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Lien HC, Lo C, Lee YH, Lin PH, Wang MY, Kuo WH, Tsai LW, Lu YS, Hu HW, Li YC, Huang CS. In situ HER2 RNA expression as a predictor of pathologic complete response of HER2-positive breast cancer patients receiving neoadjuvant chemotherapy and anti-HER2 targeted treatment. Breast Cancer Res 2024; 26:100. [PMID: 38867307 PMCID: PMC11170871 DOI: 10.1186/s13058-024-01852-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Immunohistochemistry (IHC) and in situ hybridization (ISH) remain standard biomarkers for therapeutic decisions in human epidermal growth factor 2 (HER2)-positive breast cancers (BCs); however, they are insufficient to explain the heterogeneous anti-HER2 response. METHODS We aimed to investigate the correlation of in situ HER2 RNA expression (isHRE), using RNAscope, with HER2 biomarkers and the impact of isHRE on the pathological complete response (pCR) rates of 278 patients with HER2 IHC/fluorescence ISH (FISH)-positive BC receiving neoadjuvant chemotherapy and anti-HER2 targeted treatment (NCTT). RESULTS We validated HER2 RNAscope scoring as a semiquantitative method to determine isHRE and showed a positive correlation between RNAscope scores and pCR rates, with particularly different rates between patients with a score of 5 versus 1-4 BCs (66.7% vs. 15.9%, p < 0.0001). There were higher RNAscope scores and pCR rates in patients with HER2 IHC 3 + versus IHC 2+/FISH + BCs and HER2 RNAscope scores and pCR rates showed similar non-linear positive correlations with HER2 copy numbers and HER2/centromere 17 ratios. Moreover, in each HER2-positive IHC/FISH category, higher pCR rates were observed in patients with RNAscope scores of 5 versus 1-4 BC. Patients achieving pCR had BCs with notably higher HER2 RNAscope scores. Multivariate analysis identified HER2 RNAscope 5 as a strong pCR predictor [odds ratio = 10.865, p < 0.001]. The combined impact of multivariate analysis-defined pCR predictors demonstrated that a higher pCR rate was observed in patients with a score of 5 versus a score of 1-4 BCs regardless of the status of hormone receptor and mono-or dual anti-HER2 blockade. CONCUSIONS Our results demonstrated that high isHRE (RNAscope score 5) is a strong pCR predictor in patients with HER2-positive BCs receiving NCTT, highlighting the complementary role of isHRE in stratifying HER2 status in tissue. Such stratification is relevant to anti-HER2 therapeutic efficacy, particularly using the cutoff of score 1-4 versus 5.
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Affiliation(s)
- Huang-Chun Lien
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Pathology, National Taiwan University, Taipei, Taiwan
| | - Chiao Lo
- Department of Surgery, National Taiwan University Hospital, Cancer Center Branch. No.57, Ln. 155, Sec. 3, Keelung Rd., Da'an Dist., Taipei City, 106, Taiwan
| | - Yi-Hsuang Lee
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Po-Hang Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Ming-Yang Wang
- Department of Surgery, National Taiwan University Hospital, Cancer Center Branch. No.57, Ln. 155, Sec. 3, Keelung Rd., Da'an Dist., Taipei City, 106, Taiwan
| | - Wen-Hung Kuo
- Department of Surgery, National Taiwan University Hospital, Cancer Center Branch. No.57, Ln. 155, Sec. 3, Keelung Rd., Da'an Dist., Taipei City, 106, Taiwan
| | - Li-Wei Tsai
- Department of Surgery, National Taiwan University Hospital, Cancer Center Branch. No.57, Ln. 155, Sec. 3, Keelung Rd., Da'an Dist., Taipei City, 106, Taiwan
| | - Yen-Shen Lu
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsiang-Wei Hu
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Chia Li
- Graduate Institute of Pathology, National Taiwan University, Taipei, Taiwan
| | - Chiun-Sheng Huang
- Department of Surgery, National Taiwan University Hospital, Cancer Center Branch. No.57, Ln. 155, Sec. 3, Keelung Rd., Da'an Dist., Taipei City, 106, Taiwan.
