supplemental figure legends may 1 ah edited 20 gain 0.039 c19mc amp
TRANSCRIPT
1
Supplemental Figure Legends
Figure 1 Gene expression profiles define 3 molecular sub-groups of CNS-PNET
Multiple unsupervised analyses were performed on human HT-12v4 expression array (Illumina)
data from 51 primary CNS-PNET samples. Cluster patterns were determined re-iteratively using
an initial set of 1000 genes with the highest co-efficient of variation to establish the most stable
tumour clusters achievable with a minimal sub-set of genes. Three molecular sub-groups of
CNS-PNETs were independently indicated by A. Unsupervised Hierarchical Cluster
(HCL)analyses, B.Non-negative Matrix Factorization (NMF) and,C. Principal Component
Analysis (PCA). Individual tumours corresponding to sub-groups 1, 2 and 3 are respectively
indicated by green, blue and purple coloured boxes or spheres.
Figure 2 Validation of sub-group specific gene expression signatures
Quantitative RT-PCR analysis was performed to confirm gene expression patterns observed from
supervised analyses of microarray data; gene expression levels (∆Ct) determined relative to actin
are represented.
A. Expression levels of select qRT-PCR validated genes significantly enriched within each
tumour group (p≤0.05) is shown in a global skyline plot; a mean value of n=3 is plotted/sample.
B.Meanexpression levels of individual specific lineage/signalling genes (n=3 replicas) with
robust and significant over-expression in each tumour sub-group are represented with SEM for
specific mRNA (horizontal bars). Group 1, 2 and 3 specific genes are indicated by green, blue
and purple bars or spheres respectively.
Figure 3 Immuno-histochemical analyses of IGF2
Placental trophoblastic cells are known to express high levels of IGF2 and exhibit cytoplasmic
and membranous IGF2 immuno-stain patterns (www.proteinatlas.org), thus polyclonal IGF2
antibodies (Santa Cruz, California) were tested for IHC analyses using placental tissues as
2
positive controls as described in methods. Staining patterns of placenta tissue treated with
primary IGF2 antibody at 1:50 (A), 1:75 (B), 1:100 (C) dilutions, and no primary antibody as
negative control (D) are shown.
Figure 4 Immuno-histochemical analyses of LIN28 and OLIG2 expression in CNS-PNET
A. LIN28 and OLIG2 which exhibited highest differential gene expression levels between
tumour sub-groups, was tested by corresponding immuno-assays on a test cohort of 22 CNS-
PNET for which sub-group specific gene expression patterns had been established
(Supplementary Table 1). Levels of LIN28 and OLIG2 protein expression in tumours of each
sub-group was determined by IHC analyses of tumour cores on TMA or on individual tumour
slides and scored as described in methods;protein expression levels are represented as SEM.
B.Heat map shows gene expression values for LIN28 and OLIG2 as determined from Illumina
HT-12 v4 expression arrays, in relation to LIN28 and OLIG2 IHC scores determined for each of
the 22 individual tumours as described in Figure A.
C. Summaryof all CNS-PNET samplesthat could be classified into molecular sub-groups based
on gene expression profiles and/or immuno-histochemical analyses of LIN28 and OLIG2.
Figure 5 Expression of lineage and signalling pathway genes in CNS-PNETs
A. Gene expression patterns of glial and neurogenic markers conventionally used to distinguish
malignant glial from neural tumours in CNS-PNET sub-groups 1, 2 and 3. Normalized array
expression values and significance of enrichment, derived from supervised t-test of sub-group
specific gene sets, are represented in relation to tumour sub-groups. For enrichment of specific
genes in individual sub-groups, sub-groups were collapsed to allow binary comparisons.
B. Quantitative RT-PCR analyses of cell lineage genes in 51 CNS-PNET primary samples
profiled with Illumina gene expression arrays. Meanexpression levels (Ct) of individual
specific lineage genes (n=3 replicas) in each tumour sub-group are represented in relation to
3
SEM for specific mRNA (horizontal bars). Group 1, 2 and 3 specific genes are indicated by
green, blue and purple bars or spheres respectively.
