PDF - 47K, Additional experimental data including clinical sample analysis, principal component a... more PDF - 47K, Additional experimental data including clinical sample analysis, principal component analysis, RNA sequencing/expression analysis profile, ingenuity pathway analysis, and RNA expression validation through quantitative real-time RT-PCR
PDF - 192K, IPA networks generated by genes identified to be differentially methylated in samples... more PDF - 192K, IPA networks generated by genes identified to be differentially methylated in samples carrying the t(12;21) translocation
PDF - 2252K, Hierarchical clustering of pre-B ALL sample-derived methylation levels in defined Cp... more PDF - 2252K, Hierarchical clustering of pre-B ALL sample-derived methylation levels in defined CpG-site regions
XLSX file - 370K, Annotation of CpG-site interrogating probes (S1); Summary of RNA-sequencing gen... more XLSX file - 370K, Annotation of CpG-site interrogating probes (S1); Summary of RNA-sequencing generated for each patient sample on the SOLiD 4 system (S2); Percentage of probes within a given cross-sample standard deviation (SD)-range for normal (N) and tumor (T) samples (S3); Tumor sample methylation level variability (S4); Amount of gene-associated CpG-sites, amount of RefSeq genes and their isoforms in each CpG-site region, and region-specific median Spearman's rho (S5); Spearman's ranked correlation rho between methylation and transcript expression level with significance level for each patient in each CpG-site region (S6); Probes displaying significant differential methylation in samples carrying the t(12;21) translocation (S7); Genes associated with t(12;21)-specifically methylated probes (S8); Genes identified as uniformely hypo- or hypermethylated in samples carrying the t(12;21) translocation, and associated methylation and transcript expression levels (S9); Gene networks generated by IPA (S10)
Epigenetics is defined as the modulation of gene expression without changes to the underlying DNA... more Epigenetics is defined as the modulation of gene expression without changes to the underlying DNA sequence. Epigenetic alterations, as a consequence of in utero malnutrition, may play a role in susceptibility to develop adulthood diseases and inheritance. However, the mechanistic link between epigenetic modifications and abnormalities in nutrition remains elusive. This review provides an update on the association of suboptimal nutritional environment and the high propensity to produce adult-onset chronic illnesses with a particular focus on modifications in genome functions that occur without alterations to the DNA sequence. We will mention the drivers of the phenotype and pattern of epigenetic markers set down during the reprogramming along with novel preventative and therapeutic strategies. New knowledge of epigenetic alterations is opening a gate toward personalized medicine.
To identify regions of aberrant DNA methylation in acute lymphoblastic leukemia (ALL) cells of di... more To identify regions of aberrant DNA methylation in acute lymphoblastic leukemia (ALL) cells of different subtypes on a genome-wide scale. Whole-genome bisulfite sequencing (WGBS) was used to determine the DNA methylation levels in cells from four pediatric ALL patients of different subtypes. The findings were confirmed by 450k DNA methylation arrays in a large patient set. Compared with mature B or T cells WGBS detected on average 82,000 differentially methylated regions per patient. Differentially methylated regions are enriched to CpG poor regions, active enhancers and transcriptional start sites. We also identified approximately 8000 CpG islands with variable intermediate DNA methylation that seems to occur as a result of stochastic de novo methylation. WGBS provides an unbiased view and novel insights into the DNA methylome of ALL cells.
PDF - 47K, Additional experimental data including clinical sample analysis, principal component a... more PDF - 47K, Additional experimental data including clinical sample analysis, principal component analysis, RNA sequencing/expression analysis profile, ingenuity pathway analysis, and RNA expression validation through quantitative real-time RT-PCR
PDF - 192K, IPA networks generated by genes identified to be differentially methylated in samples... more PDF - 192K, IPA networks generated by genes identified to be differentially methylated in samples carrying the t(12;21) translocation
PDF - 2252K, Hierarchical clustering of pre-B ALL sample-derived methylation levels in defined Cp... more PDF - 2252K, Hierarchical clustering of pre-B ALL sample-derived methylation levels in defined CpG-site regions
XLSX file - 370K, Annotation of CpG-site interrogating probes (S1); Summary of RNA-sequencing gen... more XLSX file - 370K, Annotation of CpG-site interrogating probes (S1); Summary of RNA-sequencing generated for each patient sample on the SOLiD 4 system (S2); Percentage of probes within a given cross-sample standard deviation (SD)-range for normal (N) and tumor (T) samples (S3); Tumor sample methylation level variability (S4); Amount of gene-associated CpG-sites, amount of RefSeq genes and their isoforms in each CpG-site region, and region-specific median Spearman's rho (S5); Spearman's ranked correlation rho between methylation and transcript expression level with significance level for each patient in each CpG-site region (S6); Probes displaying significant differential methylation in samples carrying the t(12;21) translocation (S7); Genes associated with t(12;21)-specifically methylated probes (S8); Genes identified as uniformely hypo- or hypermethylated in samples carrying the t(12;21) translocation, and associated methylation and transcript expression levels (S9); Gene networks generated by IPA (S10)
Epigenetics is defined as the modulation of gene expression without changes to the underlying DNA... more Epigenetics is defined as the modulation of gene expression without changes to the underlying DNA sequence. Epigenetic alterations, as a consequence of in utero malnutrition, may play a role in susceptibility to develop adulthood diseases and inheritance. However, the mechanistic link between epigenetic modifications and abnormalities in nutrition remains elusive. This review provides an update on the association of suboptimal nutritional environment and the high propensity to produce adult-onset chronic illnesses with a particular focus on modifications in genome functions that occur without alterations to the DNA sequence. We will mention the drivers of the phenotype and pattern of epigenetic markers set down during the reprogramming along with novel preventative and therapeutic strategies. New knowledge of epigenetic alterations is opening a gate toward personalized medicine.
To identify regions of aberrant DNA methylation in acute lymphoblastic leukemia (ALL) cells of di... more To identify regions of aberrant DNA methylation in acute lymphoblastic leukemia (ALL) cells of different subtypes on a genome-wide scale. Whole-genome bisulfite sequencing (WGBS) was used to determine the DNA methylation levels in cells from four pediatric ALL patients of different subtypes. The findings were confirmed by 450k DNA methylation arrays in a large patient set. Compared with mature B or T cells WGBS detected on average 82,000 differentially methylated regions per patient. Differentially methylated regions are enriched to CpG poor regions, active enhancers and transcriptional start sites. We also identified approximately 8000 CpG islands with variable intermediate DNA methylation that seems to occur as a result of stochastic de novo methylation. WGBS provides an unbiased view and novel insights into the DNA methylome of ALL cells.
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