# Deep Learning based Prediction of MSI using MMR Markers in Colorectal Cancer

arXiv: https://arxiv.org/abs/2203.00449 · HTML: https://mlsanity.com/paper/2203.00449/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 6 of its 25 references that are in the map.
- First posted on arXiv 24 Feb 2022.

## Builds on (most cited first, 6 of 6)

- [HoVer-Net: Simultaneous Segmentation and Classification of Nuclei in Multi-Tissue Histology Images](https://mlsanity.com/paper/1812.06499/) (2018)
- [MILD-Net: Minimal Information Loss Dilated Network for Gland Instance Segmentation in Colon Histology Images](https://mlsanity.com/paper/1806.01963/) (2018)
- [Context-Aware Convolutional Neural Network for Grading of Colorectal Cancer Histology Images](https://mlsanity.com/paper/1907.09478/) (2019)
- [Understanding the Impact of Label Granularity on CNN-based Image Classification](https://mlsanity.com/paper/1901.07012/) (2019)
- [Deep Feature based Cross-slide Registration](https://mlsanity.com/paper/2202.09971/) (2022)
- [An End-to-End Deep Learning Histochemical Scoring System for Breast Cancer Tissue Microarray](https://mlsanity.com/paper/1801.06288/) (2018)

## Abstract (arXiv)

The accurate diagnosis and molecular profiling of colorectal cancers are critical for planning the best treatment options for patients. Microsatellite instability (MSI) or mismatch repair (MMR) status plays a vital role in appropriate treatment selection, has prognostic implications and is used to investigate the possibility of patients having underlying genetic disorders (Lynch syndrome). NICE recommends that all CRC patients should be offered MMR/MSI testing. Immunohistochemistry is commonly used to assess MMR status with subsequent molecular testing performed as required. This incurs significant extra costs and requires additional resources. The introduction of automated methods that can predict MSI or MMR status from a target image could substantially reduce the cost associated with MMR testing. Unlike previous studies on MSI prediction involving training a CNN using coarse labels (MSI vs Microsatellite Stable (MSS)), we have utilised fine-grain MMR labels for training purposes. In this paper, we present our work on predicting MSI status in a two-stage process using a single target slide either stained with CK8/18 or H&E. First, we trained a multi-headed convolutional neural network model where each head was responsible for predicting one of the MMR protein expressions. To this end, we performed the registration of MMR stained slides to the target slide as a pre-processing step. In the second stage, statistical features computed from the MMR prediction maps were used for the final MSI prediction. Our results demonstrated that MSI classification can be improved by incorporating fine-grained MMR labels in comparison to the previous approaches in which only coarse labels were utilised.