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Mini oral session on Developmental and precision medicine

LBA3 - Early detection and localization of multiple cancers using a blood-based methylation assay (ELSA-seq)

Date

20 Nov 2020

Session

Mini oral session on Developmental and precision medicine

Presenters

Qiang Gao

Citation

Annals of Oncology (2020) 31 (suppl_6): S1358-S1365. 10.1016/annonc/annonc362

Authors

Q. Gao1, B. Li2, S. Cai3, J. Xu2, C. Wang2, S. Fang2, F. Qiu2, J. Su2, F. Xu2, X. Wen3, Y. Zhang3, G. Wang3, H. Liu3, Z. Zhang2

Author affiliations

  • 1 Liver Cancer Institute, Zhongshan Hospital, Fudan University, 200032 - Shanghai/CN
  • 2 Research And Development, Burning Rock Biotech, 201112 - Shanghai/CN
  • 3 Medical Affair, Burning Rock Biotech, 201112 - Shanghai/CN
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Resources

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Abstract LBA3

Background

Early detection of cancer can potentially offer clinical benefits, particularly for those without effective screening methods. The PREDICT study (NCT 04383353) is a prospective, multi-center, longitudinal study that aims to identify multiple cancers non-invasively in early stages. As a pilot project, the THUNDER (THe UNintrusive Detection of Early-stage canceR) study is designed for development and validation of ELSA-seq, a sensitive targeted methylation sequencing assay that interrogates epigenetic alterations from circulating cell-free DNA (cfDNA). Herein we report results from the second THUNDER sub study (THUNDER-II), which focused on malignancies developed in liver, colon/rectum, esophagus, pancreas, lung and ovary.

Methods

THUNDER-II comprises four independent steps: marker discovery, model training, validation, and single-blind test. By combining data generated in-house and from public sources, a targeted methylation panel was designed. A total of 625 patients and 483 non-cancer controls were enrolled and divided into a training set (274 cancer and 195 non-cancer) and an independent validation set (351 cancer and 288 non-cancer).

Results

The cancer patients and non-cancer controls were generally comparable with respect to age, gender, and smoking status. Various stages were represented in the cancer group, and 79.5% patients were diagnosed at early stages (I-III). At 99.5% training specificity (95%CI: 96.7-100%), the cross-validated sensitivity was 79.9% (95%CI: 74.6-84.4%). The results were consistent in the validation set, with 98.3% specificity (95%CI: 95.8-99.4%) and 80.6% (76.0-84.6%) sensitivity across stages and cancer types. In terms of tracking diseased organ(s), the classifier returned a tissue-of-origin (TOO) result in 98.6% cases, and 81.0% (95%CI: 77.2-84.3%) of these predictions were correct.

Conclusions

Results from the THUNDER-II study demonstrated that early cancer signals could be identified by ELSA-seq with high specificity. This method also enabled accurate prediction of TOO, offering guidance for subsequent diagnostic work-up. Together these findings highlight the potential implementation of this sensitive and robust assay as a multi-cancer detection test.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

The authors.

Funding

Burning Rock Biotech.

Disclosure

B. Li: Shareholder/Stockholder/Stock options, Full/Part-time employment: Burning Rock Biotech. S. Cai, J. Xu, C. Wang, S. Fang, F. Qiu, J. Su, F. Xu, X. Wen, Y. Zhang, G. Wang: Full/Part-time employment: Burning Rock Biotech. H. Liu, Z. Zhang: Leadership role, Shareholder/Stockholder/Stock options, Full/Part-time employment: Burning Rock Biotech.

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