8/9/2019 Child CNS

1/16

INVITED PAPER

Current concepts in the molecular genetics of pediatric

brain tumors: implications for emerging therapies

Mandeep S. Tamber & Krishan Bansal & Muh-Lii Liang &

Todd G. Mainprize & Bodour Salhia & Paul Northcott &

Michael Taylor & James T. Rutka

Received: 14 March 2006 / Published online: 2 September 2006# Springer-Verlag 2006

AbstractBackground The revolution in molecular biology that has

taken place over the past 2 decades has provided research-

ers with new and powerful tools for detailed study of the

molecular mechanisms giving rise to the spectrum of

pediatric brain tumors. Application of these tools has

greatly advanced our understanding of the molecular

pathogenesis of these lesions.

Review After familiarizing readers with some promising

new techniques in the field of oncogenomics, this review

will present the current state of knowledge as it pertains to

the molecular biology of pediatric brain neoplasms. Along

the way, we hope to highlight specific instances where thedetailed mechanistic knowledge acquired thus far may be

exploited for therapeutic advantage.

Keywords Brain neoplasms . Molecular biology .

Pediatrics . Review . Therapeutics

Introduction

In the past 2 decades, the textbooks on the molecular

biology of pediatric brain tumors have been rewritten

several times. This has been principally due to the

tremendous advances that have been made in our under-

standing of these tumors from a basic science standpoint,

a dv an ce s which a re in large p art d ue to the n ew

technologies that have come forward to query the genetic

underpinnings of these lesions. Suffice it to say that we are

now poised, greater than ever before, to utilize the

information that has been garnered toward tangible

improvements in the way children with brain tumors are

treated.

In this review, we will summarize the salient molecular

genetic changes that characterize pediatric astrocytomas,

both low- and high-grade lesions, ependymoma, medullo-

blastoma and primitive neuroectodermal tumors, atypical

teratoid rhabdoid tumor (AT/RT), germ cell tumors (GCTs),

and sarcomas. During the review of each tumor type, we

will attempt to provide clues as to how detailed knowledge

of the molecular pathogenesis of these lesions may be

harnessed toward translational research opportunities

designed to improve patient outcomes.

New techniques in the field of oncogenomics

In the past 30 years, advanced cancer cytogenetics have

been applied to numerous cancer subtypes, including many

of the pediatric brain tumors. For additional details

regarding these techniques, the interested reader is referred

to several excellent review articles on this topic [ 136, 159].

Here we will describe array comparative genomic hybrid-

Childs Nerv Syst (2006) 22:13791394

DOI 10.1007/s00381-006-0187-3

M. S. Tamber: K. Bansal : M.-L. Liang : T. G. Mainprize :

B. Salhia: P. Northcott: M. Taylor: J. T. Rutka

Division of Neurosurgery, The Hospital for Sick Children,

The University of Toronto,

Toronto, Ontario, Canada

M. S. Tamber: K. Bansal : M.-L. Liang : T. G. Mainprize :

B. Salhia: P. Northcott: M. Taylor: J. T. Rutka

Arthur and Sonia Labatt Brain Tumor Research Centre,

The Hospital for Sick Children, The University of Toronto,

Toronto, Ontario, Canada

J. T. Rutka (*)

The Division of Neurosurgery, Suite 1504,

The Hospital for Sick Children,

555 University Avenue,

Toronto, Ontario 518, Canada

e-mail: james.rutka@sickkids.ca

8/9/2019 Child CNS

2/16

ization (CGH), single nucleotide polymorphism (SNP)

arrays, microarray analysis of gene expression, and exon

resequencing as new techniques which have been and will

be applied to the study of pediatric brain tumors (Table 1).

Array comparative genomic hybridization

Array comparative genomic hybridization is similar toCGH, but instead of hybridizing the labeled probes

to metaphase chromosomes, the probes are hybridized to

microarray slides in which thousands of fragments of DNA

that span the genome have been arrayed out [29, 70, 114,

115]. The array CGH chip can be spotted with DNA

composed of genomic clones, cDNA sets, or oligonucleo-

tide probes depending on the array design. A major

advantage of array CGH over traditional CGH is the

significantly higher resolution offered by the array plat-

form, allowing investigators to identify smaller areas of

aberration. For example, bacterial artificial chromosome

(BAC) arrays consisting of greater than 30,000 BAC clonesrepresenting the entire human genome are now widely used

in array CGH, permitting whole-genome copy number

analysis at resolutions of less than 1 Mb, compared with the

much lower resolution achieved using traditional CGH

(~5 Mb) [72, 83].

The highest resolution for array CGH is now provided

by genome tiling arrays which interrogate entire genomes

with evenly spaced oligonucleotide probes [8, 19]. The

increased resolution offered by modern array CGH plat-

forms will allow for the incredibly fine mapping of focal

amplifications and deletions not possible using previous

generation arrays. Weaknesses of array CGH include an

inability to detect structural anomalies such as reciprocaltranslocations and the inability to detect copy-number-

neutral loss of heterozygosity (LOH) events.

Array CGH technology has recently been applied by a

number of groups studying DNA copy number changes in

pediatric brain tumors [24, 68, 99, 135, 161, 164]. Using a

combination of array CGH and oligonucleotide gene

expression arrays (discussed below) in a study of ependy-

moma, Taylor et al. recently reported that histologically

similar anatomical subtypes of ependymoma could be

distinguished based upon their distinct patterns of copy-

number-driven gene expression [161]. These authors also

used array CGH and expression microarrays to identify anumber of genes that are both amplified and overexpressed

in ependymoma (i.e., oncogenes). The results of this study

emphasize the power of array CGH in the identification of

genomic aberrations in cancer and demonstrate its utility

when combined with complementary technical platforms

such as gene expression arrays.

Table 1 Summary of molecular and cytogenetic techniques discussed in the text

Technique CGH SKY Array CGH SNP array Expression

array

Exon

resequencing

Primary

application

Mapping regions

of amplification

and deletion

Identification of

structural

aberrations

Copy number

analysis

Copy number

analysis; LOH

mapping

Gene

expression

profiling

Mutation

detection

Platform type Fluorescence

microscopy

Fluorescence

microscopy

Microarray:

BAC,

oligonucleotide

Microarray:

oligonucleotide

Microarray:

oligonucleotide

Dideoxy

sequencing

Starting

material

Genomic DNA Metaphase

chromosomes from

cultured cells

Genomic DNA Genomic DNA Total RNA or

mRNA

Genomic DNA

Advantages Assay only

requires genomic

DNA

Capacity to detect

balanced

translocations

Good resolution;

whole-genome

screening

High

resolution;

whole-genome

screening

Whole

transcriptome

screening

possible

Highest

resolution;

no restriction

on choice of

genes

Disadvantages Poor resolution;

unable to detect

balanced

translocations

Prone to erroneous

interpretations and

classification errors

LOH mapping

not possible

Data analysis

intensive

Data analysis

and

interpretation

issues

Limited to user-

defined genes

and gene

families;

expensive

Listed are some of the current platforms employed in cancer genetics to identify novel disease-causing genes, highlighting the type of platform

used, biological material required, as well as primary strengths and weaknesses of each technique. Detailed information for each assay type,

including relevant clinical examples, is described in the text.

CGH comparative genomic hybridization, SKY spectral karyotyping, SNP single nucleotide polymorphism, LOH loss of heterozygosity,

BAC bacterial artificial chromosome

1380 Childs Nerv Syst (2006) 22:13791394

8/9/2019 Child CNS

3/16

Single nucleotide polymorphism arrays

Single nucleotide polymorphisms represent the most com-

mon form of genetic variation in the human genome [2, 62,

137, 169]. SNPs are naturally occurring variations in DNA

sequence that occur regularly throughout the genome, with

an average frequency of one SNP for every 200 bases of

DNA. Recently, array-based technologies that use SNPs asa means of investigating both DNA copy number and SNP

genotype have become commercially available [67, 79, 95,

96]. Unlike array CGH which involves simultaneous

cohybridization of both a test sample and a reference

sample to the microarray, SNP arrays hybridize only a test

sample, with DNA copy number calculated by comparison

of signal intensity data obtained from a test sample to data

from control samples hybridized to the same array type. In

SNP array analysis, DNA from a test sample is first

digested with a specific restriction enzyme (e.g., Hind or

Xba) and then ligated to an adaptor which permits

amplification of the digested fragments. Amplified DNA

is subsequently fragmented and labeled before hybridiza-

tion to a specific SNP array (e.g. 50K Hind or 50K Xba

array) (Fig. 1).The arrays consist of 25-mer oligonucleotide probes

that are designed to genotype the test sample for either of

two alleles of a given SNP (arbitrarily designated A and B

alleles). Each SNP is represented by a set of perfect match

A and perfect match B probes, as well as an equal number

of mismatch probes for both alleles. For any given SNP,

the possible genotypes for a test sample include AA, BB,

Fig. 1 Analysis of LOH and chromosomal copy number using SNP

arrays. Data obtained from SNP array experiments can be analyzed

visually to identify instances of LOH and copy number gains and

losses. a Inferred LOH view of a medulloblastoma cell line exhibiting

genetic loss on chromosome 17p. The middle panel depicts inferred

regions of LOH in blue and those retaining heterozygosity in yellow.

The significance curve shown on the right demonstrates a high

probability of LOH on 17p for this sample. b Copy number view of a

medulloblastoma cell line with high-level genomic amplifications on

chromosome 8q24. Copy number is displayed in the middle panel

using a user-defined scale, with gains and losses represented by darker

and lighter color intensities, respectively. The right panel clearly

identifies the 8q24 amplifications in this sample as sharp peaks in copy

number, with values dramatically exceeding the threshold value of 2 at

these loci

Childs Nerv Syst (2006) 22:13791394 1381

8/9/2019 Child CNS

4/16

or AB, with genotype determined by the pattern of perfect

match and mismatch signal intensities obtained for that

SNP. Accuracy of SNP genotyping relies on the availabil-

ity of a highly purified DNA sample; analysis of tumor

tissue may therefore be problematic due to the presence of

contaminating normal cells. Modern array platforms

interrogate from 100,000 to 500,000 SNPs, resulting in

high-resolution genome coverage with median SNPspacing of ~8.5 and ~2.5 kb, respectively. This resolution

is more than 1,000 times better than classic CGH. As a

result of the high resolution and sensitivity associated

with SNP arrays, it is possible to identify microamplifi-

cations and microdeletions present in cancer samples, as

well as larger aberrations including aneuploidy. A major

advantage of SNP array technology over other platforms

used in cancer genetics is the simultaneous acquisition of

both copy number and genotype information. Whereas

copy number data are critical for mapping regions of

amplification and homozygous deletion in tumor samples,

genotyping information can identify loci which haveundergone loss of heterozygosity without a decrease in

copy number (copy-number-neutral LOH). Although

SNP-array-based approaches have not yet been reported

for pediatric brain tumors, they have proven to be a

valuable tool when applied to studies of other tumor types

[49, 65, 140, 162, 176, 179, 180].

