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CytoGPS: A Web-Enabled Karyotype Analysis Tool for Cytogenetics

By Zachary B. Abrams, Lin Zhang, Lynne V Abruzzo, Nyla A Heerema, Suli Li, Tom Dillon, Ricky Rodriguez, Kevin R Coombes, Philip R. O. Payne

Posted 13 Mar 2019
bioRxiv DOI: 10.1101/575423 (published DOI: 10.1093/bioinformatics/btz520)

Karyotype data are the most common form of genetic data that is regularly used clinically. They are collected as part of the standard of care in many diseases, particularly in pediatric and cancer medicine contexts. Karyotypes are represented in a unique text-based format, with a syntax defined by the International System for human Cytogenetic Nomenclature (ISCN). While human-readable, ISCN is not intrinsically machine-readable. This limitation has prevented the full use of complex karyotype data in discovery science use cases. To enhance the utility and value of karyotype data, we developed a tool named CytoGPS. CytoGPS first parses ISCN karyotypes into a machine-readable format. It then converts the ISCN karyotype into a binary Loss-Gain-Fusion (LGF) model, which represents all cytogenetic abnormalities as combinations of loss, gain, or fusion events, in a format that is analyzable using modern computational methods. Such data is then made available for comprehensive "downstream" analyses that previously were not feasible.

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