optical methylation mapping  (BioNano Genomics)

Journal: Bioinformatics

Article Title: Long reads capture simultaneous enhancer–promoter methylation status for cell-type deconvolution

doi: 10.1093/bioinformatics/btab306

Figure Lengend Snippet: Methylation states in predicted enhancer–promoter pairs. ( A ) schematic illustration of possible methylation states for a promoter and enhancers, and potential interaction between them. ( B ) Bionano Genomics optical methylation map of a region in chromosome 17 in GM12878 DNA. The region contains the gene TP53, its promoter (small blue box), and several predicted enhancers (pink boxes). Dark blue dots denote unmethylated sites and orange dots denote genetic tags used for alignment to the hg38 reference.

Article Snippet: Despite focusing on Bionano Genomics’ optical methylation mapping ( Gabrieli et al. , 2021 ; Sharim et al. , 2019 ), which currently provides the highest coverage of long reads, the principles are valid to other future datasets such as those produced by Oxford Nanopore ultralong-read sequencing protocol.

Techniques: Methylation

Journal: Bioinformatics

Article Title: Long reads capture simultaneous enhancer–promoter methylation status for cell-type deconvolution

doi: 10.1093/bioinformatics/btab306

Figure Lengend Snippet: Deconvolution of mixtures containing B-lymphocytes and myoblast cells by different methods using methylation states in promoters alone and enhancer–promoter pairs, accounting for one enhancer per promoter. ( A ) Calculated mixing ratio according to the different methods versus the known mixing ratio. ( B ) The mean error in calculated mixing ratio, calculated as the absolute distance from the known ratio, in the different methods.

Article Snippet: Despite focusing on Bionano Genomics’ optical methylation mapping ( Gabrieli et al. , 2021 ; Sharim et al. , 2019 ), which currently provides the highest coverage of long reads, the principles are valid to other future datasets such as those produced by Oxford Nanopore ultralong-read sequencing protocol.

Techniques: Methylation

Journal: Bioinformatics

Article Title: Long reads capture simultaneous enhancer–promoter methylation status for cell-type deconvolution

doi: 10.1093/bioinformatics/btab306

Figure Lengend Snippet: Deconvolution of B-lymphocytes and myoblast cells mixtures by different methods using methylation states in all predicted enhancer–promoter pairs. ( A ) calculated mixing ratio according to the different methods versus the known mixing ratio. ( B ) the mean error in calculated mixing ratio, calculated as the absolute distance from the known ratio, in the different methods.

Article Snippet: Despite focusing on Bionano Genomics’ optical methylation mapping ( Gabrieli et al. , 2021 ; Sharim et al. , 2019 ), which currently provides the highest coverage of long reads, the principles are valid to other future datasets such as those produced by Oxford Nanopore ultralong-read sequencing protocol.

Techniques: Methylation

Journal: Bioinformatics

Article Title: Long reads capture simultaneous enhancer–promoter methylation status for cell-type deconvolution

doi: 10.1093/bioinformatics/btab306

Figure Lengend Snippet: Methylation states in predicted enhancer–promoter pairs. ( A ) schematic illustration of possible methylation states for a promoter and enhancers, and potential interaction between them. ( B ) Bionano Genomics optical methylation map of a region in chromosome 17 in GM12878 DNA. The region contains the gene TP53, its promoter (small blue box), and several predicted enhancers (pink boxes). Dark blue dots denote unmethylated sites and orange dots denote genetic tags used for alignment to the hg38 reference.

Article Snippet: In order to establish the analytical framework for such data, we analyzed whole genome Bionano Genomics optical methylation maps ( Sharim et al. , 2019 ).

Techniques: Methylation

Journal: Bioinformatics

Article Title: Long reads capture simultaneous enhancer–promoter methylation status for cell-type deconvolution

doi: 10.1093/bioinformatics/btab306

Figure Lengend Snippet: Deconvolution of mixtures containing B-lymphocytes and myoblast cells by different methods using methylation states in promoters alone and enhancer–promoter pairs, accounting for one enhancer per promoter. ( A ) Calculated mixing ratio according to the different methods versus the known mixing ratio. ( B ) The mean error in calculated mixing ratio, calculated as the absolute distance from the known ratio, in the different methods.

Article Snippet: In order to establish the analytical framework for such data, we analyzed whole genome Bionano Genomics optical methylation maps ( Sharim et al. , 2019 ).

Techniques: Methylation

Journal: Bioinformatics

Article Title: Long reads capture simultaneous enhancer–promoter methylation status for cell-type deconvolution

doi: 10.1093/bioinformatics/btab306

Figure Lengend Snippet: Deconvolution of B-lymphocytes and myoblast cells mixtures by different methods using methylation states in all predicted enhancer–promoter pairs. ( A ) calculated mixing ratio according to the different methods versus the known mixing ratio. ( B ) the mean error in calculated mixing ratio, calculated as the absolute distance from the known ratio, in the different methods.

Article Snippet: In order to establish the analytical framework for such data, we analyzed whole genome Bionano Genomics optical methylation maps ( Sharim et al. , 2019 ).

Techniques: Methylation