in POLG subjects ( n = 8). ( B ) Comparison of variants detected in the blood DNA in healthy control ( n = 7), POLG ( n = 4) and OPA1 ( n = 7) subjects shows that variants are present, but less common than in the skeletal muscle DNA with the absence of higher level variants ( > 2% heteroplasmy) and no difference between patient groups.

    Journal: Human Molecular Genetics

    Article Title: Universal heteroplasmy of human mitochondrial DNA

    doi: 10.1093/hmg/dds435

    Figure Lengend Snippet: Very low-level heteroplasmic mtDNA variance was detected by ultra-deep amplicon resequencing. ( A ) Comparison of variants detected in the skeletal muscle (skm) DNA within the MT-HV2 amplicon in different patient groups shows no difference between healthy control ( n = 7) and OPA1 ( n = 8) subjects, but a significant excess of variance at all heteroplasmy levels in POLG subjects ( n = 8). ( B ) Comparison of variants detected in the blood DNA in healthy control ( n = 7), POLG ( n = 4) and OPA1 ( n = 7) subjects shows that variants are present, but less common than in the skeletal muscle DNA with the absence of higher level variants ( > 2% heteroplasmy) and no difference between patient groups.

    Article Snippet: We, therefore, sought to improve the depth of resolution for very low-frequency heteroplasmy by developing an amplicon-based resequencing method on the Roche 454 GS FLX platform.

    Techniques: Amplification