Microarray analysis of gene expression

In recent years, microarrays designed to study global gene

expression profiles have become an indispensable tool for

cancer researchers [16, 127, 142]. Significant improve-

ments with respect to array design, in combination with a

more comprehensive knowledge of the human transcrip-

tome, has resulted in the evolution of arrays which allow

for evaluation of the expression of every known human

gene [47, 60, 87, 88, 141]. In addition, new-generation

high-resolution arrays have recently been developed,

including platforms which interrogate every annotated

human exon. Now, genome tiling arrays capable of

measuring gene expression every 25 base pairs across

entire genome have been developed in order to measure

expression from cryptic transcriptional units [21, 75, 78].

This technology has found expression of countless tran-

scripts that previously lacked annotation, many from so-

called gene deserts.

Conventional arrays for gene expression analysis consist

of 25-mer oligonucleotide probes that are complementary in

sequence to their target, with multiple perfect match and

mismatch probes existing for each interrogated target and

multiple probe sets present for each gene represented on the

array. Total RNA from a tumor sample is first reverse-

transcribed using a T7-oligo(dT) promoter primer to

generate first-strand cDNA. First-strand cDNA is then

converted to double-stranded cDNA which serves as a

template for the synthesis of complementary RNA (cRNA)

in an in vitro transcription (IVT) reaction. IVT is carried out

by T7 RNA polymerase in the presence of biotin-labeled

ribonucleotides. The biotinylated cRNA is subsequently

purified, fragmented, and hybridized to an expression array.

Hybridized arrays are then stained, washed, and scanned todetermine the signal intensity for each probe on the array,

with the signal intensity being proportional to the amount

of bound target. Data obtained from such a gene expression

array can then be used to identify the gene expression

profile characteristic of a particular tumor [100]. Gene

expression arrays have proven useful in the identification of

aberrantly expressed genes and gene families in pediatric

brain tumors, with some of these candidates potentially

representing important prognostic markers and/or serving

as targets for future therapeutics [44, 51, 92, 119].

Exon resequencing

Advances in DNA sequencing technologies, along with the

availability of comprehensive genomic databases, have

recently led to a number of large-scale resequencing efforts

aimed at identifying novel mutations in groups or families

of preselected candidate genes [7, 27, 28, 122, 145, 146,

170, 171]. The resequencing approach involves choosing a

set of genes for analysis (e.g., kinases) and performing

polymerase chain reaction (PCR) amplification of all

coding exons including the intronexon splice site junctions

for that set of genes, with genomic DNA isolated from

patient tumor samples or cell lines serving as a template.

The PCR is carried out using a high-fidelity polymerase to

avoid introduction of de novo mutations during the

amplification reaction. PCR products are purified and then

subjected to bidirectional dideoxy sequencing to identify

putative mutations. Ideally, patient-matched normal DNA is

analyzed using the same procedure and then compared with

results from sequencing of the tumor DNA to allow for

distinction between possible mutations and natural poly-

morphisms. This strategy for mutation identification has

been successfully applied in studies of lung, colorectal,

breast, and brain tumors [7, 27, 28, 122, 145, 146, 170,

171]. For example, a resequencing project analyzing the

receptor tyrosine kinase family of genes in human

glioblastomas found mutations of the fibroblast growth

receptor-1 gene and the platelet-derived growth factor

receptor (PDGFR) gene [122]. To date, exon resequenc-

ing has been most extensively applied to the tyrosine kinase

and associated phosphatase gene families [7, 27, 28, 122,

145, 146, 171]; however, there are no limitations on the

types or families of genes that can be interrogated using this

strategy.

1382 Childs Nerv Syst (2006) 22:13791394

8/9/2019 Child CNS

5/16

Molecular genetics of specific pediatric brain tumors

High-grade astrocytoma

High-grade astrocytomas in children are relatively rare

lesions when compared with adults. Whereas the prognosis

of children with anaplastic astrocytoma or glioblastoma

multiforme may be better than that of adults with acomparable histological lesion, the majority of children

will still succumb from progressive disease within 25 years

after diagnosis [152]. What has been very interesting, and

as yet incompletely characterized, is the fact that the genetic

alterations that accompany the childhood high-grade astro-

cytic neoplasms are distinct from those that occur in adults.

The genetic alterations that are the hallmark of adult

anaplastic astrocytomasloss of p53, PTEN, p14ARF, and

amplification of the epidermal growth factor receptor

(EGFR) III mutantare relatively rare in pediatric anaplas-

tic astrocytomas (see below). In light of this and other

evidence, it appears as if the development of pediatric high-grade astrocytomas may follow pathways distinct from the

well-established primary and secondary paradigm of adult

glioblastomas.

Common chromosomal losses in pediatric high-grade

gliomas include those of chromosome 16p, 17p, 19p, 19q,

and 22 [59, 129]. Within the spectrum of high-grade

gliomas, distinct cytogenetic changes are observed in

pediatric anaplastic astrocytomas, which are typified by

gains of chromosome 5q and losses of chromosomes 6q,

9q, 12q, and 22q, and in pediatric glioblastoma, which is

characterized by gains in chromosomes 1q and 16p and

losses of chromosomes 8q and 17p [129]. The finding of 1q

amplification is noteworthy because it may be a marker of

poor survival.

Whereas microsatellite instability appears to be generally

absent in the setting of adult high-grade astrocytomas,

nearly 25% of pediatric malignant astrocytomas may

display a microsatellite instability phenotype as a manifes-

tation of mutations in various DNA mismatch repair genes

[1, 22].

In addition to being characterized by their respective

patterns of structural chromosomal abnormalities, pediatric

high-grade astrocytomas may be distinguished from their

adult counterparts on the basis of differential expression of

oncogenes and tumor suppressor genes that are involved in

signal transduction pathways critical to the process of

gliomagenesis. The pertinent pathways for the adult tumors

include the growth factor/growth factor receptor/PI3-kinase/

Akt/PTEN pathway, the p53/MDM2/p14ARF pathway, and

the pRB/cyclinD1/cyclin-dependent kinase (CDK) 4/p16

pathway. The interested reader is referred to a review by

Ichimura et al. for a recent synopsis of the interplay of these

various pathways in the molecular pathogenesis of astro-

cytic tumors [69]. In the remainder of this section, each

pathway will be examined in turn in order to characterize

the patterns of abnormality present within and to highlight

the often dichotomous nature of the importance of an

individual pathway to the genesis of pediatric vs adult high-

grade gliomas.

Although amplification of the EGFR gene is observed in

up to 40% of adult glioblastomas and 15% of adultanaplastic astrocytomas, it is not a common finding in

pediatric high-grade astrocytomas [22, 121, 148]. Similarly,

whereas de novo adult glioblastomas have a high frequency

of mutations in the PTEN tumor suppressor gene, pediatric

malignant gliomas rarely contain such mutations. Although

LOH at 10q2325 may be present in as many as 80% of

informative cases, homozygous deletions of the PTEN gene

are seen in only 8% of pediatric high-grade astrocytomas

[22]. Where mutations of PTEN are observed, they may

herald a poor prognosis for children with high-grade

astrocytomas.

The majority of adult secondary glioblastomas demon-strate mutations of the p53 tumor suppressor gene located

on chromosome 17p. A relatively small subset of high-

grade gliomas, mostly occurring in older children, may also

harbor frequent p53 mutations. In this population, there

appears to be a nearly 2:1 frequency of p53 gene mutations

in high-grade brainstem astrocytomas as opposed to non-

brainstem astrocytomas [22, 90, 117].

Homozygous deletions of the CDKN2A/pl4ARF locus at

9p21, which encodes both the p16 and p14ARFproteins, are

found in 10% of pediatric malignant astrocytomas [103].

Overexpression of the MDM2 oncogene is seen in 67% of

pediatric malignant astrocytomas, although there is no

concomitant amplification of the MDM2 gene at a genomic

level [148]. Overall, inactivation of the p53/MDM2/p14ARF

pathway, either by mutation of p53, overexpression of

MDM2, or deletion of p14ARF, is seen in more than 95% of

pediatric malignant astrocytomas, a situation which is

similar to the observed frequency of p53/MDM2/p14ARF

pathway inactivation in the setting of adult malignant

astrocytomas [148]. However, as outlined earlier, mutations

of p53 are seldom seen in malignant gliomas of children

younger than 3 years, once again suggesting that malignant

gliomas in very young children may follow a distinct

molecular pathway as compared with older children and

adults [118].

Sure et al. were able to demonstrate loss of expression of

p16 in 11 of 18 pediatric glioblastomas [149]. However, the

pRb/cyclin D1/CDK4/p16 pathway appears to be inacti-

vated in only about 25% of pediatric malignant astrocyto-

mas, as opposed to inactivation in more than 80% of the

corresponding adult tumors [148].

To date, there have been no published reports of cDNA

microarray analyses on pediatric high-grade gliomas.

Childs Nerv Syst (2006) 22:13791394 1383

8/9/2019 Child CNS

6/16

Low-grade astrocytoma

Whereas tremendous advances have been made in the

understanding of the molecular pathogenesis of pediatric

high-grade astrocytomas, there have been comparatively

few studies focusing on the low-grade and pilocytic

astrocytomas of childhood.

Consistent with the fact that they are low-grade lesions,cytogenetic studies have revealed a normal karyotype in the

majority of pilocytic astrocytomas examined, and where

abnormal profiles have been observed, no consistent

karyotype abnormalities have been identified [138, 178].

Pediatric pilocytic astrocytomas show fewer chromosomal

changes than adult tumors; where observed, they are

usually gains of only a single chromosome, such as

chromosome 7 or 8, as has been demonstrated in

approximately one third of pediatric pilocytic astrocytomas

using fluorescent in situ hybridization (FISH) analysis

[173].

Individuals with neurofibromatosis type I (NF1) have anincreased propensity to develop pilocytic astrocytomas,

especially of the optic/hypothalamic region. As sporadic

pilocytic astrocytomas occasionally show LOH on chro-

mosome 17q (the location of the NF1 tumor suppressor

gene), one would predict that mutations of the NF1 gene

with consequent loss of expression would be found in

sporadic pilocytic astrocytomas. In fact, this appears not to

be the case. In actuality, the expression of the NF1 tumor

suppressor gene in sporadic pilocytic astrocytomas is often

upregulated, perhaps as a reactive response to excessive

cellular proliferation [116, 175]. This is in contrast to

pilocytic astrocytomas arising in NF1 patients, where loss

of NF1 expression is an obligatory finding [54]. The precise

origin of the differing contribution of the NF1 gene product

in the setting of NF1 vs non-NF1 pilocytic astrocytomas

remains to be elucidated.

