SNP array data for Wilms Tumor harboring de novo germline mutation in CTCF
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE193017 | GEO | 2022/01/11
REPOSITORIES: GEO
Similar Datasets
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
Project description:SNP array data for Wilms Tumor harboring de novo germline mutation in CTCF
| PRJNA794136 | ENA
Project description:Chromosome 1p LOH was seen in one-third of cases. LOH events on chromosomes 11q and 1p were generally accompanied by copy number loss. The one exception was on chromosome 11p, where LOH in all 4 cases was accompanied by normal copy number or diploidy, implying uniparental disomy. Amplification of MYCN was also noted, and also, amplification of a second gene, ALK, in a single case. Keywords: SNP array analysis
2007-06-30 | GSE8333 | GEO
Project description:BACKGROUND: Cervical carcinoma develops as a result of multiple genetic alterations. Different studies investigated genomic alterations in cervical cancer mainly by means of metaphase comparative genomic hybridization (mCGH) and microsatellite marker analysis for the detection of loss of heterozygosity (LOH). Currently, high throughput methods such as array comparative genomic hybridization (array CGH), single nucleotide polymorphism array (SNP array) and gene expression arrays are available to study genome-wide alterations. Integration of these 3 platforms allows detection of genomic alterations at high resolution and investigation of an association between copy number changes and expression. RESULTS: Genome-wide copy number and genotype analysis of 10 cervical cancer cell lines by array CGH and SNP array showed highly complex large-scale alterations. A comparison between array CGH and SNP array revealed that the overall concordance in detection of the same areas with copy number alterations (CNA) was above 90%. The use of SNP arrays demonstrated that about 75% of LOH events would not have been found by methods which screen for copy number changes, such as array CGH, since these were LOH events without CNA. Regions frequently targeted by CNA, as determined by array CGH, such as amplification of 5p and 20q, and loss of 8p were confirmed by fluorescent in situ hybridization (FISH). Genome-wide, we did not find a correlation between copy-number and gene expression. At chromosome arm 5p however, 22% of the genes were significantly upregulated in cell lines with amplifications as compared to cell lines without amplifications, as measured by gene expression arrays. For 3 genes, SKP2, ANKH and TRIO, expression differences were confirmed by quantitative real-time PCR (qRT-PCR). CONCLUSION: This study showed that copy number data retrieved from either array CGH or SNP array are comparable and that the integration of genome-wide LOH, copy number and gene expression is useful for the identification of gene specific targets that could be relevant for the development and progression in cervical cancer. Keywords: DNA copynumber RNA expression correlation
2007-07-31 | GSE8605 | GEO
Project description:Retinoblastoma is a childhood retinal tumor that initiates in response to biallelic RB1 inactivation. We show that post-mitotic human cone precursors are uniquely sensitive to the oncogenic effects of Rb depletion. Rb knockdown induced cone precursor proliferation in prospectively isolated populations. SNP-array analysis of two Rb/p130-depleted cone precursor cell lines, revealing no megabase-size loss of heterozygosity (LOH) or copy number alterations (CNAs). SNP-array analysis of one Rb/p130-depleted (tumor 1) or one Rb-depleted (tumor 2) cone precursor-derived tumors, revealing no megabase-size LOH or CNAs, consistent with the lack of DNA copy number alterations in some retinoblastomas. Thus, the cone precursor tumors resembled human retinoblastomas at the molecular cytogenetic level.
2014-08-25 | GSE60720 | GEO
Project description:Affymetrix 10K SNP mapping arrays were used to profile 14 basal cell carcinomas (BCCs) with matched blood DNA samples. Loss of heterozygosity (LOH) and copy number abnormality (CNA) profiles were derived from each tumour-blood pair. Keywords: Genomic DNA on Affymetrix 10K SNP array
2005-07-21 | GSE2959 | GEO
Project description:Single nucleotide polymorphism (SNP) microarrays are commonly applied to tumors to identify genomic regions with copy number alterations (CNA) or loss of heterozygosity (LOH). However, in typical tumor specimens collected in clinical studies, up to 60% of the DNA derives from stromal cells with a normal genome, resulting in attenuated sensitivity to true somatic aberrations in the tumor. Here we describe SNPfilter, a model-based method to decompose SNP array data from heterogeneous tumor specimens into their corresponding normal and tumor profiles. Unlike existing methods, SNPfilter does not require paired normal control data. We assessed the performance of this method using SNP array data representing cancer cell lines with aberrant genomes, B-cell lymphoblastoid cell lines with normal genomes, and defined mixtures of the two. In the pure tumor samples, SNPfilter identified CNA and LOH regions with accuracy similar to existing methods. In the mixture samples containing 40–80% tumor genomic DNA, SNPfilter yielded prediction sensitivity superior to existing methods. Thus, SNPfilter provides a powerful tool for discovery of clinically relevant somatic aberrations in tumor genomes.
2011-12-30 | GSE34754 | GEO
Project description:SNP profiles from 78 pheochromocytomas and paragangliomas were analyzed to detect copy number changes and LOH.
2012-09-11 | GSE38525 | GEO
Project description:Renal tumors with complex morphology require extensive workup for accurate classification. Chromosomal aberrations that define subtypes of renal epithelial neoplasms have been reported. We explored if whole-genome chromosome copy number and loss-of-heterozygosity analysis with single nucleotide polymorphism (SNP) arrays can be used to identify these aberrations in cases where morphology was unable to definitively classify these tumors. Keywords: Chromosome copy number and LOH analysis (virtual karyotyping) with SNP Genotyping Arrays Keywords: Genome variation profiling by SNP array
2008-11-01 | GSE11447 | GEO
Project description:In the study of tumor genetics, formalin-fixed paraffin-embedded (FFPE) tumors are the most readily available tissue samples. While DNA derived from FFPE tissue has been validated for array comparative genomic hybridization (aCGH) application, the suitability of such fragmented DNA for single-nucleotide polymorphism (SNP) array analysis has not been well examined. Furthermore, whole-genome amplification (WGA) has been used in the study of small precursor lesions to produce sufficient amount of DNA for aCGH analysis. It is unclear whether the same approach can be extended to SNP analysis. In this study, we examined the utility and limitations of genotyping platform performed on whole-genome amplified DNA from FFPE tumor samples for both copy number and SNP analyses. We analyzed the results obtained using DNA derived from matched FFPE and frozen tissue samples on Affymetrix 250K Nsp SNP array. Two widely used WGA methods, Qiagen (isothermal protocol) and Sigma (thermocycling protocol), were used to determine how WGA methods affect the results. We found that the use of DNA derived from FFPE tumors (without or with WGA) for high-resolution SNP array application can produce a significant amount of false positive and false negative findings. While some of these misinterpretations appear to cluster in genomic regions with high or low GC contents, the majority appears to occur randomly. Only large-scale chromosome LOH (>10Mb) can be reliably detected from FFPE tumor DNA samples (without or with WGA) but not smaller LOH or copy number alterations. Our findings here indicate a need for caution in SNP array data interpretation when using FFPE tumor-derived DNA, particularly with WGA.
2011-08-15 | GSE27399 | GEO