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Precision Medicine and Imaging

Development and Validation of a Next-Generation Sequencing–Based Multigene Assay to Predict the Prognosis of Estrogen Receptor–Positive, HER2-Negative Breast Cancer

Han-Byoel Lee, Sae Byul Lee, Minsu Kim, Sunyoung Kwon, Jeonghee Jo, Jinkyoung Kim, Hee Jin Lee, Han-Suk Ryu, Jong Won Lee, Chungyeul Kim, Jaehwan Jeong, Hyoki Kim, Dong-Young Noh, In-Ae Park, Sei-Hyun Ahn, Sun Kim, Sungroh Yoon, Aeree Kim and Wonshik Han
Han-Byoel Lee
1Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea.
2Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.
3Cancer Research Institute, Seoul National University, Seoul, Republic of Korea.
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  • ORCID record for Han-Byoel Lee
Sae Byul Lee
4Department of Surgery, Asan Medical Center, Seoul, Republic of Korea.
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Minsu Kim
5Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea.
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Sunyoung Kwon
6Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea.
7School of Biomedical Convergence Engineering, College of Information and Biomedical Engineering, Pusan National University, Yangsan, Republic of Korea.
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Jeonghee Jo
8Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
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Jinkyoung Kim
9Department of Pathology, Korea University Guro Hospital, Seoul, Republic of Korea.
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Hee Jin Lee
10Department of Pathology, Asan Medical Center, Seoul, Republic of Korea.
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Han-Suk Ryu
11Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea.
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Jong Won Lee
4Department of Surgery, Asan Medical Center, Seoul, Republic of Korea.
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Chungyeul Kim
9Department of Pathology, Korea University Guro Hospital, Seoul, Republic of Korea.
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Jaehwan Jeong
12Celemics Inc., Seoul, Republic of Korea.
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Hyoki Kim
12Celemics Inc., Seoul, Republic of Korea.
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Dong-Young Noh
1Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea.
3Cancer Research Institute, Seoul National University, Seoul, Republic of Korea.
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In-Ae Park
11Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea.
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Sei-Hyun Ahn
4Department of Surgery, Asan Medical Center, Seoul, Republic of Korea.
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Sun Kim
5Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea.
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Sungroh Yoon
6Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea.
8Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
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Aeree Kim
9Department of Pathology, Korea University Guro Hospital, Seoul, Republic of Korea.
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Wonshik Han
1Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea.
2Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.
3Cancer Research Institute, Seoul National University, Seoul, Republic of Korea.
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  • For correspondence: hanw@snu.ac.kr
DOI: 10.1158/1078-0432.CCR-20-2107 Published December 2020
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Abstract

Purpose: Multigene assays provide useful prognostic information regarding hormone receptor (HR)-positive breast cancer. Next-generation sequencing (NGS)-based platforms have numerous advantages including reproducibility and adaptability in local laboratories. This study aimed to develop and validate an NGS-based multigene assay to predict the distant recurrence risk.

Experimental Design: In total, 179 genes including 30 reference genes highly correlated with the 21-gene recurrence score (RS) algorithm were selected from public databases. Targeted RNA-sequencing was performed using 250 and 93 archived breast cancer samples with a known RS in the training and verification sets, respectively, to develop the algorithm and NGS–Prognostic Score (NGS-PS). The assay was validated in 413 independent samples with long-term follow-up data on distant metastasis.

Results: In the verification set, the NGS-PS and 21-gene RS displayed 91.4% concurrence (85/93 samples). In the validation cohort of 413 samples, area under the receiver operating characteristic curve plotted using NGS-PS values classified for distant recurrence was 0.76. The best NGS-PS cut-off value predicting distant metastasis was 20. Furthermore, 269 and 144 patients were classified as low- and high-risk patients in accordance with the cut-off. Five- and 10-year estimates of distant metastasis–free survival (DMFS) for low- versus high-risk groups were 97.0% versus 77.8% and 93.2% versus 64.4%, respectively. The age-related HR for distant recurrence without chemotherapy was 9.73 (95% CI, 3.59–26.40) and 3.19 (95% CI, 1.40–7.29) for patients aged ≤50 and >50 years, respectively.

Conclusions: The newly developed and validated NGS-based multigene assay can predict the distant recurrence risk in ER-positive, HER2-negative breast cancer.

Footnotes

  • Note: Supplementary data for this article are available at Clinical Cancer Research Online (http://clincancerres.aacrjournals.org/).

  • Clin Cancer Res 2020;26:6513–22

  • Received May 30, 2020.
  • Revision received August 26, 2020.
  • Accepted September 28, 2020.
  • Published first October 7, 2020.
  • ©2020 American Association for Cancer Research.
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Clinical Cancer Research: 26 (24)
December 2020
Volume 26, Issue 24
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Development and Validation of a Next-Generation Sequencing–Based Multigene Assay to Predict the Prognosis of Estrogen Receptor–Positive, HER2-Negative Breast Cancer
Han-Byoel Lee, Sae Byul Lee, Minsu Kim, Sunyoung Kwon, Jeonghee Jo, Jinkyoung Kim, Hee Jin Lee, Han-Suk Ryu, Jong Won Lee, Chungyeul Kim, Jaehwan Jeong, Hyoki Kim, Dong-Young Noh, In-Ae Park, Sei-Hyun Ahn, Sun Kim, Sungroh Yoon, Aeree Kim and Wonshik Han
Clin Cancer Res December 15 2020 (26) (24) 6513-6522; DOI: 10.1158/1078-0432.CCR-20-2107

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Development and Validation of a Next-Generation Sequencing–Based Multigene Assay to Predict the Prognosis of Estrogen Receptor–Positive, HER2-Negative Breast Cancer
Han-Byoel Lee, Sae Byul Lee, Minsu Kim, Sunyoung Kwon, Jeonghee Jo, Jinkyoung Kim, Hee Jin Lee, Han-Suk Ryu, Jong Won Lee, Chungyeul Kim, Jaehwan Jeong, Hyoki Kim, Dong-Young Noh, In-Ae Park, Sei-Hyun Ahn, Sun Kim, Sungroh Yoon, Aeree Kim and Wonshik Han
Clin Cancer Res December 15 2020 (26) (24) 6513-6522; DOI: 10.1158/1078-0432.CCR-20-2107
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Clinical Cancer Research
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