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Ajabnoor R, Zhang G, Hu Y, Gao Y, Finkelman BS, Turner BM, Yi S, Dhakal A, Audeh W, Li Z, Li X, Hicks DG, Zhang H. Breast Cancer With HER2 Immunohistochemical Score 2 and Average HER2 Signals/Cell 6 or More and HER2/CEP17 Ratio Less Than 2 ('ISH Group 3'): A Multiinstitutional Cohort Analysis Emphasizing Outcome and Molecular Subtype. Mod Pathol 2024; 37:100530. [PMID: 38810729 DOI: 10.1016/j.modpat.2024.100530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 05/31/2024]
Abstract
Breast cancer (BC) with average human epidermal growth factor receptor 2 (HER2) signals/cell ≥6 and HER2/chromosome enumeration probe 17 (CEP17) ratio <2 (in situ hybridization [ISH] group 3) is very rare, accounting for 0.4% to 3.0% of cases sent for the dual-probe ISH assay. Although such patients are currently eligible for treatment with HER2-targeted therapy, their characteristics and outcomes remain poorly understood. Sixty-two BCs with equivocal HER2 immunohistochemical score (2+) and reflex ISH group 3 results were identified across 4 institutions. Available clinicopathologic characteristics, MammaPrint and BluePrint molecular results, and follow-up information were retrospectively analyzed. Most BCs with HER2 equivocal immunohistochemical and ISH group 3 results were histologic grade 2 or 3 (100%), estrogen receptor (ER) positive (90.3%), with an average HER2 signals/cell of 7.3. Molecular profiles revealed that 80% (16/20) of tumors were luminal subtypes, and HER2 molecular subtype was identified in 10% of tumors (2/20). Twelve (19.4%) out of 62 patients developed local recurrence and/or distant metastasis with a median follow-up of 50 months. One (10%) of 10 patients achieved pathologic complete response after neoadjuvant chemotherapy. Forty-nine (79%) out of 62 patients completed anti-HER2 agents, and exploratory analysis showed no statistically significant difference in disease outcomes between patients who completed anti-HER2 treatment and those who did not. Univariate analysis revealed advanced clinical stage, and ER/progesterone receptor negativity was associated with unfavorable disease outcomes, and exploratory multivariate analysis demonstrated that clinical stage was the most significant factor associated with disease outcomes in the studied population. These findings increase our understanding of this rare, but clinically important HER2 category. Large-scale prospective randomized studies are needed to further evaluate the role of perioperative HER2-targeted therapy in this patient population.
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Affiliation(s)
- Rana Ajabnoor
- Department of Pathology, University of Rochester Medical Center, Rochester, New York; Department of Pathology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Gloria Zhang
- Department of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Yan Hu
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Yuan Gao
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, Georgia
| | - Brian S Finkelman
- Department of Pathology, University of Rochester Medical Center, Rochester, New York
| | - Bradley M Turner
- Department of Pathology, University of Rochester Medical Center, Rochester, New York
| | - Sha Yi
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, Georgia
| | - Ajay Dhakal
- Department of Medicine, University of Rochester Medical Center, Rochester, New York
| | - William Audeh
- Department of Medical Affairs, Agendia Inc, Irvine, California
| | - Zaibo Li
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Xiaoxian Li
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, Georgia
| | - David G Hicks
- Department of Pathology, University of Rochester Medical Center, Rochester, New York
| | - Huina Zhang
- Department of Pathology, University of Rochester Medical Center, Rochester, New York.
