Working with Groups

After import, data are stored in the system group "NEW". Now it is your task to create groups and sub groups of patients and to fill them with the appropriate patients.

Creating a new group

Select the "File � New" menu on the main form to open the form for creating new groups or sub groups.

By default, "Group" is selected for creating a new group.

In the field "Short Name" enter an abbreviation for the name of your new group which may be upto 5 characters long. In the field "Description" enter the name or a short description of your group; you can use upto 255 characters.

You may want to populate the new group with patients with the patients imported into the system group NEW. For that purpose, you can select "Move patients from system group New into this group" (default) or "Copy patients from system group New into this group"; while both versions will copy the patient IDs into the new group, those IDs will additionally remain in the system group NEW with the former version and removed from the system group NEW in the latter version.

If the newly created group is aimed to be the group for further analysis, tick "Select as Active Group" (default).

Creating a New Subgroup

Select the "File � New" menu on the main form to open the form for creating new groups or sub groups.

By default, "Group" is selected for creating a new group; tick "SubGroup" to create a new sub group.

In the upper field "Short Name" enter an abbreviation for the name of your new subgroup which may be upto 5 characters long. In the upper field "Description" enter the name or a short description of your subgroup; you can use upto 255 characters.

The new subgroup can be created in an existing group or in a new group. The latter version is set by default. In the lower "Short Name" enter an abbreviation for the name of your new group which may be upto 5 characters long. In the lower field "Description" enter the name or a short description of your group; you can use upto 255 characters.

If you prefer to create the subgroup in an existing group, tick "existing":

From the combobox, select the desired group in which the new subgroup is to be created.

You may want to populate the new subgroup with patients with the patients imported into the system group NEW. For that purpose, you can select "Move patients from system group New into this group" (default) or "Copy patients from system group New into this group"; while both versions will copy the patient IDs into the new group, those IDs will additionally remain in the system group NEW with the former version and removed from the system group NEW in the latter version.If the newly created subgroup is aimed to be the group for further analysis, tick "Select as Active Group" (default).

Opening a Group or Subgroup

CyDAS analyses the data of patients which are found in the "Active Group". In order to make a group or subgroup of patients your active group, the respective group must be opened.

From the "File" menu, choose, "Open". The form for selecting a group / subgroup is displayed:

From the combobox "Group", select the appropriate group. You may wish to inspect the group before opening it. For that purpose, click the "View" button on the right from the combobox to open the PatientViewer.

If you wish to create a new group instead, click on the "New" button next to the combobox. The form for creating a new group / subgroup is opened. For more information on creating a new group, see above.

For opening a subgroup, select first the group that subgourp resides in from the upper combobox. Then tick "SubGroup" and select a subgroup from the lower combobox. Only subgroups residing in the group selected from the upper combobox are displayed.

As above, the subgroup can be expected by clicking the "View" button next to the combobox. Also a new subgroup can be created by clicking the "New" button.

Be sure not to tick "SubGroup" if you do not want to open a subgroup. Leaving the combox empty while "SubGroup" is ticked may cause an error.

After the desired group or subgroup is selected, click "OK" to activate this group. Data are loaded from the database which may take some time depending on the size of the group.

Editing a Group or Subgroup

When a group or subgroup is to be edited, it must be selected before as the active group by opening it; for more information on opening a group or subgroup, see above.

On the main windows of the CyDAS application, chose "Group" from the "Edit" menu. The form for editing is opened with the first tab being displayed and all its other tabs locked.

Adding or Removing Patients

By clicking on the "Add Patients" button on the first tab, the "Criteria" tab will be opened where you can select the criteria the patients have to fulfill to be added into the active group.

After entering the search criteria, click "View" to see the patients to be added in the PatientViewer. Only patients which are not yet in the ActiveGroup will be shown (no duplicate entries).

To remove patients from the ActiveGroup, click on "Remove Patients" on the first tab. Again, the criteria tab is opened where you can select the criteria the patients have to fulfill to be removed from the active group.

After entering the search criteria, click "View" to see the patients to be removed the PatientViewer.

In the PatientViewer, you may select "Add All" or "Remove All" to add or to remove all patients shown. You may also select single patients to be added or removed. Here, click onto the "Add Selected" or "Remove Selected" button.

