Performance evaluation for rapid detection of pan-cancer microsatellite instability with MANTIS

Abstract

In current clinical practice, microsatellite instability (MSI) and mismatch repair deficiency detection is performed with MSI-PCR and immunohistochemistry. Recent research has produced several computational tools for MSI detection with next-generation sequencing (NGS) data; however a comprehensive analysis of computational methods has not yet been performed. In this study, we introduce a new MSI detection tool, MANTIS, and demonstrate its favorable performance compared to the previously published tools mSINGS and MSISensor. We evaluated 458 normal-tumor sample pairs across six cancer subtypes, testing classification performance on variable numbers of target loci ranging from 10 to 2539. All three computational methods were found to be accurate, with MANTIS exhibiting the highest accuracy with 98.91% of samples from all six diseases classified correctly. MANTIS displayed superior performance among the three tools, having the highest overall sensitivity (MANTIS 97.18%, MSISensor 96.48%, mSINGS 76.06%) and specificity (MANTIS 99.68%, mSINGS 99.68%, MSISensor 98.73%) across six cancer types, even with loci panels of varying size. Additionally, MANTIS also had the lowest resource consumption (<1% of the space and <7% of the memory required by mSINGS) and fastest running times (49.6% and 8.7% of the running times of MSISensor and mSINGS, respectively). This study highlights the potential utility of MANTIS in classifying samples by MSI-status, allowing its incorporation into existing NGS pipelines.

Accurate Pan-Cancer Molecular Diagnosis of Microsatellite Instability by Single-Molecule Molecular Inversion Probe Capture and High-Throughput Sequencing

“…Notably, this discordant endometrial tumor was also classified as MSS by MSI-PCR, and the consistency between these two assays raises the possibility that the tumor’s molecular signature may legitimately reflect a mutational process that is distinct from MSI (10,23). Regardless of this possibility, our findings reinforce the narrow validity of MSI-PCR only within colorectal cancers (15–17) and demonstrate that informed selection of larger numbers of informative markers by smMIP can recapitulate the pan-cancer performance of exome or genome-scale NGS diagnostic approaches for MSI (10,22,24,25). …”

“…By virtue of their ability to broadly interrogate the genome, these approaches offer substantial advantages over conventional methods in terms of diagnostic accuracy and applicability across cancer types (10,22,24,25). Nevertheless, determination of MSI by NGS currently requires large-scale targeted gene enrichment or exome sequencing data, which is material-limiting for many clinical specimens and results in a high cost of testing.…”

“…Consequently, such diagnostics are typically reserved for late-stage or widely metastatic disease (26). Moreover, most analytic approaches require sequence data from matched normal material (23,24), increasing costs and workflow demands. NGS methods for determining MSI are consequently impractical as primary screening tests and are presently provided as value-added information for larger, panel-based sequencing tests when they are applied to advanced or otherwise recalcitrant malignancies.…”

Landscape of Microsatellite Instability Across 39 Cancer Types

“…MSI analysis with MANTIS (version 1.0.3; commit #942061f) was performed as previously described 17 for all cases by using an average distance threshold of 0.4 to differentiate MSI-H from MSS tumors. Coordinates for 2,539 microsatellite loci within or near the exome—originally introduced by Salipante et al 15 and used by later studies 17 — were converted from hg19 to hg38 by using Lift- Over.…”

“…Examples of such software include mSINGS, 15 MSISensor, 16 and MANTIS. 17 A recent study by our group 17 demonstrated that MANTIS achieves high sensitivity (97%) and specificity (99%) across six cancer types—tested using samples with known MSI status by MSIPCR—and provides stable performance with varying numbers of microsatellite loci. Because of this, MANTIS is particularly well suited for application to a wider variety of cancer types.…”