C. Quantitative RT-PCR analyses of cell signalling genes, PDGFRA and ERBB3, in primary 51
CNS-PNET. Meanexpression levels (Ct) of individual specific signalling genes (n=3 replicas)
in each tumour sub-group are represented in relation to SEM for specific mRNA (horizontal
bars). Group 1, 2 and 3 specific genes are indicated by green, blue and purple bars or spheres
respectively.
Figure 6 Recurrent focal copy number abnormalities (CNAs) in CNS-PNETs
DNA copy number profiles of 85 primary CNS-PNETs were generated using the Human Omni
2.5 Quad SNP array, and analysed using Partek genomics and dChip.Heat map and copy number
profiles of specific CNAs were generated using dChip and plotted relative to chromosome
ideograms.
A. Heat map and copy number plots of recurrent focal C19MC locus amplification on
chr19q13.41 in group 1 tumours.
B. Heat map and copy number plotsof recurrent chr2 gains in group 1 CNS-PNET.
C. Copy number plot and FISH analyses of focal MYCNamplification on chr2p24 in one sub-
group 3 tumour.
D. Heat map, copy number plot and FISH validation of focal CDKN2A/B loss on chr9p21 seen in
10primary group 2 and 3 CNS-PNET.
Figure 7 Molecular sub-groups of CNS-PNET have distinct DNA copy number patterns
DNA copy number profiles of primary CNS-PNET were generated using the Human Omni 2.5
Quad SNP array and recurrent copy number patterns established using CNV partition (Partek)
analyses. Significant enrichment of specific copy number abnormalities (CN lesion) in tumour
sub-groups was determined based on 59 primary samples with known molecular sub-grouping.
4
Heat map shows select CN lesions which correlate significantly, as determined using Chi-square
analyses, with specific CNS-PNET sub-groups. Recurrent focal lesions targeting CDKN2A/2B in
group 2 and 3, and C19MC in group 1 CNS-PNET are indicated by asterisks.
Picard et al Supplemental Fig 1
2 4 6 8 10
0.88
0.94
1.00
Cophenetic Coefficient
k
Cop
hene
tic c
orre
latio
n
2 4 6 8 10
0.85
0.95
Cophenetic Coefficient
k
Cop
hene
tic c
orre
latio
n
2 4 6 8 10
0.85
0.95
Cophenetic Coefficient
k
Cop
hene
tic c
orre
latio
n
2 4 6 8 10
0.85
0.95
Cophenetic Coefficient
k
Cop
hene
tic c
orre
latio
n
2 4 6 8 10
0.85
0.95
Cophenetic Coefficient
k
Cop
hene
tic c
orre
latio
n
2 4 6 8 10
0.80
0.90
1.00
Cophenetic Coefficient
k
Cop
hene
tic c
orre
latio
n
2 4 6 8 10
0.86
0.92
0.98
Cophenetic Coefficient
k
Cop
hene
tic c
orre
latio
n
2 4 6 8 10
0.85
0.95
Cophenetic Coefficient
k
Cop
hene
tic c
orre
latio
n
2 4 6 8 10
0.80
0.90
1.00
Cophenetic Coefficient
k
Cop
hene
tic c
orre
latio
n
2 4 6 8 10
0.80
0.90
1.00
Cophenetic Coefficient
k
Cop
hene
tic c
orre
latio
n
2 4 6 8 10
0.80
0.90
1.00
Cophenetic Coefficient
k
Cop
hene
tic c
orre
latio
n
200 genes 250 genes
