Clinical Classification Systems

With many types of leucaemic disorders, risk classification of patients is done based on their karyotypes. The "Clinical Classification Systems" module comprises functionality for the definition, editing, and application of such classification system.

The Classification Systems Start Window

The Clinical Classification Systems are accessed from the main window via the "Edit - Classification" menu. In the start window, the first classification system in the database is displayed:

In the present preliminary form, the menu is given by a series of buttons.

Select Menu

Here, you can select a classification system from the database. All available classification systems are displayed in a tree view control showing its contents in a bound level.

The information on the system proper includes the internal identifier, its short name, and its description.
For each item of content, the classification system id, the classification value, the description of the item, and an SQL condition are displayed.

The button "Collaps All" displays the system headers only, while the button "Expand All" will open the contents.

You can select a classification system by either clicking on its header or somewhere in its contents sections and then "OK". "Cancel" closes the window without selecting a classification system.

New Menu

You may change the text(s) shown in the text fields for the short name and the description and there after you can save this modified system as a new system. You will be propted if you really want to do so.

Note that this functionality just creates a new classification system which does not yet have any contents and the contents must be entered later. If you prefer to copy from an existing system, use the "Copy New" functionality.

Update Menu

You may change the text(s) shown in the text fields for the short name and the description and there after you can upadte this information for the presently selected system.

Delete Menu

With the Delete menu, you can remove the presently seleted classification system and all subsequent data pertaining to it from the CyDAS database. You will be prompted if you really want to do so.

Close Menu

The Close menu allows you to leave the clinical classification systems.

Edit Scores Menu

This menus opens the form for editing, deleting, and creating classification score values. It is described below.

Copy New Menu

With the "Copy New" functionality you can copy the presently selected classification system into a new classification system. You will be prompted to enter a short name for the system. The description is automatically set to "Copy of <short name of origin>".

All classification scores will be copied, but no results of classifications previously performed with the original system. The copy will be selected as the active classification system and may be edit as described above for its short name and description or its classification scores.

Classify Menu

With the Classify menu, the classification is performed for the Active Group with the presently selected classification system.

Classification is done at the level of the investigation. I.e. a patient with several investigations can receive distinct classifications for his/her investigations, which reflects the changes in risk due to karyotype evolution.

Technically, classification starts with the lowest classification score value, upto the highest. If the SQL condition fits the karyotype(s) of the investigation, its classification score is update to the present value. Hence, higher values will overwrite lower values. Thus no care need be taken to exclude investigations of higher value from the condition for a lower value, since that low value would later be overwritten.

Export Menu

Here you can export the classification results for the selected classification system and the active group into a text file.

Each line conatins five elements:
The CyDAS patient identifier, the CyDAS investigation identifier, the external patient identifier (as taken during data import), the external investigation identifier (as taken during data import), and the classification score value for the respective investigation.

Do not forget to perform the classification before exporting the data.

Report Menu

A report on the classification is generated. For each classification score which was used, it shows the value, its description, the number of investigations which were classified with this value, and the percentage of investigations.

Do not forget to perform the classification before generating the report.

The Classification Score Window

The Classification Score Window is opened from the "Edit Scores" menu of the classification systems start window.

UIpon opening, the first classification score value of the selected classification system is selected and displayed.

For information, the short name of the classification system and its description are displayed on the top of the edit window.

"Score" displays the selected score.
"Description" shows a description for the score.
"Condition" display an SQL condition for performing the classification. It can be edited additionally to direct typing into the field by a special editor.

Reset Menu

If data for the classification score were edited but not yet saved, the changes can be undone using the Reset menu.

Cancel Menu

This menu closes the classification score window. You will be prompted if you want to save the changes you made.

Editor Menu

The Editor menu opens a special editor for editing the SQL condition of the classification value. More information on the editor is available in its chapter.

OK Menu

This menu closes the form and automatically applies the changes you have made.

