Breast Cancer Molecular Subtyping in Practice - A Real-World Study of the APIS Breast Cancer Subtyping Assay in a Consecutive Series of Breast Core Biopsies

Sep 22, 2026

mRNA-based APIS Breast Cancer Subtyping Kit evaluates seven parameters, including routine biomarkers ER, PR and HER-2 plus four genes (MKI67, PCNA, CCNA2, KIF23) to generate a molecular subtype for each sample. Results are benchmarked against immunohistochemistry (IHC) and/or in situ hybridisation (ISH) in 100 cases from 98 pre-operative core biopsies and two nodal metastasis biopsies. ER concordance reaches 97%, PR 89%, and HER-2 100%. Discordance for Ki-67 is 3% versus MKI67 alone and 24% versus the four-gene proliferation signature, supporting high concordance for ER/PR/HER-2 and potential routine clinical adoption.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages13

Reading Time33 min

AccessFree to download

Introduction

Clinical standard of biomarker assessment in breast cancer

Molecular subtypes from gene expression profiling

Surrogate IHC testing and related applications

Need for refined tests and proliferation-focused approaches

RNA-based expression tests and clinical integration

Communication Breast Cancer Molecular Subtyping in Practice: A Real-World Study of the APIS Breast Cancer Subtyping Assay in a Consecutive Series of Breast Core Biopsies Silvana Di Palma 1,*, Panagiotis Koliou 2, Alex Simonovic 1, Daniela Costa 3, Catherine Faulkes 3, Brenda Kobutungi 3, Felicity Paterson 2, Jonathan David Horsnell 4, Farrokh Pakzad 4, Tracey Irvine 4, Polly Partlett 4, Elizabeth Clayton 4 and Nadine Collins 3 Citation: Di Palma, S.; Koliou, P.; Simonovic, A.; Costa, D.; Faulkes, C.; Kobutungi, B.; Paterson, F.; Horsnell, J.D.; Pakzad, F.; Irvine, T.; et al. Breast Cancer Molecular Subtyping in Practice: A Real-World Study of the APIS Breast Cancer Subtyping Assay in a Consecutive Series of Breast Core Biopsies. Int. J. Mol. Sci. 2024, 25, 2616 . [https://doi.org/10.3390/](https://doi.org/10.3390/)[ ](https://doi.org/10.3390/)ijms25052616 Academic Editor: Elena Bonanno Received: 8 January 2024 Revised: 25 January 2024 Accepted: 26 January 2024 Published: 23 February 2024 Copyright: © 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ([https://](https://)[ ](https://)[creativecommons.org/licenses/by/](creativecommons.org/licenses/by/)[ ](creativecommons.org/licenses/by/)[4.0/](4.0/)) . 1 Department of Cellular Pathology, Berkshire & Surrey Pathology Services, The Royal Surrey Hospital NHS Foundation Trust, University of Surrey, Egerton Road, Guildford GU2 7XX, UK; [alexandra.simonovic@nhs.net](alexandra.simonovic@nhs.net) 2 Department of Oncology, The Royal Surrey Hospital NHS Foundation Trust, Egerton Road, Guildford GU2 7XX, UK; [panagiotis.koliou@nhs.net](panagiotis.koliou@nhs.net) (P.K.); [felicity.paterson1@nhs.net](felicity.paterson1@nhs.net) (F.P.) 3 Molecular Diagnostics, Berkshire & Surrey Pathology Services, The Royal Surrey Hospital NHS Foundation Trust, Egerton Road, Guildford GU2 7XX, UK; [daniela.costa1@nhs.net](daniela.costa1@nhs.net) (D.C.); [c.faulkes@nhs.net](c.faulkes@nhs.net) (C.F.); [b.kobutungi@nhs.net](b.kobutungi@nhs.net) (B.K.); [nadine.collins@nhs.net](nadine.collins@nhs.net) (N.C.) 4 Breast Unit, The Royal Surrey Hospital NHS Foundation Trust, Egerton Road, Guildford GU2 7XX, UK; [j.horsnell@nhs.net](j.horsnell@nhs.net) (J.D.H.); [f.pakzad@nhs.net](f.pakzad@nhs.net) (F.P.); [traceyirvine1@nhs.net](traceyirvine1@nhs.net) (T.I.); [ppartlett@nhs.net](ppartlett@nhs.net) (P.P.); [elizabethclayton1@nhs.net](elizabethclayton1@nhs.net) (E.C.) * Correspondence: [sdipalma@nhs.net](sdipalma@nhs.net) Abstract: The APIS Breast Cancer Subtyping Kit is an mRNA-based assessment of the seven parameters including three biomarkers routinely assessed in all the newly diagnosed breast cancers (BC), oestrogen receptor (ER), progesterone receptor (PR) and HER-2 and an additional four genes that create a novel proliferation signature, MKI67, PCNA, CCNA2 and KIF23 . Taken together, the data are used to produce a molecular subtype for every sample. The kit was evaluated against the current standard protocol of immunohistochemistry (IHC) and/or in situ hybridisation (ISH) in breast cancer patients. The data were presented at the weekly breast multidisciplinary team (MDT) meeting. A total of 98 consecutive cases of pre-operative breast cancer core biopsies and two core biopsies of nodal metastases yielding 100 cases were assessed. IHC and APIS results were available for 100 and 99 cases. ER was concordant in 97% cases, PR was concordant in 89% and HER-2 results were concordant with IHC/ISH in 100% of the cases. Ki-67 IHC was discordant in 3% of cases when compared with MK167 alone but discordant in 24% when compared with the four-gene proliferation signature. In conclusion, our study indicates that the APIS Breast Cancer Subtyping Kit is highly concordant when compared to the results produced for ER/PR/HER-2 by IHC and/or ISH. The assay could

FAQs

What biomarkers and genes does the APIS Breast Cancer Subtyping Kit measure?

It includes ER, PR, and HER-2 plus four proliferation-signature genes: MKI67, PCNA, CCNA2, and KIF23.

How was the APIS assay evaluated in the study?

APIS results were compared with the standard IHC and/or ISH protocols, using data presented at the weekly breast multidisciplinary team meeting.

What were the main concordance outcomes for ER, PR, and HER-2?

ER concordance was 97%, PR concordance was 89%, and HER-2 concordance with IHC/ISH was 100% across the assessed cases.

Sep 22, 2026

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