target enrichment Search Results


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  • 94
    Agilent technologies sureselect target enrichment
    Maternal transmission of EGL305's chromothripsis. ( A ) A combination of G-banding and FISH revealed EGL305's four-way translocation between Chromosomes 1, 4, 7, and 15. <t>SureSelect</t> and Illumina HiSeq targeted to the Chromosome 1 deletion and Chromosome 7 duplication captured two junctions, and we inferred additional breakpoints. ( B ) EGL305's mother carries a more balanced form of the same four-way translocation.
    Sureselect Target Enrichment, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 227 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sureselect target enrichment/product/Agilent technologies
    Average 94 stars, based on 227 article reviews
    Price from $9.99 to $1999.99
    sureselect target enrichment - by Bioz Stars, 2020-04
    94/100 stars
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    93
    Agilent technologies haloplex target enrichment
    Maternal transmission of EGL305's chromothripsis. ( A ) A combination of G-banding and FISH revealed EGL305's four-way translocation between Chromosomes 1, 4, 7, and 15. <t>SureSelect</t> and Illumina HiSeq targeted to the Chromosome 1 deletion and Chromosome 7 duplication captured two junctions, and we inferred additional breakpoints. ( B ) EGL305's mother carries a more balanced form of the same four-way translocation.
    Haloplex Target Enrichment, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 45 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/haloplex target enrichment/product/Agilent technologies
    Average 93 stars, based on 45 article reviews
    Price from $9.99 to $1999.99
    haloplex target enrichment - by Bioz Stars, 2020-04
    93/100 stars
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    95
    Agilent technologies sureselectxt target enrichment
    Maternal transmission of EGL305's chromothripsis. ( A ) A combination of G-banding and FISH revealed EGL305's four-way translocation between Chromosomes 1, 4, 7, and 15. <t>SureSelect</t> and Illumina HiSeq targeted to the Chromosome 1 deletion and Chromosome 7 duplication captured two junctions, and we inferred additional breakpoints. ( B ) EGL305's mother carries a more balanced form of the same four-way translocation.
    Sureselectxt Target Enrichment, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 95/100, based on 92 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sureselectxt target enrichment/product/Agilent technologies
    Average 95 stars, based on 92 article reviews
    Price from $9.99 to $1999.99
    sureselectxt target enrichment - by Bioz Stars, 2020-04
    95/100 stars
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    91
    Celemics target enrichment kit
    Maternal transmission of EGL305's chromothripsis. ( A ) A combination of G-banding and FISH revealed EGL305's four-way translocation between Chromosomes 1, 4, 7, and 15. <t>SureSelect</t> and Illumina HiSeq targeted to the Chromosome 1 deletion and Chromosome 7 duplication captured two junctions, and we inferred additional breakpoints. ( B ) EGL305's mother carries a more balanced form of the same four-way translocation.
    Target Enrichment Kit, supplied by Celemics, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 91 stars, based on 5 article reviews
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    target enrichment kit - by Bioz Stars, 2020-04
    91/100 stars
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    93
    RainDance Technologies raindance target enrichment
    Maternal transmission of EGL305's chromothripsis. ( A ) A combination of G-banding and FISH revealed EGL305's four-way translocation between Chromosomes 1, 4, 7, and 15. <t>SureSelect</t> and Illumina HiSeq targeted to the Chromosome 1 deletion and Chromosome 7 duplication captured two junctions, and we inferred additional breakpoints. ( B ) EGL305's mother carries a more balanced form of the same four-way translocation.
    Raindance Target Enrichment, supplied by RainDance Technologies, used in various techniques. Bioz Stars score: 93/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 93 stars, based on 4 article reviews
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    raindance target enrichment - by Bioz Stars, 2020-04
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    96
    Agilent technologies sureselect target enrichment kit
    Low oxygen conditions induce TET enzyme expression and Foxp3 CNS2 demethylation in iTregs. (A) iTregs were induced in the presence of 10 µg ml −1 vitamin C (Vit.C) or under the 5% O 2 condition. The expressions of indicated genes were analyzed by quantitative real-time PCR. (B) 5hmC content in iTregs induced with indicated conditions was determined by LC-MS/MS analysis. (C, D) Methylation status determined by bisulfite conversion of the CpG sites of Foxp3 CNS2 in iTregs generated under the 5% O 2 condition and/or 10 µg ml −1 vitamin C (C), Ctla4 , Ikzf4 , Tnfrsf18 and Il2ra in iTregs generated under the 5% O 2 condition and 10 µg ml −1 vitamin C (D). The methylation status of tTregs is shown as a positive control in (C). (E) Violin plot showing the genome-wide methylation levels of CpG sites under 5% oxygen and normoxic conditions as detected by <t>SureSelect-PBAT.</t> * P
    Sureselect Target Enrichment Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 96/100, based on 253 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sureselect target enrichment kit/product/Agilent technologies
    Average 96 stars, based on 253 article reviews
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    sureselect target enrichment kit - by Bioz Stars, 2020-04
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    99
    Agilent technologies sureselect target enrichment system