300 genes 350 genes 400 genes
450 genes 500 genes 550 genes
600 genes 750 genes 1000 genes
200 genesk= 3
Cophenetic coef.= 0.9711samples
sam
ples
sam
ples
BGROUP 1 GROUP 2 GROUP 3
Tumour Sub-groups
Hierachical ClusteringA
Picard et al Supplemental Fig 1
C
46-17
-71
-13
-9
-5
-1
%2.51 2# CP
3
7
11
15
19
23
PCA Mapping (46.6%)
912.7
16.420.1
23.8
PC #3 9.43%
27.531.2
34.938.6
42.3
-29.7 -23.8
-65.1 -59.2 -53.3 -47.4
PC #1 21.9%
-41.5 -35.6
-17.9-12
PC #
2 15
.2%
PC #1 21.9 %
PC #3 9.43%
Principal Component Analysis(46.6%)
0
0.5
1
1.5
2
2.5
3
3.5
Picard et al Supplemental Fig 2
A
B
OLIG1
p=0.0056
p=0.0015
NKX6-2
MSX1 ZIC2p=0.020 p=0.045
mR
NA
Rel
ativ
e to
Act
in (1
0 )-1
mR
NA
Rel
ativ
e to
Act
in (1
0 )-2
CRABP1
GLI2
p<0.001
p=0.0077
vp=0.043v
Group 1Group 2
Group 3
Grp 1 Grp 2 Grp 3
Grp 1 Grp 2 Grp 3
Grp 1 Grp 2 Grp 3
Grp 1 Grp 2 Grp 3
Grp 1 Grp 2 Grp 3
Grp 1 Grp 2 Grp 3
Grp 1 Grp 2 Grp 3
TGFBR3
0
5
10
15
20
0
1
2
3
4
5
0
5
10
15
0
2
4
6
8
10
0
5
10
15
0
20
40
60
0
2
4
6
Picard et al Supplemental Fig 3
A
C
50µm
50µm50µm
B
D
50µm
Picard et al Supplemental Fig 4
ALIN28 OLIG2
Ave
rage
%
Imm
uno-
posi
tive
Cel
ls * p<0.01
1 2 3 1 2 3
BTumour Sub-group
*
*
IHC
1 2 3 Total samples
Gene Expression
14 22 15 51
IHC 15 14 28 57
Total Samples / Group
29 36 43 108
% / Group 27% 33% 40% 100%
Tumour Sub-group
010203040506070
C
109 111 138 3 5 6 158 171 173 174 187 191 196 22 30 4 132 172 197 20 25 9PNET
Expression
IHC score
Expression
IHC score
LIN28
OLIG2
Group 1 Group 2 Group 3
137Expression
IHC Pos Neg
1
Picard et al Supplemental Fig 5
LIN28B ASCL1
PDGFRA
GFAPNEUROG2 TUBB3
ERBB3
p=0.031
p=0.065
p=0.31
p=0.18 p=0.091 p=0.12
p=0.12
NESTINp=0.11
A
B
C
mR
NA
Rel
ativ
e to
Act
in (1
0 )-1
mR
NA
Rel
ativ
e to
Act
in (1
0 )-1
mR
NA
Rel
ativ
e to
Act
in (1
0 )-1
mR
NA
Rel
ativ
e to
Act
in (1
0 )-1
mR
NA
Rel
ativ
e to
Act
in (1
0 )-2
p Value
0.042
0.058
0.64
0.36
0.35
0.26
0.049
0.42
<0.001
<0.001
0.0012
Group 1 Group 2 Group 3
Grp 1 Grp 2 Grp 3
Grp 1 Grp 2 Grp 3
Grp 1 Grp 2 Grp 3
Grp 1 Grp 2 Grp 3
Grp 1 Grp 2 Grp 3
Grp 1 Grp 2 Grp 3
Grp 1 Grp 2 Grp 3
NEUROG2
NEUROG1
NEUROD2
NEUROD1
NES
MAP2
SYP
ATOH1
ASCL1
GFAP
SYPL1
Genes Comparison
grp 2 vs 1&3
grp 1 vs 2&3
grp 3 vs 1&2
grp 2 vs 1&3
grp 1 vs 2&3
grp 3 vs 1&2
Grp 1 Grp 2 Grp 3
0
1
2
3
0
1
2
3
4
0
20
40
60
80
100
mR
NA
Rel
ativ
e to
Act
in
0
50
100
150
mR
NA
Rel
ativ
e to
Act
in
0
1
2
3
4
5
0
100
200
300
400
500
mR
NA
Rel
ativ
e to
Act
in
0
2
4
6
0
5
10
15
20
25
Picard et al Supplemental Fig 6
A B
CDKN2A
CDKN2B
MYCN
DDX12p24
.32p
24.1
9p21
.39p
21.1
C D
Tumour FISH Tumours FISH
19q1
3.41
Chr
omos
ome
2
C19MC
PNET111
PNET135
PNET138
PNET14
PNET148
PNET15
PNET109PNET3
PNET40
PNET42
PNET43PNET5
PNET54PNET6
PNET91
PNET93
PNET94 2.20092 8750 Sample ID
2q2p
MYCN, Chr2p24.3
