Abstract 4113
Background
TMB has emerged as a predictive biomarker of response to immune checkpoint inhibitors. CheckMate 227 demonstrated that patients with non-small cell lung cancer (NSCLC) with TMB ≥10 mutations/megabase derived enhanced benefit from first-line treatment with nivolumab + ipilimumab vs chemotherapy (Hellmann et al. NEJM 2018). Standardized approaches for the measurement and reporting of TMB are essential for the real-world implementation of TMB. This study aimed to refine a bioinformatic pipeline for mutation calling and annotation of whole exome sequencing (WES) data for TMB assessment.
Methods
In CheckMate 026, TMB was assessed by WES on formalin-fixed, paraffin-embedded tumor samples and matched blood from 312 patients with NSCLC (Carbone et al. NEJM 2017). Data from each sample were aligned to a reference human genome and somatic mutations were called by comparing matched tumor and blood samples using the TNsnv and Strelka algorithms. The somatic mutations were additionally filtered for germline variants in public databases. TMB scores were compared with data from 710 NSCLC samples in The Cancer Genome Atlas (TCGA) dataset. We examined the concordance of TMB estimates using several mutation filtering schemes, with and without matched germline controls.
Results
TMB scores including synonymous, indel, frameshift, and nonsense mutations (all mutations) were ∼3-fold higher than matched data filtered for missense mutations only, but values were highly correlated (Spearman’s r = 0.99). Scores including missense mutations only were similar to those generated from TCGA, but those including all mutations were on average higher. Using public databases for germline subtraction showed a trend for race-dependent increases in TMB scores.
Conclusions
Standardization of bioinformatic analyses is critical to the clinical implementation of TMB assessment. TMB assessment is sensitive to variations in bioinformatic parameters (eg, which type of mutation to include), which may affect the identification of patients likely to respond to immunotherapy. These results show that data from different pipelines are highly correlated, suggesting that reliable assessment of TMB across different centers and platforms is achievable.
Clinical trial identification
NCT02041533.
Legal entity responsible for the study
Bristol-Myers Squibb.
Funding
Bristol-Myers Squibb.
Editorial Acknowledgement
Medical writing assistance was provided by Stuart Rulten, PhD, of Spark Medica Inc. (US), funded by Bristol-Myers Squibb.
Disclosure
H. Chang, S. Srinivasan, A. Sasson, R. Golhar, D. Greenawalt, J.D. Szustakowski: Employment and stock ownership: Bristol-Myers Squibb. S. Kirov: Stock ownership and compensation: Bristol-Myers Squibb.
Resources from the same session
5877 - TCR beta chain convergence defines the tumor infiltrating T cell repertoire of melanoma and non-small cell lung carcinoma.
Presenter: Timothy Looney
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
Resources:
Abstract
3212 - PI3K inhibition and modulation of immune and tumor microenvironment markers by copanlisib in patients with non-Hodgkin's lymphoma or advanced solid tumors
Presenter: Ahmad Awada
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
Resources:
Abstract
3574 - Pan-squamous genomic profiling stratified by anatomic tumor site and viral association
Presenter: Meagan Montesion
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
Resources:
Abstract
4468 - Prediction of primary resistance to anti-PD1 therapy (APD1) in 2nd line NSCLC
Presenter: Egbert Smit
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
Resources:
Abstract
4570 - Immunomodulatory germline variation impacts the development of multiple primary melanoma (MPM).
Presenter: Robert Ferguson
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
Resources:
Abstract
1169 - Leukocyte telomere length and recurrence risk after EGFR-TKIs therapy in patients with advanced lung adenocarcinoma
Presenter: Ming Yang
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
Resources:
Abstract
1707 - Gene embedding: a novel machine learning approach to identify gene candidates related to immunotherapy responsiveness
Presenter: Chi Tung Choy
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
Resources:
Abstract
2123 - Common and rare DPYD variants are predictive for 5FU/capecitabine (5FU) toxicity: The MRC COIN and COIN-B trials
Presenter: Ayman Madi
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
Resources:
Abstract
5671 - The landscape of NTRK fusions in Chinese solid tumor patients
Presenter: Qi Ling
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
Resources:
Abstract
4679 - Correlative analyses of serum biomarkers and efficacy outcomes in the randomized phase 2 trial of lenvatinib (LEN), everolimus (EVE), or LEN+EVE in patients with metastatic renal cell carcinoma
Presenter: Chung-Han Lee
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
Resources:
Abstract