    The workflow for designing the <t>SureSelect</t> library specific for bisulfite-converted DNA.
    Sureselect Target Enrichment System, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 648 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sureselect target enrichment system/product/Agilent technologies
    Average 99 stars, based on 648 article reviews
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    sureselect target enrichment system - by Bioz Stars, 2020-04
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    98
    Agilent technologies sureselect target enrichment protocol
    The workflow for designing the <t>SureSelect</t> library specific for bisulfite-converted DNA.
    Sureselect Target Enrichment Protocol, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 98/100, based on 150 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sureselect target enrichment protocol/product/Agilent technologies
    Average 98 stars, based on 150 article reviews
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    sureselect target enrichment protocol - by Bioz Stars, 2020-04
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    93
    Agilent technologies haloplex target enrichment kit
    Validation of <t>HaloPlex</t> SNVs in the 5’ UTR of GNAI3 by Sanger Sequencing. A. Homozygous SNV (c.-72C > T) of Patient 2. At the top of the Figure the track annotation panel shows the Chr1 location of the C > T variant at position 109548649. Next, the forward sequences of the reference (R) and test sample (S) are shown, followed by the confidence score of the peak corresponding to the variant. From the bottom up, the reverse sequences of the reference and test sample peak profiles and the confidence score demonstrate the same variant. The red arrows point to the mutated nucleotide. B. Heterozygous SNV (c.-61C > T) of Patient 10. Same as A, except for the track annotation panel, which shows the C > T SNV at position 109548660 in Chr1.
    Haloplex Target Enrichment Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 81 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 93 stars, based on 81 article reviews
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    haloplex target enrichment kit - by Bioz Stars, 2020-04
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    88
    Thermo Fisher targetseq target enrichment kit
    Validation of <t>HaloPlex</t> SNVs in the 5’ UTR of GNAI3 by Sanger Sequencing. A. Homozygous SNV (c.-72C > T) of Patient 2. At the top of the Figure the track annotation panel shows the Chr1 location of the C > T variant at position 109548649. Next, the forward sequences of the reference (R) and test sample (S) are shown, followed by the confidence score of the peak corresponding to the variant. From the bottom up, the reverse sequences of the reference and test sample peak profiles and the confidence score demonstrate the same variant. The red arrows point to the mutated nucleotide. B. Heterozygous SNV (c.-61C > T) of Patient 10. Same as A, except for the track annotation panel, which shows the C > T SNV at position 109548660 in Chr1.
    Targetseq Target Enrichment Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 88 stars, based on 7 article reviews
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    targetseq target enrichment kit - by Bioz Stars, 2020-04
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    99
    Agilent technologies haloplex target enrichment system
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
    Haloplex Target Enrichment System, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 285 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 285 article reviews
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    haloplex target enrichment system - by Bioz Stars, 2020-04
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    80
    Roche seqcap target enrichment kit
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
    Seqcap Target Enrichment Kit, supplied by Roche, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    seqcap target enrichment kit - by Bioz Stars, 2020-04
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    94
    Illumina Inc sureselectxt target enrichment system
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
    Sureselectxt Target Enrichment System, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 160 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sureselectxt target enrichment system/product/Illumina Inc
    Average 94 stars, based on 160 article reviews
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    sureselectxt target enrichment system - by Bioz Stars, 2020-04
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    94
    Agilent technologies haloplex target enrichment protocol
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
    Haloplex Target Enrichment Protocol, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/haloplex target enrichment protocol/product/Agilent technologies
    Average 94 stars, based on 10 article reviews
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    haloplex target enrichment protocol - by Bioz Stars, 2020-04
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    94
    Agilent technologies sureselectqxt target enrichment system
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
    Sureselectqxt Target Enrichment System, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 38 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sureselectqxt target enrichment system/product/Agilent technologies
    Average 94 stars, based on 38 article reviews
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    sureselectqxt target enrichment system - by Bioz Stars, 2020-04
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    91
    Agilent technologies sureselect target enrichment reagent
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
