Database structure for storing and automatic analysis of text GTG and fish cytogenetic results

• Autorzy: Kostorz I. , Sikora M. , Stęclik T.
• Języki publikacji: EN

Abstrakty

EN

The paper presents research on storing text cytogenetic tests data conducted with GTG and FISH methods for browsing and automatic processing of its string results. It presents analysis of the text cytogenetic test result and a two proposal structures of the databases (the storing data and the analytical one) used for anonymised text GTG and FISH cytogenetic test results storing and their processing. Presented structures were queried with known chromosome aberrations for T-cell acute lymphoblastic leukaemia (T-ALL), B-cell acute lymphoblastic leukaemia (B-ALL) and both T-ALL and B-ALL in the proposed database. Additionally, the analytical database was filled with the set of Mittelman database results and browsed with non-standard queries. Conducted tests demonstrated that the proposed analitical structure is useful for GTG and FISH cytogenetic test results text mining.

Słowa kluczowe

EN

automatic GTG text analysis; cytogenetic text test; GTG methods; FISH methods; database; cytogenetics; automatic analysis

PL

analiza automatyczna tekstu GTG; test cytogenetyczny tekstu; metoda GTG; metoda FISH; baza danych; cytogenetyka; analiza automatyczna

• Wydawca: University of Silesia, Institute of Informatics, Computer Systems Department
• Czasopismo: Journal of Medical Informatics & Technologies
• Rocznik: 2018
• Tom: Vol. 27
• Strony: 41--48
• Opis fizyczny: Bibliogr. 11 poz., rys., tab.

Twórcy

autor

Kostorz I.

• Institute of Innovative Technologies EMAG, Poland, Katowice, ul. Leopolda 31

autor

Sikora M.

• Institute of Innovative Technologies EMAG, Poland, Katowice, ul. Leopolda 31

autor

Stęclik T.

• Institute of Innovative Technologies EMAG, Poland, Katowice, ul. Leopolda 31

Bibliografia

• [1] Atlas of Genetics and Cytogenetics in Oncology and Haematology. 2018. http://atlasgeneticsoncology.org/Anomalies/Anomliste.htmlB-ALL [Online; accessed 2018-11-02].
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• [3] ABRAMS Z. B. A translational bioinformatics approach to parsing and mapping iscn karyotypes: A computational cytogenetic analysis of chronic lymphocytic leukemia (cll). 2016.
• [4] BARTLETT J. M. S. Fluorescence in situ hybridization. Molecular Diagnosis of Cancer: Methods and Protocols, 2004. Humana Press, Totowa, NJ, pp. 77–87.
• [5] EITAN, R. SHAMIR R. Reconstructing cancer karyotypes from short read data: the half empty and half full glass. BMC Bioinformatics, 2017. p. 18(1):488.
• [6] HOELZER D., GOKBUGET N., OTTMANN O., PUI C.-H., RELLING M. V., APPELBAUM F. R., VAN DONGEN J. J.,SZCZEPANSKI T. Acute lymphoblastic leukemia. ASH Education Program Book, 2002, Vol. 2002. American Society of Hematology, pp. 162–192.
• [7] JORDE, L. CAREY J. B. M. Medical genetics. 2010. MOSBY ELSEVIER.
• [8] MCGOWAN-JORDAN, J. SIMONS A. S. M. Iscn 2016 an international system for human cytogenomic nomenclature (2016) reprint of: Cytogenetic and genome research 2016. 2016. Karger Verlag.
• [9] MITELMAN F J. B., (EDS.) M. F. ”mitelman database of chromosome aberrations and gene fusions in cancer (2018). 2018. http://cgap.nci.nih.gov/Chromosomes/Mitelman [Online; accessed 2018-10-02].
• [10] SOSZYNSKA, K. MUCHA B. D. R. S. K. D. E. K. A. W. M. H. O. The application of conventional cytogenetics, fish, and rt-pcr to detect genetic changes in 70 children with all. Annals of Hematology, 2008, Vol. 87. pp. 991–1002.
• [11] SZCZEPANSKI, T. HARRISON J. V. D. C. Genetic aberrations in paediatric acute leukaemias and implications for management of patients. The lancet oncology, 2010, Vol. 11. pp. 880–9.

Uwagi

PL

Opracowanie rekordu w ramach umowy 509/P-DUN/2018 ze środków MNiSW przeznaczonych na działalność upowszechniającą naukę (2019).