Even with the use of various sensitive p53 mutation

detection assays, it appears that p53 mutations are absent or

at most infrequently present in the setting of pediatric

pilocytic astrocytomas [23, 71, 174]. Such results are in

concordance with the low frequency of allelic loss detected

at the p53 locus on chromosome 17p [23, 71, 174]. Taken

together, these findings indicate that abnormalities of p53

do not contribute in any significant way to the genesis of

pilocytic astrocytomas.

Most cases of pediatric pilocytic astrocytoma show

immunopositivity for p16 and CDK4, indicating that

abnormalities in the pRb/cyclinD1/CDK4/p16 pathway

likely do not play an important role in the evolution of

these tumors [23]. PTEN mutations are also likely not a

significant contributor to the pathogenesis of these lesions

[23, 37], as mutations in this tumor suppressor gene tend to

be reserved for higher-grade tumors [123].

Ependymoma

Chromosomal 22 defects are frequently found in ependy-

moma. Mutation of the NF-2 gene product on chromosome

22 has been documented to predispose to the formation of

various tumor types, including ependymoma, especially in

patients with NF-2 [41]. However, the vast majority of

sporadic (non-NF-2) cases lack mutations in the NF-2 gene.The most plausible explanation for these findings is the

existence of another oncogene or tumor suppressor gene on

chromosome 22 that is more commonly involved in the

genesis of sporadic ependymoma than the NF-2 gene

product [166].

Pediatric intracranial ependymomas appear to have a

chromosomal signature distinct from their adult counter-

parts. Pediatric tumors, which often occur in the

infratentorial compartment, display balanced CGH pro-

files in 3050% of cases, in comparison to only 10% of

adult tumors [38, 63]. This finding suggests that pediatric

intracranial ependymomas may progress along substantiallydifferent pathways than those giving rise to adult supra-

tentorial or spinal ependymomas [161].

Where chromosomal aberrations are observed in pediat-

ric ependymomas, monosomy 17 appears to be one of the

most common lesions, with an approximately 50% fre-

quency [166]. The p53 tumor suppressor gene resides on

17p, and individual case reports have identified some

instances of p53 mutation in ependymoma patients,

including a family who had concurrent mutation in

chromosome 22 [46, 104].

Gain of chromosome 1q is also a frequent finding in

pediatric ependymoma [38]. A putative region of interest on

chromosome 1q may be the region between 1q22 and 31

[82]. Several studies have made an association between the

presence of 1q gain and a poor clinical course, suggesting

that the presence of one or more genes located on 1q may

be responsible for tumor progression and/or response to

therapy [38, 63].

Loss of a region on 6q has been documented in a number

of case reports; however, no known oncogene or tumor

suppressor gene has yet been implicated at this locus [82,

125, 131]. Other frequent chromosomal alterations include

losses of chromosomes 1p, 6, 9q, 11, 13q, 16p, 16q, 19q,

20p, and 20q, and gains of 1q, 2, 5, 9, 12, 15, 18, 20q, and

X [63, 163].

Microarray experiments designed to document the gene

expression profile of ependymomas have been performed.

A recent examination of a panel of 12,627 genes identified

a subset of 112 genes as being abnormally expressed in

pediatric ependymoma when compared with normal brain

controls [147]. Genes with increased expression included

the oncogene WNT5A, the p53 homologue p63, and

several cell cycle, cell adhesion, and cell proliferation

1384 Childs Nerv Syst (2006) 22:13791394

8/9/2019 Child CNS

7/16

genes. Underexpressed genes included the NF2 interacting

gene SCHIP-1 and the adenomatous polyposis coli (APC)-

associated gene EB1 among others. These genes represent

candidate genes for further study; further validation work is

necessary in order to clarify their precise contribution to

ependymoma tumorigenesis.

Our understanding of the origins of ependymoma

increased dramatically with the recent publication of Tayloret al. in which histologically identical, but genetically

distinct, ependymomas showed patterns of gene expression

that recapitulate those of radial glia cells in corresponding

regions of the central nervous system [161]. In this study,

supratentorial, infratentorial, and intraspinal ependymomas

demonstrated distinct genetic signatures and were shown to

arise from restricted populations of radial glia stem cells.

For the supratentorial tumors, CDK4 and several Notch

signaling pathway genes were overexpressed; for the

infratentorial tumors, IFG-1 and several HOX homeobox

genes were overexpressed; and for the spinal tumors, the ID

genes and the aquaporins were overexpressed. The impli-cations of this study are that ependymomas should be

treated with therapies that target the cell signal pathways

that maintain subsets of ependymoma stem cells rather than

the histological or clinical forms of the disease [161].

Atypical teratoid rhabdoid tumor

Molecular studies have been able to distinguish CNS AT/RT

from the other primitive pediatric brain tumors, establishing

it as a unique pathological entity [55, 133, 134]. AT/RT

frequently demonstrates deletion of the long arm of

chromosome 22q11.2, and further molecular studies have

led to the identification of the INI1/hSNF5 tumor suppres-

sor gene at this location [1013, 165]. A somatic mutation

in this gene predisposes children to develop AT/RT

[1013]. The hSNF5 protein is the smallest member of a

highly conserved family of proteins that function in

chromatin remodeling via the nucleosome. By winding

and unwinding DNA, this complex changes the config-

uration of genomic DNA, thus allowing or denying

transcription factors access to the DNA, consequently

changing patterns of gene expression.

Some children with AT/RT are born with heterozygous

germ line mutations of the hSNF5 gene, suggesting that

these children were predisposed to develop AT/RT [155]; in

most cases, however, these germ line mutations arise de

novo.

Heterozygous mSNF5 +/ knockout mice develop

tumors resembling AT/RT, supporting the role of hSNF5 as

a tumor suppressor gene [130]. Although most AT/RTs

show evidence of some genetic derangement at the hSNF5

locus, mutational analysis of the hSNF5 gene in a series of

primitive neuroectodermal tumors/medulloblastomas dis-

covered mutations in only 4 of 52 tumors [155]. Of those

four, two were reclassified as AT/RT upon reexamination of

the pathology, but there was insufficient clinical material to

establish an accurate diagnosis in the other two cases. This

suggests that tumors which are histologically diagnosed as

primitive neuroectodermal tumors/medulloblastomas but

which also harbor hSNF5 mutations are most likely AT/RT.

Although mutation/deletion of hSNF5 is not currentlysufficient for a diagnosis of AT/RT, it appears to be related

to the clinical outcome; consequently, determination of the

status of the AT/RT gene by DNA sequence analysis, FISH,

or immunohistochemistry is rapidly becoming an integral

part of the neuropathological diagnosis of primitive

pediatric malignant brain tumors (Fig. 2).

Medulloblastoma

Recent gene expression studies have shown that medullo-

blastoma is molecularly distinct from the supratentorial

primitive neuroectodermal tumors (sPNETs) [119]. TheSonic Hedgehog (SHH), Wingless(WNT/WG), and

receptor tyrosine kinase I family ERBB pathway are

emerging as central developmental signaling pathway

systems in the formation of medulloblastoma [17, 110].

The specific contributions of these pathways to the genesis

of medulloblastoma will be discussed in turn.

Medulloblastoma has been reported in the setting of a

number of different hereditary cancer syndromes, including

nevoid basal cell carcinoma syndrome (NBCCS), Turcot

syndrome, LiFraumeni syndrome and RubensteinTaybi

syndrome [156]. In the mid-1990s, it was discovered that

NBCCS arises from germ line mutations of PTCH1, which

Fig. 2 Pattern of INI-1 staining in AT/RTs of childhood. Immuno-

histochemical staining with an anti-INI-1 antibody fails to stain the

nuclei of tumor cells but does stain the nuclei of normal or reactive

tissues in the vicinity

Childs Nerv Syst (2006) 22:13791394 1385

8/9/2019 Child CNS

8/16

encodes the receptor for the Hedgehog (Hh) family of

signaling proteins. PTCH1 is a 12-pass transmembrane

receptor protein that represses activity of the Hh signaling

pathway in its unbound state by suppressing the activity of

the seven-pass transmembrane protein Smoothened

(SMOH) [56, 74, 94]. Upon ligand binding, PTCH1s tonic

inhibition of SMOH is lifted, leading to the release of GLI

transcription factor from a tetra-protein complex which alsoincludes suppressor of fused (SUFU), fused (FU), and

costal-2 (COS2). Upon its release, GLI is activated and

translocated to the nucleus where it binds to promoters in a

sequence-specific fashion to increase the transcription of

various growth-promoting genes such as cyclin D [94].

Mutations in the various molecules comprising this signal-

ing complex, including SHH, PTCH1, SMOH, and SUFU,

have been shown to occur in both familial and sporadic

tumors [43, 113, 126, 158]. Another recent report demon-

strated a crucial role for polycomb group gene Bmi1 in

clonal expansion of granule cell precursors in vivo and

linked overexpression of BMI1 and patched (PTCH), afinding that is suggestive of an alternative or additive

mechanism of SHH pathway activation in the pathogenesis

of medulloblastomas [84]. A novel putative tumor suppres-

sor, human REN(KCTD11), incidentally maps to 17p13.2,

a chromosomal region which is frequently lost in medul-

loblastoma [45]. The REN tumor suppressor inhibits

medulloblastoma growth by impairing both Gli2-dependent

gene transcription and SHH-enhanced expression of the

target Gli1 mRNA, thereby decreasing the expression of

downstream genes [34, 35].

Cyclopamine, a plant-derived teratogen that binds to

SMOH and interrupts its ability to activate downstream

signaling, may have some important therapeutic implica-

tions. Mice harboring human medulloblastoma explants

showed tumor regression upon drug administration. Less

toxic derivatives of cyclopamine are being used in

preclinical trials of medulloblastoma. Although this com-

pound will probably only be effective for patients with

NBCCS or those whose tumors harbor PTCH and SMOH

mutations, it carries great potential as a targeted molecular

therapy in such instances [9, 151].

