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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 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE85035 | GEO | 2016/08/02

SECONDARY ACCESSION(S): PRJNA336004

REPOSITORIES: GEO

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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 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.

2016-08-02 | E-GEOD-85035 | 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

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

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

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

Copy number data and Stage I/II Breast Cancer

Project description:Search for copy number imbalances and allelotype in 971 early stage breast cancer using molecular inversion probe arrays Affymetrix MIP arrays were performed according to the manufacturer's directions on DNA extracted from paraffin embedded formalin fixed Stage I and II Breast Cancers Copy number analysis of Affymetrix Oncoscan Version 1 MIP arrays was performed for 971 Stage I and II breast cancers.

2011-08-16 | E-GEOD-31424 | biostudies-arrayexpress

Affymetrix OncoScan SNP arrays for profiling somatic copy-number alterations in blastic plasmacytoid dendritic cell neoplasm

Project description:Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive malignancy assumed to originate from plasmacytoid dendritic cells (pDCs), which affects the skin and bone marrow and sequentially other organ systems. Here, we used Affymetrix OncoScan CNV arrays to characterize somatic copy number variations in 45 BPDCN cases.

2022-04-05 | GSE200113 | GEO

Cross-laboratory validation of the OncoScan FFPE Assay, a multiplex tool for whole genome tumour profiling

Project description:162 FFPE samples, representing six different tumour types, were profiled in triplicate across three independent laboratories. OncoScan¬ FFPE assay data was then analysed for reproducibility of genome-wide copy number, loss of heterozygosity and somatic mutations.

2015-02-18 | E-MTAB-2914 | biostudies-arrayexpress

RNA-Seq of ILC and IDC breast cancer cell lines in attached (2D) and suspension (ultra-low attachment) cultures

Project description:Invasive lobular carcinoma (ILC) is a histological subtype of breast cancer with distinct molecular and clinical features from the more common subtype invasive ductal carcinoma (IDC). ILC cells exhibit anchorage-independent growth in ultra-low attachment (ULA) suspension cultures, which is largely attributed to the loss of E-cadherin. In addition to anoikis resistance, herein we show that human ILC cell lines exhibit enhanced cell proliferation in ULA cultures as compared to IDC cells. Proteomic comparison of ILC and IDC cell lines identified induction of PI3K/Akt and p90-RSK pathways specifically in ULA culture in ILC cells. Further transcriptional profiling uncovered unique upregulation of the inhibitors of differentiation family transcription factors ID1 and ID3 in ILC ULA culture, the knockdown of which diminished the anchorage-independent growth of ILC cell lines through cell cycle arrest. We find that ID1 and ID3 expression is higher in human ILC tumors as compared to IDC, correlated with worse prognosis uniquely in patients with ILC and associated with upregulation of angiogenesis and matrisome-related genes. Altogether, our comprehensive study of anchorage independence in human ILC cell lines provides mechanistic insights and clinical implications for metastatic dissemination of ILC and implicates ID1 and ID3 as novel drivers and therapeutic targets for lobular breast cancer.

2020-06-23 | GSE130650 | GEO

DNA-Seq of human Acute Panmyelosis with Myelofibrosis (APMF) Samples

Project description:FFPE Bone marrow core biopsis of a cohort of 16 APMF Samples were analysed by OncoScan copy number analysis (E-MTAB-7888). 5 out of this 16 Samples had enough DNA available for NGS using the Illumina TruSight Myeloid and/or Tumor 15 NGS Gene Panels.

2020-04-11 | E-MTAB-7891 | biostudies-arrayexpress

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