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A database to store and annotate Stem cell gEnetic Abnormalities
KTH, School of Computer Science and Communication (CSC).
2014 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

Human pluripotent stem cells (hPSC) are important in medicine due to several of their distinctive features. However, genomic abnormalities are observed in PSC, which arise either during cell culture or during the process of cell reprogramming. These genomic abnormalities are a serious concern for the use of hPSC. To assess the threat of these abnormalities it is essential to distinguish polymorphisms from bona fide mutational events, and to distinguish incidental abnormalities from those that are bona fide altering the biology and/or security of hPSC. An important aspect of PSC genetic abnormalities is that they are often recurrent possibly due to a strong selective advantage in culture for cells. Such selective advantage is reminiscent of precancerous or cancerous lesions and should be avoided. It is therefore mandatory to carefully catalogue all the genomic alterations that are found in hPSC and identify those that are recurrent as well as those that are shared with cancer. With these requirements, I set up SEAdb, a database indexing and annotating hPSC genomic abnormalities. This database has been curated with most of the abnormalities reported in the scientific literature. It integrates a tool to easily focus on hotspots. It also integrates information from databases reporting common polymorphisms and genetic abnormalities implied in cancer.

Place, publisher, year, edition, pages
National Category
Computer Science
URN: urn:nbn:se:kth:diva-153660OAI: diva2:753077
Available from: 2014-11-21 Created: 2014-10-07 Last updated: 2014-11-21Bibliographically approved

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