A Novel Algorithm for Detecting Microsatellite Instability Based on Next-Generation Sequencing Data.

ABSTRACT:

Objectives

Microsatellite instability (MSI) is the condition of genetic hypermutability caused by spontaneous acquisition or loss of nucleotides during the DNA replication. MSI has been discovered to be a useful immunotherapy biomarker clinically. The main DNA-based method for MSI detection is polymerase chain reaction (PCR) amplification and fragment length analysis, which are costly and laborious. Thus, we developed a novel method to detect MSI based on next-generation sequencing (NGS) data.

Methods

We chose six markers of MSI. After alignment and reads counting, a histogram was plotted showing the counts of different lengths for each marker. We then designed an algorithm to discover peaks in the generated histograms so that the peak numbers discovered in NGS data resemble

SUBMITTER: Li S 

PROVIDER: S-EPMC9280483 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature