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TranscriptomicsGenome-wide analysis of esopageal adenocarcinoma tumor biopsy using high-density single-nucleotide polymorphism arrays.
We applied whole-genome single nucleotide polymorphism (SNP) arrays to define a comprehensive genetic profile of 23 esophageal adenocarcinoma (EAC) primary tumor biopsies based on loss of heterozygosity (LOH) and DNA copy number changes. Alterations were common, averaging 97 (range 23-208) per tumor...
ORGANISM(S): Homo sapiens 
2008-06-01 | E-GEOD-10506 | biostudies-arrayexpress
TranscriptomicsA statistical method for detecting genomic aberrations in heterogeneous tumour samples from single nucleotide polymorphism genotyping data
SNP array analysis of microdissected tumor vs stroma vs surgically obtained tumor DNA was extracted from total tumor material, from microdissected stroma and microdissected, pure tumor tissue
ORGANISM(S): Homo sapiens 
2010-08-25 | E-GEOD-23785 | biostudies-arrayexpress
TranscriptomicsComparison of primary neuroblastoma tumors and derivative early-passage cell lines using genome-wide SNP array analysis
Stromal contamination is one of the major confounding factors in the analysis of primary solid tumor samples by single nucleotide polymorphism (SNP) arrays. As we propose to employ genome-wide SNP microarray analysis as a diagnostic platform for neuroblastoma, the sensitivity, specificity, and accur...
ORGANISM(S): Homo sapiens 
2009-01-31 | E-GEOD-14656 | biostudies-arrayexpress
TranscriptomicsCombined arrayCGH and SNP-loss of heterozygosity analysis in cervical cancer
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 heterozygos...
ORGANISM(S): Homo sapiens 
2010-06-05 | E-GEOD-8605 | biostudies-arrayexpress
TranscriptomicsMolecular Analyses of 10q hemizygous deletions and parents
We report on the analyses of four unrelated patients with de novo, overlapping, hemizygous deletions of the long arm of chromosome 10. These include two small terminal deletions (10q26.2 to 10qter), a larger terminal deletion (10q26.12 to 10qter), and an interstitial deletion (10q25.3q26.13). Single...
ORGANISM(S): Homo sapiens 
2009-07-01 | E-GEOD-11958 | biostudies-arrayexpress
TranscriptomicsIllumina SNP and CNV data for the HuRef individual
The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation. Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger stru...
ORGANISM(S): Homo sapiens 
2013-02-12 | E-GEOD-20284 | biostudies-arrayexpress
TranscriptomicsGSTM3 single nucleotide polymorphism (rs7483) associated with peripheral BMC expression in Alzheimer disease
Comparisons between the sample groups (normal elderly control (NEC) and Alzheimer disease (AD)) allowed the identification of genes with disease expression patterns associated with the glutathione S-transferase M3 single nucleotide polymorphism rs7483. Keywords: biological repeat Peripheral blood mo...
ORGANISM(S): Homo sapiens 
2010-06-24 | E-GEOD-4227 | biostudies-arrayexpress
TranscriptomicsTranscriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection.
Purpose: Water stress limits plant survival and production in many parts of the world. Identification of genes and alleles responding to water stress conditions is important in breeding plants better adapted to drought. Currently there are no studies examining the transcriptome wide gene and allelic...
ORGANISM(S): Eucalyptus camaldulensis 
2012-07-17 | E-GEOD-39369 | biostudies-arrayexpress
TranscriptomicsAffymetrix SNP and CNV data for the HuRef individual
The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation. Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger stru...
ORGANISM(S): Homo sapiens 
2013-02-12 | E-GEOD-20275 | biostudies-arrayexpress
TranscriptomicsGenotyping of human basal cell carcinomas unveils uniparental disomy as a key domatic event.
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. Experiment Overall Design: 14 BCC/Blood pairs were used in this stu...
ORGANISM(S): Homo sapiens 
2008-06-12 | E-GEOD-2959 | biostudies-arrayexpress
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