As part of his Master’s program in Bioinformatics and Systems Biology at the Vrije Universiteit Amsterdam, Tim Mocking performed research at the Pathology department at Cancer Center Amsterdam. Under supervision of Dr. Yongsoo Kim, Tim helped develop a novel algorithm that could generate chromosomal “fingerprints” from DNA information extracted from tumors in patients.
Creating a clear fingerprint based on cancer DNA
”Extracting the chromosomal fingerprint of a tumor is not straightforward. It is rare that a particular tumor can be defined by one exact fingerprint,” Tim Mocking explains. “As tumors develop and grow, there are chromosomal gains or losses of DNA fragments over generations, leading to a heterogeneous collection of DNA fingerprints in practice. In addition, the techniques that are used to construct these fingerprints in the lab introduces all kinds of artifacts and noise, making interpretation more difficult.”
Central to the newly created algorithm ‘CNP-ALIGN’ was the perception that patterns of chromosomal abnormalities in cancer do not entirely occur by chance. In addition, some specific chromosomes have additional copies in more than half of all analyzed tumors, while other chromosomes hardly ever reveal copy number changes.
“It is somewhat similar to identifying a parent and child by recognizing multiple shared features, like bushy eye brows in combination with freckles, rather than just looking at their brown colored hair, which is very common,” says Tim. Therefore, CNP-ALIGN places more focus on chromosomal features that are shared between multiple tumors in one patient, and pays less attention to copy number alterations that are common among all tumors.
Jury recognizes potential
Among several selection criteria, the Master's Thesis Award Jury Report highlighted the anticipated impact of Tim’s work. ”The jury is convinced that Tim’s results are highly promising. The jury therefore not only awards the prize to Tim for his fantastically readable and illustrated thesis, but also to encourage him to keep up the great work.”
Tim Mocking has now embarked on a PhD project in the Department of Hematology at Cancer Center Amsterdam, where he intends to apply computational analysis to uncover clinical meaningful strategies against myeloid malignancies.
For more information, contact Tim Mocking .
Other scientist can access the open-source CNP-ALIGN algorithm here
More information on the 2021 Vrije Universiteit Thesis awards is available here
People involved at Cancer Center Amsterdam:
Tim Mocking
Yongsoo Kim
Bárbara Barbosa
Bauke Ylstra
Text by Henri van de Vrugt