Research article
Computer aided analysis of additional chromosome aberrations in Philadelphia chromosome positive acute lymphoblastic leukaemia using a simplified computer readable cytogenetic notation
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* Corresponding author: Harald Rieder rieder@mailer.uni-marburg.de
1 Institute of Clinical Genetics, Philipps-University, Bahnhofstraβe 7, Marburg, 35037, Germany
2 Institute for Medical Biology, University of Vienna, Währinger Straβe 10, Vienna, 1090, Austria
3 Clinic of Haematology and Oncology, University Hospital, Parkstr.11, Ulm, 89073, Germany
4 Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 328, Heidelberg, 69120, Germany
5 Clinic of Haematology and Oncology, University Hospital, Fetscherstraβe 74, Dresden, 07307, Germany
6 Department of Internal Medicine III, University of Munich, Marchionistraβe 15, Munich, 81377, Germany
BMC Bioinformatics 2003, 4:4 doi:10.1186/1471-2105-4-4
Published: 28 January 2003Abstract
Background
The analysis of complex cytogenetic databases of distinct leukaemia entities may help to detect rare recurring chromosome aberrations, minimal common regions of gains and losses, and also hot spots of genomic rearrangements. The patterns of the karyotype alterations may provide insights into the genetic pathways of disease progression.
Results
We developed a simplified computer readable cytogenetic notation (SCCN) by which chromosome findings are normalised at a resolution of 400 bands. Lost or gained chromosomes or chromosome segments are specified in detail, and ranges of chromosome breakpoint assignments are recorded. Software modules were written to summarise the recorded chromosome changes with regard to the respective chromosome involvement. To assess the degree of karyotype alterations the ploidy levels and numbers of numerical and structural changes were recorded separately, and summarised in a complex karyotype aberration score (CKAS). The SCCN and CKAS were used to analyse the extend and the spectrum of additional chromosome aberrations in 94 patients with Philadelphia chromosome positive (Ph-positive) acute lymphoblastic leukemia (ALL) and secondary chromosome anomalies. Dosage changes of chromosomal material represented 92.1% of all additional events. Recurring regions of chromosome losses were identified. Structural rearrangements affecting (peri)centromeric chromosome regions were recorded in 24.6% of the cases.
Conclusions
SCCN and CKAS provide unifying elements between karyotypes and computer processable data formats. They proved to be useful in the investigation of additional chromosome aberrations in Ph-positive ALL, and may represent a step towards full automation of the analysis of large and complex karyotype databases.