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Germline Variant in Ctcf Links Mental Retardation to Wilms Tumor Predisposition

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE193235 | GEO | 2022/01/11

REPOSITORIES: GEO

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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

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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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The Genetic and Epigenetic Features of Bilateral Wilms Tumor Predisposition

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-11-09 | GSE226480 | GEO

Mental Retardation Patients

Project description:Profiling the genomic profiles of mental retardation patients. 13 mental retardation patients were selected for detection of genomic aberrations.

2009-12-16 | GSE19457 | GEO

Mental Retardation Patients

Project description:Profiling the genomic profiles of mental retardation patients. 13 mental retardation patients were selected for detection of genomic aberrations. Patient's DNA were hybridized against Promega control on Agilent G4426B arrays and scanned with the Agilent G2505B scanner.

2010-05-18 | E-GEOD-19457 | biostudies-arrayexpress

Biallelic germline nonsense variant of MLH3 underlies polyposis predisposition.

Project description:PurposeSome 10% of familial adenomatous polyposis (FAP) and 80% of attenuated polyposis (AFAP) cases remain molecularly unexplained. We scrutinized such cases by exome-wide and targeted methods to search for novel susceptibility genes.MethodsExome sequencing was conducted on 40 unexplained (mainly sporadic) cases with FAP or AFAP from Finland. The DNA mismatch repair (MMR) gene MLH3 (MutL Homolog 3) was pinpointed and prompted a subsequent screen of ~1000 Swedish patients referred to clinical panel sequencing for colon tumor susceptibility.ResultsThree homozygous carriers of a truncating variant in MLH3, c.3563C>G, p.Ser1188Ter, were identified among the index cases from the Finnish series. An additional biallelic carrier of the same variant was present in the Swedish series. All four patients shared a 0.8-Mb core haplotype around MLH3, suggesting a founder variant. Colorectal polyps from variant carriers showed no instability at mono-, di-, tri-, or tetranucleotide repeats, in agreement with previous findings of a minor role of MLH3 in MMR. Multiple loci were affected by loss of heterozygosity, suggesting chromosomal instability.ConclusionOur results show that a biallelic nonsense variant of MLH3 underlies a novel syndrome with susceptibility to classical or attenuated adenomatous polyposis and possibly extracolonic tumors, including breast cancer.

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ARX transcription factor implicated in mental retardation and epilepsy

Project description:This SuperSeries is composed of the SubSeries listed below.

2011-12-22 | GSE30191 | GEO

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

Integrating somatic variant data and biomarkers for germline variant classification in cancer predisposition genes.

Project description:In its landmark paper about Standards and Guidelines for the Interpretation of Sequence Variants, the American College of Medical Genetics and Genomics (ACMG), and Association for Molecular Pathology (AMP) did not address how to use tumor data when assessing the pathogenicity of germline variants. The Clinical Genome Resource (ClinGen) established a multidisciplinary working group, the Germline/Somatic Variant Subcommittee (GSVS) with this focus. The GSVS implemented a survey to determine current practices of integrating somatic data when classifying germline variants in cancer predisposition genes. The GSVS then reviewed and analyzed available resources of relevant somatic data, and performed integrative germline variant curation exercises. The committee determined that somatic hotspots could be systematically integrated into moderate evidence of pathogenicity (PM1). Tumor RNA sequencing data showing altered splicing may be considered as strong evidence in support of germline pathogenicity (PVS1) and tumor phenotypic features such as mutational signatures be considered supporting evidence of pathogenicity (PP4). However, at present, somatic data such as focal loss of heterozygosity and mutations occurring on the alternative allele are not recommended to be systematically integrated, instead, incorporation of this type of data should take place under the advisement of multidisciplinary cancer center tumor-normal sequencing boards.

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