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Copy number profiling of gastric cancer cell lines and gastric tumor tissues

ABSTRACT: Copy number profiling of 27 gastric cancer cell lines and 105 gastric tumor tissues. we hypothesized that a detailed fine-scale survey of genomic CNAs might reveal potential genes disrupted by fusion events in gastric cancer. We inferred the locations of likely chromosomal breakpoints by identifying regions where closely-spaced microarray probes exhibited striking transitions in copy number.

ORGANISM(S): Homo sapiens

PROVIDER: GSE22694 | GEO | 2010/12/31

SECONDARY ACCESSION(S): PRJNA128303

REPOSITORIES: GEO

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Copy number profiling of gastric cancer cell lines and gastric tumor tissues

Project description:Copy number profiling of 27 gastric cancer cell lines and 105 gastric tumor tissues. we hypothesized that a detailed fine-scale survey of genomic CNAs might reveal potential genes disrupted by fusion events in gastric cancer. We inferred the locations of likely chromosomal breakpoints by identifying regions where closely-spaced microarray probes exhibited striking transitions in copy number. 27 gastric cancer cell lines and 105 gastric tumor tissues were profiled by Agilent 244K microarray.

2010-12-31 | E-GEOD-22694 | biostudies-arrayexpress

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Project description:Early gastric cancers (EGC) precede advanced gastric cancers (AGC) with a favorable clinical outcome compared to advanced gastric cancers (AGC). To understand the progression mechanisms of EGC to AGC, it is required to disclose the EGC and AGC genomes in terms of the the mutational and evolutionary perspectives. In this study, we performed whole-exome sequencing and copy number profiling of nine microsatellite (MS)-unstable (MSI-H) (5 EGC and 4 AGC) and eight MS-stable (MSS) gastric cancers (4 EGC and 4 AGC). Unexpectedly, we observed no substantial differences in the number, sequence composition and functional consequences (potential driver mutations and affected pathways) of the mutations and CNAs between EGC and AGC genomes in both MSI-H and MSS cases. Gastrectomy tissues from 17 GC patients were used for this study. The hospital pathology department confirmed pathologic features of the GC (e.g., EGC vs. AGC, differentiation, lymph node metastasis and TNM stage). All of the picked areas from tumor and normal areas were frozen, cut, and stained with hematoxylin & eosin (H&E). Two pathologists selected cases with rich tumor cell population (at least 60%), which were subsequently used in the study. Copy number profiling was performed using Agilent 180K platform according to the manufacturer's protocol.

2014-06-30 | E-GEOD-57176 | biostudies-arrayexpress

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2012-02-10 | GSE31168 | GEO

Patterns of Copy-Number Loss in Gastric Adenocarcinoma

Project description:Genome-wide DNA copy number profiling of gastric tumors and matched non-maligant samples to determine patterns of copy-number loss. Other samples included in this study can be found under accession number GSE31168.

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Genetic Landscape of Copy Number Alterations in Gastric Cancer

Project description:Genome-wide DNA copy number profiling of gastric tumors and matched non-maligant samples. The affymetrix SNP6 array was used to obtain DNA copy number profiles in 193 gastric tumors and 98 matched gastric non-malignant samples. Genomic DNA extracted from 193 gastric tumors and 98 matched gastric non-malignant (normal) tissues was hybridized on Affymetrix SNP6 genotyping arrays.

2012-02-10 | E-GEOD-31168 | biostudies-arrayexpress

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