Biomedical Engineering Reference
In-Depth Information
PROTOCOL 3.5 Visualization of Genotyping and LOH Data
in Spotfire
Equipment and reagents
A PC with the following specification:
— Intel Pentium 2.0 GHz or above
—memory size
≥
2GB
—hard drive
≥
100 GB
— video display 1280
×
1024 (recommended)
— 17 inch LCD monitor (recommended)
— operating system Windows XP-SP2 (32 bits) or Windows XP-SP2 (64 bits)
•
Microsoft NET framework 1.1 (or above)
•
Microsoft Access 2003
•
Spotfire DecisionSite 9.1 for Functional Genomics (Spotfire, Somerville, MA, USA)
•
Method
1 Open Spotfire DecisionSite for Functional Genomics.
2 Paste the data from the final query containing all sample information (Protocol 3.5,
step 14) from the Access database into Spotfire.
3 Spotfire automatically generates a scatter plot.
o
However, some settings have to be
changed to visualize SNP and LOH information for every tumor sample (see
Figure 3.2).
(a) Select Start Position (bp) on the
x
-axis. This shows the base pair position of the
SNPs from p-ter to q-ter.
(b) Select the ABnormRationorm for one of the tumors on the
y
-axis to visualize the
quality scores relating to possible LOH.
(c) Go to Edit Properties. Select the Trellis tab and Add variable Chromosome Name
(Bind To Columns). Set Columns to 1 and Rows, for example, to 5 to generate a
visualization for sets of five chromosomes per sample.
(d) Select the Markers tab and set Color By the ABnormRationorm for the selected
tumor and Categorical. Customize the Shape to Diamonds. Set Labels to
Locus_Name.
4 In the Query Devices pane, select the Heterozygous SNPs for the paired Normal of the
tumor sample under analysis by deselecting the AA and BB genotypes. This confines the
analysis to the SNPs that are heterozygous in the normal.
