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TranscriptomicsChromosome 11q and its association with CCND1 gene amplification and tamoxifen resistance in premenopausal breast cancer
Background: The amplification event occurring at chromosome locus 11q13, reported in several different cancers, includes a number of potential oncogenes. We have previously reported amplification of one such oncogene, CCND1, to be correlated with an adverse effect of tamoxifen in premenopausal breas...
ORGANISM(S): Homo sapiens 
2008-10-07 | E-GEOD-12759 | biostudies-arrayexpress
TranscriptomicsMolecular subtypes of breast cancer are associated with characteristic DNA methylation patterns
Introduction: Five different molecular subtypes of breast cancer have been identified through gene expression profiling. Each subtype has a characteristic expression pattern suggested to partly depend on cellular origin. We aimed to investigate whether the molecular subtypes also display distinct me...
ORGANISM(S): Homo sapiens 
2010-06-09 | E-GEOD-22210 | biostudies-arrayexpress
TranscriptomicsNon-coding antisense transcription detected by conventional and single-stranded cDNA microarray
Recent bioinformatic studies revealed that many mammalian protein-coding genes also transcribe their complementary strands. This phenomenon raises questions regarding the validity of data obtained from double-stranded cDNA microarrays since hybridization to both strands may occur. To analyze experim...
ORGANISM(S): Homo sapiens 
2007-09-01 | E-GEOD-7860 | biostudies-arrayexpress
TranscriptomicsIdentification of new microRNAs in paired normal and tumor breast tissue suggests a dual role for the ERBB2/Her2 gene
To comprehensively characterize microRNA (miRNA) expression in breast cancer, we performed the first extensive next-generation sequencing expression analysis of this disease. We sequenced small RNA from tumors with paired samples of normal and tumor-adjacent breast tissue. Our results indicate that ...
ORGANISM(S): Homo sapiens 
2012-07-06 | E-GEOD-39162 | biostudies-arrayexpress
TranscriptomicsNormalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios
Illumina Infinium whole genome genotyping (WGG) arrays are increasingly being applied in cancer genomics to study gene copy number alterations and allele-specific aberrations such as loss-of-heterozygosity (LOH). Methods developed for normalization of WGG arrays have mostly focused on diploid, norma...
ORGANISM(S): Homo sapiens 
2008-10-04 | E-GEOD-11977 | biostudies-arrayexpress
TranscriptomicsHigh-resolution aCGH analyses of copy number alterations in HER2-amplified breast cancer
HER2 gene amplification and protein overexpression (HER2+) define a clinically challenging subgroup of breast cancer with variable prognosis and response to therapy. Although gene expression profiling has identified an ERBB2 molecular subtype of breast cancer, it is clear that HER2+ tumors reside in...
ORGANISM(S): Homo sapiens 
2010-04-14 | E-GEOD-21259 | biostudies-arrayexpress
TranscriptomicsBreast tumors from CHEK2 1100delC mutation carriers: genomic landscape and clinical implications (CGH)
Abstract Introduction: CHEK2 is a moderate penetrance breast cancer risk gene, whose truncating mutation 1100delC increases the risk about two fold. We pursued to investigate gene copy number aberrations and gene expression profiles that are typical for breast tumors of CHEK2 1100delC mutation carri...
ORGANISM(S): Homo sapiens 
2011-05-10 | E-GEOD-24698 | biostudies-arrayexpress
TranscriptomicsBreast tumors from CHEK2 1100delC mutation carriers: genomic landscape and clinical implications (GEX)
Introduction: CHEK2 is a moderate penetrance breast cancer risk gene, whose truncating mutation 1100delC increases the risk about two fold. We pursued to investigate gene copy number aberrations and gene expression profiles that are typical for breast tumors of CHEK2 1100delC mutation carriers. Mat...
ORGANISM(S): Homo sapiens 
2011-05-10 | E-GEOD-24697 | biostudies-arrayexpress
TranscriptomicsScreening for copy-number alterations and LOH in CLL - a comparative study of four microarray platforms
Screening for gene copy-number alterations (CNAs) has improved by applying genome-wide microarrays, where SNP arrays also allow analysis of loss of heterozygozity (LOH). We here analyzed 10 chronic lymphocytic leukemia (CLL) samples using four different high-resolution platforms: BAC arrays (32K), o...
ORGANISM(S): Homo sapiens 
2008-12-10 | E-GEOD-13557 | biostudies-arrayexpress
TranscriptomicsIdentification of subtypes in HER2-positive breast cancer reveals a gene signature prognostic of outcome
Purpose HER2 gene amplification or protein overexpression (HER2+) defines a clinically challenging subgroup of breast cancer with variable prognosis and response to therapy. We aimed to investigate the heterogeneous biological appearance and clinical behavior of HER2+ tumors using molecular profilin...
ORGANISM(S): Homo sapiens 
2010-03-16 | E-GEOD-18328 | biostudies-arrayexpress
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