control, Chr2q11.2
CDKN2A/B, Chr9p21
control, Chr9p21
Tumours Tumours
Chr 19q13 CN Profile Chr 2 CN Profile
Chr 2p CN Profile Chr 9p CN Profile
Loss Gain Loss Gain
Loss GainLoss Gain
2 2
2 2
Picard et al Supplemental Fig 7
Group 1 Group 2 Group 3
Loss Gain
5
8
9
10
4
11
7
12
13
3
14
15
16
2
17
18
19
1
202122
6
Chr 2 Gain
CN Lesion p Value
<0.001
Chr 3 Gain 0.039
Chr 9 p Loss 0.009CDKN2A/B Loss 0.004
Chr 14 Loss 0.009
Chr 20 Gain 0.039C19MC Amp <0.0001
Chr 8 p Gain 0.027
Chr
omos
ome
Chr 13 Gain 0.009
Supplemental Table 1: Participating Centres
1. Hospital for Sick Children, Toronto, Canada.
2. Queen’s Medical Centre, Nottingham, UK.
3. John Hopkins University School of Medicine, Baltimore, USA.
4. Seoul National University Children’s Hospital, Seoul, South Korea
5. Asan Medical Center, Seoul, Korea
6. German Cancer Research Center, Heidelberg, Germany
7. Children’s Memorial Hospital, Chicago, USA
8. Schneider Hospital, PetachTikva, Israel
9. Kumamoto University, Japan
10. Virginia Commonwealth University, Virginia, USA
11. Newcastle University, Newcastle Upon Tyne, United Kingdom
12. Alberta Children's Hospital, Calgary, Canada
13. Children’s Hospital Boston, Boston, USA
14. Texas Children’s Hospital, Texas, USA
15. Chinese University of Hong Kong, Hong Kong, China
16. Institute of Cancer Research, Sutton, United Kingdom
17. St. Jude Research Hospital, Memphis, USA
18. Birmingham Children’s Hospital, Birmingham, UK
19. Cookridge Hospital, Leeds, UK
Supplemental Table 2: Clinicopathologic characteristics of tumour samples
Annotation Alternate
Annotation Group Gender Diagnosis
Age at Diagnosis
(years) Treatment
Metastasis Status
Survival Status
Survival Time
(years)
Illumina HT-12 v4
OmniQuad 2.5 SNP
Immunohistochemistry
PNET3 Group 1 female PNET/EP 4.08 Chemo M0 Dead 0.50 √ √ √
PNET4 Group 2 female PNET 10.75 Chemo/XRT M0 Dead 0.67 √ √ √
PNET5 Group 1 female PNET/EP 1.67 Chemo M0 Dead 0.58 √ √ √
PNET6 Group 1 female PNET/EP 2.42 Chemo M0 Dead 1.00 √ √ √
PNET7 Group 2 male PNET n/a n/a n/a n/a n/a √ √ no material
PNET8 Group 3 male PNET 6.00 n/a M+ Alive n/a no material √ √
PNET9 Group 3 male PNET 4.08 n/a M+ Alive 0.42 √ √ √
PNET10 n/a n/a PNET n/a n/a n/a n/a n/a no material √ no material
PNET11 n/a n/a PNET n/a n/a n/a n/a n/a no material √ no material
PNET15 Group 1 male PNET/ME 0.42 None M0 Alive n/a √ √ no material
PNET17 Group 3 male PNET 1.83 Chemo/XRT M0 Dead 6.33 √ √ no material
PNET20 Group 3 female PNET 11.00 n/a n/a Dead 1.00 √ √ √
PNET22 Group 2 female PNET 9.67 n/a n/a Dead 2.00 √ √ √
PNET25 Group 3 male PNET 2.00 n/a n/a n/a n/a √ √ √
PNET28 Group 3 male PNET 4.00 n/a n/a n/a n/a no material √ √
PNET30 Group 2 male PNET 12.00 n/a n/a n/a n/a √ √ √