    Sureselect Target Enrichment Reagent, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 91/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sureselect target enrichment reagent/product/Agilent technologies
    Average 91 stars, based on 3 article reviews
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    sureselect target enrichment reagent - by Bioz Stars, 2020-04
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    92
    Agilent technologies haloplexhs target enrichment system
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
    Haloplexhs Target Enrichment System, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/haloplexhs target enrichment system/product/Agilent technologies
    Average 92 stars, based on 5 article reviews
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    haloplexhs target enrichment system - by Bioz Stars, 2020-04
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    93
    Agilent technologies sureselectxt target enrichment kit
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
    Sureselectxt Target Enrichment Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sureselectxt target enrichment kit/product/Agilent technologies
    Average 93 stars, based on 14 article reviews
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    sureselectxt target enrichment kit - by Bioz Stars, 2020-04
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    88
    Agilent technologies sureselect target enrichment workflow
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
    Sureselect Target Enrichment Workflow, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 88/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sureselect target enrichment workflow/product/Agilent technologies
    Average 88 stars, based on 3 article reviews
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    sureselect target enrichment workflow - by Bioz Stars, 2020-04
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    86
    Agilent technologies sureselectxt target enrichment protocol
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
    Sureselectxt Target Enrichment Protocol, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 86/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sureselectxt target enrichment protocol/product/Agilent technologies
    Average 86 stars, based on 15 article reviews
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    sureselectxt target enrichment protocol - by Bioz Stars, 2020-04
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    94
    Illumina Inc sureselect target enrichment system
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
    Sureselect Target Enrichment System, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 73 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sureselect target enrichment system/product/Illumina Inc
    Average 94 stars, based on 73 article reviews
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    sureselect target enrichment system - by Bioz Stars, 2020-04
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    97
    Agilent technologies target enrichment
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
    Target Enrichment, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 97/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/target enrichment/product/Agilent technologies
    Average 97 stars, based on 19 article reviews
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    target enrichment - by Bioz Stars, 2020-04
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    95
    Agilent technologies sureselectqxt target enrichment kit
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
    Sureselectqxt Target Enrichment Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 95/100, based on 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sureselectqxt target enrichment kit/product/Agilent technologies
    Average 95 stars, based on 26 article reviews
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    sureselectqxt target enrichment kit - by Bioz Stars, 2020-04
    95/100 stars
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    92
    Agilent technologies v6 target enrichment kits
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
    V6 Target Enrichment Kits, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 92 stars, based on 5 article reviews
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    v6 target enrichment kits - by Bioz Stars, 2020-04
    92/100 stars
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    80
    Roche hypercap target enrichment kit
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
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    Agilent technologies sureselect target enrichment v3
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
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    Agilent technologies suredesign target enrichment kit
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
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    Agilent technologies haloplexhs target enrichment kit
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
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    Agilent technologies sureselectxt2 target enrichment system
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
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    Agilent technologies haloplextm target enrichment system
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
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    Agilent technologies haloplex target enrichment panel
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
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    Roche nimblegen seqcapex target enrichment
    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the <t>HaloPlex</t> exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .
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    Image Search Results


