Analysis of ISCN Formulae
CyDAS can also analyse the ISCN formula of single cases. An ISCN formula may describe a single clone or may be ployclonal. Virtually all information available from the formula is extracted.
This function is opened from the menu of the main window. Select "Other
- Analyse ISCN" from its menu.
There upon the application window is opened.
In the textbox, the ISCN formual is entered. If it is polyclonal, the distinct clone have to be separated by a forward slash ("/").
After entering the formula, click the "Analyse" button. In the text field below, the result is shown.
The karyotypes(s) entered are re-written in strict adherence to the ISCN specification. All abbreviations are removed, "idem" terms are replaced by the respective rearrangements. Minor errors which can be resolved are removed from the formula(e) giving raise to the description which should be used in publications etc.
In case of errors which cannot be resolved, a message stating the error will be given. Typical errors are missing break points, bogus derivative chromosomes, and typos.
If a polyclonal karyotype was given, a composite karyoytpe is calculated and the follwoing analysis is based upon that composite karyotype.
"Is composite karyotype" indicates if the karyotype is marked
"Clone size" shows the clone size indicated in the karyotype. It is 0 if no clone size was given.
"Is incomplete" indicates if the karyoytpe is marked incomplete.
"Double Minutes" displays the term describing the double minutes.
"Markers" displays the term describing the marker chromosomes.
"Marker count" shows the minimum and maximum number for marker chromosomes given. It is 0 if no markers were denoted. Both values are the same if the number of markers was not given as a range.
"Rings" displays the term describing the ring chromosomes of unknown origin.
"Ring count" shows the minimum and maximum number for such ring chromosomes given. It is 0 if no rings were denoted. Both values are the same if the number of rings was not given as a range.
"Chromosome count field" displays the text of the chromosome count field.
"Chomosome count" shows the minium and maximum number given for the chromosome count. Both values are the same if an exact number instead of a range was given.
"Ploidy level" indicates the ploidy of the karyotype as explicitly stated in the chromosome count field or calculated from the chromosome count.
"Sex chromosomes" shows the sex chromosomes as given in the sex chromosomes field.
There after, information is given on each rearrangement. Each section
is headed by "Aberration" and a number.
"ISCN" displays the ISCN fomrula for that aberration.
"Break points" lists the break points inferred by that aberration.
"Quantitative" lists gains and losses in the SCCN style.
"Qualitative" list structural rearrangements in the SCCN style.
"Junctions" describes the points where chromosomal material is newly joined. A standard method for the description of junctions which also includes their directions is not yet defined.
"Deriavtive Chromosome" describes the derivative chromosome in ISCN detailed style, if the aberration started with a "der()" clause.
After the statements for each rearrangement, a summary follows summing up the data of the distinct aberrations. Additionally, structural and quantitative aberrations are calculated at a resolution of 400 bands per haploid set (bphs), and a the complex karyotype aberration score (CKAS) is displayed.
Next, the cytoband lists follows showing the number of gains, losses, and structural rearrangements (chromosomal breaks) for each chromosomal band at a resolution of 400 bands per haploid set (bphs).