Counting Unique Molecular IdentifiersUsing PCR-branching Models

Abstract

DNA sequencing technology plays an essential role in biomedical research, especially in cancer genetics. However, errors in the sequencing process can confuse the results of detecting the actual variants. In order to distinguish these two mutations, researchers add Unique Molecular Identifiers(UMI), a unique tag sequence to each fragment of the original DNA molecules and do UMI counting on the sequenced molecules. Since the whole sequencing process, including DNA barcoding and amplification, is complex. Many parameters are invisible in actual biological experiments. A DNA barcoding algorithm based on level order traversal and a mathematical model of DNA amplification assuming molecules with memory and based on the growth patterns of population and molecular diversity is introduced, which are the critical steps for simulation. The project aims to obtain simulation results similar to the actual laboratory data by adjusting the model parameters and thereby determining the appropriate parameter values to help biological experiments perform better.