direct barcoding barcoded fusion primers Search Results


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    Thermo Fisher solid total rna seq star seq kit
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    dntp  (TaKaRa)
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    TaKaRa dntp
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    Roche amplicon sequencing
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    Illumina Inc illumina miseq system
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    Thermo Fisher ion total rna seq kit v2
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    Pacific Biosciences unique barcodes
    Direct barcoding results. Direct barcoding results for the technical replicate with different <t>barcodes.</t> A : UCSC browser screenshot illustrating the detected variants (red lines) of the two fully‐phased haplogroup sequences for each sample barcode relative to the GRCh38 reference. The CYP2D6 gene is located on the negative strand. Exon numbers are indicated in white based on the NM_000106.5 transcript sequence. For the haplogroup 2 sequences, the variants determining the CYP2D6 * 35 call are indicated. B : Identity and distribution of all 27 variants across the haplogroup sequences. Order in this table (top to bottom) is identical to those in Figure 2A (left to right). Variants in bold determine the CYP2D6 * 35 haplotype; * indicates that the variant was included on the Roche AmpliChip CYP450 test; # indicates that the variant was included in PharmGKB (February 4, 2016); and “HG” and “i” denote haplogroup and index, respectively.
    Unique Barcodes, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 91/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher phusion taq master mix
    Direct barcoding results. Direct barcoding results for the technical replicate with different <t>barcodes.</t> A : UCSC browser screenshot illustrating the detected variants (red lines) of the two fully‐phased haplogroup sequences for each sample barcode relative to the GRCh38 reference. The CYP2D6 gene is located on the negative strand. Exon numbers are indicated in white based on the NM_000106.5 transcript sequence. For the haplogroup 2 sequences, the variants determining the CYP2D6 * 35 call are indicated. B : Identity and distribution of all 27 variants across the haplogroup sequences. Order in this table (top to bottom) is identical to those in Figure 2A (left to right). Variants in bold determine the CYP2D6 * 35 haplotype; * indicates that the variant was included on the Roche AmpliChip CYP450 test; # indicates that the variant was included in PharmGKB (February 4, 2016); and “HG” and “i” denote haplogroup and index, respectively.
    Phusion Taq Master Mix, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Beckman Coulter amplure xp spri beads
    Direct barcoding results. Direct barcoding results for the technical replicate with different <t>barcodes.</t> A : UCSC browser screenshot illustrating the detected variants (red lines) of the two fully‐phased haplogroup sequences for each sample barcode relative to the GRCh38 reference. The CYP2D6 gene is located on the negative strand. Exon numbers are indicated in white based on the NM_000106.5 transcript sequence. For the haplogroup 2 sequences, the variants determining the CYP2D6 * 35 call are indicated. B : Identity and distribution of all 27 variants across the haplogroup sequences. Order in this table (top to bottom) is identical to those in Figure 2A (left to right). Variants in bold determine the CYP2D6 * 35 haplotype; * indicates that the variant was included on the Roche AmpliChip CYP450 test; # indicates that the variant was included in PharmGKB (February 4, 2016); and “HG” and “i” denote haplogroup and index, respectively.
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    Pacific Biosciences pacbio smrt cell
    Direct barcoding results. Direct barcoding results for the technical replicate with different <t>barcodes.</t> A : UCSC browser screenshot illustrating the detected variants (red lines) of the two fully‐phased haplogroup sequences for each sample barcode relative to the GRCh38 reference. The CYP2D6 gene is located on the negative strand. Exon numbers are indicated in white based on the NM_000106.5 transcript sequence. For the haplogroup 2 sequences, the variants determining the CYP2D6 * 35 call are indicated. B : Identity and distribution of all 27 variants across the haplogroup sequences. Order in this table (top to bottom) is identical to those in Figure 2A (left to right). Variants in bold determine the CYP2D6 * 35 haplotype; * indicates that the variant was included on the Roche AmpliChip CYP450 test; # indicates that the variant was included in PharmGKB (February 4, 2016); and “HG” and “i” denote haplogroup and index, respectively.
    Pacbio Smrt Cell, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 88/100, based on 57 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Pacific Biosciences cyp2d6
    Direct barcoding results. Direct barcoding results for the technical replicate with different barcodes. A : UCSC browser screenshot illustrating the detected variants (red lines) of the two fully‐phased haplogroup sequences for each sample barcode relative to the GRCh38 reference. The <t>CYP2D6</t> gene is located on the negative strand. Exon numbers are indicated in white based on the NM_000106.5 transcript sequence. For the haplogroup 2 sequences, the variants determining the CYP2D6 * 35 call are indicated. B : Identity and distribution of all 27 variants across the haplogroup sequences. Order in this table (top to bottom) is identical to those in Figure 2A (left to right). Variants in bold determine the CYP2D6 * 35 haplotype; * indicates that the variant was included on the Roche AmpliChip CYP450 test; # indicates that the variant was included in PharmGKB (February 4, 2016); and “HG” and “i” denote haplogroup and index, respectively.
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    Image Search Results


    Direct barcoding results. Direct barcoding results for the technical replicate with different barcodes. A : UCSC browser screenshot illustrating the detected variants (red lines) of the two fully‐phased haplogroup sequences for each sample barcode relative to the GRCh38 reference. The CYP2D6 gene is located on the negative strand. Exon numbers are indicated in white based on the NM_000106.5 transcript sequence. For the haplogroup 2 sequences, the variants determining the CYP2D6 * 35 call are indicated. B : Identity and distribution of all 27 variants across the haplogroup sequences. Order in this table (top to bottom) is identical to those in Figure 2A (left to right). Variants in bold determine the CYP2D6 * 35 haplotype; * indicates that the variant was included on the Roche AmpliChip CYP450 test; # indicates that the variant was included in PharmGKB (February 4, 2016); and “HG” and “i” denote haplogroup and index, respectively.