You may return to the "General" tab, or to the "Criteria" tab to add other criteria and repeat the addition or removal of patients. To finish your actions, click on "Done" on the bottom of the form. The (changed) ActiveGroup will then be reloaded.

For further information on the PatientViewer, see the page "PatientViewer".

Data Source

"Data source" is available when adding patients only. If patients are to be removed, the ActiveGroup is selected automatically.

First of all, a source of the patient data has to be selected:

• Tick "All patients in database" if the patients may stem from any group or subgroup.
• Tick "Group" and select the appropriate group from the combobox next to it, if the patients stem from a specific group.
• Tick "SubGroup" and select the appropriate subgroup from the combobox next to it, if the patients stem from a specific subgroup.

Make sure that the appropriate radio button is ticked.

Filters

Next, a series of filters can be applied. If several criteria are used, every type of criterion must be fulfilled for at least one karyotype of the patient. Selection works at the level of the patient, i.e. also investigations and karyotypes which do not meet the criteria will be included if at least one karyotype in a patient fulfills them.

Diagnosis / Morphology

The diagnosis of the patient (or the morphology of the tumor in case of Mitelman data).

All values available in the database are displayed in the multi-select combobox. You may select more than one diagnosis / morphology by holding down the shift or control key while clicking with the mouse.
Make sure to tick the checkbox if the diagnoses are to be used.

In the example above, patients with leukemia of FAB types L1, L2, or L3 are selected.

Topography

Selet the topography of the tumour.

All values available in the database are displayed in the multi-select combobox. You may select more than one topography by holding down the shift or control key while clicking with the mouse.
Make sure to tick the checkbox if the topographies are to be used.

In the example above, patients with tumours in brain or kidney are selected.

Sex

Select the sex of the patient. Make sure to tick the checkbox if the sex is to be used as a criterion. If it does not matter, do not check the checkbox.

In the example above, female patients are selected.

Date of Birth

Select a range of dates the date of birth of the patient has to be between. You can enter the dates either directly or select them from a calendar element. Make sure to tick the checkbox if the date of birth is to be used.

In the above example, patients whose birth date is between 1.1.1950 and 1.1.1980 are selected.

Date of Death

Select a range of dates the date of death of the patient has to be between. You can enter the dates either directly or select them from a calendar element. Make sure to tick the checkbox if the date of death is to be used.

In the above example, patients who died in the first half of 2005 are selected.

Clinical Classification

A selection for clinical classification scores is not yet implemented.

ISCN

Enter a text which has to be found in the ISCN formula of a karyotype. Check "NOT" if that text has to absent. Make sure to tick the checkbox if the ISCN is to be used.

In the above example, patients with at least one karyotype showing an isochromosome of the long arm of chromosome 7 are selected.
If "NOT" was also checked, all patients who have at least one karyotype without the isochromosome 7q are selected; i.e. patients for whom several karyotypes were found may also be selected if the isochromosome was not found in all karyotypes.

SCCN Quantitative

Enter a text which has to be found in the quantitative part of the SCCN formula of a karyotype. Check "NOT" if that text has to absent. Make sure to tick the checkbox if the Quantitative residue of SCCN is to be used.

In the above example, patients with at least one karyotype showing a gain of the complete long arm of chromosome 7 are selected.
To select patients having a gain somewhere on the long arm of chromosome 7, use "+(7)(q".
To select patients having a gian of the whole chromosome 7, use "+(7),".
Always use the band numbers instead of abbrevations like "cen" or "ter".

For more information on the SCCN, see here.

SCCN Qualitative

Enter a text which has to be found in the qualitative part of the SCCN formula of a karyotype. Check "NOT" if that text has to absent. Make sure to tick the checkbox if the Qualitative residue SCCN is to be used.

In the above example, patients with at least one karyotype with 22q11 involved in a translocation are selected. This will also select patients with aberrant Philadelphia translocations, and patients where the Philadelphia translocation is found in derivative chromosomes only.

For more information on the SCCN, see here.

SCCN Extra

Enter a text which has to be found in the qualitative part of the SCCN formula (using extra symbols) of a karyotype. Check "NOT" if that text has to absent. Make sure to tick the checkbox if the Qualitative Extra residue of SCCN is to be used.

