Oops, you're using an old version of your browser so some of the features on this page may not be displaying properly.

MINIMAL Requirements: Google Chrome 24+Mozilla Firefox 20+Internet Explorer 11Opera 15–18Apple Safari 7SeaMonkey 2.15-2.23

Poster display session: Biomarkers, Gynaecological cancers, Haematological malignancies, Immunotherapy of cancer, New diagnostic tools, NSCLC - early stage, locally advanced & metastatic, SCLC, Thoracic malignancies, Translational research

3748 - Accurate measurement of tumor mutation burden in liquid biopsy (bTMB) using a 500 gene panel

Date

20 Oct 2018

Session

Poster display session: Biomarkers, Gynaecological cancers, Haematological malignancies, Immunotherapy of cancer, New diagnostic tools, NSCLC - early stage, locally advanced & metastatic, SCLC, Thoracic malignancies, Translational research

Presenters

Tingting Jiang

Citation

Annals of Oncology (2018) 29 (suppl_8): viii14-viii57. 10.1093/annonc/mdy269

Authors

T. Jiang, S. Zhang, A. Jager, S. Katz, J. Lococo, P. Le, B. Andrian, C. Zhao, D. Baker, T. Pawlowski, S. Bilke

Author affiliations

  • Clinical Genomics, Illumina, Inc, 92122 - San diego/US
More

Resources

Abstract 3748

Background

Tumor mutation burden (TMB) has been shown as a new predictive biomarker for immune checkpoint inhibitor in various cancer types. It is typically measured by processing tumor tissue with substantial input which limits its clinical utility in patients with metastatic or unresectable disease. Meanwhile, there is increasing interest in circulating tumor DNA (ctDNA) that act as a noninvasive real-time biomarker for cancer patients. Therefore, here we develop a new next generation sequencing assay that can identify patients with sufficient tumor fraction in plasma and accurately measures the TMB from blood (bTMB).

Methods

Cell free DNA (cfDNA) was extracted from plasma across four original tissue types by different tumor stages. CfDNA Assay was performed with unique molecular identifier (UMI) , sequenced on the Illumina® platforms and analyzed using an internal pipeline for variants down to 0.4%. By integrating the fragment size distribution and the clonal mutation frequency, we were able to estimate the tumor fraction per plasma sample. A bTMB score was also derived using all the coding variants on a 1.3M panel across 500+ genes. The matched TMB score is derived by the same assay using FFPE tissue.

Results

Our assay has generated sufficient results from 1-4ml plasma for variant detection down to 0.4%. Across four tissue types by various cancer stages, our assay and pipeline yield a variant concordance of 70% between cfDNA and FFPE. Majority of mutations only found in plasma may be associated with clonal hematopoiesis in genes such as TET2, DMBT3A and etc. By combining fragment size distribution and driver mutation frequency, we were able to estimate tumor fraction in plasma. Tumor fraction in plasma is significantly associated with tumor stage that >50% of metastatic cancers and > 25% early stage lung cancers contain high tumor fraction. In patients with at least 1% tumor content, there is high correlation between bTMB measured by plasma and TMB measured by FFPE (R2=0.92).

Conclusions

We have developed a ctDNA assay to detect somatic variants and determine bTMB with high accuracy and precision with input as low as 10 ng of cfDNA. Our assay yield accurate measurement of TMB compared to tissue biopsy.

Clinical trial identification

Legal entity responsible for the study

Illumina, Inc.

Funding

Has not received any funding.

Editorial Acknowledgement

Disclosure

T. Jiang, S. Zhang, A. Jager, S. Katz, J. Lococo, P. Le, B. Andrian, C. Zhao, D. Baker, T. Pawlowski, S. Bilke: Employee and shareholder: Illumina, Inc.

This site uses cookies. Some of these cookies are essential, while others help us improve your experience by providing insights into how the site is being used.

For more detailed information on the cookies we use, please check our Privacy Policy.

Customise settings
  • Necessary cookies enable core functionality. The website cannot function properly without these cookies, and you can only disable them by changing your browser preferences.