Select Menu

The Select menu allows you to select the classification value to be edited. Similar to the Select menu of the Classification start window, a tree view is shown with all the classification scores of the selected classification system. Click on a value and the on OK to select it.

Update Menu

You can change the values in the text fields of the edit form. To apply the changes, click on "Update".

New Menu

You can change the values in the text fields of the edit form. To save the values as a new classification score, click on "New". You will be prompted if you really want to do so.

Delete Menu

With the delete menu, you can delete the selected classification score. You will be prompted if you really want to do so.

The Classification Score Editor Window

The Classification Score Editor Window is opened from the "Editor" menu of the Classification Score Window.

The SQL condition of the selected score is analysed and displayed as a series of elementary conditions. Note that the editor is a quite simple one which does not cope with e.g. brackets; in such a case, an error message would be shown.

For each item in the SQL condition, a line is shown. At first, the parameter involved is named. Next, the condition can be negated (i.e. check the "NOT" check box). An operator for comparison follows. Possible types of comparison are:

  • "=" indicates that the parameter must have an exact value.
  • "Between" indicates that the parameter must be between the both values given; a second field for the parameter value will be displayed automatically if this operator is selected.
  • ">" indicates that the parameter must be greater than the value.
  • "<" indicates that the parameter must be less than the value.
  • ">="  indicates that the parameter must be greater than or equal to the value.
  • "<=" indicates that the parameter must be less than or equal to the value.
  • "Like" indicates that the parameter fulfills the pattern (using the appropriate SQL wild cards) given.
  • "Contains" indicates that the parameter contains the text given; appropriate SQL wildcards are added automatically.
  • "StartsWith" indicates that the parameter starts with the text given; appropriate SQL wildcards are added automatically.
  • "EndsWith" indicates that the parameter ends with the text given; appropriate SQL wildcards are added automatically.

The last field(s) take up the compare value for the parameter; generally, it is one field only, but for the "Between" operator two fields are required.

The conditions for the parameters can be joined with the "AND" or "OR" qualifiers. Note that bracketing is not possible with this editor, but brackets can be added manually in the text field for the SQL condition later.

An item can be removed by clicking into it and then selecting "Edit - Remove" from the menu.

Items can be added via the "AddItem" menu. It contains a submenus listing all types of parameters which can be used.

  • "Age" stands for the age of the patient at the time of investigation
  • "Metaphases" is the number of metaphases analysed in the investigation.
  • "KaryotypeNumber" indicates the number of the clone in a polyclonal karyotype. Sometimes, the main line clone (karyotype number = 1) is requested.
  • "ISCNFormula" means the karyotype description according to the ISCN.
  • "CGHFormula" means the results of a cgh analysis.
  • "SCCNQualitative" stands for the structural aberrations denoted in SCCN style.
  • "SCCNQuantitative" stands for the gains and losses denoted in SCCN style.
  • "CKASOverall" stands for the overall value of the complex karyotype aberration score (CKAS).
  • "CKASPloidy" stands for the ploidy residue of the complex karyotype aberration score (CKAS).
  • "CKASNumeric" stands for the numerical residue of the complex karyotype aberration score (CKAS).
  • "CKASBalanced" stands for the balanced residue of the complex karyotype aberration score (CKAS).
  • "CKASUnbalanced" stands for the unbalanced residue of the complex karyotype aberration score (CKAS).
  • "CKASUnclassified" stands for the unclassified residue of the complex karyotype aberration score (CKAS).
  • "Error" stands for errors encountered during the automated analysis of the karyotype formula.
  • "AberrationCount" is the number of aberration elements in the ISCN formula (a simple measure for karyotype complexity).
  • "CloneSize" is the size of the clone.
  • "OTHER CONDITION" opens a textfields where other conditions can be entered as in an SQL clause.

After editing the conditions, click on "OK" to return to the Classification Score Window and to update its "Condition" field; the changed condition is not yet stored in the database.