Assessment of Tumor Mutational Burden in Pediatric Tumors by Real-Life Whole-Exome Sequencing and In Silico Simulation of Targeted Gene Panels: How the Choice of Method Could Affect the Clinical Decision?

Hana Noskova; Michal Kyr; Karol Pal; Tomas Merta; Peter Mudry; Kristyna Polaskova; Tina Catela Ivkovic; Sona Adamcova; Tekla Hornakova; Marta Jezova; Leos Kren; Jaroslav Sterba; Ondrej Slaby

doi:10.3390/cancers12010230

Assessment of Tumor Mutational Burden in Pediatric Tumors by Real-Life Whole-Exome Sequencing and In Silico Simulation of Targeted Gene Panels: How the Choice of Method Could Affect the Clinical Decision?

Cancers (Basel). 2020 Jan 17;12(1):230. doi: 10.3390/cancers12010230.

Authors

Hana Noskova^{1

2}, Michal Kyr^{2

3

4}, Karol Pal^{1

5}, Tomas Merta^{2

3

4}, Peter Mudry^{2

3

4}, Kristyna Polaskova^{2

3

4}, Tina Catela Ivkovic¹, Sona Adamcova¹, Tekla Hornakova¹, Marta Jezova⁶, Leos Kren⁶, Jaroslav Sterba^{2

3

4

7}, Ondrej Slaby^{1

3

6}

Affiliations

¹ Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
² Department of Pediatric Oncology, University Hospital Brno, 613 00 Brno, Czech Republic.
³ Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic.
⁴ International Clinical Research Center, St. Anne's University Hospital, 65691 Brno, Czech Republic.
⁵ Department of Hematology, University Hospital Schleswig-Holstein, 24105 Kiel, Germany.
⁶ Department of Pathology, University Hospital Brno, 62500 Brno, Czech Republic.
⁷ Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 60200 Brno, Czech Republic.

Abstract

Background: Tumor mutational burden (TMB) is an emerging genomic biomarker in cancer that has been associated with improved response to immune checkpoint inhibitors (ICIs) in adult cancers. It was described that variability in TMB assessment is introduced by different laboratory techniques and various settings of bioinformatic pipelines. In pediatric oncology, no study has been published describing this variability so far.

Methods: In our study, we performed whole exome sequencing (WES, both germline and somatic) and calculated TMB in 106 patients with high-risk/recurrent pediatric solid tumors of 28 distinct cancer types. Subsequently, we used WES data for TMB calculation using an in silico approach simulating two The Food and Drug Administration (FDA)-approved/authorized comprehensive genomic panels for cancer.

Results: We describe a strong correlation between WES-based and panel-based TMBs; however, we show that this high correlation is significantly affected by inclusion of only a few hypermutated cases. In the series of nine cases, we determined TMB in two sequentially collected tumor tissue specimens and observed an increase in TMB along with tumor progression. Furthermore, we evaluated the extent to which potential ICI indication could be affected by variability in techniques and bioinformatic pipelines used for TMB assessment. We confirmed that this technological variability could significantly affect ICI indication in pediatric cancer patients; however, this significance decreases with the increasing cut-off values.

Conclusions: For the first time in pediatric oncology, we assessed the reliability of TMB estimation across multiple pediatric cancer types using real-life WES and in silico analysis of two major targeted gene panels and confirmed a significant technological variability to be introduced by different laboratory techniques and various settings of bioinformatic pipelines.

Keywords: TMB; gene panel sequencing; immune checkpoint inhibitors; pediatric tumors; tumor mutational burden; whole-exome sequencing.

Abstract

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