Counting Unique Molecular IdentifiersUsing PCR-branching Models
Typ
Examensarbete för masterexamen
Program
Publicerad
2022
Författare
Zhan, Hongyi
Gu, Yizhe
Modellbyggare
Tidskriftstitel
ISSN
Volymtitel
Utgivare
Sammanfattning
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.
Beskrivning
Ämne/nyckelord
DNA sequencing, Polymerase Chain Reaction(PCR), Unique Molecular Identifiers(UMI), Size-dependent branching