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The ELSA-seq Assay Provides Early Detection and Localisation Information in Multiple Cancers

The non-invasive ELSA-seq blood-based methylation sequencing assay demonstrated sensitivity and specificity
20 Nov 2020
Diagnosis, Imaging and Staging;  Personalised medicine

The ELSA-seq assay was able to detect diverse cancer types at early stages with high specificity and to provide information regarding the tissue of origin, according to findings presented at the ESMO Asia Virtual Congress 2020, held from 20 to 22 November 2020.

Qiang Gao of the Liver Cancer Institute, Zhongshan Hospital, Fudan University in Shanghai, China discussed the underlying rationale for the prospective, multicentre, longitudinal PREDICT study (NCT04383353), which aimed to identify multiple cancers non-invasively at early stages. According to Professor Gao, early detection of cancer offers clinical benefits, particularly for cancer types that do not have effective screening methods.

He further explained that a pilot project, the THUNDER (THe UNintrusive Detection of Early-stage canceR) study was designed to develop and validate ELSA-seq, a sensitive targeted methylation sequencing assay that detects epigenetic alterations from circulating cell-free DNA.

He presented findings from the second THUNDER substudy (THUNDER-II) that focused on detecting malignancies in the liver, colon/rectum, oesophagus, pancreas, lung, and ovary.

The THUNDER-II substudy was composed of four independent steps: marker discovery, model training, validation, and single-blind test. The investigators combined data generated in-house and from public sources to design a targeted methylation panel.

The substudy analyzed 625 patients and 483 non-cancer controls who were categorised into a training set comprising 274 cancer patients and 195 non-cancer controls or an independent validation set with 351 cancer and 288 non-cancer participants.

The assay shows promise as a multi-cancer detection tool

The cancer patients and non-cancer controls were generally matched with respect to age, gender, and smoking status.

Among the cancer patients, 79.5% of patients had been diagnosed with cancer at early stages (I-III).

Regarding the assay, at 99.5% training specificity (95% confidence interval [CI] 96.7-100), the cross-validated sensitivity was 79.9% (95% CI 74.6-84.4). These results were consistent in the validation set, which demonstrated 98.3% specificity (95% CI 95.8-99.4) and 80.6% (76.0-84.6) sensitivity across disease stages and the diverse cancer types.

In terms of tracking the location of the malignancies, the classifier returned a tissue-of-origin result in 98.6% of cases, and 81.0% (95% CI 77.2-84.3) of these predictions were correct.


Summary of ELSA-seq sensitivities at given specificities (training: 99.5%; validation: 98.3%). A) Sensitivities across different clinical stages; B) Sensitivities across different cancer types.

© Qiang Gao.


According to the authors, 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 information on the tissue of origin, which may provide guidance for subsequent diagnostic work-up. Further independent validation results of the THUNDER-II will be reported in the near future. 

Based on these findings, the authors suggest potential implementation of this sensitive and robust assay as a multi-cancer detection test.

This study was funded by Burning Rock Biotech.


LBA3 – Gao Q, Li B, Cai S, et al. Early detection and localization of multiple cancers using a blood-based methylation assay (ELSA-seq). ESMO Asia Virtual Congress 2020 (20-22 November).

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