The Experts below are selected from a list of 225 Experts worldwide ranked by ideXlab platform

Liqing Zhang - One of the best experts on this subject based on the ideXlab platform.

  • Investigating Bisulfite short-read mapping failure with hairpin Bisulfite sequencing data
    BMC Genomics, 2015
    Co-Authors: Jacob Porter, Ming-an Sun, Hehuang Xie, Liqing Zhang
    Abstract:

    Background DNA methylation is an important epigenetic mark relevant to normal development and disease genesis. A common approach to characterizing genome-wide DNA methylation is using Next Generation Sequencing technology to sequence Bisulfite treated DNA. The short sequence reads are mapped to the reference genome to determine the methylation statuses of Cs. However, despite intense effort, a much smaller proportion of the reads derived from Bisulfite treated DNA (usually about 40-80%) can be mapped than regular short reads mapping (> 90%), and it is unclear what factors lead to this low mapping efficiency. Results To address this issue, we used the hairpin Bisulfite sequencing technology to determine sequences of both DNA double strands simultaneously. This enabled the recovery of the original non-Bisulfite-converted sequences. We used Bismark for Bisulfite read mapping and Bowtie2 for recovered read mapping. We found that recovering the reads improved unique mapping efficiency by 9-10% compared to the Bisulfite reads. Such improvement in mapping efficiency is related to sequence entropy. Conclusions The hairpin recovery technique improves mapping efficiency, and sequence entropy relates to mapping efficiency.

  • Investigating Bisulfite short-read mapping failure with hairpin Bisulfite sequencing data.
    BMC genomics, 2015
    Co-Authors: Jacob Porter, Ming-an Sun, Hehuang Xie, Liqing Zhang
    Abstract:

    DNA methylation is an important epigenetic mark relevant to normal development and disease genesis. A common approach to characterizing genome-wide DNA methylation is using Next Generation Sequencing technology to sequence Bisulfite treated DNA. The short sequence reads are mapped to the reference genome to determine the methylation statuses of Cs. However, despite intense effort, a much smaller proportion of the reads derived from Bisulfite treated DNA (usually about 40-80%) can be mapped than regular short reads mapping (> 90%), and it is unclear what factors lead to this low mapping efficiency. To address this issue, we used the hairpin Bisulfite sequencing technology to determine sequences of both DNA double strands simultaneously. This enabled the recovery of the original non-Bisulfite-converted sequences. We used Bismark for Bisulfite read mapping and Bowtie2 for recovered read mapping. We found that recovering the reads improved unique mapping efficiency by 9-10% compared to the Bisulfite reads. Such improvement in mapping efficiency is related to sequence entropy. The hairpin recovery technique improves mapping efficiency, and sequence entropy relates to mapping efficiency.

  • ICCABS - Improving Bisulfite short-read mapping efficiency with hairpin-Bisulfite data
    2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2014
    Co-Authors: Jacob Porter, Ming-an Sun, Hehuang Xie, Liqing Zhang
    Abstract:

    DNA methylation is an important epigenetic mark relevant to normal development and disease genesis. A common approach to characterizing genome-wide DNA methylation is to use Next Generation Sequencing technology to sequence Bisulfite treated DNA. The short sequence reads are mapped to the reference genome to determine the methylation status of Cs. However, despite intense effort, a much smaller proportion of the reads derived from Bisulfite treated DNA (usually about 40-80%) can be mapped than regular short reads mapping (≥ 90%), and it is unclear what factors lead to this low mapping efficiency. To address this issue, we used the hairpin sequencing technology to determine sequences of both DNA double strands simultaneously. This enabled the recovery of the original non-Bisulfite-converted sequences. Recovered reads had a higher unique mapping efficiency than the Bisulfite reads, and one reason could be that mapping efficiency relates to entropy, and entropy may be lost due to Bisulfite treatment. Bismark was used to map Bisulfite reads, and Bowtie2 was used to map recovered untreated reads.

Mike G Makrigiorgos - One of the best experts on this subject based on the ideXlab platform.

  • precision and performance characteristics of Bisulfite conversion and real time pcr methylight for quantitative dna methylation analysis
    The Journal of Molecular Diagnostics, 2006
    Co-Authors: Shuji Ogino, Takako Kawasaki, Mohan Brahmandam, Mami Cantor, Gregory J Kirkner, Donna Spiegelman, Mike G Makrigiorgos
    Abstract:

    Assays to measure DNA methylation, which are important in epigenetic research and clinical diagnostics, typically rely on conversion of unmethylated cytosine to uracil by sodium Bisulfite. However, no study has comprehensively evaluated the precision and performance characteristics of sodium Bisulfite conversion and subsequent quantitative methylation assay. We developed quantitative real-time polymerase chain reaction (MethyLight) to measure percentage of methylated reference (PMR, ie, degree of methylation) for the MGMT, MLH1, and CDKN2A (pl6) promoters. To measure the precision of Bisulfite conversion, we Bisulfite-treated seven different aliquots of DNA from each of four paraffin-embedded colon cancer samples. To assess run-to-run variation, we repeated MethyLight five times. Bisulfite-to-Bisulfite coefficient of variation (CV) of PMR ranged from 0.10 to 0.38 (mean, 0.21), and run-to-run CV of PMR ranged from 0.046 to 0.60 (mean, 0.31). Interclass correlation coefficients were 0.74 to 0.84 for the three loci, indicating good reproducibility. DNA mixing study with methylated and unmethylated DNA showed good linearity of the assay. Of 272 colorectal cancers evaluated, most showed PMR either 10, and promoter methylation (PMR >4) was tightly associated with loss of respective protein expression (P

Shuji Ogino - One of the best experts on this subject based on the ideXlab platform.

