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Elementary Analysis

During import, data are analysed in some elementary way:

All karyotypes are checked for errors. If an error was encountered which cannot be corrected automatically, the analysis of that karyotype is stopped and a description of the error is put into the error field.

Errors may be in the syntax (e.g. wrong symbols, wrong number of distinct chromosomes or bands), but also in the meaning: a deletion of a centromer is not possible (the acentric fragment would be lost at the next cell division), and sometimes highly aberrant chromosomes cannot be reconstructed from the rearrangements denoted.

Automatic correction is possible for minor errors only. Such errors include the wrong position of question marks (after instead before the chromosome), dots missing or in the wrong position, or also wrong semicola in case of insertions.

If no uncorrectable error was encountered, the ISCN formula is rewritten in strict obediance to the standard, with the "idem" term replaced by the appropriate rearrangements.

SCCN

The ISCN formula is evaluated for gains and losses of chromosomal material and for structural changes. Those data are denoted using the "Simplified Computer readable Cytogenetic Notation"  ("SCCN"). The SCCN was introduced in
Jutta Bradtke, Harald Balz, Christa Fonatsch, Barbara Heinze, Anna Jauch, Brigitte Mohr, Claudia Schoch, Harald Rieder:
"Computer aided analysis of additional chromosome aberrations in Philadelphia chromosome positive acute lymphoblastic leukaemia using a simplified computer readable cytogenetic notation",
BMC Bioinformatics 2003, 4:4 (28 January 2003)

Hallmark of SCCN is the separation of structural and quantitative aberrations.All evaluated data are calculated for a virtual banding resolution of two digits after the arm.

Special Symbols

For further special analysis, a number of special symbols was introduced. These special symbols allow for greater details with some types of rearrangements, e.g. insertions and translocations.
Symbol Meaning
deln non-terminal (i.e. interstitial) Deletion
delt terminal Deletion
insa intrachromosomal Insertion
insr interchromosomal Insertion
tbc Translocation between 2 chromosomes
tbcqb Translocation between 2 chromosomes with 4 breaks (exhange of interstitial fragments)
ttc Translocation between 3 chromosomes
ttchb Translocation between 3 chromosomen with 6 breaks (exchange interstitial fragments)
tqc Translocation between 4 chromosomes
tpc Translocation between 5 chromosomes
thc Translocation between 6 chromosomes
tsc Translocation between 7 chromosomes
toc Translocation between 8 chromosomes
tnc Translocation between 9 chromosomes
tdc Translocation between 10 chromosomes

CKAS

The "Complex Karyotype Aberration Score" ("CKAS") was introduced togetehr with the SCCN. It is a measure for karyoytpe complexity. It counts the events behind the description of aberrations.

Band List

A list of gains, losses and structural changes per affected band is calculated. The resolution for the band is two digits behind the arm.

Markers, Rings, Double Minutes

The presence of marker chromosomes, ring chromosomes, and duoble minutes is stored in their respective fields. With ring chromosomes, not only ring shaped marker chromosomes of unknown origin are meant, but also well defined ring chromosomes described with the symbols "r" or "der(...)r" in the ISCN. Their presence may be indicated also in case of errors in a karyotype.