    Journal: Human Mutation

    Article Title: Flexible and Scalable Full‐Length CYP2D6 Long Amplicon PacBio Sequencing

    doi: 10.1002/humu.23166

    Figure Lengend Snippet: Direct barcoding results. Direct barcoding results for the technical replicate with different barcodes. A : UCSC browser screenshot illustrating the detected variants (red lines) of the two fully‐phased haplogroup sequences for each sample barcode relative to the GRCh38 reference. The CYP2D6 gene is located on the negative strand. Exon numbers are indicated in white based on the NM_000106.5 transcript sequence. For the haplogroup 2 sequences, the variants determining the CYP2D6 * 35 call are indicated. B : Identity and distribution of all 27 variants across the haplogroup sequences. Order in this table (top to bottom) is identical to those in Figure 2A (left to right). Variants in bold determine the CYP2D6 * 35 haplotype; * indicates that the variant was included on the Roche AmpliChip CYP450 test; # indicates that the variant was included in PharmGKB (February 4, 2016); and “HG” and “i” denote haplogroup and index, respectively.

    Article Snippet: Initial analysis of one individual was performed using two technical replicate libraries with unique barcodes, prepared and sequenced together on one PacBio SMRT cell.

    Techniques: Sequencing, Variant Assay

    Barcoding schemes. Direct versus two‐step sample barcoding. A : In the direct barcoding scheme the sample specific barcodes, indicated by the blue and red for patients 1 and 2, respectively, are attached to the gene‐specific sequences (black arrows) and are introduced in a single PCR reaction. B : For the two‐step procedure for each individual, the region of interest is first amplified with a pair of gene‐specific primers with M13 forward (green) and reverse (purple) sequence tails. A symmetrical sample barcode, indicated by blue and red for patients 1 and 2, respectively, is introduced in a second PCR using a set of M13 barcode primers. A 5' padding sequence (black) is present on the index primers for both the direct and two‐step barcoding schemes to give all fragment identical end sequences to avoid ligation biases during the SMRT bell library preparation.

    Journal: Human Mutation

    Article Title: Flexible and Scalable Full‐Length CYP2D6 Long Amplicon PacBio Sequencing

    doi: 10.1002/humu.23166

    Figure Lengend Snippet: Barcoding schemes. Direct versus two‐step sample barcoding. A : In the direct barcoding scheme the sample specific barcodes, indicated by the blue and red for patients 1 and 2, respectively, are attached to the gene‐specific sequences (black arrows) and are introduced in a single PCR reaction. B : For the two‐step procedure for each individual, the region of interest is first amplified with a pair of gene‐specific primers with M13 forward (green) and reverse (purple) sequence tails. A symmetrical sample barcode, indicated by blue and red for patients 1 and 2, respectively, is introduced in a second PCR using a set of M13 barcode primers. A 5' padding sequence (black) is present on the index primers for both the direct and two‐step barcoding schemes to give all fragment identical end sequences to avoid ligation biases during the SMRT bell library preparation.

    Article Snippet: Initial analysis of one individual was performed using two technical replicate libraries with unique barcodes, prepared and sequenced together on one PacBio SMRT cell.

    Techniques: Polymerase Chain Reaction, Amplification, Sequencing, Ligation

    Direct barcoding results. Direct barcoding results for the technical replicate with different barcodes. A : UCSC browser screenshot illustrating the detected variants (red lines) of the two fully‐phased haplogroup sequences for each sample barcode relative to the GRCh38 reference. The CYP2D6 gene is located on the negative strand. Exon numbers are indicated in white based on the NM_000106.5 transcript sequence. For the haplogroup 2 sequences, the variants determining the CYP2D6 * 35 call are indicated. B : Identity and distribution of all 27 variants across the haplogroup sequences. Order in this table (top to bottom) is identical to those in Figure 2A (left to right). Variants in bold determine the CYP2D6 * 35 haplotype; * indicates that the variant was included on the Roche AmpliChip CYP450 test; # indicates that the variant was included in PharmGKB (February 4, 2016); and “HG” and “i” denote haplogroup and index, respectively.

    Journal: Human Mutation

    Article Title: Flexible and Scalable Full‐Length CYP2D6 Long Amplicon PacBio Sequencing

    doi: 10.1002/humu.23166

    Figure Lengend Snippet: Direct barcoding results. Direct barcoding results for the technical replicate with different barcodes. A : UCSC browser screenshot illustrating the detected variants (red lines) of the two fully‐phased haplogroup sequences for each sample barcode relative to the GRCh38 reference. The CYP2D6 gene is located on the negative strand. Exon numbers are indicated in white based on the NM_000106.5 transcript sequence. For the haplogroup 2 sequences, the variants determining the CYP2D6 * 35 call are indicated. B : Identity and distribution of all 27 variants across the haplogroup sequences. Order in this table (top to bottom) is identical to those in Figure 2A (left to right). Variants in bold determine the CYP2D6 * 35 haplotype; * indicates that the variant was included on the Roche AmpliChip CYP450 test; # indicates that the variant was included in PharmGKB (February 4, 2016); and “HG” and “i” denote haplogroup and index, respectively.

    Article Snippet: M13 Sequence‐Based Two‐Step Barcoding Scheme For Multiplexing of CYP2D6 Although the direct barcoding scheme is able to deliver high‐quality results and accurate CYP2D6 phenotype predictions, the setup is rigid.

    Techniques: Sequencing, Variant Assay