Germ line mutations of APC in patients with Turcot

syndrome have been reported to increase the risk of

developing medulloblastomas [58]. The inactivation of the

APC gene leads to aberrant signaling in the WNT pathway,

resulting in the inability of the multiprotein complex

containing APC, axin, and glycogen synthase kinase-3

(GSK-3) to phosphorylate and cause degradation of -

catenin. This leads to an overabundance of -catenin and

its translocation to the nucleus where it activates the TCF/

LEF transcriptional complex. The -catenin/TCF dimer

activates the transcription of other growth-regulating genes,

some of which are known oncogenes (e.g., c-MYC and

cyclin D) [42, 101, 150]. Mutations in WNT pathway

members occur in about 15% of sporadic medulloblastoma

[25, 66, 77, 181]. A recent report also demonstrated that

mutations in SUFU can cause a decreased efficiency of-

catenin nuclear export, thereby also resulting in increased

-catenin/TCF signaling [160].

The ERBB or epidermal growth factor family of receptor

tyrosine kinases plays a crucial role in regulating cellular proliferation, apoptosis, migration, and differentiation.

Activation of these receptors through ligand binding,

dimerization, and autophosphorylation culminate in down-

stream signaling through mitogen-activated protein kinase

(MAPK), AKT, and STAT [107]. Interestingly, one of the

four members of the ERBB family, ERBB2, has been

shown to be highly expressed in medulloblastoma [52]. A

high level of ERBB2 and ERBB4 coexpression signifies an

increased risk of metastases and is associated with poor

prognosis in cases of medulloblastoma [48, 50]. Microarray

analysis of medulloblastoma cell lines demonstrate that

S100A4, a prometastatic gene known to be linked to breastand bladder cancers, is a direct target of ERBB2 signaling

in medulloblastoma cells via the AKT/PI3K pathway [61].

Compounds such as OSI-774 (erlotinib, also known as

gefitinif) inhibit ERBB2 signaling in human medulloblas-

toma cells and may have therapeutic potential [61].

The PDGFR and downstream activation of the RAS/

MAPK signaling pathway (including MAP2K1, MAP2K2,

and MAPK1/3) have also been uncovered as potential

mediators of medulloblastoma metastasis [33, 51, 92].

The mRNA expression level of TrkC, a neurotrophin

signaling receptor, was identified as a positive prognostic

factor for progression-free and overall survival in medul-

loblastoma [53, 124]. The MYC protooncogenes (MYCN

and MYCC) are amplified and/or overexpressed in a

subset of large cell medulloblastomas and also correlate

with poor clinical outcome [39, 40]. However, other

studies of TrkC, MYCC, and MYCN mRNA expression

or immunoreactivity did not demonstrate a significant

prognostic effect [48, 80].

Loss of chromosome 17p, often through the formation of

an isochromosome 17q i(17)(q10), is the most common

chromosome aberration in childhood medulloblastoma,

occurring in about 25% to 35% of cases. Either isolated

17p deletion or i(17)(q10) has been reported as a significant

negative prognostic factor [50, 109]. Recent cytogenetic

analysis using matrix CGH suggested that overexpression

of CDK6 correlates with a worse prognosis [99].

Most of the tumor suppressor genes shown to play a role

in the formation of medulloblastoma have been identified

through mutations; however, other epigenetic phenomena

may lead to their decreased expression. Aberrant methyla-

tion of CpG islands located in promoter regions represents

one of the major mechanisms for silencing of cancer-related

1386 Childs Nerv Syst (2006) 22:13791394

8/9/2019 Child CNS

9/16

genes in tumor cells. Extensive hypermethylation of the

RASSF1A gene (ras-association domain family protein 1,

isoform A), an identified tumor suppressor gene located at

chromosome 3p21.3, occurs in about 80% of primary

medulloblastomas [86, 91]. Furthermore, complete methyl-

ation of the putative tumor suppressor HIC-1 (hyper-

methylated in cancer) and the apoptosis effector molecule

caspsase-8 has been found in a subset of medulloblastoma[132, 168, 182].

Germ cell tumors

Although the exact molecular and cytogenetic aberrations

in GCTs are still not well defined, the most consistent

cytogenetic abnormality observed in such tumors is

isochromosome 12p (i12p) [26, 31, 89]. Some tumors

without i12p have overrepresentation of 12p by other

mechanisms, such as duplication of the entire chromosome.

The exact role of genes implicated in 12p overrepresenta-tion in GCTs remains uncertain, but evidence suggests that

the genes located on this chromosome, such as cyclin D2,

may play a role in facilitating entry into S phase of the cell

cycle. The rather frequent finding of i12p is also highly

indicative of the existence of novel putative oncogenes on

12p which may be involved in the pathogenesis of GCTs.

Other chromosomal aberrations have also been observed

in pineal GCTs. In a study of 15 pineal region GCTs,

Rickert et al. reported that the most common chromosomal

imbalances in pineal germinomas were losses of 13q and

18q, and loss of chromosomes 4 and 5 [128]. Interestingly,

these authors infrequently found gain of 12p. A summary

of other reported genetic aberrations in these tumors can be

found in a recent review by Taylor et al. [157].

Although most GCTs are sporadic, a few genetic

syndromes do predispose individuals to their development.

Pineal germinomas or teratomas in patients with Klinefelter

syndrome have been reported [120]. That patients with

Klinefelter syndrome generally have increased risk of

developing malignancy is in keeping with the idea of the

existence of a putative oncogene on the X chromosome.

Patients with trisomy 21 have an increased risk of a number

of cancers including leukemia and gonadal and extragona-

dal GCTs [139].

Ewing sarcoma

Primary Ewing sarcoma (ES)/peripheral primitive neuro-

ectodermal tumors (pPNET) of the central nervous system

constitute a clinically important, albeit rare, subset of

pediatric soft tissue tumors. They typically arise extracra-

nially or paraspinally and often result in secondary invasion

of critical neural structures [18].

In recent years, an examination of the genetic alterations

present within the spectrum of pediatric soft tissue tumors

has demonstrated a fairly specific (although not absolute)

association between specific nonrandom reciprocal chro-

mosomal translocations and individual soft tissue tumor

types [20]. Ongoing study of these fusion products has

yielded profound insights into the biology of these tumors

and may hold great promise for novel diagnostic andtherapeutic applications.

Ewing sarcoma/pPNET-associated translocations charac-

teristically involve the EWS gene on 22q12 and various

members of the ETS family of protooncogenes (Fig. 3).

Approximately 85% of ES/pPNET tumors harbor the

translocation t(11;22)(q24;q12); in this subset of tumors,

the translocation partner for EWS is the FLI1 gene product

found on 11q24 [32]. In nearly 10% of cases, the

translocation partner is ERG [t(21;22)(q22;q12)] [144],

and in rare cases, EWS may be fused to the ETS domains

of ETV-1 [t(7;22)(p22;q12)] [73], E1AF [t(17;22)(q12;

q12)] [76], or FEV [t(2;22)(q33;q12)] [111].The EWS gene product is a member of a growing family

of highly conserved RNA-binding proteins [105]. Although

the exact biological function of wild-type EWS and its

homologues remains largely unknown, a growing body of

evidence suggests that they are involved in mRNA

transcription. EWS has been shown to form an adaptor

ternary complex with RNA polymerase II and other

heterogeneous RNA-binding proteins [112]; these findings

are highly suggestive of an important role of EWS in basic

transcriptional regulation.

ETS-domain-containing proteins are DNA-binding tran-

scription factors that are implicated in the control of cellular

proliferation. ETS family members appear to cooperate

with other nuclear proteins to help establish promoter

specificity, modulate transcriptional regulation, and facili-

tate linkage to various signal transduction pathways,

including RAS [36, 64, 143, 172].

The ES/pPNET-associated translocations result in chi-

meric proteins containing the N-terminal domain of EWS

fused to the site-specific nucleic acid binding domain of the

ETS transcription factor translocation partner (Fig. 3). This

structure suggests that the chimeric protein is directed at the

promoter region of specific genes recognized by the

translocated DNA-binding domain of the ETS member [5,

106]. However, the ultimate targets of the EWS-ETS

chimeric protein may not be solely dependent on the ETS

domain; rather, other proteinprotein interactions unique to

the chimeric molecule may be at play [98]. The actual

target genes contributing to tumorigenesis are not known,

but analysis of mRNAs differentially expressed in cell lines

stably transfected with the EWS-FLI1 fusion has produced

some interesting candidates, including manic fringe, c-myc,

cyclin D1, mE2-C, MMP-1, and TGF-RIII [4, 6, 14].

Childs Nerv Syst (2006) 22:13791394 1387

8/9/2019 Child CNS

10/16

The fairly consistent presence of these recombinant gene

products in ES/pPNET suggests that they play a critical role

in the underlying biology of these tumors (Fig. 3). Trans-fection of EWS-FLI1 or EWS-ERG can transform mouse

NIH-3T3 cells if both the EWS and ETS domains are

functionally intact [98]. EWS-FLI1 antisense RNA trans-

fected into ES/pPNET cells results in marked growth

inhibition, suggesting that the EWS-ETS gene rearrange-

ment may also be necessary for maintaining the malignant

phenotype of ES/pPNET cell lines [153]. Furthermore,

expression of EWS-ETS fusion constructs may contribute

to tumorigenesis via inhibition of apoptosis; not surprisingly,

antisense inhibition of EWS-ETS fusion genes may enhance

susceptibility to chemotherapy-induced apoptosis [177].

The gene fusions characteristic of ES/pPNET exhibit an

underlying molecular heterogeneity. There are two under-

lying sources of variability: the specific ETS fusion partner

and the breakpoint location within the genes. A better

outcome for patients with localized tumors expressing the

most common chimeric transcript (type I: EWS exon 7

fused to FLI1 exon 6) compared with the next most

common fusion types (type II: EWS exon 7 fused to FLI1

exon 5 or type III: EWS exon 10 fused to FLI1 exon 6) has

been reported, raising the possibility that heterogeneity in

chimeric transcripts may reliably define clinically distinct

risk groups [30, 85]. Preliminary work suggests that the

better outcome associated with type I fusion transcripts maybe related to the weaker transcriptional activation properties

of the type I transcript [30].

Other less common numerical and structural chromo-

somal aberrations may also be found in ES/pPNET [3, 15,

97, 102, 108, 154]. The most common numerical abnor-

malities are +1q, +8, +12, and +20, and 1p, 16q, and

19q. More complex, multichromosome translocations,

such as t(11;14;22)(q24;q11;q12) and t(10;11;22)(p11.2;

q24;q12), may also occur and generally portend a poor

prognosis.

Changes in known tumor suppressor genes may be

observed in some cases. Homozygous deletion of

CDKN2A (p14ARF) on 9p21 has been described in

approximately 30% of cases [81]. Although mutations in

p53 have been described in up to 50% of ES/pPNET cell

lines [57], this appears to be a rare event in primary tumors

[167]. Amplification of the MDM2 gene, an inactivator of

p53, is also rare in ES/pPNET, consistent with the

hypothesis that p53 and regulators of its activity may not

play a dominant role in the pathogenesis of ES/pPNET

[93].