In the above example, patients with at least one karyotype with a three-way translocation involving 22q11 are selected. The band (at a resolution of two digits after the arm) follows in brackets.

For more information on the SCCN with extra symbols, see here.

Bandlist

Enter a bandlist description for the change on band level. "G" means gain, "L" loss, and "S" structrual change (break point). Check "NOT" if that text has to absent. Make sure to tick the checkbox if the Bandlist is to be used.

In the above example, patients with at least one karyotype giving raise to a gain in 9q34 are selected.

Age

Enter the minimum and maximum age of the patient at examination into the text fields.  Make sure to tick the checkbox if the Age is to be used.

In the above example, patients between 50 and 59 years old (both values included) when examined are selected. Note that "Age" does not necessarily reflect the present age of the patient.
To select patients older than a specific age (e.g. at least 60 years), enter the minumum ("60") into the first text field and set the second text field to a very high value which no patient will reach (e.g. "200").
To select patients younger than a specific age (e.g. not elder than 14 years), enter the maximum ("14") into the second text field and set the first text field to 0.

Aberration Count

Enter the minimum and maximum number of aberrations to be found in the ISCN formula into the text fields. Make sure to tick the checkbox if the Aberration Count is to be used.

In the above example, patients having at least one karyotype with two or three aberrations are selected.
To select patients having a karyotype with more than a specific number of aberrations (e.g. at least 10), enter the minumum ("10") into the first text field and set the second text field to a very high value which no patient will reach (e.g. "10000").
To select patients having a karyotype with less than a specific number of aberrations (e.g. not more than 2), enter the maximum ("2") into the second text field and set the first text field to 0.
To select patients having a karyotype with exactly a specific number of aberrations (e.g. exactly 2), enter the same value ("2") into both fields.

CKAS (Complex Karyotype Aberration Score)

Enter the minimum and maximum value for the CKAS into the text fields. Make sure to tick the checkbox if the CKAS is to be used.

In the above example, patients having at least one karyotype giving raise to a CKAS of two or three aberrations are selected.
To select patients having a karyotype giving raise to a specific minimum CKAS value (e.g. at least 10), enter the minumum ("10") into the first text field and set the second text field to a very high value which no patient will reach (e.g. "10000").
To select patients having a karyotype giving raise to a specific maximum CKAS value (e.g. not more than 2), enter the maximum ("2") into the second text field and set the first text field to 0.
To select patients having a karyotype giving raise to a specific CKAS value (e.g. exactly 2), enter the same value ("2") into both fields.

For more information on the CKAS, see here.

Errors in the ISCN Formula

Check this field if you want to select for patients with at least one bogus karyotype. This is specially useful for finding karyotypes which need re-analysis.

Additionally check "NO" to select patients with at least one correct karyotype.

Double Minutes

Check this field if you want to select for patients with at least one karyotype with Double Minutes.
Additionally check "NO" to select for patients with at least one karyotype without double minutes.

Marker Chromosomes

Check this field if you want to select for patients with at least one karyotype with Marker Chromosomes.
Additionally check "NO" to select for patients with at least one karyotype without Marker Chromosomes.

Ring Chromosomes

Check this field if you want to select for patients with at least one karyotype with Ring Chromosomes.
Additionally check "NO" to select for patients with at least one karyotype without Ring Chromosomes.

"Ring chromosomes" can be both ring shaped marker chromosomes ("+r") or well defined ring ring chromosomes ("r(...)") or derivative ring chromosomes ("der(...)r(...)").

Other Changes

On the first tab, click on "Other Changes" to open the "Other Changes" tab.

Renaming a Group / Subgroup

Enter the new short name for the group into the text field directly on the right to the "Rename" button, and the new description of the group into the next field, the click "Rename".

Removing All Patients of a Group / Subgroup

All patients can be removed from a group / subgroup using the "Clear Group" button. By default, all patient data remain in the data base, only their link to the group is deleted. If also the patients have to be removed from the database, tick the checkbox near "Remove patient data from database".

Deleting a Group / Subgroup

A group / subgroup can be deleted using the "Delete Group" button. By default, all patient data remain in the data base, only their link to the group is deleted. If also the patients have to be removed from the database, tick the checkbox near "Remove patient data from database".