Online Analysis

Deutsche Version

Some example programs are available for online analysis of cytogenetic data:

ISCN Analysis

allows the user to analyse simple or polyclonal karyotypes (more...).

Drawing ideograms of aberrant chromosomes

draws ideograms of derivative chromosomes (more...).

Drawing a Karyogram

draws the ideograms of all derivative and non-derivative chromosomes of the karyotype (more...).

Analysis of Data Sets for Gains, Losses and Breakpoints

analyses large data sets, e.g. downloaded from the Mitelman DB, for gains and losses, and breakpoints (more...).

Dependence Network

shows statistical dependence between pairs of rearrangements (more...).

Evolution Tree

shows putative pathways of karyotype development during tumour progression. (more...).

Dependence on Karyotype Complexity

shows how often a selected rearrangement was encountered in relation to the total number of rearrangements encountered in the karyotypes. (more...).

CyDASControl

is an Internet Explorer embedded control for ISCN analysis, drawing ideograms of aberrant chromosomes, and developing karyograms (more...).

Web Service

Some functionality is already available as a Web Service. For the Web Service's documentation see here.

ISCN Analysis

This simple program allows the user to analyse both simple (monoclonal) karyotypes as well as polyclonal karyotype.

In the description field, a textual description of the karyotype(s) is entered. A simple karyotype is analysed as such, while for a polyclonal karyotype a composite karyotype is calculated first, and then that composite karyotype is analysed.

The analysis comprises lots of information which can be extracted from the ISCN formula:

composite karyotype: denotes whether the karyotype was marked "composite" ("[cp]")
clone size: size of the clone, if it was noted, otherwise 0.
incomplete: shows whether the karyotyoe was marked "incomplete" ("inc")
double minutes: the double minutes of the karyotype
markers: the marker chromosomes in the karyotype
rings: ring chromosomes whose origin could not be described more closely
chromosome count field: the data given in the chromosome count field
chromosome count: lower and upper limit of the chromosome count
ploidy level: ploidy calculated from chromosome count or taken from ploidy information in the chromosome count field
sex chromosomes: non-aberrant sex chromosomes
count of aberration elements
aberration <number>: a description of each aberration element, the number of metaphases the aberration was found in, its quantitative changes in SCCN, qualitative changes in SCCN, and break points; in case of derivative chromosomes ("der" or "ider" aberrations), the ISCN detailed description is shown; in some cases, fusion products may be given (the feature "fusions" is still in early development)
in the summary section, break points, structural and quantitative aberrations are shown summed up for all aberrations of the karyotype, as well as a Complex Karyotype Aberration Score.
a table shows then the amounts of gains, losses and structural aberrations per chromosomal band.

If errors are encountered during analysis, they are shown in the text field instead of the result.

Drawing aberrant chromosomes

With this program, ideograms for derivative chromosome(s) can be drawn.

In the description field, the textual description of a rearrangement giving raise to one or more derivative chromosome(s) is entered, either using the ISCN detailed notation (e.g. "der(22)(22pter->22q112::9q34->9qter)" (the detailed notation showing symbols for aberration type, e.g. "t(9;22)(9pter->q34::22q112->22qter;22pter->22q112::9q34->9qter)" is not supported because it does not work with more complicated rearrangements) or the ISCN short notation (e.g. "t(9;22)(q34;q112)"). After selecting the desired resolution of the ideogram and the coloring (black and white only or default colors; the desk top version allows for changing the colors), a map viewer to be linked with the chromosomal bands, and the scale, the button "Draw" is clicked and the chromosome is drawn. If an error was encountered in the description of the rearrangement, a message is displayed to show the problem.

Drawing a Karyogram

The ideograms of all chromosomes - both derivative and non-derivative - inferred from an ISCN formula are shown.

In the description field, the ISCN formula is entered following the ISCN standards. Minor errors (e.g. slightly wrong chromosome count, sloppily denoted sex chromosomes, upper case instead of lower case characters, ...) are automatically corrected and the corrected version is shown in the description field.