Fig. 3 Schematic representation

of the two commonest fusion

genes in Ewing sarcoma and the

proposed effects of the onco-

genic chimeric protein on cellu-

lar proliferation and

tumorigenicity

1388 Childs Nerv Syst (2006) 22:13791394

8/9/2019 Child CNS

11/16

Conclusions

As is evident from this review, our understanding of the

fundamental mechanisms of brain tumorigenesis in children

has increased markedly over the past 2 decades. The pace

of subsequent advances will only quicken, owing to such

monumental technical feats as the sequencing of the human

genome. Concomitant developments in the field of bio-informatics will be equally important as they will allow us

to make sense of the volumes of data that will undoubtedly

emerge from the ongoing interrogation of the fundamental

molecular processes at work in the genesis of pediatric

brain tumors. The challenge for the next 2 decades will be

to consolidate our understanding of the molecular patho-

genesis of childhood brain tumors and to apply this

sophisticated knowledge toward the development of clini-

cally useful treatment strategies.

Acknowledgements This work was supported by grants from the

National Cancer Institute of Canada, the Pediatric Brain Tumor

Foundation, the Wiley Fund, and the Laurie Berman Fund for BrainTumor Research.

References

1. Alonso M, Hamelin R, Kim M, Porwancher K, Sung T, Parhar P,

Miller DC, Newcomb EW (2001) Microsatellite instability

occurs in distinct subtypes of pediatric but not adult central

nervous system tumors. Cancer Res 61:21242128

2. Altshuler D, Brooks LD, Chakravarti A, Collins FS, Daly MJ,

Donnelly P, International HapMap Consortium (2005) A

haplotype map of the human genome. Nature 437:12991320

3. Armengol G, Tarkkanen M, Virolainen M et al (1997) Recurrent

gains of 1q, 8 and 12 in the Ewing family of tumors by

comparative genomic hybridization. Br J Cancer 75:14031409

4. Baer C, Nees M, Breit S et al (2004) Profiling and functional

annotation of mRNA gene expression in pediatric rhabdomyo-

sarcoma and Ewings sarcoma. Int J Cancer 110:687694

5. Bailly RA, Bosselut R, Zucman J et al (1994) DNA-binding and

transcriptional activation properties of the EWS-FLI-1 fusion

protein resulting from the t(11;22) translocation in Ewing

sarcoma. Mol Cell Biol 14:32303241

6. Bandres E, Malumbres R, Escalada A et al (2005) Gene

expression profile of Ewing sarcoma cell lines differing in their

EWS-FLI1 fusion type. J Pediatr Hematol Oncol 27:537542

7. Bardelli A, Parsons DW, Silliman N, Ptak J, Szabo S, Saha S,

Markowitz S, Willson JK, Parmigiani G, Kinzler KW, Vogelstein

B, Velculescu VE (2003) Mutational analysis of the tyrosinekinome in colorectal cancers. Science 300:949

8. Barrett MT, Scheffer A, Ben-Dor A, Sampas N, Lipson D,

Kincaid R, Tsang P, Curry B, Baird K, Meltzer PS, Yakhini Z,

Bruhn L, Laderman S (2004) Comparative genomic hybridiza-

tion using oligonucleotide microarrays and total genomic DNA.

Proc Natl Acad Sci USA 101:1776517770

9. Berman DM, Karhadkar SS, Hallahan AR, Pritchard JI,

Eberhart CG, Watkins DN et al (2002) Medulloblastoma

growth inhibition by hedgehog pathway blockade. Science

297:15591561

10. Biegel JA, Rorke LB, Packer RJ et al (1990) Monosomy 22 in

rhabdoid or atypical tumors of the brain. J Neurosurg 73:710 714

11. Biegel JA, Zhou JY, Rorke LB et al (1999) Germ-line and

acquired mutations of INI1 in atypical teratoid and rhabdoid

tumors. Cancer Res 59:7479

12. Biegel JA, Fogelgren B, Zhou JY, James CD, Janss AJ, Allen JC,

Zagzag D, Raffel C, Rorke LB (2000) Mutations of the INI1

rhabdoid tumor suppressor gene in medulloblastomas and

primitive neuroectodermal tumors of the central nervous system.

Clin Cancer Res 6:27592763

13. Biegel JA, Tan L, Zhang F, Wainwright L, Russo P, Rorke LB

(2002) Alterations of the hSNF5/INI1 gene in central nervous

system atypical teratoid/rhabdoid tumors and renal and extra-

renal rhabdoid tumors. Clin Cancer Res 8:34613467

14. Braun BS, Frieden R, Lessnick SL et al (1995) Identification

of target genes for the Ewings sarcoma EWS/Fli fusion

protein by representational difference analysis. Mol Cell Biol

15:46234630

15. Brisset S, Schleiermacher G, Peter M et al (2001) CGH analysis

of secondary genetic changes in Ewing tumors: correlation with

metastatic disease in a series of 43 cases. Cancer Genet

Cytogenet 130:5761

16. Bucca G, Carruba G, Saetta A, Muti P, Castagnetta L, Smith CP

(2004) Gene expression profiling of human cancers. Ann N Y

Acad Sci 1028:2837

17. Buhren J, Christoph AH, Buslei R, Albrecht S, Wiestler OD,

Pietsch T (2000) Expression of the neurotrophin receptor

p75NTR in medulloblastomas is correlated with distinct

histological and clinical features: evidence for a medulloblasto-

ma subtype derived from the external granule cell layer. J

Neuropathol Exp Neurol 59:229240

18. Carlotti CG Jr, Drake JM, Hladky JP, Teshima I, Becker LE,

Rutka JT (1999) Primary Ewings sarcoma of the skull in

children. Utility of molecular diagnostics, surgery and adjuvant

therapies. Pediatr Neurosurg 31:307315

19. Carvalho B, Ouwerkerk E, Meijer GA, Ylstra B (2004) High

resolution microarray comparative genomic hybridisation analy-

sis using spotted oligonucleotides. J Clin Pathol 57:644646

20. Chang CC, Shidham VB (2003) Molecular genetics of pediatric

soft tissue tumors. J Mol Diagn 5:143154

21. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S,

Long J, Stern D, Tammana H, Helt G, Sementchenko V,

Piccolboni A, Bekiranov S, Bailey DK, Ganesh M, Ghosh S,

Bell I, Gerhard DS, Gingeras TR (2005) Transcriptional maps of

10 human chromosomes at 5-nucleotide resolution. Science

308:11491154

22. Cheng Y, Ng HK, Zhang SF, Ding M, Pang JC, Zheng J, Poon

WS (1999) Genetic alterations in pediatric high-grade astrocyto-

mas. Hum Pathol 30:12841290

23. Cheng Y, Pang JC, Ng HK, Ding M, Zhang SF, Zheng J, Liu

DG, Poon WS (2000) Pilocytic astrocytomas do not show most

of the genetic changes commonly seen in diffuse astrocytomas.

Histopathology 37:437444

24. Cowell JK, Matsui S, Wang YD, LaDuca J, Conroy J, McQuaid

D, Nowak NJ (2004) Application of bacterial artificial chromo-

some array-based comparative genomic hybridization and spec-tral karyotyping to the analysis of glioblastoma multiforme.

Cancer Genet Cytogenet 151:3651

25. Dahmen RP, Koch A, Denkhaus D et al (2001) Deletions of

AXIN1, a component of the WNT/wingless pathway, in sporadic

medulloblastomas. Cancer Res 61:70397043

26. Dal Cin P, Dei Tos AP, Qi H, Giannini C, Furlanetto A, Longatti

PL, Marynen P, Van den Berghe H (1998) Immature teratoma of

the pineal gland with isochromosome 12p. Acta Neuropathol

(Berl) 95:107110

27. Davies H, Bignell GR, Cox C, Stephens P, Edkins S, Clegg S,

Teague J, Woffendin H, Garnett MJ, Bottomley W, Davis N,

Dicks E, Ewing R, Floyd Y, Gray K, Hall S, Hawes R, Hughes J,

Childs Nerv Syst (2006) 22:13791394 1389

8/9/2019 Child CNS

12/16

Kosmidou V, Menzies A, Mould C, Parker A, Stevens C, Watt S,

Hooper S, Wilson R, Jayatilake H, Gusterson BA, Cooper C,

Shipley J, Hargrave D, Pritchard-Jones K, Maitland N,

Chenevix-Trench G, Riggins GJ, Bigner DD, Palmieri G, Cossu

A, Flanagan A, Nicholson A, Ho JW, Leung SY, Yuen ST, Weber

BL, Seigler HF, Darrow TL, Paterson H, Marais R, Marshall CJ,

Wooster R, Stratton MR, Futreal PA (2002) Mutations of the

BRAF gene in human cancer. Nature 417:949954

28. Davies H, Hunter C, Smith R, Stephens P, Greenman C, Bignell

G, Teague J, Butler A, Edkins S, Stevens C, Parker A, OMeara S,Avis T, Barthorpe S, Brackenbury L, Buck G, Clements J, Cole J,

Dicks E, Edwards K, Forbes S, Gorton M, Gray K, Halliday K,

Harrison R, Hills K, Hinton J, Jones D, Kosmidou V, Laman R,

Lugg R, Menzies A, Perry J, Petty R, Raine K, Shepherd R, Small

A, Solomon H, Stephens Y, Tofts C, Varian J, Webb A, West S,

Widaa S, Yates A, Brasseur F, Cooper CS, Flanagan AM, Green

A, Knowles M, Leung SY, Looijenga LH, Malkowicz B, Pierotti

MA, Teh BT, Yuen ST, Lakhani SR, Easton DF, Weber BL,

Goldstraw P, Nicholson AG, Wooster R, Stratton MR, Futreal PA

(2005) Somatic mutations of the protein kinase gene family in

human lung cancer. Cancer Res 65:75917595

29. Davies JJ, Wilson IM, Lam WL (2005) Array CGH technologies

and their applications to cancer genomes. Chromosome Res

13:237248

30. de Alava E, Panizo A, Antonescu CR, Huvos AG, Pardo-Mindan

FJ, Barr FG, Ladanyi M (2000) Association of EWS-FLI1 type 1

fusion with lower proliferative rate in Ewings sarcoma. Am J

Pathol 156:849855

31. de Bruin TW, Slater RM, Defferrari R, Geurts van Kessel A,

Suijkerbuijk RF, Jansen G, de Jong B, Oosterhuis JW (1994)

