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Validating a clinically based MS-MLPA threshold through comparison with Sanger sequencing in glioblastoma patients.
Clin Epigenetics
January 2025
Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and 1st Faculty of Medicine of Charles University in Prague, U Nemocnice 499/2, 128 00, Prague, Czech Republic.
Background: Glioblastoma is the commonest malignant brain tumor and has a very poor prognosis. Reduced expression of the MGMT gene (10q26.3), influenced primarily by the methylation of two differentially methylated regions (DMR1 and DMR2), is associated with a good response to temozolomide treatment.
View Article and Find Full Text PDFAge-invariant genes: multi-tissue identification and characterization of murine reference genes.
Aging (Albany NY)
January 2025
Department of Pathology, Yale University School of Medicine, New Haven, CT 06519, USA.
Studies of the aging transcriptome focus on genes that change with age. But what can we learn from age-invariant genes-those that remain unchanged throughout the aging process? These genes also have a practical application: they can serve as reference genes in expression studies. Reference genes have mostly been identified and validated in young organisms, and no systematic investigation has been done across the lifespan.
View Article and Find Full Text PDFThe multi-omics signatures of telomere length in childhood.
BMC Genomics
January 2025
Centre for Environmental Health, Hasselt University, Hasselt, Belgium.
Background: Telomere length is an important indicator of biological age and a complex multi-factor trait. To date, the telomere interactome for comprehending the high-dimensional biological aspects linked to telomere regulation during childhood remains unexplored. Here we describe the multi-omics signatures associated with childhood telomere length.
View Article and Find Full Text PDFmethylGrapher: genome-graph-based processing of DNA methylation data from whole genome bisulfite sequencing.
Nucleic Acids Res
January 2025
Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Genome graphs, including the recently released draft human pangenome graph, can represent the breadth of genetic diversity and thus transcend the limits of traditional linear reference genomes. However, there are no genome-graph-compatible tools for analyzing whole genome bisulfite sequencing (WGBS) data. To close this gap, we introduce methylGrapher, a tool tailored for accurate DNA methylation analysis by mapping WGBS data to a genome graph.
View Article and Find Full Text PDFBlood-based epigenome-wide association study and prediction of alcohol consumption.
Clin Epigenetics
January 2025
Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
Alcohol consumption is an important risk factor for multiple diseases. It is typically assessed via self-report, which is open to measurement error through recall bias. Instead, molecular data such as blood-based DNA methylation (DNAm) could be used to derive a more objective measure of alcohol consumption by incorporating information from cytosine-phosphate-guanine (CpG) sites known to be linked to the trait.
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