Project description:Methylation profiles of chr12-16 were generated by meDIP and array hybridisation in 3 cases with maternal uniparental disomy of chromosome 15, and three cases of paternal uniparental disomy of chromosome 15. Comparison of these profiles reveals differentially methylated (imprinted) regions on chromosome 15.
Project description:Methylation profiles of chr12-16 were generated by meDIP and array hybridisation in 3 cases with maternal uniparental disomy of chromosome 15, and three cases of paternal uniparental disomy of chromosome 15. Comparison of these profiles reveals differentially methylated (imprinted) regions on chromosome 15. Methylated DNA was enriched by immunoprecipitation using antibodies against 5-methylcytosine. meDIP and input DNA was labeled with cy5 and cy3 respectively and hybridized to Nimblegen arrays comprising 2.1 million 50-85mers covering human chromosomes 12-16 at a mean density of ~1 probe per 100bp. Resulting log2 fluorescence ratios correspond to methylation levels. Six samples were analyzed, with technical replicates for each DNA.
Project description:Utilizing reciprocal genome-wide uniparental disomy samples presenting with Beckwith-Wiedemann and Silver-Russell syndrome-like phenotypes, we have analyzed ~0.1% of CpG dinucleotides present in the human genome for imprinted differentially methylated regions (DMRs) using the Illumina Infinium HumanMethylation27 BeadChip microarray. This approach identified 15 imprinted DMRs associated with previously characterized imprinted domains, and confirmed the maternal methylation of the RB1 DMR. In addition, we discovered two novel DMRs: a maternally methylated region overlapping the FAM50B promoter CpG island, which results in paternal expression of this retrotransposon, and a paternally methylated region located between maternally expressed ZNF597 and NAT15 genes. We analyzed reciprocal genome-wide uniparental disomy samples (one maternal UPD and three paternal UPD samples) and six different normal somatic tissues derived from the three germinal layers (lymphocytes, buccal cells, placenta, brain, muscle, and fat) .
Project description:Utilizing reciprocal genome-wide uniparental disomy samples presenting with Beckwith-Wiedemann and Silver-Russell syndrome-like phenotypes, we have analyzed ~0.1% of CpG dinucleotides present in the human genome for imprinted differentially methylated regions (DMRs) using the Illumina Infinium HumanMethylation27 BeadChip microarray. This approach identified 15 imprinted DMRs associated with previously characterized imprinted domains, and confirmed the maternal methylation of the RB1 DMR. In addition, we discovered two novel DMRs: a maternally methylated region overlapping the FAM50B promoter CpG island, which results in paternal expression of this retrotransposon, and a paternally methylated region located between maternally expressed ZNF597 and NAT15 genes.
Project description:We describe a stromal predominant Wilms tumor with a complex, tumor specific chromosome 11 aberration: a homozygous deletion of the entire WT1 gene within a heterozygous 11p13 deletion and an additional region of uniparental disomy (UPD) limited to 11p15.5-p15.2 including the IGF2 gene. The tumor carried a heterozygous p.T41A mutation in CTNNB1. Cells established from the tumor carried the same chromosome 11 aberration, but a different, homozygous p.S45Î CTNNB1 mutation. Uniparental disomy (UPD) 3p21.3pter lead to the homozygous CTNNB1 mutation. The tumor cell line was immortalized with telomerase (TERT) and a novel triple ts mutant SV40 large T antigen (LT). This cell line is cytogenetically stable and can be grown indefinitely. It is a valuable tool to study the effect of a complete lack of WT1 in tumor cells. The tumor cell line and the immortalized cells have a limited potential for muscle/osteogenic/adipogenic differentiation similar to all other WT1 mutant cell lines. Array expression experiment of Wilms tumor cell lines
Project description:We describe a stromal predominant Wilms tumor with a complex, tumor specific chromosome 11 aberration: a homozygous deletion of the entire WT1 gene within a heterozygous 11p13 deletion and an additional region of uniparental disomy (UPD) limited to 11p15.5-p15.2 including the IGF2 gene. The tumor carried a heterozygous p.T41A mutation in CTNNB1. Cells established from the tumor carried the same chromosome 11 aberration, but a different, homozygous p.S45Δ CTNNB1 mutation. Uniparental disomy (UPD) 3p21.3pter lead to the homozygous CTNNB1 mutation. The tumor cell line was immortalized with telomerase (TERT) and a novel triple ts mutant SV40 large T antigen (LT). This cell line is cytogenetically stable and can be grown indefinitely. It is a valuable tool to study the effect of a complete lack of WT1 in tumor cells. The tumor cell line and the immortalized cells have a limited potential for muscle/osteogenic/adipogenic differentiation similar to all other WT1 mutant cell lines.
Project description:Comparison of gene expression levels between matUPD12 and patUPD12 15.5 dpc whole embryo or placenta samples (maternal versus paternal uniparental disomy of Chr 12). Identification of highly differentially expressed transcripts. Keywords: genetic modification
