N51: A Novel Tool For Quantitative Analysis Of Microsatellite Mutations And Frameshift Neoantigens

A. Ballhausen1, M. Przybilla2, M. Jendrusch2, S. Krausert2, J. Janikovits2, A. Ahadova2, D. Heid2, S. Kalteis2, E. Pfaffendorf2, J. Gebert2, J. Krzykalla3, A. Benner3, M. von Knebel Doeberitz2, M. Kloor2

1 – Department of Applied Tumor Biology, University Hospital Heidelberg. 2 – University Hospital Heidelberg. 3 – German Cancer Research Center.


Aim: Lynch syndrome cancers are caused by DNA mismatch repair (MMR) deficiency. MMR deficiency leads to microsatellite instability (MSI) and to a high mutational load. Insertion/deletion mutations (indels) of coding microsatellites are drivers of MSI cancer development and responsible for the accumulation of immunogenic frameshift neoantigens. Next-generation sequencing has a limited sensitivity for detecting such indels. We have developed a novel tool to provide a high-resolution map of the MSI cancer mutation and neoantigen landscape.

Method: The ‘qMSI’ algorithm processes fragment length analysis data, removing stutter band artifacts using a linear matrix. QMSI allows the quantification of the true allele frequency of mutations and the distinction of different mutation types that give rise to distinct frameshift neoantigens.

Results: Using qMSI for 40 target genes in MSI colorectal cancers (n=139) we demonstrate that most indels in MSI cancer are single-nucleotide deletions (77%) followed by two-nucleotide deletions and single-nucleotide insertions (21%). Neoantigen-inducing mutations were surprisingly similar across different MSI cancers.

Conclusion: The qMSI algorithm is a powerful tool to identify driver genes and mutational neoantigens in MSI cancer. The identification of shared, recurrent neoantigen-inducing mutations indicates that a vaccine for tumor prevention in Lynch syndrome is highly promising.