    Maternal transmission of EGL305's chromothripsis. ( A ) A combination of G-banding and FISH revealed EGL305's four-way translocation between Chromosomes 1, 4, 7, and 15. SureSelect and Illumina HiSeq targeted to the Chromosome 1 deletion and Chromosome 7 duplication captured two junctions, and we inferred additional breakpoints. ( B ) EGL305's mother carries a more balanced form of the same four-way translocation.

    Journal: Genome Research

    Article Title: Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis

    doi: 10.1101/gr.191247.115

    Figure Lengend Snippet: Maternal transmission of EGL305's chromothripsis. ( A ) A combination of G-banding and FISH revealed EGL305's four-way translocation between Chromosomes 1, 4, 7, and 15. SureSelect and Illumina HiSeq targeted to the Chromosome 1 deletion and Chromosome 7 duplication captured two junctions, and we inferred additional breakpoints. ( B ) EGL305's mother carries a more balanced form of the same four-way translocation.

    Article Snippet: We used Agilent SureSelect Target Enrichment to pull down 40-kb regions around breakpoints fine-mapped by custom array CGH.

    Techniques: Transmission Assay, Fluorescence In Situ Hybridization, Translocation Assay

    Low oxygen conditions induce TET enzyme expression and Foxp3 CNS2 demethylation in iTregs. (A) iTregs were induced in the presence of 10 µg ml −1 vitamin C (Vit.C) or under the 5% O 2 condition. The expressions of indicated genes were analyzed by quantitative real-time PCR. (B) 5hmC content in iTregs induced with indicated conditions was determined by LC-MS/MS analysis. (C, D) Methylation status determined by bisulfite conversion of the CpG sites of Foxp3 CNS2 in iTregs generated under the 5% O 2 condition and/or 10 µg ml −1 vitamin C (C), Ctla4 , Ikzf4 , Tnfrsf18 and Il2ra in iTregs generated under the 5% O 2 condition and 10 µg ml −1 vitamin C (D). The methylation status of tTregs is shown as a positive control in (C). (E) Violin plot showing the genome-wide methylation levels of CpG sites under 5% oxygen and normoxic conditions as detected by SureSelect-PBAT. * P

    Journal: International Immunology

    Article Title: Improvement of Foxp3 stability through CNS2 demethylation by TET enzyme induction and activation

    doi: 10.1093/intimm/dxx049

    Figure Lengend Snippet: Low oxygen conditions induce TET enzyme expression and Foxp3 CNS2 demethylation in iTregs. (A) iTregs were induced in the presence of 10 µg ml −1 vitamin C (Vit.C) or under the 5% O 2 condition. The expressions of indicated genes were analyzed by quantitative real-time PCR. (B) 5hmC content in iTregs induced with indicated conditions was determined by LC-MS/MS analysis. (C, D) Methylation status determined by bisulfite conversion of the CpG sites of Foxp3 CNS2 in iTregs generated under the 5% O 2 condition and/or 10 µg ml −1 vitamin C (C), Ctla4 , Ikzf4 , Tnfrsf18 and Il2ra in iTregs generated under the 5% O 2 condition and 10 µg ml −1 vitamin C (D). The methylation status of tTregs is shown as a positive control in (C). (E) Violin plot showing the genome-wide methylation levels of CpG sites under 5% oxygen and normoxic conditions as detected by SureSelect-PBAT. * P

    Article Snippet: SureSelect-PostBisulfite Adaptor tagging library preparation and data analysis One hundred and nine megabases of mouse genome, which contain CpG island, tissue-specific differentially methylated regions and open regulatory regions, were captured using the SureSelect Mouse Methyl-Seq kit and the SureSelect Target Enrichment kit (Agilent Technologies).

    Techniques: Expressing, Real-time Polymerase Chain Reaction, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, Methylation, Generated, Positive Control, Genome Wide

    The workflow for designing the SureSelect library specific for bisulfite-converted DNA.

    Journal: Nucleic Acids Research

    Article Title: In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes

    doi: 10.1093/nar/gks1467

    Figure Lengend Snippet: The workflow for designing the SureSelect library specific for bisulfite-converted DNA.

    Article Snippet: To this end, we developed a protocol for the Agilent SureSelect Target Enrichment System involving the bisulfite treatment step before the hybrid capture (see Materials and Methods).