PNET31 Group 2 female PNET n/a n/a n/a n/a n/a √ √ no material
PNET36 Group 2 male PNET 10.00 Chemo/XRT n/a Alive 4.00 √ √ no material
PNET37 Group 3 female PNET 8.00 Chemo/XRT n/a Alive 3.92 √ √ no material
PNET40 Group 1 male PNET 2.50 None M0 Dead 0.01 √ √ no material
PNET42 Group 1 female PNET 3.17 Chemo/XRT M0 Dead 0.83 √ √ no material
PNET43 Group 1 male PNET 1.50 Chemo M+ Dead 0.83 √ √ no material
PNET44 Group 2 male PNET 11.00 Chemo M0 Dead 1.75 √ √ no material
PNET47 Group 2 female PNET 2.58 Chemo/XRT M+ Alive 11.17 √ √ no material
PNET48 Group 3 female PNET 1.00 Chemo M0 Dead 2.33 √ √ no material
PNET49 n/a male PNET 17 n/a n/a n/a n/a no material √ no material
PNET51 n/a female PNET 3 n/a n/a n/a n/a no material √ no material
PNET52 n/a female PNET 8 n/a n/a n/a n/a no material √ no material
PNET53 n/a female PNET 3 n/a n/a n/a n/a no material √ no material
PNET54 Group 1 male PNET/EP 3 n/a M0 n/a n/a no material √ no material
PNET55 n/a female PNET 2 n/a n/a n/a n/a no material √ no material
PNET56 Group 1 female PNET/ETNATR 1.67 n/a M0 Dead 0.25 no material no material √
PNET59 Group 3 n/a PNET n/a n/a n/a n/a n/a no material no material √
PNET61 Group 3 female PNET 0.67 n/a n/a Dead n/a no material no material √
PNET62 Group 3 female PNET 1.00 n/a n/a Dead n/a no material no material √
PNET64 Group 3 male PNET 16.00 n/a n/a Alive n/a no material no material √
PNET65 Group 3 male PNET 10.00 n/a n/a Alive n/a no material no material √
PNET66 Group 2 female PNET 6.00 n/a n/a Dead n/a no material no material √
PNET67 Group 1 male PNET/ETNATR 3.00 n/a n/a Dead n/a no material no material √
PNET68 Group 3 male PNET 2.00 n/a n/a Alive n/a no material no material √
PNET71 Group 2 male PNET 7.00 n/a n/a Alive n/a no material no material √
PNET72 Group 3 male PNET 0.06 n/a n/a Dead n/a no material no material √
PNET75 Group 3 male PNET 0.92 n/a n/a Dead n/a no material no material √
PNET78 Group 3 male PNET 4.00 n/a n/a Alive n/a no material no material √
PNET79 Group 3 male PNET/ME 4.00 n/a n/a Dead n/a no material no material √
PNET81 Group 1 female PNET/ETNATR 3.00 n/a n/a Alive n/a no material no material √
PNET82 Group 1 female PNET/ME 12.00 n/a n/a Alive n/a no material no material √
PNET91 Group 1 female PNET n/a n/a n/a n/a n/a √ √ no material
PNET93 Group 1 female PNET n/a n/a n/a n/a n/a √ √ no material
PNET94 Group 1 female PNET 15.00 n/a n/a n/a n/a √ √ no material
PNET95 Group 3 female PNET 3.08 n/a n/a n/a n/a √ √ no material
PNET96 Group 3 male PNET 8.00 n/a n/a n/a n/a √ √ no material
PNET97 Group 2 male PNET 12.00 n/a n/a n/a n/a √ √ no material
PNET99 n/a male PNET 6 n/a M+ Dead 1.25 no material √ no material
PNET100 n/a female PNET 11 n/a M+ Dead 8.7 no material √ no material
