Sir Peter MacCallum Department of Oncology - Research Publications

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Author: Fox, Stephen × Author: Gorringe, Kylie × Author: Kader, Tanjina × Author: Goode, David ×

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    Atypical ductal hyperplasia is a multipotent precursor of breast carcinoma
    Kader, T ; Hill, P ; Zethoven, M ; Goode, DL ; Elder, K ; Thio, N ; Doyle, M ; Semple, T ; Sufyan, W ; Byrne, DJ ; Pang, J-MB ; Murugasu, A ; Miligy, IM ; Green, AR ; Rakha, EA ; Fox, SB ; Mann, GB ; Campbell, IG ; Gorringe, KL (WILEY, 2019-07)
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    Molecular comparison of interval and screen-detected breast cancers
    Cheasley, D ; Li, N ; Rowley, SM ; Elder, K ; Mann, GB ; Loi, S ; Savas, P ; Goode, DL ; Kader, T ; Zethoven, M ; Semple, T ; Fox, SB ; Pang, J-M ; Byrne, D ; Devereux, L ; Nickson, C ; Procopio, P ; Lee, G ; Hughes, S ; Saunders, H ; Fujihara, KM ; Kuykhoven, K ; Connaughton, J ; James, PA ; Gorringe, KL ; Campbell, IG (WILEY, 2019-06)
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    The genetic architecture of breast papillary lesions as a predictor of progression to carcinoma
    Kader, T ; Elder, K ; Zethoven, M ; Semple, T ; Hill, P ; Goode, DL ; Thio, N ; Cheasley, D ; Rowley, SM ; Byrne, DJ ; Pang, J-M ; Miligy, IM ; Green, AR ; Rakha, EA ; Fox, SB ; Mann, GB ; Campbell, IG ; Gorringe, KL (NATURE PORTFOLIO, 2020-03-12)
    Intraductal papillomas (IDP) are challenging breast findings because of their variable risk of progression to malignancy. The molecular events driving IDP development and genomic features of malignant progression are poorly understood. In this study, genome-wide CNA and/or targeted mutation analysis was performed on 44 cases of IDP, of which 20 cases had coexisting ductal carcinoma in situ (DCIS), papillary DCIS or invasive ductal carcinoma (IDC). CNA were rare in pure IDP, but 69% carried an activating PIK3CA mutation. Among the synchronous IDP cases, 55% (11/20) were clonally related to the synchronous DCIS and/or IDC, only one of which had papillary histology. In contrast to pure IDP, PIK3CA mutations were absent from clonal cases. CNAs in any of chromosomes 1, 16 or 11 were significantly enriched in clonal IDP lesions compared to pure and non-clonal IDP. The observation that 55% of IDP are clonal to DCIS/IDC indicates that IDP can be a direct precursor for breast carcinoma, not limited to the papillary type. The absence of PIK3CA mutations and presence of CNAs in IDP could be used clinically to identify patients at high risk of progression to carcinoma.
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    Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
    Kader, T ; Goode, DL ; Wong, SQ ; Connaughton, J ; Rowley, SM ; Devereux, L ; Byrne, D ; Fox, SB ; Arnau, GM ; Tothill, RW ; Campbell, IG ; Gorringe, KL (BMC, 2016-11-15)
    Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. LC WGS improved CN profiles of samples that performed poorly using MIP arrays. Our technique enables identification of driver and prognostic CNAs in archival patient samples previously deemed unsuitable for genomic analysis due to DNA limitations.