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Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [SNP_genotyping]

ABSTRACT: SNP genotyping of human breast tumors

ORGANISM(S): Homo sapiens

PROVIDER: GSE100529 | GEO | 2019/04/17

REPOSITORIES: GEO

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Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas

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

2017-03-31 | GSE97293 | GEO

Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [aCGH]

Project description:DNA copy number alterations play an important role in cancer development and progression by changing the transcriptional levels of key cancer-related genes. However, gene expression patterns may also be affected by other mechanisms. To test these basic principles, we have applied genome-wide screening techniques to 53 invasive breast tumors with array comparative genomic hybridization and gene expression microarrays to assess the direct effect of gene dosage on gene expression levels and independently to test the effect of other mechanisms on transcriptional levels. Low-level gain, high-level gain/amplification, heterozygous loss and homozygous deletion (henceforth referred to as gain, amplification, loss and deletion) were defined as log2 ratio thresholds set at +0.2, ≥+0.5, -0.2 and ≤-1.0, respectively.

2017-03-31 | GSE97292 | GEO

Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [expression]

Project description:Transcriptomic profiling of human breast tumors. Genomic and expression profiling using 38K BAC array-CGH and Illumina HT-12 beadchips were performed on 53 invasive breast tumors to assess the impact of gene dosage on gene expression patterns and the effect of other mechanisms on transcriptional levels. Array-CGH results was validated by FISH using tumors showing 8p11-p12 DNA amplification and expression profiling was confirmed using qPCR for 11 transcripts. Low-level gain, high-level gain/amplification, heterozygous loss and homozygous deletion (henceforth referred to as gain, amplification, loss and deletion) were defined as log2 ratio thresholds set at +0.2, >= +0.5, -0.2 and <=-1.0, respectively.

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Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [RNA-seq]

Project description:Transcriptomic profiling of human breast tumors using RNA sequencing

2019-04-17 | GSE100799 | GEO

Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas

Project description:Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas

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Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma.

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Frequent MYC coamplification and DNA hypomethylation of multiple genes on 8q in 8p11-p12-amplified breast carcinomas.

Project description: Not available

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Transforming properties of 8p11-12 amplified genes in human breast cancer.

Project description: Not available

| S-EPMC3089754 | biostudies-literature

SNP genotyping of cryptic complexity in structural chromosome abnormalities previously detected by cytogenetic analysis

Project description:Purpose: The purpose of this study was to evaluate SNP genotyping methodology as a means to detect chromosomal abnormalities previously diagnosed by G-band karyotype or fluorescence in situ hybridization (FISH) analysis and to determine the frequency of sub-microscopic (cryptic) chromosomal alterations in these subjects. Methods: We used the Illumina HumanHap Beadchip platform to genotype 40 individuals having previously detected chromosomal anomalies (by G-banded and/or FISH analysis). The resulting data were analyzed for signal intensity (log R ratio) and allelic composition (B allele frequency). Results: SNP array analysis detected 100% of previously identified cytogenetic abnormalities. Changes or clarifications of the ISCN karyotype designation assigned by conventional cytogenetic and/or FISH analysis were made in 82 % of the cases (32 of 39). Nine of the 39 cases (23%) involved a reassignment of an abnormal band while an additional 9 of the 39 (23%) resulted in a clarification of a sub-band assignment. In 8 more of the 39 cases (21%) the previously reported alterations were confirmed, however the SNP analysis also identified related cryptic alterations. SNP analysis not only confirmed FISH-detected abnormalities but also more precisely mapped the breakpoints of 6/6 patients. Investigations into the origin of de novo abnormalities in 15 trio families established that 12 /15 occurred on the paternal chromosome. Conclusions: SNP genotyping array analysis, confirmed all previously detected structural chromosomal abnormalities and provided additional, clinically-relevant genomic information in 82% of these alterations.

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Multi-omics approaches for revealing the complexity of cardiovascular disease.

Project description: Not available

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