PNET101 n/a male PNET 3 n/a M0 Alive 6.6 no material √ no material
PNET105 n/a female PNET n/a n/a n/a n/a n/a no material √ no material
PNET106 n/a male PNET n/a n/a n/a n/a n/a no material √ no material
PNET109 Group 1 female PNET 1.58 n/a n/a Dead n/a √ √ √
PNET111 Group 1 male PNET 2.33 n/a n/a Dead n/a √ √ √
PNET112 Group 2 male PNET 2.00 n/a n/a Dead n/a no material no material √
PNET113 Group 3 male PNET 7.00 n/a n/a Dead n/a no material no material √
PNET114 Group 2 male PNET n/a n/a n/a n/a n/a √ √ no material
PNET116 Group 2 male PNET 14.20 Chemo/XRT M0 Dead 1.79 no material no material √
PNET118 Group 1 male PNET 2.90 XRT M0 Dead 0.38 no material no material √
PNET119 Group 2 male PNET 17.90 Chemo/XRT M0 Dead 0.58 no material no material √
PNET122 Group 3 male PNET 16.70 Chemo/XRT M0 Dead 4.33 no material no material √
PNET123 Group 2 male PNET 17.90 Chemo M+ Dead 0.88 no material no material √
PNET126 Group 2 male PNET 3.00 n/a n/a n/a n/a no material no material √
PNET129 Group 2 male PNET 8.00 n/a n/a n/a n/a no material no material √
PNET131 Group 3 female PNET 0.83 n/a n/a n/a n/a no material no material √
PNET132 Group 3 male PNET 4.00 n/a n/a n/a n/a √ no material √
PNET135 Group 1 male PNET n/a n/a n/a Dead 0.00 √ √ no material
PNET138 Group 1 male PNET 2.83 n/a M0 Dead 1.58 √ √ √
PNET139 n/a n/a PNET n/a n/a n/a n/a n/a no material √ no material
PNET140 n/a n/a PNET n/a n/a n/a n/a n/a no material √ no material
PNET141 n/a n/a PNET n/a n/a n/a n/a n/a no material √ no material
PNET142 n/a n/a PNET n/a n/a n/a n/a n/a no material √ no material
PNET143 Group 2 female PNET 1.92 n/a M0 Dead 0.75 √ √ no material
PNET146 Group 3 male PNET 10.58 n/a M+ Alive 3.58 √ √ no material
PNET148 Group 1 female PNET 2.2 n/a M0 Alive 3.6 no material √ no material
PNET149 Group 2 male PNET 6.42 n/a M0 Dead 1.25 √ √ no material
PNET157 Group 3 male PNET 2.25 n/a M0 Dead 8.17 √ √ no material
PNET158 Group 2 male PNET 0.03 n/a M0 Dead 6.08 √ √ √
PNET160 Group 3 male PNET 5.75 XRT M+ Alive 1.75 no material no material √
PNET161 Group 1 female PNET 1.75 Chemo/XRT M0 Dead 3.17 no material no material √
PNET163 Group 2 female PNET 1.42 Chemo M0 Dead 0.08 no material no material √
PNET164 Group 1 female PNET 8.92 n/a M+ Dead 1.33 no material no material √
PNET166 n/a female PNET 0.06 n/a M0 Dead 0.25 no material no material √
PNET167 Group 3 female PNET 1.08 n/a n/a Dead 2.71 no material no material √
PNET169 Group 2 female PNET 4.08 n/a n/a Dead 0.17 no material no material √
PNET170 Group 2 female PNET n/a None n/a n/a n/a √ √ no material
PNET171 Group 2 male PNET 11.17 Chemo/XRT M+ Dead 4.42 √ √ √
PNET172 Group 3 female PNET 3.50 Chemo/XRT M0 Alive 2.17 √ √ √
PNET173 Group 2 male PNET 13.17 Chemo/XRT M0 Dead 1.83 √ √ √
