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SNP array data for Wilms Tumor harboring de novo germline mutation in CTCF

ABSTRACT: SNP array data for Wilms Tumor harboring de novo germline mutation in CTCF

PROVIDER: PRJNA794136 | ENA |

REPOSITORIES: ENA

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SNP array data for Wilms Tumor harboring de novo germline mutation in CTCF

Project description:SNP array was combined with next generation sequencing (NGS) to identify a unique de novo germline mutation in CTCF that became homozygous in the tumor. SNP array shows an LOH through chr16q where CTCF is located.

2022-01-11 | GSE193017 | GEO

Germline Variant in Ctcf Links Mental Retardation to Wilms Tumor Predisposition

Project description:SNP arrays was combined with next generation sequencing (NGS) to identify an LOH in 16q together with an unreported CTCF missense variant in its zinc finger domain. CTCF is within 16q LOH. We found that germline heterozygous variant I446K became homozygous in the tumor due to a loss of heterozygosity rearrangement affecting the whole q arm on chromosome 16. Based on CTCF role in regulating the epigenetic architechture of the genome, our findings reveal CTCF variant I446K as a link between MRD21 and Wilms tumor predisposition.

2022-01-11 | GSE193233 | GEO

Germline Variant in *Ctcf* Links Mental Retardation to Wilms Tumor Predisposition

Project description:Germline Variant in *Ctcf* Links Mental Retardation to Wilms Tumor Predisposition

| PRJNA795462 | ENA

Germline Variant in Ctcf Links Mental Retardation to Wilms Tumor Predisposition

Project description:Germline Variant in Ctcf Links Mental Retardation to Wilms Tumor Predisposition

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De novo mutations in the genome organizer CTCF cause Intellectual Disability (RNA-Seq)

Project description:An increasing number of genes involved in chromatin structure and epigenetic regulation has been implicated in a variety of developmental disorders, often including intellectual disability. By trio exome sequencing and subsequent mutational screening we now identified two de novo frameshift mutations and one de novo missense mutation in the CTCF gene in individuals with intellectual disability, microcephaly and growth retardation. Furthermore, a patient with a larger deletion including CTCF was identified. CTCF (CCCTC-binding factor) is one of the most important chromatin organizers in vertebrates and is involved in various chromatin regulation processes such as higher order of chromatin organization, enhancer function, and maintenance of three-dimensional chromatin structure. Transcriptome analyses in all three patients with point mutations revealed deregulation of genes involved in signal transduction and emphasized the role of CTCF in enhancer-driven expression of genes. Our findings indicate that haploinsufficiency of CTCF affects genomic interaction of enhancers and their regulated gene promoters that drive developmental processes and cognition. Comparison of lymphocyte gene expression between 3 de novo CTCF mutation patients and 8 controls (4 technical replicates each, no biological replicates).

2013-06-01 | E-GEOD-46831 | biostudies-arrayexpress

De novo mutations in the genome organizer CTCF cause Intellectual Disability (ChIP-Seq)

Project description:An increasing number of genes involved in chromatin structure and epigenetic regulation has been implicated in a variety of developmental disorders, often including intellectual disability. By trio exome sequencing and subsequent mutational screening we now identified two de novo frameshift mutations and one de novo missense mutation in the CTCF gene in individuals with intellectual disability, microcephaly and growth retardation. Furthermore, a patient with a larger deletion including CTCF was identified. CTCF (CCCTC-binding factor) is one of the most important chromatin organizers in vertebrates and is involved in various chromatin regulation processes such as higher order of chromatin organization, enhancer function, and maintenance of three-dimensional chromatin structure. Transcriptome analyses in all three patients with point mutations revealed deregulation of genes involved in signal transduction and emphasized the role of CTCF in enhancer-driven expression of genes. Our findings indicate that haploinsufficiency of CTCF affects genomic interaction of enhancers and their regulated gene promoters that drive developmental processes and cognition. ChIP-seq analysis of CTCF genomic binding sites in lymphocytes of a control individual (no replicates).

2013-06-01 | E-GEOD-46832 | biostudies-arrayexpress

De novo mutations in the genome organizer CTCF cause Intellectual Disability (ChIP-Seq)

2013-06-01 | GSE46832 | GEO

De novo mutations in the genome organizer CTCF cause Intellectual Disability (RNA-Seq)

2013-06-01 | GSE46831 | GEO

Gene-expression profiling according to the Wilms tumor 1 (WT1) single nucleotide polymorphism rs16754 in adult de novo cytogenetically normal acute myeloid leukemia.

Project description:Gene-expression profiling according to the Wilms tumor 1 (WT1) single nucleotide polymorphism rs16754 in adult de novo cytogenetically normal acute myeloid leukemia.

2012-06-09 | E-TABM-1165 | biostudies-arrayexpress

microRNA-expression profiling according to the Wilms tumor 1 (WT1) single nucleotide polymorphism rs16754 in adult de novo cytogenetically normal acute myeloid leukemia patients 60 years.\//\<

Project description:microRNA-expression profiling according to the Wilms tumor 1 (WT1) single nucleotide polymorphism rs16754 in adult de novo cytogenetically normal acute myeloid leukemia patients <60 years.

2012-06-09 | E-TABM-1166 | biostudies-arrayexpress

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