  • precision and performance characteristics of Bisulfite conversion and real time pcr methylight for quantitative dna methylation analysis
    The Journal of Molecular Diagnostics, 2006
    Co-Authors: Shuji Ogino, Takako Kawasaki, Mohan Brahmandam, Mami Cantor, Gregory J Kirkner, Donna Spiegelman, Mike G Makrigiorgos
    Abstract:

    Assays to measure DNA methylation, which are important in epigenetic research and clinical diagnostics, typically rely on conversion of unmethylated cytosine to uracil by sodium Bisulfite. However, no study has comprehensively evaluated the precision and performance characteristics of sodium Bisulfite conversion and subsequent quantitative methylation assay. We developed quantitative real-time polymerase chain reaction (MethyLight) to measure percentage of methylated reference (PMR, ie, degree of methylation) for the MGMT, MLH1, and CDKN2A (pl6) promoters. To measure the precision of Bisulfite conversion, we Bisulfite-treated seven different aliquots of DNA from each of four paraffin-embedded colon cancer samples. To assess run-to-run variation, we repeated MethyLight five times. Bisulfite-to-Bisulfite coefficient of variation (CV) of PMR ranged from 0.10 to 0.38 (mean, 0.21), and run-to-run CV of PMR ranged from 0.046 to 0.60 (mean, 0.31). Interclass correlation coefficients were 0.74 to 0.84 for the three loci, indicating good reproducibility. DNA mixing study with methylated and unmethylated DNA showed good linearity of the assay. Of 272 colorectal cancers evaluated, most showed PMR either 10, and promoter methylation (PMR >4) was tightly associated with loss of respective protein expression (P

Jacob Porter - One of the best experts on this subject based on the ideXlab platform.

  • Investigating Bisulfite short-read mapping failure with hairpin Bisulfite sequencing data
    BMC Genomics, 2015
    Co-Authors: Jacob Porter, Ming-an Sun, Hehuang Xie, Liqing Zhang
    Abstract:

    Background DNA methylation is an important epigenetic mark relevant to normal development and disease genesis. A common approach to characterizing genome-wide DNA methylation is using Next Generation Sequencing technology to sequence Bisulfite treated DNA. The short sequence reads are mapped to the reference genome to determine the methylation statuses of Cs. However, despite intense effort, a much smaller proportion of the reads derived from Bisulfite treated DNA (usually about 40-80%) can be mapped than regular short reads mapping (> 90%), and it is unclear what factors lead to this low mapping efficiency. Results To address this issue, we used the hairpin Bisulfite sequencing technology to determine sequences of both DNA double strands simultaneously. This enabled the recovery of the original non-Bisulfite-converted sequences. We used Bismark for Bisulfite read mapping and Bowtie2 for recovered read mapping. We found that recovering the reads improved unique mapping efficiency by 9-10% compared to the Bisulfite reads. Such improvement in mapping efficiency is related to sequence entropy. Conclusions The hairpin recovery technique improves mapping efficiency, and sequence entropy relates to mapping efficiency.

  • Investigating Bisulfite short-read mapping failure with hairpin Bisulfite sequencing data.
    BMC genomics, 2015
    Co-Authors: Jacob Porter, Ming-an Sun, Hehuang Xie, Liqing Zhang
    Abstract:

    DNA methylation is an important epigenetic mark relevant to normal development and disease genesis. A common approach to characterizing genome-wide DNA methylation is using Next Generation Sequencing technology to sequence Bisulfite treated DNA. The short sequence reads are mapped to the reference genome to determine the methylation statuses of Cs. However, despite intense effort, a much smaller proportion of the reads derived from Bisulfite treated DNA (usually about 40-80%) can be mapped than regular short reads mapping (> 90%), and it is unclear what factors lead to this low mapping efficiency. To address this issue, we used the hairpin Bisulfite sequencing technology to determine sequences of both DNA double strands simultaneously. This enabled the recovery of the original non-Bisulfite-converted sequences. We used Bismark for Bisulfite read mapping and Bowtie2 for recovered read mapping. We found that recovering the reads improved unique mapping efficiency by 9-10% compared to the Bisulfite reads. Such improvement in mapping efficiency is related to sequence entropy. The hairpin recovery technique improves mapping efficiency, and sequence entropy relates to mapping efficiency.

