Preferential Occurrence of Chromosome Breakpoints within Early Replicating Regions in Neuroblastoma.
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Isabelle Janoueix-Lerosey1, Philippe Hupé2,4, Zofia Maciorowski3, Philippe La Rosa4, Gudrun Schleiermacher1, Gaelle Pierron5, Stéphane Liva4, Emmanuel Barillot4 and Olivier Delattre1
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1 INSERM U509, Laboratoire de Pathologie Moléculaire des Cancers, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
2 UMR 144 CNRS, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
3 Service de Cytométrie, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
4 Service Bioinformatique, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
5 Unité de Genétique Somatique, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
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This replication timing data analysis was based on the GLAD algorithm (Hupé et al, 2004) and the VAMP software (La Rosa et al, submitted) developed by the Bioinformatics group from Institut Curie.
Abstract
Data
description
Data visualization
withing VAMP
Guidelines to visualize data:
Raw Data
Abstract
Neuroblastoma
(NB) is a frequent paediatric extra cranial solid tumour
whose genetic hallmark is the occurrence of unbalanced translocations.
Previous analysis of NB cell lines using chromosomal CGH and 24-colour
karyotyping suggested that the majority of the breakpoints
corresponding
to these unbalanced translocations mapped to early replicating
chromosome
bands. In order to better evaluate the relationship between the
position
of the breakpoints corresponding to unbalanced translocations and
replication timing in NB cell lines, we have now used genome wide
arrays
containing 3400 PAC/BAC clones spaced at approximately 1 Mb intervals:
(1) to further refine the mapping of breakpoints in 28 NB cell lines by
a
classical array-CGH
method; (2) to assess replication timing of
sequences
during the S phase of the cell cycle in 7 NB cell lines, using the
method
recently described by K. Woodfine et al (2004).
Data
description
Data
corresponding to these experiments are visualized using VAMP
(Visualization and Analysis of CGH array, transcriptome and other
Molecular Profiles) and organized into 4 folders:
The BREAKPOINTS
folder contains the position of the 142 breakpoints associated to
colour transition and gain or loss of genetic material by cCGH that
have been further mapped by array-CGH. Breakpoint
positions were determined using the DAGLAD algorithm (Hupé
et al,
manuscript in preparation), a recently modified version of GLAD
(Hupé
et al, 2004).
The CELL-LINES-CGH
folder contains the array-CGH profiles
for the 28 NB cell lines.
The CELL-LINES-RT
folder contains the replication timing
profiles for the 7 cell lines : for each cell line, 2 profiles were
obtained since replication timing was evaluated after a sort of the
total
S phase or a sort of the first quarter of the S phase (S1). This folder
also contains the Average-Total S phase and Average-S1 profiles
obtained
after calculating an average replicating ratio for the 7 samples, in
total S or S1 fractions, respectively.
The SANGER-RT
folder
contains the replication timing
profile drawn from the data obtained by K. Woodfine et al (2004) on a
human lymphoblastoid cell line of normal karyotype after a total S
phase
sort.
Each
folder includes 2 subfolders, “arrays”
and “chromosomes”
that enable the visualization of the whole genome profiles or the
visualization of only a selected chromosome, respectively.
Data visualization
within VAMP
You have to launch the VAMP interface clicking the button below:
Warning: configure your java
virtual machine according the following
instructions. Your browser must allow java to be used.
Guidelines to visualize data
Some guidelines are given below to help the user visualizing the data
within VAMP interface:
1 - Replication
Timing Data
Close
the previous window and open a new window
View
-> New View -> Double View -> Point View
Import the
averaged replication timing data
File
-> Import -> In Top Panel -> CELL-LINES-RT -> Arrays-> average-TotalS
View
-> Current View -> Top Panel -> Gained/Lost Color Codes
Import the
other replication timing array data
File
-> Import -> In Bottom Panel -> CELL-LINES-RT -> Arrays
(and select the array you want to visualize then click on Import data)
View
-> Current View -> Bottom Panel -> Gained/Lost Color Codes
Red = early replicated
Green = Late replicated
2 - Comparison
between Sanger's data and Curie's data
Close
the previous window and open a new window
View
-> New View
-> Simple View -> Point View
File
-> Import -> SANGER-RT -> Arrays ->
SANGER-RT
File
-> Import -> CELL-LINES-RT -> Arrays ->
average-TotalS
View
-> Current View -> GNL Color Codes
View
-> Current View -> Show Smoothing Line
Scale
the data in Y axis
3 - Array
CGH data
Import
all the array CGH data
File -> Import
-> CELL-LINES-CGH -> Arrays
Select All the arrays and then click on Import data
Increase
the scale in Y axis and X axis
Add
the results of the analysis by the GLAD algorithm
View -> Current
View -> Show Smoothing Line
View -> Current View -> Show Breakpoints
View -> Current View -> Gained/Lost Color Codes
Green = Loss
Yellow = Normal
Red = Gain
Blue = Amplicon
Select
and copy all the array CGH data
Edit -> Select
All and Copy
Paste
the data in karyotype view
View -> New View
-> Simple View -> Karyotype Classic View
Edit -> Paste
View -> Current View -> Gained/Lost Color Codes
View -> Current View -> Show Smoothing Line
Scale the data in Y axis
N.B. The default behaviour is to plot the data in LogRatio. If you want
to
switch to Ratio then:
Edit
-> Select All
Tools
-> CGH
-> Change CGH Ratio L to M
4 - Comparison
between breakpoints position and replication timing
Open
a new window
View
-> New View -> Double View -> Point View
Import the
averaged replication timing data
File
-> Import -> In Bottom Panel -> CELL-LINES-RT ->
Arrays -> average-TotalS
View
-> Current View -> Bottom Panel -> Gained/Lost Color Codes
Import the
breakpoins data
File
-> Import -> In Top Panel ->
BREAKPOINTS -> Arrays
-> Breakpoints
Click on Y-range
and set Max
to 2 and Apply
Hightlight the region early replicated
Tools
-> In Bottom Panel -> CGH -> Minimal Alteration
Select "widens regions"
unselect "Amplicon" and "Lost"
Click on OK
Raw Data
Raw data (gpr files) for the 28 cell line array CGH profiles can de downloaded here.
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The breakpoints
detection has been performed using the GLAD
algorithm
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To download the java plugin click
here