PNET174 Group 2 male PNET 7.83 Chemo/XRT M0 Dead 2.33 √ √ √
PNET187 CNS PNET
44 Group 2 female PNET 15.83 Chemo/XRT M0 Alive 2.92 √ √ √
PNET188 Group 2 male PNET 1.67 Chemo M0 Dead 3.42 √ √ no material
PNET190 CNS PNET
38 Group 3 male PNET 11.75 XRT M+ Dead 2.50 √ √ √
PNET191 Group 2 female PNET 4.42 Chemo M0 Alive 5.17 √ √ √
PNET196 CNS PNET
15 Group 2 female PNET 1.67 None M0 Dead 0.00 √ √ √
PNET197 CNS PNET
35 Group 3 male PNET 10.17 Chemo/XRT M0 Alive 7.50 √ √ √
PNET199 Group 2 female PNET 9.67 Chemo/XRT M0 Dead 2.08 √ √ no material
PNET200 Group 3 female PNET 7.00 Chemo/XRT M+ Dead 1.67 √ √ no material
PNET226 Group 1 female PNET 3.4 n/a n/a Dead 0 no material √ no material
PNET255 Group 1 female PNET 1.92 Chemo/XRT M+ Alive 4.67 no material no material √
PNET256 Group 2 female PNET 13.00 Chemo/XRT M0 Dead 1.17 no material no material √
PNET258 Group 3 male PNET 7.50 Chemo/XRT M+ Alive 2.08 no material no material √
PNET259 Group 1 male PNET 3.67 Chemo/XRT M+ Dead 0.67 no material no material √
PNET260 Group 2 female PNET 8.50 XRT M0 Alive 7.75 no material no material √
PNET265 n/a female PNET 1.33 Chemo M+ Dead 0.50 no material no material √
PNET266 CNS PNET
33 Group 3 male PNET 8.92 XRT M+ Dead 5.92 no material √ √
PNET267 CNS PNET
23 n/a female PNET 4.25 Chemo/XRT M0 Dead 2.00 no material no material √
PNET268 n/a male PNET 2.75 None M0 Dead 0.00 no material no material √
PNET269 n/a male PNET 1.75 None M0 Dead 0.00 no material no material √
PNET270 n/a female PNET 0.42 Chemo M+ Dead 1.17 no material no material √
PNET271 CNS PNET
28 n/a female PNET 5.92 XRT M0 Dead 0.58 no material √ √
PNET272 CNS PNET
9 Group 1 female PNET 0.83 Chemo M+ Dead 3.42 no material √ √
PNET273 Group 1 female PNET 8.25 Chemo/XRT M0 Dead 0.67 no material no material √
PNET274 Group 3 male PNET 15.50 Chemo/XRT M0 Alive 21.33 no material no material √
PNET276 n/a male PNET 10.25 Chemo/XRT M0 Dead 1.33 no material no material √
PNET277 n/a female PNET 3.58 Chemo/XRT M0 Alive 22.00 no material no material √
PNET279 n/a female PNET 4.17 None M0 Dead 0.17 no material no material √
PNET281 Group 3 female PNET 11.75 Chemo/XRT M+ Dead 4.83 no material no material √
PNET282 Group 3 female PNET 7.08 Chemo/XRT M0 Alive 9.33 no material no material √
PNET283 CNS PNET
40 Group 3 male PNET 11.83 None M0 Dead 0.00 no material √ √
PNET284 CNS PNET
25 Group 3 male PNET 4.92 Chemo/XRT M+ Dead 0.75 no material √ √
PNET285 CNS PNET
18 n/a female PNET 2.00 Chemo M0 Dead 0.25 no material √ √
PNET286 Group 1 male PNET 5.17 Chemo M0 Dead 3.17 no material no material √
PNET287 n/a male PNET 0.50 Chemo M0 n/a 0.00 no material no material √
PNET288 Group 1 male PNET 2.25 None M0 Dead 3.17 no material no material √
PNET289 CNS PNET
