Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Landscape of somatic allelic imbalances and copy number alterations in human lung carcinoma

ABSTRACT: Lung cancer is the worldwide leading cause of death from cancer. This GEO series correspond to one of the BAC aCGH data sets used as validation cohort for the study: Landscape of somatic allelic imbalances and copy number alterations in human lung cancer, Int J Cancer 2013.

ORGANISM(S): Homo sapiens

PROVIDER: GSE29065 | GEO | 2012/10/09

SECONDARY ACCESSION(S): PRJNA142921

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Landscape of somatic allelic imbalances and copy number alterations in human lung carcinoma

Project description:Lung cancer is the worldwide leading cause of death from cancer. This GEO series correspond to one of the BAC aCGH data sets used as validation cohort for the study: Landscape of somatic allelic imbalances and copy number alterations in human lung cancer, Int J Cancer 2012. Genomic profiling of 78 lung carcinomas using 32K BAC aCGH microarrays.

2012-10-09 | E-GEOD-29065 | biostudies-arrayexpress

Genomic imbalances of lung cancer

Project description:The array comparative genomic hybridization (aCGH) was perform to identify regions with genomic imbalance in lung cancer.The aCGH analysis detected a total of 325 regions with genomic imbalance in all 8 lung cancer samples, ranging from focal rearrangements (70 kb–5 Mb) to chromosome-arm alterations with chromosomal segments amplification or deletion. Among these mutations, a total of 115 genomic imbalances were discovered occurring at high frequency varying from 25% to 50%.

2016-11-17 | GSE89927 | GEO

Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer

Project description:A survey of the somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer. Genomic profiling of 26 breast tumors with amplification of HER2 using 1M and 2.5M Illumina SNP beadchips. Sample identifiers correspond to GSE21259 where sample annotations may be extracted.

2011-12-02 | E-GEOD-31645 | biostudies-arrayexpress

Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer

Project description:A survey of the somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer.

2011-12-02 | GSE31645 | GEO

Integrated genomics approach to detect allelic imbalances in multiple myeloma

Project description:Multiple myeloma (MM) is characterized by marked genomic instability. Beyond structural rearrangements, a relevant role in its biology is represented by allelic imbalances leading to significant variations in ploidy status. To better elucidate the genomic complexity of MM, we analyzed a panel of 45 patients using combined FISH and microarray approaches. Using a self-developed procedure to infer exact local copy numbers for each sample, we identified a significant fraction of patients showing marked aneuploidy. A conventional clustering analysis showed that aneuploidy, chromosome 1 alterations, hyperdiploidy and recursive deletions at 1p and chromosomes 13, 14 and 22 were the main aberrations driving samples grouping. Then, we integrated mapping information with gene and microRNAs expression profiles: a multiclass analysis of the identified clusters showed a marked gene-dosage effect, particularly concerning 1q transcripts, also confirmed by correlating gene expression levels and local copy number alterations. A wide dosage effect affected also microRNAs, indicating that structural abnormalities in MM closely reflect in their expression imbalances. Finally, we identified several loci in which genes and microRNAs expression correlated with loss-of-heterozygosity occurrence. Our results provide insights into the composite network linking genome structure and gene/microRNA transcriptional features in MM. Keywords: Integrated genomics approach based on SNP microarray and FISH procedures to detect allelic imbalances in multiple myeloma.

2009-04-14 | GSE13591 | GEO

Integrated genomics approach to detect allelic imbalances in multiple myeloma, SNP data

Project description:A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma: an integrated genomics approach reveals a wide dosage effect on gene and microRNA expression Multiple myeloma (MM) is characterized by marked genomic instability. Beyond structural rearrangements, a relevant role in its biology is represented by allelic imbalances leading to significant variations in ploidy status. To better elucidate the genomic complexity of MM, we analyzed a panel of 45 patients using combined FISH and microarray approaches. Using a self-developed procedure to infer exact local copy numbers for each sample, we identified a significant fraction of patients showing marked aneuploidy. A conventional clustering analysis showed that aneuploidy, chromosome 1 alterations, hyperdiploidy and recursive deletions at 1p and chromosomes 13, 14 and 22 were the main aberrations driving samples grouping. Then, we integrated mapping information with gene and microRNAs expression profiles: a multiclass analysis of the identified clusters showed a marked gene-dosage effect, particularly concerning 1q transcripts, also confirmed by correlating gene expression levels and local copy number alterations. A wide dosage effect affected also microRNAs, indicating that structural abnormalities in MM closely reflect in their expression imbalances. Finally, we identified several loci in which genes and microRNAs expression correlated with loss-of-heterozygosity occurrence. Our results provide insights into the composite network linking genome structure and gene/microRNA transcriptional features in MM. Keywords: Integrated genomics approach based on SNP microarray and FISH procedures to detect allelic imbalances in multiple myeloma.

2009-05-16 | GSE16121 | GEO

A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma

Project description:A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma: an integrated genomics approach reveals a wide dosage effect on gene and microRNA expression This SuperSeries is composed of the following subset Series: GSE13591: Integrated genomics approach to detect allelic imbalances in multiple myeloma GSE16121: Integrated genomics approach to detect allelic imbalances in multiple myeloma, SNP data Refer to individual Series

2009-05-16 | E-GEOD-16122 | biostudies-arrayexpress

Allelic Imbalances in bladder tumors based on high-density SNP array

Project description:Comparison between germline (blood) and microdissected bladder tumors to determine allelic imbalances. The GeneChip® Mapping 10K Early Access Array Affymetrix, Santa Clara, CA was used to determine the number of heterozygous SNPs in DNA from blood compared to the number of heterozygous SNPs in DNA from tumor in the same patient. Keywords: repeat sample

2005-04-15 | GSE2258 | GEO

Allelic Imbalances in bladder tumors based on high-density SNP array

Project description:Comparison between germline (blood) and microdissected bladder tumors to determine allelic imbalances. The GeneChipÂ® Mapping 10K Early Access Array Affymetrix, Santa Clara, CA was used to determine the number of heterozygous SNPs in DNA from blood compared to the number of heterozygous SNPs in DNA from tumor in the same patient.

2010-06-10 | E-GEOD-2258 | biostudies-arrayexpress

A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma

2009-05-16 | GSE16122 | GEO