Supplemental Figure Legends May 1 AH edited 20 Gain 0.039 C19MC Amp

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

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tic c

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latio

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2 4 6 8 10

0.85

0.95


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0.95


k

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200 genes 250 genes

300 genes 350 genes 400 genes



200 genesk= 3

Cophenetic coef.= 0.9711samples

sam

ples

sam

ples

BGROUP 1 GROUP 2 GROUP 3

Tumour Sub-groups

Hierachical ClusteringA


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


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


A

C

50µm

50µm50µm

B

D

50µm


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


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


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


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



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 √ √ √



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


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



PNET54 Group 1 male PNET/EP 3 n/a M0 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 √


PNET64 Group 3 male PNET 16.00 n/a n/a Alive 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 √



PNET72 Group 3 male PNET 0.06 n/a n/a Dead 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 √



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 √ √ √



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 √



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 √


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 √ √ √





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 √


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 √ √


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 √




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 √


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

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Supplemental Figure Legends May 1 AH edited 20 Gain 0.039 C19MC Amp