    Techniques:

    Validation of HaloPlex SNVs in the 5’ UTR of GNAI3 by Sanger Sequencing. A. Homozygous SNV (c.-72C > T) of Patient 2. At the top of the Figure the track annotation panel shows the Chr1 location of the C > T variant at position 109548649. Next, the forward sequences of the reference (R) and test sample (S) are shown, followed by the confidence score of the peak corresponding to the variant. From the bottom up, the reverse sequences of the reference and test sample peak profiles and the confidence score demonstrate the same variant. The red arrows point to the mutated nucleotide. B. Heterozygous SNV (c.-61C > T) of Patient 10. Same as A, except for the track annotation panel, which shows the C > T SNV at position 109548660 in Chr1.

    Journal: PLoS ONE

    Article Title: GNAI3: Another Candidate Gene to Screen in Persons with Ocular Albinism

    doi: 10.1371/journal.pone.0162273

    Figure Lengend Snippet: Validation of HaloPlex SNVs in the 5’ UTR of GNAI3 by Sanger Sequencing. A. Homozygous SNV (c.-72C > T) of Patient 2. At the top of the Figure the track annotation panel shows the Chr1 location of the C > T variant at position 109548649. Next, the forward sequences of the reference (R) and test sample (S) are shown, followed by the confidence score of the peak corresponding to the variant. From the bottom up, the reverse sequences of the reference and test sample peak profiles and the confidence score demonstrate the same variant. The red arrows point to the mutated nucleotide. B. Heterozygous SNV (c.-61C > T) of Patient 10. Same as A, except for the track annotation panel, which shows the C > T SNV at position 109548660 in Chr1.

    Article Snippet: Capture HaloPlex target enrichment system A library of DNA restriction fragments from all coding exons, introns and UTRs (5’ and 3’) of the GNAI3 gene was prepared with a HaloPlex target enrichment kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer's instructions.

    Techniques: Sequencing, Variant Assay

    Variants identified in the 5’UTR and non-coding exon 9/3’ UTR using the HaloPlex target enrichment system/IIlumina MiSeq sequencing and visualized with the Integrative Genomics Viewer (IGV). A. SNVs found in the 5’ UTR of the GNAI3 gene, represented by the blue horizontal bar before the start codon encoding Methionine (green), at the beginning of exon 1. B . SNVs, insertions and deletions found in the GNAI3 2109 bp of non-coding exon 9/3’ UTR, represented by the blue horizontal bar. Variants are homozygous [red or blue (lower frequency)] and heterozygous (half blue and half red).

    Journal: PLoS ONE

    Article Title: GNAI3: Another Candidate Gene to Screen in Persons with Ocular Albinism

    doi: 10.1371/journal.pone.0162273

    Figure Lengend Snippet: Variants identified in the 5’UTR and non-coding exon 9/3’ UTR using the HaloPlex target enrichment system/IIlumina MiSeq sequencing and visualized with the Integrative Genomics Viewer (IGV). A. SNVs found in the 5’ UTR of the GNAI3 gene, represented by the blue horizontal bar before the start codon encoding Methionine (green), at the beginning of exon 1. B . SNVs, insertions and deletions found in the GNAI3 2109 bp of non-coding exon 9/3’ UTR, represented by the blue horizontal bar. Variants are homozygous [red or blue (lower frequency)] and heterozygous (half blue and half red).

    Article Snippet: Capture HaloPlex target enrichment system A library of DNA restriction fragments from all coding exons, introns and UTRs (5’ and 3’) of the GNAI3 gene was prepared with a HaloPlex target enrichment kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer's instructions.

    Techniques: Sequencing

    GNAI3 gene locus in human Chr1, Agilent Haloplex amplicons and Median coverage of GNAI3 . A . GNAI3 is located in the p arm of chromosome 1, band 13.3 (red line). B. Agilent Haloplex Amplicons designed to amplify the GNAI3 9 exons, introns and 100 bp of each 5’ and 3’ UTRs are depicted in green and show that all regions of the gene were effectively covered. The GNAI3 RefSeq is shown in black and was aligned against the GRCh37/hg19 human genome using the UCSC-BLAT browser. C. The median coverage level varied from 14 to 8,009 across the targeted GNAI3 region analyzed in the HaloPlex design; only 1.2% of the target GNAI3 region was not covered.

