KaryoReader©

BACKGROUND: Characterization of non-random recurrent chromosomal aberrations has proven to be a very useful instrument for identification of genes related to human cancers and other genetic diseases and for improving diagnosis and prognosis of certain types of cancers. However, cytogenetic data are very cryptic and chromosomal aberrations show a high degree of complexity, making the systematical analysis of cytogenetic data very challenging. More critical chromosomal breakpoints and complex cytogenetic patterns characteristic of genetic diseases await to be discovered using comprehensive cytogenetic data analyzed with new strategies and methodologies.

KaryoReader© is a computer program that parses the karyotypic data and calculates the detailed chromosomal changes aiming to facilitate systematic analysis of cytogenetic data at large scales, such as the data in the Mitelman Database of Chromosome Aberrations in Cancer, and to identify novel cytogenetic signatures associated with specific genetic diseases.

INPUT DATA REQUIREMENTS: KaryoReader© is designed to work with karyotypic data strictly following the International System for Human Cytogenetic Nomenclature (ISCN 1995)(A list of ISCN Abbreviated Terms and Symbols is available here). Input data needs to be put into a plain text file with the fields delimited by certain characters. The processing by KR only involves the Case ID, the tumor type, the tumor site, and the karyotype description. If you have your own data, please follow the section below to tell KR the structure of your data.The text file retrieved from the Mitelman Database can be directly used as the input.

Data input from plain text file
(A test file--420 cases of Wilms' tumors from Mitelman database is available here)

Is the data format strictly follows the format used by the Mitelman Database?
Yes     No

If no, please specify your own format below by giving the column number for each of the fields:
Karyotype     Unique Identifier AND (Leave the second box as "none" if just one identifier)
Additional columns to keep in the output AND AND AND AND AND

Select or unselect the options for data processing:

Exclude polyploid     Exclude uncertainty data     Breakpoints only     Parse idem

Select output format:

A. Aberration frequency (See an example; A frequency plot like this example is also available)
To make a frequency plot using previously downloaded frequency data (output option A), click here

B. Aberrations in binary format (see an example)    
Option for A & B: minimal frequency (%) to be listed (a number between 0 and 100, default is 0 to list all aberrations)

C. One aberration per line (see an example)

D. One case per line (see an example)    


A list of syntax used in the output
This service is provided by the Bioinformatics Group of Roswell Park Cancer Institute and is partially supported NCI grant CA16056 to RPCI, NCI grant CA101515 and a Roswell Alliance Foundation to Dr. Ping Liang. Please cite this web site in your publications involving the use of this program. Should you have any comments/suggestion, please send to Dr. Ping Liang.   Last modified: Friday, 09-Mar-2007 15:42:54 EST.