Open Access Highly Accessed Research article

Molecular characterisation of cell line models for triple-negative breast cancers

Anita Grigoriadis1*, Alan Mackay2, Elodie Noel1, Pei Jun Wu1, Rachel Natrajan2, Jessica Frankum2, Jorge S Reis-Filho23 and Andrew Tutt1

Author Affiliations

1 Breakthrough Breast Cancer Research Unit, Guy’s Hospital, King’s Health Partners AHSC, King’s College London School of Medicine, London, SE1 9RT, UK

2 The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK

3 Current affiliation: Department of Pathology and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA

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BMC Genomics 2012, 13:619  doi:10.1186/1471-2164-13-619

Published: 14 November 2012

Additional files

Additional file 1:

Table S1. Clinicopathological features of breast cell lines. Clinicopathological characteristics of BC cell lines.

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Additional file 2:

Table S2. Gene signatures with relevance in ER-negative breast tumours. Compendium of gene signatures, listing their genes, their citation and their relevance for triple-negative BCs.

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Additional file 3:

Figure S1. aCGH profiles Of BCCLs.zip. Folder provided aCGH-profiles for each BCCL individually. Gains are coloured in green, while copy number loss is shown in red.

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Additional file 4:

Figure S2. Distribution of CNAs over 3 gene expression clusters. Genomic instability varies between different BC cell lines expression clusters. For each BC cell line the genomic instability was determined, defined as the fraction of altered genome, and compared between the three expression clusters. Total genomic aberrations, amplifications and deletions were investigated separately. P_values (Welch t-test) for pairwise comparison are shown in red.

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Additional file 5:

Table S3. Recurrent amplicons of 56 Grade 3 TNBC in BCCLs. Recurrent amplicons of TNBC found in BC cell lines of “Cluster 1, 2 and 3”.

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Additional file 6:

Table S4. Gene centric analysis in 25 BCCL. Gene centric table of BC cell lines, showing the copy number state of each gene in each BC cell line, their un/adjusted Pearson’s correlation between gene expression and copy number; their correlation between gene expression and copy number in triple-negative BCs (both taken from Turner [31] their methylation states in BC cell lines, their Pearson’s correlation between methylated state and their gene expression in BC cell lines and basal-like BCs [38].

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Additional file 7:

Figure S3. Hierarchical clustering of BCCL methylation data. Unsupervised hierarchical clustering of BC cell lines based CpG islands. BC cell lines of ”Cluster 1, 2, 3” are shown in blue, orange and red, respectively.

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Additional file 8:

Figure S4. Distribution of methylated and unmethylated CpG islands in each BCCL. representation of BC specific un/methylated CpG sites in BC cell lines. Methylation marks for triple-negative BC were retrieved from Holm’s methylation profiling analysis [38]. Barplots represent the number of un/methylated CpG islands in each BC cell lines as identified of being un/methylated in BCs. BC cell lines of ”Cluster 1, 2, 3” are shown in blue, orange and red, respectively. The order of the BC cell lines is based on their gene expression clustering.

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Additional file 9:

Sweave Documentation. Sweave documentation of analysis.

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