Develop a Karyogram
A karyogram is the graphical and abstract representation of all chromosomes of a karyotype. Apart from showing the band composition of the derivative chromosomes (the application "Derivative Chromosome" is meant for that purpose), it also displays non-derivative chromosomes and thus gives hints about lost, gained or replaced normal chromosomes. Thus, a further application for checking the correctness of a karyotype is offered.
The Application Window
This function is opened from the menu of the main window. Select "Other
- Develop Karyogram" from its menu.
There upon the application window is opened. It will always maximise automatically because the graphics will require a lot of space.
In the yellow line, the ISCN formula of the presently displayed karyogram is shown. It can be entered by double-clicking that line or via the "File - Karyotype" menu.
Minor errors in the formula are automatically corrected. Among these are: not exact number of chromosomes, sex chromosomes, some description errors in the aberrations.
Additional aberrations can be introduced via the "Rearrange" menu. Breakpoints are selected from the karyogram and the ISCN formula is updated according to the ISCN standards and the corresponding karyogram is displayed.
Chromosomal bands are linked with a map viewer (NCBI or Ensembl). When the mouse is hovering over them, the band number is shown. Below the chromosomes, the number of the chromosome (for non-derivative chromosomes) or a "#" sign (for chromosomes derived from an aberration) is displayed. Hovering over the "#", information on the chromosome (the aberration which gives raise to this chromosome, and the band composition of the chromosome) are displayed.
Ring chromosomes are linearized. Marker chromosomes are shown as chromosomes of unknown origin ("?"). For unknown fragments or bands, no differentiation concerning the length of the unknown segment or on the presence / absence of a centromere is possible.
The Menu
The File Menu
Setting / Editing the ISCN Formula
The "Karyotype" menu opens a window for editing the ISCN formula. It can also be accessed by double-clicking the yellow line with the ISCN formula.
In the large text box, the formula can be entered or the present formula can be edited.
Clicking on the "Check" button calls a routine which checks the karyotype for errors. A message box shows if the karyotype is ok or which errors where encountered and must be corrected.
Click on "OK" to close the window and have the karyogram displayed. "Cancel" closes the window without changing the formula.
Save the Karyogram
The "Save Image" menu allows you to save the graphic which is displayed in the viewer panel into an image file. Regrettably, the imagemap information gets lost during that process.
Close the Application
"Close" closes the window.
The Edit Menu
Editing the Parameters
The parameters for the karyogram are edited via a dedicated form which is accessed through the "Edit - Parameters" menu. The parameters are changed on their respective tabs.
All parameter changes will come into effect when the karyogram is redrawn. I.e. after changing the parameters, use the "View - Refresh" menu to see the changes with the present karyotype.
Colors
The "Use Colors" checkbox determines if chromosomes are drawn with their individual colors (default) or in black.
Next to the "Background Color" button, the current background color is displayed. Clicking the button opens a common windows color dialog. Since there is no "transparent" color defined in the dialog, it can be set by clicking "Cancel" in that dialog; a message box will pop up asking you if you want to set the background color to transparent. Click "OK" to do so, or "Cancel" to keep the present color.
The colors used for drawing the chromosomes are adjusted via a dedicated form which is opened upon clicking on the "Chromosome Colors" button. They are originally defined in the resources file.
All chromosomes are displayed with their number written in their respective color. Click on a chromosome to open the standard windows color dialog as above.
The "Reset" button causes the default colors to be reloaded.
"Apply" saves the changes, but keeps the dialog opened.
"Cancel" closes the dialog while discarding the changes since saving
them last.
"OK" saves the changes and closes the dialog.
Banding Resolution
The banding resolution for the ideogram can be adjusted from the "Resolution" tab of the "Edit Parameters" form.
The desired resolution can be selected from three predefined values:
- "2 Digits": This is a virtual resolution not defined by the ISCN manual. It means that bands are denoted by their chromosome, arm and exactly two further digits. Note that there is no standard definition for ideograms at this resolution.
- "400 bphs": This is the 400 bands per haploid set resolution as defined in the ISCN manual.
- "550 bphs": This is the 550 bands per haploid set resolution as defined in the ISCN manual.
- "800 bphs": This is the 800 bands per haploid set resolution as defined in the ISCN manual.