  • ICCABS - Improving Bisulfite short-read mapping efficiency with hairpin-Bisulfite data
    2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2014
    Co-Authors: Jacob Porter, Ming-an Sun, Hehuang Xie, Liqing Zhang
    Abstract:

    DNA methylation is an important epigenetic mark relevant to normal development and disease genesis. A common approach to characterizing genome-wide DNA methylation is to use Next Generation Sequencing technology to sequence Bisulfite treated DNA. The short sequence reads are mapped to the reference genome to determine the methylation status of Cs. However, despite intense effort, a much smaller proportion of the reads derived from Bisulfite treated DNA (usually about 40-80%) can be mapped than regular short reads mapping (≥ 90%), and it is unclear what factors lead to this low mapping efficiency. To address this issue, we used the hairpin sequencing technology to determine sequences of both DNA double strands simultaneously. This enabled the recovery of the original non-Bisulfite-converted sequences. Recovered reads had a higher unique mapping efficiency than the Bisulfite reads, and one reason could be that mapping efficiency relates to entropy, and entropy may be lost due to Bisulfite treatment. Bismark was used to map Bisulfite reads, and Bowtie2 was used to map recovered untreated reads.

Ming-an Sun - One of the best experts on this subject based on the ideXlab platform.

  • Investigating Bisulfite short-read mapping failure with hairpin Bisulfite sequencing data
    BMC Genomics, 2015
    Co-Authors: Jacob Porter, Ming-an Sun, Hehuang Xie, Liqing Zhang
    Abstract:

    Background DNA methylation is an important epigenetic mark relevant to normal development and disease genesis. A common approach to characterizing genome-wide DNA methylation is using Next Generation Sequencing technology to sequence Bisulfite treated DNA. The short sequence reads are mapped to the reference genome to determine the methylation statuses of Cs. However, despite intense effort, a much smaller proportion of the reads derived from Bisulfite treated DNA (usually about 40-80%) can be mapped than regular short reads mapping (> 90%), and it is unclear what factors lead to this low mapping efficiency. Results To address this issue, we used the hairpin Bisulfite sequencing technology to determine sequences of both DNA double strands simultaneously. This enabled the recovery of the original non-Bisulfite-converted sequences. We used Bismark for Bisulfite read mapping and Bowtie2 for recovered read mapping. We found that recovering the reads improved unique mapping efficiency by 9-10% compared to the Bisulfite reads. Such improvement in mapping efficiency is related to sequence entropy. Conclusions The hairpin recovery technique improves mapping efficiency, and sequence entropy relates to mapping efficiency.

  • Investigating Bisulfite short-read mapping failure with hairpin Bisulfite sequencing data.
    BMC genomics, 2015
    Co-Authors: Jacob Porter, Ming-an Sun, Hehuang Xie, Liqing Zhang
    Abstract:

    DNA methylation is an important epigenetic mark relevant to normal development and disease genesis. A common approach to characterizing genome-wide DNA methylation is using Next Generation Sequencing technology to sequence Bisulfite treated DNA. The short sequence reads are mapped to the reference genome to determine the methylation statuses of Cs. However, despite intense effort, a much smaller proportion of the reads derived from Bisulfite treated DNA (usually about 40-80%) can be mapped than regular short reads mapping (> 90%), and it is unclear what factors lead to this low mapping efficiency. To address this issue, we used the hairpin Bisulfite sequencing technology to determine sequences of both DNA double strands simultaneously. This enabled the recovery of the original non-Bisulfite-converted sequences. We used Bismark for Bisulfite read mapping and Bowtie2 for recovered read mapping. We found that recovering the reads improved unique mapping efficiency by 9-10% compared to the Bisulfite reads. Such improvement in mapping efficiency is related to sequence entropy. The hairpin recovery technique improves mapping efficiency, and sequence entropy relates to mapping efficiency.

  • ICCABS - Improving Bisulfite short-read mapping efficiency with hairpin-Bisulfite data
    2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2014
    Co-Authors: Jacob Porter, Ming-an Sun, Hehuang Xie, Liqing Zhang
    Abstract:

    DNA methylation is an important epigenetic mark relevant to normal development and disease genesis. A common approach to characterizing genome-wide DNA methylation is to use Next Generation Sequencing technology to sequence Bisulfite treated DNA. The short sequence reads are mapped to the reference genome to determine the methylation status of Cs. However, despite intense effort, a much smaller proportion of the reads derived from Bisulfite treated DNA (usually about 40-80%) can be mapped than regular short reads mapping (≥ 90%), and it is unclear what factors lead to this low mapping efficiency. To address this issue, we used the hairpin sequencing technology to determine sequences of both DNA double strands simultaneously. This enabled the recovery of the original non-Bisulfite-converted sequences. Recovered reads had a higher unique mapping efficiency than the Bisulfite reads, and one reason could be that mapping efficiency relates to entropy, and entropy may be lost due to Bisulfite treatment. Bismark was used to map Bisulfite reads, and Bowtie2 was used to map recovered untreated reads.