Isochromosome 12p-positive pineal germ cell tumor. Cancer Res

54:15421544

32. Delattre O, Zucman J, Plougastel B et al (1992) Gene fusion with

an ETS DNA-binding domain caused by chromosome translo-

cation in human tumors. Nature 359:162165

33. Del Valle L, Enam S, Lassak A, Wang JY, Croul S et al (2002)

Insulin-like growth factor I receptor activity in human medullo-

blastomas. Clin Cancer Res 8:18221830

34. De Smaele E, Di Marcotullio L, Ferretti E, Screpanti I, Alesse E,

Gulino A (2004) Chromosome 17p deletion in human medullo-

blastoma: a missing checkpoint in the Hedgehog pathway. Cell

Cycle 3:12631266

35. Di Marcotullio L, Ferretti E, De Smaele E, Argenti B, Mincione

C et al (2004) REN(KCTD11) is a suppressor of Hedgehog

signaling and is deleted in human medulloblastoma. Proc Natl

Acad Sci USA 101:1083310838

36. Dittmer J, Nordheim A (1998) ETS transcription factors and

human disease. Biochim Biophys Acta 1377:F1F11

37. Duerr EM, Rollbrocker B, Hayashi Y, Peters N, Meyer-Puttlitz

B, Louis DN, Schramm J, Wiestler OD, Parsons R, Eng C, von

Deimling A (1998) PTEN mutations in gliomas and glioneuronal

tumors. Oncogene 16:22592264

38. Dyer S, Prebble E, Davison V, Davies P, Ramani P, Ellison D,

Grundy R (2002) Genomic imbalances in pediatric intracranial

ependymomas define clinically relevant groups. Am J Pathol

161:21332141

39. Eberhart CG, Kepner JL, Goldthwaite PT et al (2002) Histo-

pathologic grading of medulloblastomas: a Pediatric Oncology

Group study. Cancer 94:552560

40. Eberhart CG, Kratz J, Wang Y, Summers K, Stearns D et al

(2004) Histopathological and molecular prognostic markers in

medulloblastoma: c-myc, n-myc, TrkC, and anaplasia. J

Neuropathol Exp Neurol 63:441449

41. Ebert C, von Haken M, Meyer-Puttlitz B, Wiestler OD,

Reifenberger G, Pietsch T, von Deimling A (1999) Molecular

genetic analysis of ependymal tumors. NF2 mutations and

chromosome 22q loss occur preferentially in intramedullary

spinal ependymomas. Am J Pathol 155:627632

42. Elberhart CG, Tihan T, Burger PC (2000) Nuclear localization

and mutation of beta-catenin in medulloblastoma. J Neuropathol

Exp Neurol 59:333337

43. Erez A, Ilan T, Amariglio N et al (2002) GLI3 is not mutated

commonly in sporadic medulloblastomas. Cancer 95:2831

44. Fernandez-Teijeiro A, Betensky RA, Sturla LM, Kim JY,

Tamayo P, Pomeroy SL (2004) Combining gene expression

profiles and clinical parameters for risk stratification in medul-loblastomas. J Clin Oncol 22:994998

45. Ferretti E, Smaele ED, Marcotullio LD, Screpanti I, Gulino A

(2005) Hedgehog checkpoints in medulloblastoma: the chromo-

some 17p deletion paradigm. Trends Mol Med 11:537545

46. Fink KL, Rushing EJ, Schold SC Jr, Nisen PD (1996)

Infrequency of p53 gene mutations in ependymomas. J Neuro-

oncol 27:111115

47. Freeman WM, Robertson DJ, Vrana KE (2000) Fundamentals of

DNA hybridization arrays for gene expression analysis. Bio-

techniques 29:10421046, 10481055

48. Gajjar A, Hernan R, Kocak M, Fuller C, Lee Y et al (2004)

Clinical, histopathological, and molecular markers of prognosis:

toward a new disease risk stratification system for medulloblas-

toma. J Clin Oncol 22:984993

49. Garraway LA, Widlund HR, Rubin MA, Getz G, Berger AJ,

Ramaswamy S, Beroukhim R, Milner DA, Granter SR, Du J,

Lee C, Wagner SN, Li C, Golub TR, Rimm DL, Meyerson ML,

Fisher DE, Sellers WR (2005) Integrative genomic analyses

identify MITF as a lineage survival oncogene amplified in

malignant melanoma. Nature 436:117122

50. Gilbertson R, Wickramasinghe C, Hernan R, Balaji V, Hunt D et

al (2001) Clinical and molecular stratification of disease risk in

medulloblastoma. Br J Cancer 85:705712

51. Gilbertson RJ, Clifford SC (2003) PDGFRB is overexpressed in

metastatic medulloblastoma. Nat Genet 35:197198

52. Gilbertson RJ, Clifford SC, MacMeekin W, Meekin W, Wright C

et al (1998) Expression of the ErbB-neuregulin signaling network

during human cerebellar development: implications for the

biology of medulloblastoma. Cancer Res 58:39323941

53. Grotzer MA, Janss AJ, Fung KM, Biegel JA, Sutton LN, Rorke

LB (2000) TrkC expression predicts good clinical outcome in

primitive neuroectodermal brain tumors. J Clin Oncol 18:1027

1035

54. Gutmann DH, Donahoe J, Brown T, James CD, Perry A (2000)

Loss of neurofibromatosis 1 (NF1) gene expression in NF1-

associated pilocytic astrocytomas. Neuropathol Appl Neurobiol

26:361367

55. Gyure KA (2005) Newly defined central nervous system

neoplasms. Am J Clin Pathol 123(Suppl):S3S12

56. Hahn H, Wicking C, Zaphiropoulous PG, Gailani MR, Shanley S

et al (1996) Mutations of the human homolog of Drosophila

patched in the nevoid basal cell carcinoma syndrome. Cell

85:841851

57. Hamelin R, Zucman J, Melot T et al (1994) p53 mutations in

human tumors with chimeric EWS/FLI-1 genes. Int J Cancer

57:336340

58. Hamilton SR, Liu B, Parsons RE, Papadopoulos N, Jen J, Powell

SM et al (1995) The molecular basis of Turcots syndrome. N

Engl J Med 332:839847

59. Harkness W, Hayward R, Darling J, Thomas D (2001)

Identification of extensive genomic loss and gain by comparative

genomic hybridisation in malignant astrocytoma in children and

young adults. Genes Chromosomes Cancer 31:1522

60. Harrington CA, Rosenow C, Retief J (2000) Monitoring gene

expression using DNA microarrays. Curr Opin Microbiol

3:285291

1390 Childs Nerv Syst (2006) 22:13791394

8/9/2019 Child CNS

13/16

61. Hernan R, Fasheh R, Calabrese C, Frank AJ, Maclean KH et al

(2003) ERBB2 up-regulates S100A4 and several other prometa-

static genes in medulloblastoma. Cancer Res 63:140148

62. Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger

DG, Frazer KA, Cox DR (2005) Whole-genome patterns of

common DNA variation in three human populations. Science

307:10721079

63. Hirose Y, Aldape K, Bollen A, James CD, Brat D, Lamborn K,

Berger M, Feuerstein BG (2001) Chromosomal abnormalities

subdivide ependymal tumors into clinically relevant groups. AmJ Pathol 158:11371143

64. Hromas R, Klemsz M (1994) The ETS oncogene family in

development, proliferation and neoplasia. Int J Hematol 59:

257265

65. Hu N, Wang C, Hu Y, Yang HH, Giffen C, Tang ZZ, Han XY,

Goldstein AM, Emmert-Buck MR, Buetow KH, Taylor PR, Lee

MP (2005) Genome-wide association study in esophageal cancer

using GeneChip mapping 10 K array. Cancer Res 65:25422546

66. Huang H, Mahler-Araujo BM, Sankila A, Chimelli L, Yonekawa

Y, Kleihues P (2000) APC mutations in sporadic medulloblas-

tomas. Am J Pathol 156:433437

67. Huang J, Wei W, Zhang J, Liu G, Bignell GR, Stratton MR,

Futreal PA, Wooster R, Jones KW, Shapero MH (2004) Whole

genome DNA copy number changes identified by high density

oligonucleotide arrays. Hum Genomics 1:287299

68. Hui AB, Takano H, Lo KW, Kuo WL, Lam CN, Tong CY,

Chang Q, Gray JW, Ng HK (2005) Identification of a novel

homozygous deletion region at 6q23.1 in medulloblastomas

using high-resolution array comparative genomic hybridization

analysis. Clin Cancer Res 11:47074716

69. Ichimura K, Ohgaki H, Kleihues P, Collins VP (2004) Molecular

pathogenesis of astrocytic tumors. J Neurooncol 70:137160

70. Inazawa J, Inoue J, Imoto I (2004) Comparative genomic

hybridization (CGH)-arrays pave the way for identification of

novel cancer-related genes. Cancer Sci 95:559563

71. Ishii N, Sawamura Y, Tada M, Daub DM, Janzer RC, Meagher-

Villemure M, de Tribolet N, Van Meir EG (1998) Absence of

p53 gene mutations in a tumor panel representative of pilocytic

astrocytoma diversity using a p53 functional assay. Int J Cancer

76:797800

72. Ishkanian AS, Malloff CA, Watson SK, DeLeeuw RJ, Chi B,

Coe BP, Snijders A, Albertson DG, Pinkel D, Marra MA, Ling

V, MacAulay C, Lam WL (2004) A tiling resolution DNA

microarray with complete coverage of the human genome. Nat

Genet 36:299303

73. Jeon IS, Davis JN, Braun BS et al (1995) A variant Ewings

sarcoma translocation (7;22) fuses the EWS gene to the ETS

gene ETV1. Oncogene 10:12291234

74. Johnson RL et al (1996) Human homolog of patched, a candidate

gene for the basal cell nevus syndrome. Science 272:16681671

75. Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S,

Cawley S, Drenkow J, Piccolboni A, Bekiranov S, Helt G,

Tammana H, Gingeras TR (2004) Novel RNAs identified from

an in-depth analysis of the transcriptome of human chromosomes

21 and 22. Genome Res 14:331342

76. Kaneko Y, Yoshida K, Handa M et al (1996) Fusion of an ETS-

family gene, E1AF, to EWS by t(17;22)(q12;q12) chromosome

translocation in an undifferentiated sarcoma of infancy. Genes

Chromosomes Cancer 15:115121

77. Kang DE, Soriano S, Xia X, Eberhart CG, De Strooper B et al

(2002) Presenilin couples the paired phosphorylation of beta-

catenin independent of axin: implications for beta-catenin

activation in tumorigenesis. Cell 110:751762

78. Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg

RL, Fodor SP, Gingeras TR (2002) Large-scale transcriptional

activity in chromosomes 21 and 22. Science 296:916919

79. Kennedy GC, Matsuzaki H, Dong S, Liu WM, Huang J, Liu G,

Su X, Cao M, Chen W, Zhang J, Liu W, Yang G, Di X, Ryder T,

He Z, Surti U, Phillips MS, Boyce-Jacino MT, Fodor SP, Jones

KW (2003) Large-scale genotyping of complex DNA. Nat

Biotechnol 21:12331237

80. Korshunov A, Savostikova M, Ozerov S (2002) Immunohisto-

chemical markers for prognosis of average-risk pediatric medul-

loblastomas. The effect of apoptotic index, TrkC, and c-myc

expression. J Neurooncol 58:271279

81. Kovar H, Jug G, Aryee DN et al (1997) Among genes involvedin the RB dependent cell cycle regulatory cascade, the p16 tumor

suppressor gene is frequently lost in the Ewing family of tumors.

