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MGPC-Nantes / MEM

Motivation: Microsatellites are DNA sequences formed by a continuous repetition of patterns from 1 to 6 nucleotides. Deficient mismatch repair system (dMMR) induces a variation in length of microsatellites called microsatellite instability (MSI). However, MSI assessment by Next-Generation Sequencing (NGS) is difficult because replication errors occurring during the amplification steps of the sequencing process themselves induce variation in microsatellite sequence length. Results: The MSI assessment by Expectation-Maximization (MEM) algorithm attempts to closely replicate the reference PCR interpretation method for 5 microsatellites validated by the Bethesda and ESMO international guidelines (BAT-25, BAT-26, NR-21, NR-24, and NR-27). MEM identifies the stable or unstable nature of each microsatellite i- by determining the length distribution of microsatellite sequences from unmapped and quality unfiltered paired-end reads using the Smith-Waterman alignment, and ii- by determining whether the observed distribution is comparable to a reference distribution (stable) or corresponds to a mixture model, i.e. the mixture of several sub-distributions of different mean lengths (unstable) using Expectation-Maximization algorithm.
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Program test example #1

Closed xiaoquexingchen closed 1 year ago

xiaoquexingchen commented 2 years ago

Hello: I was recently reading your article "MEM: An Algorithm for the Reliable Detection of Microsatellite Instability (MSI) on a Small NGS Panel in Colorectal Cancer" and thought it was a good idea. Would like to ask how the program attached to the article should work? Can you give me a test example? Thank you very much! Best Regards！

MGPC-Nantes commented 2 years ago

Hello,

The program is a java plugin for the CLC genomics workbench software (QIAGEN). We have developed this program to meet our needs on this software, but it is not cross-platform. Unfortunately I don't have time to develop a program independent of this software, but I can help you if you want to do it.

Best regards

Dr. Guillaume HERBRETEAU

Biologiste MCU-PH, MD PhD

Laboratoire de biochimie - Plateforme de génétique des cancers

CHU de Nantes - Hôtel-Dieu

Tel : (02400) 84004

De : xiaoquexingchen @.***> Envoyé : samedi 19 février 2022 14:33 À : MGPC-Nantes/MEM Cc : Subscribed Objet : [MGPC-Nantes/MEM] Program test example (Issue #1)

Hello: I was recently reading your article "MEM: An Algorithm for the Reliable Detection of Microsatellite Instability (MSI) on a Small NGS Panel in Colorectal Cancer" and thought it was a good idea. Would like to ask how the program attached to the article should work? Can you give me a test example? Thank you very much! Best Regards!

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