30 n/a male PNET 7.00 Chemo/XRT M+ Dead 1.67 no material no material √
PNET290 Group 3 male PNET 0.17 n/a n/a Dead 0.00 no material no material √
PNET291 Group 1 female PNET 3.75 Chemo/XRT n/a Dead 1.00 no material no material √
PNET293 Group 2 female PNET 1.75 n/a n/a n/a n/a no material no material √
PNET294 Group 3 female PNET 10.00 n/a n/a n/a n/a no material no material √
PNET295 Group 2 male PNET 5.33 n/a n/a n/a n/a no material no material √
PNET296 n/a female PNET 9.17 n/a n/a n/a n/a no material no material √
PNET297 Group 3 female PNET 15.33 Chemo/XRT n/a Dead 2.08 no material no material √
PNET300 Group 3 female PNET 5.67 n/a n/a n/a n/a no material no material √
PNET301 Group 1 female PNET 3.25 Chemo M0 Alive 13.75 no material no material √
PNET302 n/a female PNET 8.75 Chemo/XRT M0 Dead 1.75 no material no material √
samples can be found with same annotation in Li, M., K. F. Lee, et al. (2009). "Frequent amplification of a chr19q13.41 microRNA polycistron in aggressive primitive neuroectodermal brain tumors." Cancer Cell 16(6): 533-546.tumors." Cancer Cell 16(6): 533-546.
samples can be found with alternate annotation in Miller, S., H. A. Rogers, et al. (2011). "Genome-wide molecular characterization of central nervous system primitive neuroectodermal tumor and pineoblastoma." NeuroOncol 13(8): 866-879.
n/a = not available Chemo = Chemotherapy XRT = Radation therapy
PNET/ME: PNET with features of medulloepithelioma PNET/EP: PNET with features of ependymal or ependymoblasticdifferentiation PNET/ETNATR: PNET variant with excess neuropil and true rosettes
Supplemental Table 3: Quantitative qRT-PCR primers and probes Gene Probe # ASCL1 Hs00269932_m1 COL1A1 Hs00164004_m1 COL1A2 Hs00164099_m1 COL5A1 Hs00609088_m1 CRABP1 Hs00171635_m1 ERBB3 Hs00176538_m1 FOXJ1 Hs00230964_m1 GFAP Hs00909233_m1 GLI2 Hs01119974_m1 GLI3 Hs00609233_m1 IGF2 Hs00171254_m1 LIN28A Hs00702808_s1 LIN28B Hs01013729_m1 MSX1 Hs00427183_m1 NCAM2 Hs00189850_m1 Nestin Hs00707120_s1 NEUROG2 Hs00702774_s1 NKX6-2 Hs00752986_s1 OLIG1 Hs00744293_s1 OLIG2 Hs00377820_m1 PDGFRA Hs00998018_m1 SMO Hs01090242_m1 TGFB3 Hs01086000_m1 TGFBR3 Hs01114253_m1 TUBB3 Hs00801390_s1 ZIC2 Hs00600845_m1
Supplemental Table 4: Samples with inconclusive IHC analyses
Annotation LIN28 OLIG2 PNET166 missing core missing core PNET265 missing core missing core PNET267 missing core missing core PNET268 missing core missing core PNET269 missing core missing core PNET270 missing core missing core PNET271 missing core missing core PNET276 failed negative PNET277 failed negative PNET279 missing core missing core PNET285 missing core missing core PNET287 missing core negative PNET289 missing core negative PNET296 missing core positive PNET302 missing core missing core