Supplemental Material
Supplemental Table 1. Pearson’s correlation coefficients of 12 Bioscored FFPE samples. In
general there is good agreement between the Bioscore and the correlation of the FFPE sample
to the original frozen sample.
Supplemental Table 2. Signal to noise, and the average number of segments fit via CBS to
matched frozen samples run on both platforms, and matched FFPE samples run on both
platforms. The number of samples for BAC FFPE is larger since many of the samples contained
more than one sample from the FFPE tissue bank.
Supplemental Table 3. BAC aCGH platform summary showing noise (MSE and MAD), signal to
noise, and average number of segments for paired samples analyzed from frozen tissue, FFPE
tissue, and whole genome amplified tissue.
Supplemental Table 4. BAC aCGH platform summary table showing the correlation between the
samples across each of the tissue procurement methods.
analyzed for comparing frozen tissue to FFPE.
Fifteen paired samples were
Eleven paired samples were analyzed for
comparing FFPE tissue to whole genome amplified tissue.
Seven paired samples were
analyzed for comparing frozen tissue to whole genome amplified tissue.
Supplemental Table 1
Bioscore
1.3
1.6
1.9
2.7
3.1
9.6
13.5
13.9
16.4
20.2
21
22
Pearson's
Correlation
0.68
0.46
0.56
0.80
0.70
0.90
0.81
0.48
0.78
0.82
0.73
0.92
Supplemental Table 2
CGH platform/
DNA source
BAC/Frozen
Agilent/Frozen
BAC/FFPE
Agilent/FFPE
#
of Signal to Noise
samples
6
8.051
6
4.186
16
7.796
10
3.256
Avg # of Segments
104.43
132.43
175.19
515.30
Supplemental Table 3
DNA source
BAC/Frozen
BAC/FFPE
BAC/WGA
#
of MAD
Samples
59
.053
24
.083
13
.110
MSE
.010
.028
.058
Signal
Noise
6.946
5.555
4.556
to Avg. # of
segments
101.63
144.87
121.39
Supplemental Table 4
Pearson: log2 T/C
Pearson: segment
Spearman: log2 T/C
Spearman: segment
Frozen : FFPE
.51
.66
.43
.62
FFPE:WGA
.75
.78
.65
.72
Frozen:WGA
.36
.56
.26
.50
2
Supplemental Figure 1. Isolation of individual Hodgkin Reed-Sternberg (HRS) cells using laser capture
microdissection. Samples were mounted on PALM membrane slides (PEN-membrane; Zeiss) and
stained for CD30 (brown) and hematoxylin-eosin counterstained. A) CD30 IHC on FFPE HD patient
sample, 63x on PALM microlaser. Arrows denote rare Hodgkin Reed-Sternberg cells. B) On the PALM
microdissection workstation, cells of interest (i) were designated (ii) for laser (UV-A) trace (iii) and isolated
by UV-A pulse catapult (iv) into a microfuge cap containing TE buffer.
Supplemental Figure 2. Confirmation of aCGH CNAs by FISH for NEDD9 and WISP3 on
chromosome 6. Top panel: The aCGH profile for chromosome 6, RP11-28L24 is circled in red.
Middle panel: The probes RP11-28L24 (WISP3; 6q21; green signal) and RP11-679B17
(NEDD9; 6p24.1; red signal) were used to assess copy number, l to r: interphase nucleus with 6
green (WISP3) and 4 red (NEDD9) signals; metaphase with same signal pattern; DAPI-banded
image of same metaphase showing the deleted 6 chromosomes (hybridize to the green probe
only). These two derivative chromosomes are der(6)del(6)(p12.3)del(6)q14.3), were confirmed
by 24-color karyotyping (lower panel), tinted fluorophore image, left, and blended fluorophore
image at right, both showing 4 copies of chromosome 6 and two copies of the der(6).
Supplemental Figure 3. Whole genome aCGH profile of a frozen sample analyzed in parallel
using BAC aCGH (top) and Agilent aCGH (bottom). CBS segmentation values are in red,
preprocessed log2 probe values are in grey.
Supplemental Figure 4. Whole genome aCGH profile of an FFPE sample analyzed in parallel
using BAC aCGH (top) and Agilent aCGH (bottom). CBS segmentation values are in red,
preprocessed log2 probe values are in grey. Note this is a different sample than analyzed in
Figure 3.
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