TechnicalNote
OncoScan® CNV FFPE Assay Kit: no need to re-validate for
existing OncoScan® assay users
OncoScan® CNV FFPE Assay Kit (P/N 902695) offers the identical DNA copy number functionality as OncoScan® FFPE Assay Kit (902293),
minus somatic mutations. The aim of this technical note is to demonstrate the concordance between copy number and quality metrics on
the two platforms, thereby reducing/removing the need to re-validate the assay for research use.
Metrics compared across the two platforms
The following metrics were used to compare the two platforms:
n
MAPD (median of the absolute values of all pairwise differences)
n
ndSNPQC (SNP Quality Control of Normal Diploid Markers)
n
Percent Match (in copy number calls between the two products)
In addition to the above metrics, whole-genome copy number plots are shown for samples analyzed using the two platforms.
MAPD
MAPD is a global measure of the variation of all microarray probes across the genome. It represents the median of the distribution of
changes in log2 ratio between adjacent probes. Since it measures differences between adjacent probes, it is a measure of short-range
“noise” in the microarray data. Lower MAPD values are indicative of lesser noise. The MAPD graph in Figure 1 shows values for 25 samples
run in two replicates across eight tumor types and three tissue types with OncoScan FFPE Assay Kit and OncoScan CNV FFPE Assay Kit. The
experimental variability observed for MAPD is similar between OncoScan FFPE and OncoScan CNV FFPE assay kits, and the distribution in
MAPD values is indistinguishable between the two platforms.
Figure 1. MAPD values for 25 samples run in two replicates for OncoScan® CNV Assay Kit and OncoScan® FFPE Assay Kit.
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ndSNPQC
The ndSNPQC metric is a measure of how well genotype
alleles are resolved in the microarray data. ndSNPQC is only
applied to normal diploid markers (i.e., those that have
been determined to have copy number = 2 in the sample).
Larger ndSNPQC values are indicative of better marker
resolution. The ndSNPQC graph in Figure 2 shows values for
25 samples run in two replicates across eight tumor types
and three tissue types with OncoScan FFPE Assay Kit and
OncoScan CNV FFPE Assay Kit. While there is some natural
variability between replicates, the difference between the
assays is unnoticeable compared to running replicates under
the OncoScan FFPE assay.
Figure 2. ndSNPQC values for 25 samples run in two replicates
for OncoScan® CNV Assay Kit and OncoScan® FFPE Assay Kit.
Percent Match in copy number calls
The “Percent Match” metric refers to the percentage of
markers that had the same copy number call across two or
more observations. Figure 3 shows the comparisons of copy
number calls when running two replicates of six normal
samples (FFPE normal and cell line) for each of the two
assays (OncoScan FFPE assay and OncoScan CNV FFPE
assay), followed by comparing replicates between assays.
The graph shows comparable performance between the
two products (OncoScan FFPE Assay Kit and OncoScan
CNV Assay Kit). On average, less than 1% of the markers
changed copy number state when comparing the two
assays on normal samples.
Figure 3. Percent Match: Percent of markers with the same copy number call between OncoScan® CNV FFPE Assay Kit and
OncoScan® FFPE Assay Kit. Six normal samples were compared: three FFPE normal and three cell line samples.
The table below shows data from the six samples run twice with OncoScan
FFPE® Assay Kit and twice with OncoScan® CNV FFPE Assay Kit. The column
Percent Match (FFPE-FFPE) shows the Percent Match between two replicates run
with OncoScan FFPE Assay Kit; Percent Match (CNV-CNV) shows the Percent Match
between two replicates run with OncoScan CNV FFPE Assay Kit; and Percent Match
(FFPE-CNV) shows the Percent Match when comparing the two replicates across
platforms, resulting in four Percent Match numbers per sample.
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Sample
Percent
Match
(FFPE-FFPE)
Percent
Match
(CNV-CNV)
s1
100.00
99.98
99.98
99.98
99.98
99.98
s2
99.97
99.96
99.96
99.96
99.96
99.99
s3
99.98
99.99
100.00
100.00
99.99
99.98
s4
99.98
99.94
99.99
99.94
99.93
99.97
s5
99.94
99.66
99.66
99.95
99.96
99.65
s6
99.94
99.95
99.91
99.92
99.96
99.95
Percent Match (FFPE-CNV)
Whole-genome view
In addition to the metrics analyzed above, whole-genome copy number plots of samples analyzed by the two platforms (OncoScan
FFPE Assay Kit and OncoScan CNV FFPE Assay Kit) were examined. Figure 4 shows that on a genome-wide scale, complex copy number
signatures are similar across platforms. The upper track in the plot represents the log2 copy number ratio, and the bottom track represents
the B-allele frequency.
Figure 4. Whole-genome copy number views of tumor samples processed with OncoScan® FFPE Assay Kit and OncoScan® CNV FFPE
Assay Kit.
Ovarian tumor, Ploidy: 2, 60% aberrant cells
Analyzed with OncoScan® FFPE Assay Kit
Analyzed with OncoScan® CNV FFPE Assay Kit
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For Research Use Only. Not for use in diagnostic procedures.
P/N GCL05777 Rev. 1
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