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Tseng YF, Li YC, Lee YH, Hu HW, Zhang MS, Hung TC, Lien HC. Correlation of In Situ HER2 RNA Expression With HER2 Immunohistochemistry and Fluorescence In Situ Hybridization Categories in Breast Cancer. Arch Pathol Lab Med 2024; 148:e48-e56. [PMID: 37639453 DOI: 10.5858/arpa.2023-0129-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2023] [Indexed: 08/31/2023]
Abstract
CONTEXT.— RNA sequencing study has demonstrated that human epidermal growth factor receptor 2 (HER2) RNA levels influence anti-HER2 therapeutic efficacy. However, in situ HER2 RNA expression (isHRE), which evaluates HER2 RNA expression in tissue, has remained unclear in breast cancers (BCs) of various HER2 immunohistochemistry (IHC)/in situ hybridization (ISH) categories. OBJECTIVE.— To correlate isHRE with all HER2 IHC/fluorescence ISH (FISH) categories in BC. DESIGN.— Formalin-fixed, paraffin-embedded tissue sections from 259 BCs, covering all IHC/FISH categories, were analyzed for isHRE by RNAscope. RESULTS.— We validated HER2 RNAscope scoring as a semiquantitative method to evaluate isHRE and demonstrated significantly higher RNAscope scores in IHC 3+ than in IHC 2+ cases, and in IHC 2+ than in IHC 0/1+ cases. Among the 5 IHC 2+/FISH groups, group 1 (G1) cases had the highest scores. The scores in G3 cases were higher than those in G2, but not significantly different from those in G4 and G5. G4 cases had significantly higher scores than those in G2. Higher HER2 copy numbers and HER2:CEP 17 (centromere 17) copy number ratios were significantly correlated with higher isHRE in G1 cases, but not in G2 to G5 cases. RNAscope scores were significantly lower in HER2-negative (IHC 0) than in HER2-low (IHC 2+/FISH- and IHC 1+) BCs but were not different between IHC 0 and 1+ BCs when analyzed separately. CONCLUSIONS.— We demonstrate the HER2 RNA expression status among BCs of various HER2 IHC/FISH categories in tissue. Such information may be relevant for anti-HER2 treatment decisions considering the role of HER2 RNA expression in predicting anti-HER2 therapeutic efficacy.
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Affiliation(s)
- Yu-Fen Tseng
- From the Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan (Tseng, Lee, Hu, Zhang, Hung, Lien)
| | - Yu-Chia Li
- the Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan (Li, Lien)
| | - Yi-Hsuan Lee
- From the Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan (Tseng, Lee, Hu, Zhang, Hung, Lien)
| | - Hsiang-We Hu
- From the Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan (Tseng, Lee, Hu, Zhang, Hung, Lien)
| | - Man-San Zhang
- From the Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan (Tseng, Lee, Hu, Zhang, Hung, Lien)
| | - Tze-Chun Hung
- From the Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan (Tseng, Lee, Hu, Zhang, Hung, Lien)
| | - Huang-Chun Lien
- the Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan (Li, Lien)
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Ivanova M, Porta FM, D'Ercole M, Pescia C, Sajjadi E, Cursano G, De Camilli E, Pala O, Mazzarol G, Venetis K, Guerini-Rocco E, Curigliano G, Viale G, Fusco N. Standardized pathology report for HER2 testing in compliance with 2023 ASCO/CAP updates and 2023 ESMO consensus statements on HER2-low breast cancer. Virchows Arch 2024; 484:3-14. [PMID: 37770765 PMCID: PMC10791807 DOI: 10.1007/s00428-023-03656-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/03/2023] [Accepted: 09/13/2023] [Indexed: 09/30/2023]
Abstract
Since the release of the DESTINY-Breast04 (DB-04) trial findings in June 2022, the field of pathology has seen a renaissance of HER2 as a predictive biomarker in breast cancer. The trial focused on patients with metastatic breast cancer who were classified as "HER2-low," i.e., those with immunohistochemistry (IHC) HER2 1 + or 2 + and negative in situ hybridization (ISH) results. The study revealed that treating these patients with trastuzumab deruxtecan (T-DXd) instead of the oncologist's chosen chemotherapy led to outstanding improvements in survival. This has challenged the existing binary HER2 pathological classification system, which categorized tumors as either positive (overexpression/amplification) or negative, as per the ASCO/CAP 2018 guideline reaffirmed by ASCO/CAP 2023 guideline update. Given that DB-04 excluded patients with HER2 IHC score 0 status, the results of the ongoing DB-06 trial may shed further light on the potential benefits of T-DXd therapy for these patients. Roughly half of all breast cancers are estimated to belong to the HER2-low category, which does not represent a distinct or specific subtype of cancer. Instead, it encompasses a diverse group of tumors that exhibit clinical, morphological, immunohistochemical, and molecular variations. However, HER2-low offers a distinctive biomarker status that identifies a specific therapeutic regimen (i.e., T-DXd) linked to a favorable prognosis in breast cancer. This unique association emphasizes the importance of accurately identifying these tumors. Differentiating between a HER2 IHC score 0 and score 1 + has not been clinically significant until now. To ensure accurate classification and avoid misdiagnosis, it is necessary to adopt standardized procedures, guidelines, and specialized training for pathologists in interpreting HER2 expression in the lower spectrum. Additionally, the utilization of artificial intelligence holds promise in supporting this endeavor. Here, we address the current state of the art and unresolved issues in assessing HER2-low status, with a particular emphasis on the score 0. We explore the dilemma surrounding the exclusion of HER2-zero patients from potentially beneficial therapy based on traditional HER2 testing. Additionally, we examine the clinical context, considering that DB-04 primarily involved heavily pretreated late-stage metastatic breast cancers. We also delve into emerging evidence suggesting that extrapolating HER2-low status from the original diagnosis may lead to misleading results. Finally, we provide recommendations for conducting high-quality testing and propose a standardized pathology report in compliance with 2023 ASCO/CAP updates and 2023 ESMO consensus statements on HER2-low breast cancer.
