Biomedical Engineering Reference
In-Depth Information
8 Use the 50th percentiles (displayed on the plots as dotted lines; see Figure 1.2) to
guide identification of gains and losses.
hh
(a)
(b)
Figure 1.2
Chromosome view output of BeadArraySNP showing examples of a colorectal
carcinoma. (a) Chromosome 8 with physical loss at the p-arm and gain at the q-arm.
(b) An example of LOH without a copy number change on chromosome 9. Each red dot
indicates the normalized individual SNP signal; the solid red lines show the smoothed copy
number with the 25th and 75th percentile interval marked with the dashed red lines. The
gray vertical bars above the ideogram show the heterozygous SNPs in the normal sample
that retained heterozygosity in the paired tumor. Black vertical bars show LOH; that is,
heterozygous in the normal and homozygous in the tumor.
Notes
y
Twelve tumor:normal pairs (24 samples) can be profiled using four pools of approximately 1500
SNPs (collectively referred to as
the linkage panel
). The SNPs are hybridized to sentrix arrays,
a matrix of 96 arrays, each detecting about 1500 SNPs. Thus, for each sample, four arrays of
approximately 1500 SNPs each are hybridized and subsequently combined to yield around 6000
genotypes. Alternatively, a genome-wide cancer SNP panel, or custom SNP panels of 1536, 768
or 384 SNPs, can be typed.
z
The allele-specific data obtained from Illumina SNP-arrays can be used to perform both
genotyping and copy number analysis. Although the Illumina software for genotyping performs
satisfactorily in most cases, we have found that there is room for improvement in performing
