Biomedical Engineering Reference
In-Depth Information
PROTOCOL 1.8 Data Analysis of Illumina SNP Beadarray
Experiments
Equipment and reagents
•
Illumina BeadScan software for genotyping and the Bioconductor
(www.bioconductor.org) BeadarraySNP package [25]
•
Quantile smoothing software [31].
Method
y
1 Perform an Illumina GoldenGate
TM
assay,
y
according to the protocol supplied by
Illumina, using 1
μ
g of activated DNA (isolated from FFPE tissue) dissolved in 60-100
μ
l
of RS1 buffer.
2Scan
z
the Illumina arrays using the Illumina BeadScan software,
aa
creating (by default)
the following types of files for each of the samples on the array:
•
locs: locations of beads on the array
•
idat: summarized intensity information (binary format)
•
XML: scanner settings.
3 Adapt the Settings.xml
bb
within the beadstudio directory in order to produce the
additional file types.
<
SavePerBeadFiles
>
true
<
\SavePerBeadFiles
>
<
SaveEIFFiles
>
false
<
\SaveEIFFiles
>
<
SaveTextFiles
>
true
<
\SaveTextFiles
>
<
CompressImages
>
true
<
\CompressImages
>
<
ExcludeOutliers
>
true
<
\ExcludeOutliers
>
<
IncludeXY
>
true
<
\IncludeXY
>
4 Perform the genotyping of the scanned images using the GenCall software,
cc
producing
the following types of files for each experiment.
dd
5 *-OPA_LocusByDNA_*.csv: genotyping and quality scores (one sample per row):
•
*-OPA_LocusByDNA_*DNA_Report.csv: summary of allele frequencies for each
sample
•
*-OPA_LocusByDNA_*Final.csv: genotyping and quality scores (each probe and
sample appear on a separate row)
•
*-OPA_LocusByDNA_*Locus_Report.csv: quality index summaries for all probes.
6 Begin copy number analysis
ee
by defining the samples in a sample sheet.
ff
Calculate the
copy number values for all the samples in the experiment using the function
standardNormalization().
7 Plot the raw and smoothed copy number data using the Quantile smoothing
software.
gg