    Journal: PLoS ONE

    Article Title: GNAI3: Another Candidate Gene to Screen in Persons with Ocular Albinism

    doi: 10.1371/journal.pone.0162273

    Figure Lengend Snippet: GNAI3 gene locus in human Chr1, Agilent Haloplex amplicons and Median coverage of GNAI3 . A . GNAI3 is located in the p arm of chromosome 1, band 13.3 (red line). B. Agilent Haloplex Amplicons designed to amplify the GNAI3 9 exons, introns and 100 bp of each 5’ and 3’ UTRs are depicted in green and show that all regions of the gene were effectively covered. The GNAI3 RefSeq is shown in black and was aligned against the GRCh37/hg19 human genome using the UCSC-BLAT browser. C. The median coverage level varied from 14 to 8,009 across the targeted GNAI3 region analyzed in the HaloPlex design; only 1.2% of the target GNAI3 region was not covered.

    Article Snippet: Capture HaloPlex target enrichment system A library of DNA restriction fragments from all coding exons, introns and UTRs (5’ and 3’) of the GNAI3 gene was prepared with a HaloPlex target enrichment kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer's instructions.

    Techniques:

    Validation of HaloPlex homozygous deletion (c.*1379_*1380delAT) of Patient 22 in the non-coding exon 9/3’ UTR of GNAI3 by Sanger Sequencing. In addition to the track annotation panel clearly indicating the deletion at positions 109593703–109593704, the figure shows the forward sequences of the reference (R) and test sample (S) and the reverse sequences. The red arrows point to the deleted nucleotides.

    Journal: PLoS ONE

    Article Title: GNAI3: Another Candidate Gene to Screen in Persons with Ocular Albinism

    doi: 10.1371/journal.pone.0162273

    Figure Lengend Snippet: Validation of HaloPlex homozygous deletion (c.*1379_*1380delAT) of Patient 22 in the non-coding exon 9/3’ UTR of GNAI3 by Sanger Sequencing. In addition to the track annotation panel clearly indicating the deletion at positions 109593703–109593704, the figure shows the forward sequences of the reference (R) and test sample (S) and the reverse sequences. The red arrows point to the deleted nucleotides.

    Article Snippet: Capture HaloPlex target enrichment system A library of DNA restriction fragments from all coding exons, introns and UTRs (5’ and 3’) of the GNAI3 gene was prepared with a HaloPlex target enrichment kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer's instructions.

    Techniques: Sequencing

    Validation of HaloPlex heterozygous insertion (c.*1994_*1995insA) of Patient 18 in the non-coding exon 9/3’ UTR of GNAI3 by Sanger Sequencing. As in the previous figures, the track annotation panel depicts the Chr1 location of the insertion at position 109594317, followed by the forward sequences of the reference (R) and test sample (S), the confidence score peaks and reverse reference and test sample sequences. The red arrows point to the insertion in the sequences.

    Journal: PLoS ONE

    Article Title: GNAI3: Another Candidate Gene to Screen in Persons with Ocular Albinism

    doi: 10.1371/journal.pone.0162273

    Figure Lengend Snippet: Validation of HaloPlex heterozygous insertion (c.*1994_*1995insA) of Patient 18 in the non-coding exon 9/3’ UTR of GNAI3 by Sanger Sequencing. As in the previous figures, the track annotation panel depicts the Chr1 location of the insertion at position 109594317, followed by the forward sequences of the reference (R) and test sample (S), the confidence score peaks and reverse reference and test sample sequences. The red arrows point to the insertion in the sequences.

    Article Snippet: Capture HaloPlex target enrichment system A library of DNA restriction fragments from all coding exons, introns and UTRs (5’ and 3’) of the GNAI3 gene was prepared with a HaloPlex target enrichment kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer's instructions.

    Techniques: Sequencing

    EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the HaloPlex exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .

    Journal: NPJ genomic medicine

    Article Title: Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care

    doi: 10.1038/npjgenmed.2016.19

    Figure Lengend Snippet: EXaCT-1 reportable range Number and percentage of common low coverage bases shared by 36 (80%) and all 45 (100%) control (germline) samples obtained from normal tissue. ( a ) The germline samples were expected to have low genomic complexity and therefore provide more accurate assessment of coverage and performance statistics. Over 95% of the HaloPlex exome bases were covered at > 10×. ( b ) These guaranteed regions that have constant higher than 10× coverage is our reportable range, which is listed on our website ( https://rubinlab.med.cornell.edu/IPMWES/Haloplex_Exome_Sequencing_reportable_region.xlsx ). This poorly covered 4.29% genomic area of the HaloPlex exome will be excluded from our reportable range. The reportable range is listed on https://rubinlab.med.cornell.edu/IPMWES/HaloPlex_low_coverage_region.xlsx .