Chromosome bands were originally measured in the ISCN manual (pp. 14-21) for 400 bphs and 550 bphs resolution. Later, information on the 800 bphs ideograms was obtained from NCBI. Band length were entered for the highest resolution a band fulfills, thus the length of a band at 400 or 550 bphs may sometimes be its length at 800 bphs differring from the corresponding ideograms in the ISCN manual.
The default value is 800 bphs.
Draw Sequence
The sequence in which the chromosomes are displayed is not derived from the default sequence defined in the chromosomes definition file. Here, chromosomes are displayed in two lines by default.
Line breaks are indicated by "BR". Chromosomes whose band composition is partially known but whose centromeric origin is unclear / marker chromosomes are represented by a question mark "?".
Scale
The scale determines the size of the chromosome idoegram. A maximum scale of 1 is allowed; here, a non-derivative chromosome 1 would measure about 1600 pixels in length.
Generally, values greter than 0,25 are not recommended because they yield very large images. If a single derivative chromosomes is needed at a greater scale, use the "Derivative Chromosome" application instead (the "View - Zoom" menu is not yet implemented).
Map Viewer
The map viewer parameter indicates an external resource in the internet to which chromosomal bands in the drawings are linked. Viewers are available from Ensembl and the National Center for Biotechnology Information (NCBI).
The default value for the MapViewer is set in the CyDAS.ini file. Also note that the MapViewer is set at a global level always; i.e. changing its value somewhere in the CyDAS application will change it for the whole CyDAS application.
Navigating between Karyograms
The "Previous Karyotypes..." and "Next Karyotypes..." menus correspond to common "Undo" / "Redo" functions.
"Previous Karyotypes..." displays a list of all karyotypes which were previously shown:
It starts with the first karyotype, and extends to the presently shown karyotype which is selected. A previous karyotype can be selected by clicking the respective radio button and then "OK" (due to a bug in the radio button component, a selection by double click only without clicking the OK button is not possible).
If you navigated back via the above function, you can navigate forward via the "Next Karyotypes..." function. Like above, a list of karyotypes is shown, now extending from the presently displayed karyotype (selected) upto the last karyotype.
Whenever further rearrangements are introduced in a karyotype selected from the list, the "next karyotypes" list is emptied and replaced with the newly added karyotypes.
The Rearrange Menu
With the "rearrange" menu, additional rearrangements can be introduced into the present karyotype. Many rearrangements are specified more exactly than with the ISCN standards.
After selection of the type of rearrangement, the Band Selection window is opened and kept in the foreground of the application. It can be dragged to other positions, but remains in the foreground.
The Band Selection window request all the required break points for the selected type of aberration (which is displayed on top). From the karyogram in the main window, select the presently requested band by clicking on the respective band. After all requested bands were entered, click on "OK" to introduce the aberration. The karyogram and its ISCN formula are updated automatically.
Sometimes, the outcome will not meet your expectations. This can be due to the limitations of the ISCN, or to limitations of the implementation of the software (see also the chapters on Known Problems below), or on wrong expectations. In such cases, you can navigate back to the previous karyotype, and try a different aberration (or the aberration in the other way round), or enter the next aberration manually.
The View Menu
The "Zoom" menu magnifies a user selected region or chromosome (not yet implemented).
The "Navigate" menu indicates if clicking onto a band will link out to the map viewer information onto that band. It is activated by default, but automatically deactivated during the selection of bands for the introduction of further aberrations.
"Refresh" recalculates the karyogram from the ISCN formula and redraws it with the present set of parameters.
The Help Menu
The Help menu leads you to the documentation available on the CyDAS
website, either the User Documentation (this page) or to the Technical
Documentation.
A local "Help" is not yet implemented.
Known Problems
If quite simple karyotypes are displayed, no problems are likely to occur. That holds especially true for the simple karyotypes generally encountered during pre- or postnatal analysis. But when analysing karyotypes of tumours, especially solid tumours, more complicated aberrations may occur which cannot be well described with the ISCN (see also the general chapter on problems with the ISCN).
Special problems do arise when the karyogram is to be calculated. For each aberration, all derivative chromosomes derived from the aberration are calculated. I.e. a "t(9;22)(q34.12;q11.23)" is transcribed into a "der(9)t(9;22)(q34.12;q11.23)" and a "der(22)t(9;22)(q34.12;q11.23)".
