Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Characterisation of an oesophageal adenocarcinoma cell line (The MFD-1)

ABSTRACT: A cell line (MFD-1) was derived from a 55-year old male with oesophageal adenocarcinoma. Using different sources of genetic material from normal and tumour tissue surgically resected, peripheral blood and the derived cell line a high concordance of genotypes calls across the whole genome confirms MFD-1 was derived from parent tumour. The SNP6 array contained 906,000 probes for the genotyping of SNPs and 946,000 probes for the genotyping of non-polymorphic copy number. Affymetrix CEL files were analysed using the tool PICNIC2 (predicting absolute allele copy number variation with microarray cancer data).

ORGANISM(S): Homo sapiens

SUBMITTER: Edwin Garcia

PROVIDER: E-MTAB-4590 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1.

Garcia Edwin E Hayden Annette A Birts Charles C Britton Edward E Cowie Andrew A Pickard Karen K Mellone Massimiliano M Choh Clarisa C Derouet Mathieu M Duriez Patrick P Noble Fergus F White Michael J MJ Primrose John N JN Strefford Jonathan C JC Rose-Zerilli Matthew M Thomas Gareth J GJ Ang Yeng Y Sharrocks Andrew D AD Fitzgerald Rebecca C RC Underwood Timothy J TJ

Scientific reports 20160907

New biological tools are required to understand the functional significance of genetic events revealed by whole genome sequencing (WGS) studies in oesophageal adenocarcinoma (OAC). The MFD-1 cell line was isolated from a 55-year-old male with OAC without recombinant-DNA transformation. Somatic genetic variations from MFD-1, tumour, normal oesophagus, and leucocytes were analysed with SNP6. WGS was performed in tumour and leucocytes. RNAseq was performed in MFD-1, and two classic OAC cell lines F ...[more]

PMID: 27600491

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Project description:Copy number variant (CNV) analysis was performed on renal cell carcinoma (RCC) specimens (chromophobe, clear cell, oncocytoma, papillary type 1, papillary type 2) using high resolution arrays (1.85 million probes). RCC samples exhibited diverse genomic changes within and across tumor types ranging from 106 CNV segments in a clear cell specimen to 2238 CNV segments in a papillary type 2 specimen. Despite the genomic heterogeneity, distinct CNV segments were common within each of 4 tumor classifications: chromophobe (7 segments), clear cell (3 segments), oncocytoma (9 segments), and papillary type 2 (2 segments). Shared segments ranged from a 6.1 Kb deletion among oncocytomas to a 208.3 Kb deletion common to chromophobes. Among common tumor type-specific variations, chromophobe, clear cell and oncocytomas comprised exclusively non-coding DNA. No CNV regions were common to papillary type 1 specimens although there were 12 amplifications and 12 deletions in 5 of 6 samples. Three microRNAs and 12 mRNA genes had M-bM-^IM-% 98% of their coding region contained within CNV regions including multiple gene families (chromophobe: amylase 1A, 1B, 1C; oncocytoma: general transcription factor 2H2, 2B, 2C, 2D). Gene deletions involved in histone modification and chromatin remodeling affected individual subtypes (clear cell: SFMBT, SETD2; papillary type 2: BAZ1A) as well as the collective RCC group (KDM4C). The genomic amplifications/deletions identified in each renal tumor type represent potential diagnostic and/or prognostic biomarkers. Tissue samples were obtained from the University of Pittsburgh Health Sciences Tissue Bank (HSTB) using an honest broker system and according to IRB approved protocol #970480. Samples were acquired as surgical specimens, flash-frozen in a 1.8 ml cryotube (NalgeNunc, Inc., Rochester, NY) followed by immediate storage at -80C. Each tumor sample (n=27) was classified into one of 5 renal cancer subtypes (chromophobe: n=5, clear cell: n=5, oncocytoma: n=5, papillary type 1: n=6, papillary type 2: n=6) by consensus evaluation of correlative hematoxylin and eosin stained slides performed independently by 3 anatomical pathologists. The three pathologists also confirmed the absence of pathological features in adjacent normal renal samples (n=9) and this normal reference group was expanded by inclusion of 14 normal thyroid samples and 8 normal lung specimens. DNA from each of these specimens was analyzed using genotyping microarrays (SNP 6.0, Affymetrix, Sunnyvale, CA).

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Dataset Information

Characterisation of an oesophageal adenocarcinoma cell line (The MFD-1)

Publications

Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1.

Similar Datasets

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