Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

32 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumour tissue

ABSTRACT: We analysed a cohort of Lifepool IDC cases treated only with wide local excision for genome-wide copy number and loss of heterozygosity using Affymetrix OncoScanÂ® MIP arrays. Cases included IDC (n=4).Benign cases were available for 2 cases. We have analysed copy number calling from the same samples using low-coverage whole genome sequencing in order to investigate the concordance between the two techniques. 4 cases of lifepool invasive ductal carcinoma (IDC) and 2 benign cases were microdissected from FFPE tissue and analysed by molecular inversion probe (MIP) copy number arrays. The data in this submission are CN values for the ~300,000 probes common to two batches performed.

ORGANISM(S): Homo sapiens

SUBMITTER: TANJINA KADER

PROVIDER: E-GEOD-85035 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumour tissue

Project description:We analysed a cohort of Lifepool IDC cases treated only with wide local excision for genome-wide copy number and loss of heterozygosity using Affymetrix OncoScan® MIP arrays. Cases included IDC (n=4).Benign cases were available for 2 cases. We have analysed copy number calling from the same samples using low-coverage whole genome sequencing in order to investigate the concordance between the two techniques.

2016-08-02 | GSE85035 | GEO

Identification of copy number alterations associated with the progression of DCIS to Invasive Ductal Carcinoma

Project description:Ductal carcinoma in situ (DCIS) is a non-obligate precursor to invasive ductal carcinoma (IDC). Annotation of the genetic differences between the two lesions may assist in the identification of genes that promote the invasive phenotype. Matched IDC and DCIS showed highly similar copy number profiles (average of 83% of the genome shared) indicating a common clonal orgin although there is evidence that the DCIS continues to evolve in parallel with the co-existing IDC. Four chromosomal regions of loss (3q, 6q, 8p and 11q) and four regions of gain (5q, 16p, 19q and 20) were recurrently affected in IDC but not in DCIS. CCND1 and MYC showed increased amplitude of gain in IDC. One region of loss (17p11.2) was specific to DCIS. 21 cases of synchronous DCIS and IDC were microdissected from FFPE tissue and analysed by molecular inversion probe (MIP) copy number arrays. The arrays were early release OncoScan arrays and the data in this submission are CN values for the ~300,000 probes common to two batches performed. Raw data is retained by Affymetrix.

2012-09-04 | E-GEOD-31892 | biostudies-arrayexpress

The genetic architecture of breast papillary lesions as a predictor of progression to carcinoma

Project description:We analysed a cohort of breast papillary lesions cases with (n=4) or without (n=7) co-existed cancer for genome-wide copy number and loss of heterozygosity using Affymetrix OncoScan® MIP arrays. Cases included pure papilloma (withoout cancer) (n=7), papilloma cases synchronous with cancer (n=4). We have analysed copy number calling from these samples including carcinoma components of synchronous cases in order to understand the precursor relationship as well any biomarker for progression from papillary lesions to carcinoma.

2020-01-29 | GSE131087 | GEO

Copy number analysis of DCIS with and without recurrence

Project description:We analysed a cohort of pure DCIS cases treated only with wide local excision for genome-wide copy number and loss of heterozygosity using Affymetrix OncoScan® MIP arrays. Cases included those without recurrence within 6 years (n=25) and with recurrence between 1-5 years after diagnosis (n=15). Additional cases were excluded for low grade (n=6) or non-clonal recurrence (n=2). Recurrence tumour was available for 8 cases. Pure DCIS were broadly similar in copy number changes compared to invasive breast cancer, with the consistent exception of a greater frequency of ERBB2 amplification in DCIS. There were no significant differences in age or ER status between the cases with a recurrence versus those without. Overall, the DCIS cases with recurrence had more copy number events than the DCIS without recurrence. The increased copy number appeared non-random with several genomic regions showing an increase in frequency in recurrent cases including 20q gain, ERBB2 amplification and 15q loss. Copy number changes may provide prognostic information for DCIS recurrence but validation in additional cohorts is required.

2015-12-01 | GSE66746 | GEO

FFPE study using MIP copy number platform

Project description:This SuperSeries is composed of the following subset Series: GSE14740: FFPE study using MIP copy number platform - kidney GSE14741: FFPE study using MIP copy number platform - bladder/colorectal/kidney/liver GSE14742: FFPE study using MIP copy number platform - colorectal GSE14743: FFPE study using MIP copy number platform - breast cancer I GSE14744: FFPE study using MIP copy number platform - breast cancer II GSE14745: FFPE study using MIP copy number platform - liver Refer to individual Series, GSE14856_quartets.txt contains list of matched samples

2010-05-06 | E-GEOD-14856 | biostudies-arrayexpress

Integrated Copy Number Analysis of Epstein Barr Virus (EBV)-Positive Diffuse Large B-Cell Lymphoma (DLBCL)

Project description:Copy number analysis was performed on EBV+ DLBCL samples compared with EBV- DLBCL. We analyzed the genomic DNA from 18 cases of EBV+ DLBCL, 21 cases of EBV- DLBCL, and 13 cases of nonneoplastic tonsillar tissues using OncoScan FFPE Express 2.0 (MIP). No technical replication were done.

2014-02-01 | E-MTAB-1971 | biostudies-arrayexpress