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

5871 - Tumor mutation burden assessment on FFPE samples using a targeted next-generation sequencing assay

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

Topics

Targeted Therapy

Presenters

Ruchi Chaudhary

Citation

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

Authors

R. Chaudhary1, D. Cyanam2, V. Mittal3, W. Tom4, J. Au-Young4, C. Allen5, S. Sadis3, F. Hyland4

Author affiliations

  • 1 Clinical Next Generation Sequencing, Thermo Fisher Scientific, 94080 - South San Francisco/US
  • 2 Clinical Next-generation Sequencing, Thermo Fisher Scientific, 95051 - Santa Clara/US
  • 3 Clinical Next-generation Sequencing, Thermo Fisher Scientific, 48104 - Ann Arbor/US
  • 4 Clinical Next-generation Sequencing, Thermo Fisher Scientific, 94080 - South San Francisco/US
  • 5 Clinical Next-generation Sequencing, Thermo Fisher Scientific, Liverpool/GB
More

Resources

Abstract 5871

Background

Tumor mutation burden (TMB) predicts durable benefit from immune checkpoint blockade in several cancer types. We demonstrate the ability of a targeted panel with fast turn-around time and low input needs to estimate TMB from research samples.

Methods

We developed a single sample analysis workflow to estimate mutation burden (TMB; nonsynonymous mutations/Mb) from FFPE and fresh frozen tumor research samples. The assay utilizes a PCR-based targeted panel that covers 409 genes and 1.7 Mb of genomic regions. The workflow requires only 10 ng of input DNA and enables a 2.5-day turn-around time from sample to the final report. Sequencing is performed on high throughput semiconductor sequencing platform to achieve sufficient depth (∼500x coverage) and accuracy. The workflow is tumor sample only, with no matched normal sample required; germ-line variants, along with background noise, are removed through filters based on population databases. The assay is research use only, not for diagnostic procedures.

Results

A comparison with whole exome sequencing (WES) on 12 FFPE tumors, where WES was performed on tumors and their matched normal using Agilent’s exome enrichment kit (∼150x coverage for tumor; ∼100x coverage for normal) on illumina platform and our assay ran on tumors only, showed high correlation (r2=0.83) between TMB estimates by our assay with that from WES. To assess reproducibility, we compared raw somatic mutations/Mb in library replicates for a cohort of 21 FFPE research samples (19 CRC, 2 Melanoma) and observed high correlation (r2=0.97). Our pipeline identifies mutation signatures consistent with specific mechanisms such as UV and tobacco damage, as well as substitutions from FFPE processing.

Conclusions

A simple workflow has been developed on the Ion Torrent sequencing platform with an AmpliSeq panel to estimate TMB from FFPE and fresh frozen tumor research samples. This solution will advance research in immuno-oncology.

Clinical trial identification

Legal entity responsible for the study

Thermo Fisher Scientific.

Funding

Thermo Fisher Scientific.

Editorial Acknowledgement

Disclosure

R. Chaudhary, D. Cyanam, V. Mittal, W. Tom, J. Au-Young, C. Allen, S. Sadis, F. Hyland: Employment: Thermo Fisher Scientific.

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.