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Selection and evolution in the genomic landscape of copy number alterations in ductal carcinoma in situ (DCIS) and its progression to invasive carcinoma of ductal/no special type: a meta-analysis

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Abstract

Ductal carcinoma in situ (DCIS) is a pre-invasive malignancy detected with an increasing frequency through screening mammography. One of the primary aims of therapy is to prevent local recurrence, as in situ or as invasive carcinoma, the latter arising in half of the recurrent cases. Reliable biomarkers predictive of its association with recurrence, particularly as invasive disease, are however lacking. In this study, we perform a meta-analysis of 26 studies which report somatic copy number aberrations (SCNAs) in 288 cases of ‘pure’ DCIS and 328 of DCIS associated with invasive carcinoma, along with additional unmatched cases of 145 invasive carcinoma of ductal/no special type (IDC) and 50 of atypical ductal hyperplasia (ADH). SCNA frequencies across the genome were calculated at cytoband resolution (UCSC genome build 19) to maximally utilize the available information in published literature. Fisher’s exact test was used to identify significant differences in the gain–loss distribution in each cytoband in different group comparisons. We found synchronous DCIS to be at a more advanced stage of genetic aberrations than pure DCIS and was very similar to IDC. Differences in gains and losses in each disease process (i.e. invasive or in situ) at each cytoband were used to infer evidence of selection and conservation for each cytoband and to define an evolutionary conservation scale (ECS) as a tool to identify and distinguish driver SCNA from the passenger SCNA. Using ECS, we have identified aberrations that show evidence of selection from the early stages of neoplasia (i.e. in ADH and pure DCIS) and persist in IDC; we postulate these to be driver aberrations and that their presence may predict progression to invasive disease.

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Acknowledgements

SUR was funded by Tata Memorial Centre, Mumbai, India; AG and HM were funded by the Breast Cancer Now funding at King’s College London and by the National Institute for Health Research Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London. Frequency plots and circle plots were created using the engine at the Progenetix website (www.progenetix.org) [15, 16].

Author contributions

SP, AG and SUR conceived the study, SUR acquired the data, performed the data analysis and generated figures and HM participated in the data analysis and generated figures. All authors were involved in writing the paper and had final approval of the submitted and published version.

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Authors and Affiliations

  1. Department of Research Oncology, King’s Health Partners AHSC, King’s College London, London, UK

    Swapnil Ulhas Rane, Hasan Mirza, Anita Grigoriadis & Sarah E. Pinder

  2. Breast Tissue and Data Bank, King’s Health Partners AHSC, King’s College London, London, UK

    Swapnil Ulhas Rane & Sarah E. Pinder

  3. Department of Pathology, Tata Memorial Centre, Tata Memorial Hospital, 8th Floor, Annexe Building, Mumbai, India

    Swapnil Ulhas Rane

  4. Breast Cancer Now, King’s College London, London, UK

    Hasan Mirza & Anita Grigoriadis

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This study involved analysis of published literature. The study did not involve any human or animal participants.

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10549_2015_3509_MOESM1_ESM.rar

Panther analysis.rar: archive of excel files containing results of PANTHER overrepresentation tests performed on gene lists corresponding to ECS groups of 13, 12–11, 10−8, 7 to −7, −8 to −10, −11 to −12, −13 and regions significantly different between pure DCIS and synchronous DCIS with an ECS of ± 8 to ± 13 (RAR 14975 kb)

Table 1

Observed aberration Frequency of 851 cytobands spanning chromosomes 1–22 and chromosome X across ADH, ‘pure’ DCIS, DCIS with synchronous IDC and ‘pure’ IDC (XLSX 157 kb)

Table 2

Observed aberration frequencies of significantly different aberrations between pure DCIS and synchronous DCIS identified using an FDR-corrected Fisher test with a p value ≤0.05(XLSX 128 kb)

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Rane, S.U., Mirza, H., Grigoriadis, A. et al. Selection and evolution in the genomic landscape of copy number alterations in ductal carcinoma in situ (DCIS) and its progression to invasive carcinoma of ductal/no special type: a meta-analysis. Breast Cancer Res Treat 153, 101–121 (2015). https://doi.org/10.1007/s10549-015-3509-x

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  • DOI: https://doi.org/10.1007/s10549-015-3509-x

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