Oncogene 15:22252232

82. Kramer DL, Parmiter AH, Rorke LB, Sutton LN, Biegel JA

(1998) Molecular cytogenetic studies of pediatric ependymomas.

J Neurooncol 37:2533

83. Krzywinski M, Bosdet I, Smailus D, Chiu R, Mathewson C,

Wye N, Barber S, Brown-John M, Chan S, Chand S, Cloutier A,

Girn N, Lee D, Masson A, Mayo M, Olson T, Pandoh P, Prabhu

AL, Schoenmakers E, Tsai M, Albertson D, Lam W, Choy CO,

Osoegawa K, Zhao S, de Jong PJ, Schein J, Jones S, Marra MA

(2004) A set of BAC clones spanning the human genome.

Nucleic Acids Res 32:36513660

84. Leung C, Lingbeek M, Shakhova O, Liu J, Tanger E,

Saremaslani P et al (2004) Bmi1 is essential for cerebellar

development and is overexpressed in human medulloblasto-

mas. Nature 428:337341

85. Lin PP, Brody RI, Hamelin AC, Bradner JE, Healey JH, Ladanyi

M (1999) Differential transactivation by alternative EWS-FLI1

fusion proteins correlates with clinical heterogeneity in Ewings

sarcoma. Cancer Res 59:14281432

86. Lindsey JC, Lusher ME, Anderton JA, Bailey S, Gilbertson RJ et

al (2004) Identification of tumor-specific epigenetic events in

medulloblastoma development by hypermethylation profiling.

Carcinogenesis 25:661668

87. Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ (1999) High

density synthetic oligonucleotide arrays. Nat Genet 21(1 Suppl):

2024

88. Lockhart DJ, Winzeler EA (2000) Genomics, gene expression

and DNA arrays. Nature 405:827836

89. Losi L, Polito P, Hagemeijer A, Buonamici L, Van den Berghe

H, Dal Cin P (1998) Intracranial germ cell tumor (embryonal

carcinoma with teratoma) with complex karyotype including

isochromosome 12p. Virchows Arch 433:571574

90. Louis DN, Rubio MP, Correa KM, Gusella JF, von Deimling A

(1993) Molecular genetics of pediatric brain stem gliomas.

Application of PCR techniques to small and archival brain

tumor specimens. J Neuropathol Exp Neurol 52:507515

91. Lusher ME, Lindsey JC, Latif F, Pearson AD, Ellison DW,

Clifford SC (2002) Biallelic epigenetic inactivation of the

RASSF1A tumor suppressor gene in medulloblastoma develop-

ment. Cancer Res 62:59065911

92. MacDonald TJ, Brown KM, LaFleur B, Peterson K, Lawlor C,

Chen Y, Packer RJ, Cogen P, Stephan DA (2001) Expression

profiling of medulloblastoma: PDGFRA and the RAS/MAPK

pathway as therapeutic targets for metastatic disease. Nat Genet

29:143152

93. Maitra A, Roberts H, Weinberg AG et al (2001) Aberrant

expression of tumor suppressor proteins in the Ewing family of

tumors. Arch Pathol Lab Med 125:12071212

94. Marigo V, Davey RA, Zuo Y, Cunningham JM, Tabin CJ et al

(1996) Biochemical evidence that Patched is the Hedgehog

receptor. Nature 384:176179

95. Matsuzaki H, Dong S, Loi H, Di X, Liu G, Hubbell E, Law J,

Berntsen T, Chadha M, Hui H, Yang G, Kennedy GC, Webster

TA, Cawley S, Walsh PS, Jones KW, Fodor SP, Mei R (2004)

Childs Nerv Syst (2006) 22:13791394 1391

8/9/2019 Child CNS

14/16

Genotyping over 100,000 SNPs on a pair of oligonucleotide

arrays. Nat Methods 1:109111

96. Matsuzaki H, Loi H, Dong S, Tsai YY, Fang J, Law J, Di X,

Liu WM, Yang G, Liu G, Huang J, Kennedy GC, Ryder TB,

Marcus GA, Walsh PS, Shriver MD, Puck JM, Jones KW, Mei

R (2004) Parallel genotyping of over 10,000 SNPs using a one-

primer assay on a high-density oligonucleotide array. Genome

Res 14:414425

97. Maurici D, Perez-Atayde A, Grier HE et al (1998) Frequency

and implications of chromosome 8 and 12 gains in Ewingsarcoma. Cancer Genet Cytogenet 100:106110

98. May WA, Gishizky ML, Lessnick SL et al (1993) Ewing

sarcoma 11;22 translocation produces a chimeric transcrip-

tion factor that requires the DNA-binding domain encoded

by FLI1 for transformation. Proc Natl Acad Sci USA

90:57525756

99. Mendrzyk F, Radlwimmer B, Joos S, Kokocinski F, Benner A,

Stange DE, Neben K, Fiegler H, Carter NP, Reifenberger G,

Korshunov A, Lichter P (2005) Genomic and protein expression

profiling identifies CDK6 as novel independent prognostic

marker in medulloblastoma. J Clin Oncol 23:88538862

100. Mischel PS, Cloughesy TF, Nelson SF (2004) DNA-microarray

analysis of brain cancer: molecular classification for therapy. Nat

Rev Neurosci 5:782792

101. Morin PJ (1999) Beta-catenin signaling and cancer. Bioessays

21:10211030

102. Mugneret F, Lizard S, Aurias A et al (1988) Chromosomes in

Ewings sarcoma. II. Nonrandom additional changes, trisomy

8 and der(16)t(1;16). Cancer Genet Cytogenet 32:239245

103. Newcomb EW, Alonso M, Sung T, Miller DC (2000) Incidence

of p14ARF gene deletion in high-grade adult and pediatric

astrocytomas. Hum Pathol 31:115119

104. Nijssen PC, Deprez RH, Tijssen CC, Hagemeijer A, Arnoldus

EP, Teepen JL, Holl R, Niermeyer MF (1994) Familial anaplastic

ependymoma: evidence of loss of chromosome 22 in tumor cells.

J Neurol Neurosurg Psychiatry 57:12451248

105. Ohno T, Ouchida M, Lee L et al (1994) The EWS gene,

involved in Ewing family of tumors, malignant melanoma of

soft parts and desmoplastic small round cell tumors, codes for

an RNA binding protein with novel regulatory domains.

Oncogene 9:30873097

106. Ohno T, Rao VN, Reddy ESP (1994) EWS/Fli-1 chimeric

protein is a transcriptional activator. Cancer Res 53:5859

5863

107. Olayioye MA, Neve RM, Lane HA, Hynes NE (2000) The ErbB

signaling network: receptor heterodimerization in development

and cancer. EMBO J 19:31593166

108. Ozaki T, Paulussen M, Poremba C et al (2001) Genetic

imbalances revealed by comparative genomic hybridization in

Ewing tumors. Genes Chromosomes Cancer 32:164171

109. Pan E, Pellarin M, Holmes E, Smirnov I, Misra A, Eberhart CG

(2005) Isochromosome 17q is a negative prognostic factor in

poor-risk childhood medulloblastoma patients. Clin Cancer Res

11:47334740

110. Park PC, Taylor MD, Mainprize TG, Becker LE, Ho M, Dura

WT et al (2003) Transcriptional profiling of medulloblastoma in

children. J Neurosurg 99:534541

111. Peter M, Couturier J, Pacquement H et al (1997) A new member

of the ETS family fused to EWS in Ewing tumors. Oncogene

14:11591164

112. Petermann R, Mossier BM, Aryee DN et al (1998) Oncogenic

EWS-Fli1 interacts with hsRPB7, a subunit of human RNA

polymerase II. Oncogene 17:603610

113. Pietsch T, Waha A, Koch A et al (1997) Medulloblastomas of the

desmoplastic variant carry mutations of the human homologue of

Drosophila patched. Cancer Res 57:20852088

114. Pinkel D, Albertson DG (2005) Array comparative genomic

hybridization and its applications in cancer. Nat Genet 37(Suppl):

S11S17

115. Pinkel D, Albertson DG (2005) Comparative genomic hybrid-

ization. Annu Rev Genomics Hum Genet 6:331354

116. Platten M, Giordano MJ, Dirven CM, Gutmann DH, Louis DN

(1996) Up-regulation of specific NF-1 gene transcripts in

sporadic pilocytic astrocytomas. Am J Pathol 149:621627

117. Pollack IF, Hamilton RL, Finkelstein SD, Campbell JW,

Martinez AJ, Sherwin RN, Bozik ME, Gollin SM (1997) Therelationship between TP53 mutations and overexpression of p53

and prognosis in malignant gliomas of childhood. Cancer Res

57:304309

118. Pollack IF, Finkelstein SD, Burnham J, Holmes EJ, Hamilton

RL, Yates AJ, Finlay JL, Sposto R (2001) Age and TP53

mutation frequency in childhood malignant gliomas: results in a

multi-institutional cohort. Cancer Res 61:74047407

119. Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M,

McLaughlin ME, Kim JY, Goumnerova LC, Black PM, Lau C,

Allen JC, Zagzag D, Olson JM, Curran T, Wetmore C, Biegel

JA, Poggio T, Mukherjee S, Rifkin R, Califano A, Stolovitzky G,

Louis DN, Mesirov JP, Lander ES, Golub TR (2002) Prediction

of central nervous system embryonal tumor outcome based on

gene expression. Nature 415:436442

120. Prall JA, McGavran L, Greffe BS, Partington MD (1995)

Intracranial malignant germ cell tumor and the Klinefelter

syndrome. Case report and review of the literature. Pediatr

Neurosurg 23:219224

121. Raffel C, Frederick L, OFallon JR, Atherton-Skaff P, Perry A,

Jenkins RB, James CD (1999) Analysis of oncogene and tumor

suppressor gene alterations in pediatric malignant astrocytomas

reveals reduced survival for patients with PTEN mutations. Clin

Cancer Res 5:40854090

122. Rand V, Huang J, Stockwell T, Ferriera S, Buzko O, Levy S,

Busam D, Li K, Edwards JB, Eberhart C, Murphy KM,

Tsiamouri A, Beeson K, Simpson AJ, Venter JC, Riggins GJ,

Strausberg RL (2005) Sequence survey of receptor tyrosine

kinases reveals mutations in glioblastomas. Proc Natl Acad Sci

USA 102:1434414349

123. Rasheed BK, Stenzel TT, McLendon RE, Parsons R, Friedman

AH, Friedman HS, Bigner DD, Bigner SH (1997) PTEN gene

mutations are seen in high grade but not in low grade gliomas.

