Biomedical Engineering Reference
In-Depth Information
1
2
1.1
1
2
2
1.1
1
3
2
1.1
1
4
2
1.
1
5
2
1.1
1
0
50000000
100000000
150000000
200000000
250000000
Figure 3.2
Spotfire Genotype and LOH visualization of a single tumor sample relative
to a paired normal sample. Five panels (1-5) for chromosomes 1-5 are shown. For each
panel, on the
x
-axis the position of each SNP is depicted in base pairs from the p-telomere
to the q-telomere of the chromosome. An SNP that is heterozygous in both the normal
sample and paired tumor is represented in yellow diamonds on the 2-line on the
y
-axis.
SNPs that are heterozygous in the normal sample but homozygous in the tumor sample are
represented in red diamonds on the 1-line, while SNPs that are heterozygous in the normal
but with a quality ratio below 0.8 in the paired tumor sample are represented in blue
diamonds on the 1.1 line. LOH is called in regions (relative to their base pair positions
on the
x
-axis), marked by more red and blue markers (SNPs) than yellow markers. (See
Plate 3.2.)
5 Analyze the scatter plot visualization to determine patterns of potential LOH as
described in Figure 3.2.
6 Repeat step 3b-5 to analyze every tumor : normal pair.
Notes
o
See [45] for more details.
PROTOCOL 3.6 Illumina Data Storage, LOH and Genotype Analysis
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)
•