Tumour View
Also note that the point of view on an ISCN formula is a tumour cytogeneticist's one: While a constitutional Turner syndrom would generally be described as "45,X", CyDAS does not see any aberrations in the formula, and will "correct" it to a normal female karyotype ("46,XX"); use the "tumour" view, i.e. "45,X,-X", instead.
Centromere Envolvement and Replacement of Normal Chromosomes
If centromeres were involved, such derivative chromosomes may each contain two centromeres and thus replace two normal chromosomes each. Internally, some of such problems can be circumvented by denoting the derivative chromosomes as additional chromosomes, with a loss of each normal chromosome. I.e. a "t(4;5)(p10;q10)" is internally represented by "+der(4;5)t(4;5)(p10;q10),+der(4;5)t(4;5)(q10;p10),-4,-5".
Such whole arm translocations are displayed correctly and are available for further rearrangements.
For duplications (triplications, quadruplications), the involvement of a centromeric region is not always accounted for. As a consequence, a simple "dup(10)(p13q21)" can still be transcribed in a "der(10)dup(10)(p13q21)" which replaces one normal chromosome 10 only, but when further aberrations are introduced, the identical origin of the centromeres gets lost and it will be transcribed into something like a "der(10;10)(...)" which replaces two normal chromosomes 10. Consequently, the karyogram shown is wrong. Use e.g. "-10,+dup(10)(p13q21)" instead when you want to introduce further aberrations into the derivative chromosome.
Though whole arm translocations between homologous chromosomes (e.g. "t(6;6)(q10;q10)") are displayed correctly, they must not be used for the introduction of further rearrangements: the ISCN formula cannot be calculated because of bugs in the ISCN (no useful way to discriminate between sister chromosomes: underlining is not plain-text compatible). You could use both isochromosomes (i.e. "i(6)(p10),i(6)(q10)") instead and introduce the further aberrations into them.
Band Selection and Ambiguous Band Notation
In a derivative chromosome, there may be more than one band for a given band name, e.g. after duplication of a chromosomal segment. The ISCN does not provide clues how such doubled bands can be denoted uniquely.
Though in the graphics, the band is selected interactively and thus just one of them is selected, only the ISCN band number is preserved and used for further analysis. Hence, the further rearrangement may take place at the other site.
Example: Introducing an addition into a "dup(5)(p15.2p13.2)" at 5p14 will introduce the addition always at the most terminal site, also when selecting the 5p14 which is closest to the centromere.
Resolution Settings
Typically, break points in rearrangements are given with two digits after the chromosomal arm only. But at a 400 bands per haploid set, very often a third digit is required; at 550 bphs even more often or even further digits. With such cases, the break points inside the derivative chromosomes cannot be determined exactly, and thus the sub-bands of the band involved as a break point are likely to be displayed incorrectly.
A typical example is the inversion which causes a longer derivative chromosome - though the length must not change of course: "inv(16)(p13q12)" causes duplications of 16p13 and 16q12. This can be circumvented by a more exact naming of the break points, e.g. "inv(16)(p13.2q12.2)".
This problem is exacerbated by even worse band descriptions like "inv(16)(p1q1)" or "inv(16)(p?q?)" which yield useless ideograms only.
Re-calculation of ISCN Short Formula
Very often, the additional aberration is introduced into a derivative chromosome. That derivative chromosome is internally represented by its fragment composition. Sometimes, the rearrangement introduced does not cause major problems for the ISCN short formula: the corresponding formula can be composed by simply adding the new rearrangement to the previous formula. But if that is not possible, or if no such simple way is known, the new derivative chromosome is available in the ISCN detailed form only. A new function was created (Chromosome.repairISCNShort()) which then tries to set up an ISCN short formula corresponding to that band composition. This feature may show up results which were perhaps not expected, but which might be a valid interpretation of the karyotype.
Example: In der(6)t(6;7)(q21;q22.3) the region from 6q14.1 to 7q33 was duplicated giving raise to der(6)(6pter->6q21::7q22.3->7q33::6q14.1->6q21::7q22.3->7qter). If now a deletion from 6q13 to 7q34 is introduced, the duplicated region gets lost, and the remaining chromosome der(6)(6pter->6q13::7q34->7qter) is translated into a der(6)t(6;7)(q13;q34).
Calculation of the Karyogram
The calculation of the karyogram is described in the technical documentation on the Karyogram class.