Cancer Res 57:41874190

124. Ray A, Ho M, Ma J, Parkes RK, Mainprize TG, Ueda S,

Mclaughlin J et al (2004) A clinical biological model

predicting survival in medulloblastoma. Clin Cancer Res

10:76137620

125. Reardon DA, Entrekin RE, Sublett J, Ragsdale S, Li H,

Boyett J, Kepner JL, Look AT (1999) Chromosome arm 6q

loss is the most common recurrent autosomal alteration

detected in primary pediatric ependymoma. Genes Chromo-

somes Cancer 24:230237

126. Reifenberger J, Wolter M, Weber RG et al (1998) Missense

mutation in SMOH in sporadic basal cell carcinoma of the skin

and primitive neuroectodermal tumors of the central nervous

system. Cancer Res 58:17981803

127. Rhodes DR, Chinnaiyan AM (2005) Integrative analysis of the

cancer transcriptome. Nat Genet 37(Suppl):S31S37

128. Rickert CH, Simon R, Bergmann M, Dockhorn-Dworniczak

B, Paulus W (2000) Comparative genomic hybridization in

pineal germ cell tumors. J Neuropathol Exp Neurol 59:815

821

129. Rickert CH, Strater R, Kaatsch P, Wassmann H, Jurgens H,

Dockhorn-Dworniczak B, Paulus W (2001) Pediatric high grade

astrocytomas show chromosomal imbalances distinct from adult

cases. Am J Pathol 158:15251532

1392 Childs Nerv Syst (2006) 22:13791394

8/9/2019 Child CNS

15/16

130. Roberts CW, Galusha SA, McMenamin ME et al (2000)

Haploinsufficiency of Snf5 (integrase interactor 1) predisposes

to malignant rhabdoid tumors in mice. Proc Natl Acad Sci USA

97:1379613800

131. Rogatto SR, Casartelli C, Rainho CA, Barbieri-Neto J (1993)

Chromosomes in the genesis and progression of ependymomas.

Cancer Genet Cytogenet 69:146152

132. Rood BR, Zhang H, Weitman DM, Cogen PH (2002) Hyper-

methylation of HIC-1 and 17p allelic loss in medulloblastoma.

Cancer Res 62:37943797133. Rorke LB, Packer R, Biegel J (1995) Central nervous system

atypical teratoid/rhabdoid tumors of infancy and childhood.

J Neurooncol 24:2128

134. Rorke LB, Packer RJ, Biegel JA (1996) Central nervous system

atypical teratoid/rhabdoid tumors of infancy and childhood:

definition of an entity. J Neurosurg 85:5665

135. Rossi MR, Conroy J, McQuaid D, Nowak NJ, Rutka JT, Cowell

JK (2006) Array CGH analysis of pediatric medulloblastomas.

Genes Chromosomes Cancer 45:290303

136. Rutka JT, Taylor M, Mainprize T, Langlois A, Ivanchuk S,

Mondal S, Dirks P (2000) Molecular biology in the third

millennium. Neurosurgery 46:10341051

137. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein

LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL,

Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J,

Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L,

Davenport R, Dante M, Fulton L, Hillier L, Waterston RH,

McPherson JD, Gilman B, Schaffner S, Van Etten WJ, Reich D,

Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann

N, Zody MC, Linton L, Lander ES, Altshuler D, International

SNP Map Working Group (2001) A map of human genome

sequence variation containing 1.42 million single nucleotide

polymorphisms. Nature 409:928933

138. Sanoudou D, Tingby O, Ferguson-Smith MA, Collins VP,

Coleman N (2000) Analysis of pilocytic astrocytoma by compar-

ative genomic hybridization. Br J Cancer 82:12181222

139. Satge D, Sommelet D, Geneix A, Nishi M, Malet P, Vekemans

M (1998) A tumor profile in Down syndrome. Am J Med Genet

78:207216

140. Schaid DJ, Guenther JC, Christensen GB, Hebbring S, Rosenow

C, Hilker CA, McDonnell SK, Cunningham JM, Slager SL,

Blute ML, Thibodeau SN (2004) Comparison of microsatellites

versus single-nucleotide polymorphisms in a genome linkage

screen for prostate cancer susceptibility loci. Am J Hum Genet

75:948965

141. Schulze A, Downward J (2001) Navigating gene expression using

microarraysa technology review. Nat Cell Biol 3:E190E195

142. Segal E, Friedman N, Kaminski N, Regev A, Koller D (2005)

From signatures to models: understanding cancer using micro-

arrays. Nat Genet 37(Suppl):S38S45

143. Sharrocks AD, Brown AL, Ling Y et al (1997) The ETS-domain

transcription factor family. Int J Biochem Cell Biol 29:13711387

144. Sorensen PH, Lessnick SL, Lopez-Terrada D et al (1994) A

second Ewings sarcoma translocation, t(21;22), fuses the EWS

gene to another ETS-family transcription factor, ERG. Nat Genet

6:146151

145. Stephens P, Hunter C, Bignell G, Edkins S, Davies H, Teague J,

Stevens C, OMeara S, Smith R, Parker A, Barthorpe A, Blow

M, Brackenbury L, Butler A, Clarke O, Cole J, Dicks E, Dike A,

Drozd A, Edwards K, Forbes S, Foster R, Gray K, Greenman C,

Halliday K, Hills K, Kosmidou V, Lugg R, Menzies A, Perry J,

Petty R, Raine K, Ratford L, Shepherd R, Small A, Stephens Y,

Tofts C, Varian J, West S, Widaa S, Yates A, Brasseur F, Cooper

CS, Flanagan AM, Knowles M, Leung SY, Louis DN, Looijenga

LH, Malkowicz B, Pierotti MA, Teh B, Chenevix-Trench G,

Weber BL, Yuen ST, Harris G, Goldstraw P, Nicholson AG,

Futreal PA, Wooster R, Stratton MR (2004) Lung cancer:

intragenic ERBB2 kinase mutations in tumors. Nature

431:525526

146. Stephens P, Edkins S, Davies H, Greenman C, Cox C, Hunter C,

Bignell G, Teague J, Smith R, Stevens C, OMeara S, Parker A,

Tarpey P, Avis T, Barthorpe A, Brackenbury L, Buck G, Butler

A, Clements J, Cole J, Dicks E, Edwards K, Forbes S, Gorton M,

Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jones D,

Kosmidou V, Laman R, Lugg R, Menzies A, Perry J, Petty R,

Raine K, Shepherd R, Small A, Solomon H, Stephens Y, Tofts C,Varian J, Webb A, West S, Widaa S, Yates A, Brasseur F, Cooper

CS, Flanagan AM, Green A, Knowles M, Leung SY, Looijenga

LH, Malkowicz B, Pierotti MA, Teh B, Yuen ST, Nicholson AG,

Lakhani S, Easton DF, Weber BL, Stratton MR, Futreal PA,

Wooster R (2005) A screen of the complete protein kinase gene

family identifies diverse patterns of somatic mutations in human

breast cancer. Nat Genet 37:590592

147. Suarez-Merino B, Hubank M, Revesz T, Harkness W, Hayward

R, Thompson D, Darling JL, Thomas DG, Warr TJ (2005)

Microarray analysis of pediatric ependymoma identifies a cluster

of 112 candidate genes including four transcripts at 22q12.1

q13.3. Neuro-oncol 7:2031

148. Sung T, Miller DC, Hayes RL, Alonso M, Yee H, Newcomb EW

(2000) Preferential inactivation of the p53 tumor suppressor

pathway and lack of EGFR amplification distinguish de novo

high grade pediatric astrocytomas from de novo adult astrocy-

tomas. Brain Pathol 10:249259

149. Sure U, Ruedi D, Tachibana O, Yonekawa Y, Ohgaki H,

Kleihues P, Hegi ME (1997) Determination of p53 mutations,

EGFR overexpression, and loss of p16 expression in pediatric

glioblastomas. J Neuropathol Exp Neurol 56:782789

150. Taipale J, Beachy PA (2001) The Hedgehog and Wnt signalling

pathways in cancer. Nature 411:349354

151. Taipale J, Chen JK, Cooper MK, Wang B, Mann RK,

Milenkovic L et al (2000) Effects of oncogenic mutations in

Smoothened and Patched can be reversed by cyclopamine.

Nature 406:10051009

152. Tamber MS, Rutka JT (2003) Pediatric supratentorial high grade

gliomas. Neurosurg Focus 14:e1 (serial online)

153. Tanaka K, Iwakuma T, Harimaya K et al (1997) EWS-Fli1

antisense oligodeoxynucleotide inhibits proliferation of human

Ewings sarcoma and primitive neuroectodermal tumor cells.

J Clin Invest 99:239247

154. Tarkkanen M, Kiuru-Kuhlefelt S, Blomqvist C et al (1999)

Clinical correlations of genetic changes by comparative genomic

hybridization in Ewing sarcoma and related tumors. Cancer

Genet Cytogenet 114:3541

155. Taylor MD, Gokgoz N, Andrulis IL et al (2000) Familial

posterior fossa brain tumors of infancy secondary to germ-line

mutation of the hSNF5 gene. Am J Hum Genet 66:14031406

156. Taylor MD, Mainprize TG, Rutka JT (2000) Molecular insight

into medulloblastoma and central nervous system primitive

neuroectodermal tumor biology from hereditary syndromes: a

review. Neurosurgery 47:888901

157. Taylor MD, Mainprize TG, Squire JA, Rutka JT (2001)

Molecular genetics of pineal region neoplasms. J Neurooncol

54:219238

158. Taylor MD, Liu L, Raffel C, Hui CC, Mainprize TG, Zhang X,

Rutka JT (2002) Mutation in SUFU predispose to medulloblas-

toma. Nat Genet 31:306310

159. Taylor MD, Mainprize TG, Rutka JT (2003) Bio