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Affiliation(s)
- Mariia Ivanova
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Francesca Maria Porta
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Marianna D'Ercole
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Carlo Pescia
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Elham Sajjadi
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
| | - Giulia Cursano
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Elisa De Camilli
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Oriana Pala
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Giovanni Mazzarol
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Konstantinos Venetis
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Elena Guerini-Rocco
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
| | - Giuseppe Curigliano
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Division of New Drugs and Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Giuseppe Viale
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Nicola Fusco
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy.
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy.
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Alinger-Scharinger B, Kronberger C, Hutarew G, Hitzl W, Reitsamer R, Frederike KF, Hager M, Fischer T, Sotlar K, Jaksch-Bogensperger H. HER2 copy number determination in breast cancer using the highly sensitive droplet digital PCR method. Virchows Arch 2023:10.1007/s00428-023-03706-3. [PMID: 37996704 DOI: 10.1007/s00428-023-03706-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023]
Abstract
Human epidermal growth factor receptor 2 (HER)-positive breast cancer (BC) is characterized by an aggressive clinical course. In the case of HER2 overexpression/amplification, patients benefit from HER2-targeting therapies. Standardized diagnostic HER2 assessment includes immunohistochemistry (IHC) and/or in situ hybridization (ISH). The aim of this study was to compare this "gold standard" with the Droplet Digital™ polymerase chain reaction (ddPCR), a method that allows sensitive and precise detection of copy number variations (CNV) in FFPE (formalin-fixed, paraffin-embedded) DNA samples. Partitioning of the PCR reaction into 20,000 droplets enables a precise quantitative "CN" discrimination also in heterogeneous samples. FFPE breast cancer samples (n = 170) with routinely assessed HER2 status by IHC/ISH were retrospectively analyzed using the ddPCR CNV ERBB2 assay. Comparison of HER2 status assessment by the two methods revealed concordant results in 92.9% (158/170) of the cases. Discrepant cases were verified and interpreted. For ddPCR, a cut off value of 3 HER2 copies was set to distinguish between HER2-negative and HER2-positive BC. Results obtained with the ddPCR CNV ERBB2 assay were consistent and reproducible, and serial dilutions demonstrated a high stability and sensitivity of the method. The ddPCR CNV ERBB2 assay may be a specific and convenient tool to quantify HER2 copy numbers in BC samples. In our study, this method showed high reproducibility in accuracy of HER2 assessment compared to IHC/ISH analysis.
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Affiliation(s)
- Beate Alinger-Scharinger
- Department of Pathology, University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria.