The desired banding resolution of the ideograms and the coloring (black and white only or default colors; the desk top version allows for changing the colors), a map viewer to be linked with the chromosomal bands, and the scale, can be adjusted.

The drawing sequence indicates the sequence in which chromosomes are to be drawn; "BR" indicates a line break. It is not necessary to include all chromosomes in the field, also duplicates are possible.

If an error was encountered in the description of the rearrangement, a message is displayed to show the problem.

An experimental page for step by step development of a karyogram is also available.

Analysis of Data Sets for Gains, Losses and Breakpoints

This program shows how large data sets can be analysed with CyDAS for recurrent gains and losses as well as recurrent break points. Data from many sources can be analysed, if they were exported into a text file in the Mitelman format (or directly downloaded from the Mitelman database; see HowTo Download data from the Mitelman database) or special other formats for karyotype banding analysis or comparative genome hybridisation (CGH) (see HowTo on Data Formats).

The location of the data file is entered into the "File" field (you may select it using the "Browse" button on the right to it. For analysing data, the maximum number of cases read, and banding resolution can be selected. For drawing, the scaling and a cutoff-level can be selected. A cutoff of 0 means that gains and losses or structural aberration, resp., will be scaled relative to their maximum value.

For technical reasons, the maximum number of cases to be analysed cannot exceed 500. The scaling factor for the images is set to a maximum of 1. Higher values will be ignored. If you want to circumvent these limitations of the online version, you may use the desktop version of CyDAS which is available from the Download section.

Dependence Network

Many distinct rearrangements occur during cancer progression and karyotype evolution. Some of the rearrangements occur preferrable together with specific other rearrangements, and other rearrangements seem to almost exclude each other. Such a dependence is visualized with the Dependence Network.

Data from many sources can be analysed, if they were exported into a text file in the Mitelman format (or directly downloaded from the Mitelman database; see HowTo Download data from the Mitelman database) or special other formats for karyotype banding analysis or comparative genome hybridisation (CGH) (see HowTo on Data Formats).

The location of the data file is entered into the "File" field (you may select it using the "Browse" button on the right to it. For analysing data, the maximum number of cases read, and a pre-processing of data can be selected. The number of rearrangements analysed and a threashold value for a dependence to be shown can be adjusted. The rearrangements shown are the most frequent rearrangements, with the most frequent displayed on top, and the other rearrangements following in clockwise direction with decreasing frequency.

For technical reasons, the maximum number of cases to be analysed cannot exceed 500. Higher values will be ignored, but may be very useful for statistical reasons. If you want to circumvent these limitations of the online version, you may use the desktop version of CyDAS which is available from the Download section. The desk top version also allows you to order the rearrangements interactively.

Evolution Tree

The rearrangements occuring during tumour progression seem to follow some common evolution pathes. Here, we try to describe these evolutionary pathes by analysing the karyotype data from many patients at many stages of tumour progression.

Dependence on Karyotype Complexity

The Aberration Count Distribution shows how often a selected rearrangement was encountered in relation to the total number of rearrangements encountered in the karyotypes.

The CyDASControl

Here, the functions of ISCN Analysis (see above), drawing ideograms of aberrant chromosomes (see above), and drawing of complete karyograms (see above) are combined in an Internet Explorer hosted .NET control running on your computer.

The karyogram functionality is far enhanced in comparison to the Online Example:
You start from a simple karyotype which need not be aberrant, and introduce aberrations step by step. Click into the yellow bar on top the window and enter the first karyotype. Then select from the menu the type of aberration you want to introduce and then click on the desired breakpoints. The ISCN formula is automatically update, even for terribly complex aberrations!

Please note that this control has some requirements:
The CyDASControl requires Microsoft Internet Explorer version 6 or later.
Scripting must be enabled.
The site "http://www.cydas.org/" must be added to the trusted zone.
The .NET Framework 2.0 must be installed (it is freely available from Microsoft).