Method and system for visualizing common aberrations from multi-sample comparative genomic hybridization data sets
A computer-implemented method for viewing comparative genomic hybridization (CGH) data is provided. In certain embodiments, the method comprises: a) inputting a plurality of CGH data sets for a corresponding plurality of genomic samples into a computer memory; b) analyzing the CGH data sets using an aberration calling method to identify chromosomal regions having aberrant copy number; and c) producing a graphical user interface that shows graphical representations of a chromosomes from each of the genomic samples.
1 . A computer-implemented method for viewing comparative genomic hybridization (CGH) data, comprising:
a) inputting a plurality of CGH data sets for a corresponding plurality of genomic samples into a computer memory;
b) analyzing said CGH data sets using an aberration calling method to identify chromosomal regions having aberrant copy number; and
c) producing a graphical user interface that shows graphical representations of a chromosome from each of said genomic samples, said graphical representations showing said chromosomal regions having aberrant copy number.
2 . The computer-implemented method of claim 1 , wherein said graphical representations of said chromosome are aligned adjacent to each other.
3 . The computer-implemented method of claim 1 , further comprising executing instructions to identify chromosomal regions having aberrant copy number that are common in said chromosome.
4 . The computer-implemented method of claim 3 , further comprising indicating said common aberrant regions on said graphical representations of said chromosome.
5 . The computer-implemented method of claim 1 , wherein said inputting is selecting or uploading.
6 . The computer-implemented method of claim 1 , wherein the copy number of said chromosomal regions having aberrant copy number is indicated by a color code.
7 . The computer-implemented method of claim 1 , wherein said method comprises selecting a sub-set of said data sets for showing on said graphical user interface.
8 . The computer-implemented method of claim 1 , wherein said method includes arranging the order of said graphical representations according to similarities in their regions having aberrant copy number.
9 . The computer-implemented method of claim 1 , wherein said method includes provides a tree in which said one or more chromosomes are grouped according to similarities in their regions having aberrant copy number.
10 . The computer-implemented method of claim 1 , wherein said method includes executing computer-readable instructions that are at a remote location to said graphical user interface and transmitting data from said remote location to said graphical user interface.
11 . The computer-implemented of claim 1 , wherein said method further includes receiving said CGH data sets from a remote location.
12 . A computer-readable medium comprising:
instructions for inputting a plurality of CGH data sets for a corresponding plurality of genomic samples into a computer memory;
instructions for analyzing said CGH data sets to identify chromosomal regions having aberrant copy number; and
instructions for producing a graphical user interface that shows graphical representations of a chromosome from each of said genomic samples, said graphical representations showing chromosomal regions having aberrant copy number.
13 . The computer-readable medium of claim 12 , wherein said graphical representations are aligned next to each other in said graphical user interface.
14 . The computer-readable medium of claim 12 , further comprising instructions to identify regions of aberrant copy number that are common to said chromosomes.
15 . The computer-readable medium of claim 14 , further comprising indicating said common regions on said graphical user interface.
16 . A computer comprising the computer readable medium of claim 12 .
17 . The computer of claim 16 , further comprising a user interface for inputting a plurality of CGH data sets into a computer memory.
18 . A method comprising:
a) performing array-based CGH assays on a plurality of genomic samples to produce a corresponding plurality of CGH data sets;
b) inputting said CGH data sets into a computer of claim 16 ; and
c) executing said instructions to produce a graphical user interface that shows graphical representations of a chromosome from each of said genomic samples, said graphical representations showing chromosomal regions having aberrant copy number.
19 . The method of claim 18 , wherein said graphical representations are aligned next to each other in said graphical user interface.
20 . The method of claim 18 , further comprising executing instructions to identify regions of aberrant copy number that are common to said chromosomes.
21 . The method of claim 20 , wherein said common regions are indicated on said graphical user interface.