| | - Cornelia Kronberger
- Department of Pathology, University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Georg Hutarew
- Department of Pathology, University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Wolfgang Hitzl
- Research Management and Technology Transfer, Paracelsus Medical University Salzburg, Strubergasse 16, 5020, Salzburg, Austria
- Department of Ophthalmology and Optometry, Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
- Research Program Experimental Ophthalmology and Glaucoma Research, Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Roland Reitsamer
- Department of Obstetrics and Gynaecology, Clinical Research Center Salzburg (CRCS), University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Klaassen-Federspiel Frederike
- Department of Obstetrics and Gynaecology, Clinical Research Center Salzburg (CRCS), University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Martina Hager
- Department of Pathology, University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Thorsten Fischer
- Department of Obstetrics and Gynaecology, Clinical Research Center Salzburg (CRCS), University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Karl Sotlar
- Department of Pathology, University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Heidi Jaksch-Bogensperger
- Department of Obstetrics and Gynaecology, Clinical Research Center Salzburg (CRCS), University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
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Balestra A, Larsimont D, Noël JC. HER2 Amplification in p53-Mutated Endometrial Carcinomas. Cancers (Basel) 2023; 15:cancers15051435. [PMID: 36900227 PMCID: PMC10001224 DOI: 10.3390/cancers15051435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/04/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
p53-mutated endometrial carcinomas tend to recur and develop distant metastases. Therefore, the detection of new potential therapeutic targets such as HER2 is particularly interesting. In this retrospective study, which considered over 118 endometrial carcinomas, the p53 mutation was detected in 29.6% of cases. In these cases, the HER2 protein profile was studied via immunohistochemistry, and an overexpression of HER2 protein (++ or +++) was noted in 31.4%. The CISH technique was used in these cases to determine if gene amplification was present. In 18% of cases, the technique was not conclusive. Amplification of the HER2 gene was observed in 36.3% of cases and 36.3% of cases showed a polysomal-like aneusomy for centromere 17. Amplification was found in serous carcinomas, clear cell carcinomas and carcinosarcomas, highlighting the future potentiality of HER2-targeted therapies in these variants of aggressive carcinomas.
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Affiliation(s)
- Ambre Balestra
- Department of Gynecology, ULB-Erasme, HUB, 808 Route de Lennik, 1070 Bruxelles, Belgium
- Correspondence: ; Tel.: +32-478966216
| | - Denis Larsimont
- Department of Pathology, Institut Bordet, ULB-Erasme, HUB, 808 Route de Lennik, 1070 Bruxelles, Belgium
| | - Jean-Christophe Noël
- Department of Pathology, Institut Bordet, ULB-Erasme, HUB, 808 Route de Lennik, 1070 Bruxelles, Belgium
- CUREPATH, Rue de Borfilet, 12A, 6040 Jumet, Belgium
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Validation of HER2 Status in Whole Genome Sequencing Data of Breast Cancers with the Ploidy-Corrected Copy Number Approach. Mol Diagn Ther 2021; 26:105-116. [PMID: 34932189 PMCID: PMC8766398 DOI: 10.1007/s40291-021-00571-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2021] [Indexed: 11/02/2022]
Abstract
BACKGROUND AND OBJECTIVE Human epidermal growth factor receptor 2 (HER2) protein overexpression is one of the most significant biomarkers for breast cancer diagnostics, treatment prediction, and prognostics. The high accessibility of HER2 inhibitors in routine clinical practice directly translates into the diagnostic need for precise and robust marker identification. Even though multigene next-generation sequencing methodologies have slowly taken over the field of single-biomarker molecular tests, the copy number alterations such as amplification of the HER2-coding ERBB2 gene are hard to validate on next-generation sequencing platforms as they are characterized by chromosomal structural heterogeneity, polysomy, and genomic context of ploidy. In our study, we tested the approach of using whole genome sequencing instead of next-generation sequencing panels to determine HER2 status in the clinical set-up. METHODS We used a large dataset of 876 patients with breast cancer whole genomes with curated clinical data and an additional set of 551 patients' external genomic data. We used the decision-tree-based algorithm for optimization of the diagnostic tool for HER2 status assessment by whole genome sequencing. RESULTS The most efficient approach to assess HER2 status in whole genome sequencing data was the ploidy-corrected copy number, utilizing ERBB2 copy number and mean tumor ploidy. The classifier achieved sensitivity of 91.18% and specificity of 98.69% on the internal validation dataset and 89.86% and 96.06% on the external data, which is similar to other next-generation sequencing methods, currently tested in the clinic. CONCLUSIONS We provide evidence that the HER2 status may be reliably determined by whole genome sequencing and is applicable across different laboratory protocols and pipelines. We suggest using the ploidy-corrected copy number for diagnostic purposes.
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