    Article Snippet: The test uses the HaloPlex Target Enrichment System (Agilent Technologies) for target amplification ((357,999 exons/21,522 genes), followed by sequencing on the Illumina system.

    Techniques: Sequencing

    Schematic view of EXaCT-1 assay workflow ( a ) (1) Slides are assessed by pathologist for neoplastic content, and tumour tissue marked and macrodissected. (2) DNA from fresh or FFPE tumour tissue and matched normal control specimen is extracted. (3) DNA is then enriched for exome sequences (357,999 exons corresponding to 21,522 genes) with HaloPlex technology described in this protocol in four major steps: fragmentation by restriction enzyme digestion, hybridisation to HaloPlex probes and introduction of Illumina sequence motifs, solid-phase capture and DNA ligation, and amplification of targeted fragments by PCR, followed by (4) sequencing on an Illumina HiSeq 2500 rapid mode, four samples per lane. (5) Paired-end reads are aligned to the human genome and (6) variant calls are made. (7) Variants are annotated and classified by our internally developed informatics pipeline, using publicly available and our own developed knowledge base. (8) The case is reviewed and results interpreted by a molecular pathologist who also signs it out in the LIS. (9) A report is then automatically generated and (10) dispensed to medical records. EXaCT-1 data analysis pipeline. ( b ) Schematic view of EXaCT-1 assay validation. ( c ) DNA derived from matched normal/tumour pairs from either fresh or FFPE specimens as well as standardised commercial DNA material were used to demonstrate the accuracy, sensitivity, specificity, reproducibility and precision of the assay using bioinformatics process for the detection of numerous types of variants (SNV, indel and CNV gain), according to NYS-DOH NGS guidelines for somatic genetic variant detection. IPM, Institute for Precision Medicine.

    Journal: NPJ genomic medicine

    Article Title: Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care

    doi: 10.1038/npjgenmed.2016.19

    Figure Lengend Snippet: Schematic view of EXaCT-1 assay workflow ( a ) (1) Slides are assessed by pathologist for neoplastic content, and tumour tissue marked and macrodissected. (2) DNA from fresh or FFPE tumour tissue and matched normal control specimen is extracted. (3) DNA is then enriched for exome sequences (357,999 exons corresponding to 21,522 genes) with HaloPlex technology described in this protocol in four major steps: fragmentation by restriction enzyme digestion, hybridisation to HaloPlex probes and introduction of Illumina sequence motifs, solid-phase capture and DNA ligation, and amplification of targeted fragments by PCR, followed by (4) sequencing on an Illumina HiSeq 2500 rapid mode, four samples per lane. (5) Paired-end reads are aligned to the human genome and (6) variant calls are made. (7) Variants are annotated and classified by our internally developed informatics pipeline, using publicly available and our own developed knowledge base. (8) The case is reviewed and results interpreted by a molecular pathologist who also signs it out in the LIS. (9) A report is then automatically generated and (10) dispensed to medical records. EXaCT-1 data analysis pipeline. ( b ) Schematic view of EXaCT-1 assay validation. ( c ) DNA derived from matched normal/tumour pairs from either fresh or FFPE specimens as well as standardised commercial DNA material were used to demonstrate the accuracy, sensitivity, specificity, reproducibility and precision of the assay using bioinformatics process for the detection of numerous types of variants (SNV, indel and CNV gain), according to NYS-DOH NGS guidelines for somatic genetic variant detection. IPM, Institute for Precision Medicine.

    Article Snippet: The test uses the HaloPlex Target Enrichment System (Agilent Technologies) for target amplification ((357,999 exons/21,522 genes), followed by sequencing on the Illumina system.

    Techniques: Formalin-fixed Paraffin-Embedded, Hybridization, Sequencing, DNA Ligation, Amplification, Polymerase Chain Reaction, Variant Assay, Generated, Derivative Assay, Next-Generation Sequencing