Genomic analysis reveals few genetic alterations
in pediatric acute myeloid leukemia
Ina Radtkea, Charles G. Mullighana, Masami Ishiia, Xiaoping Sua, Jinjun Chenga, Jing Mab, Ramapriya Gantia,
Zhongling Caia, Salil Goorhaa, Stanley B. Poundsc, Xueyuan Caoc, Caroline Obertb, Jianling Armstrongb, Jinghui Zhangd,
Guangchun Songa, Raul C. Ribeiroe, Jeffrey E. Rubnitze, Susana C. Raimondia, Sheila A. Shurtleffa,
and James R. Downinga,1
Departments ofaPathology,cBiostatistics, andeOncology, and thebHartwell Center for Bioinformatics and Biotechnology, St. Jude Children’s Research
Hospital, 262 Danny Thomas Place, Memphis, TN 38105; anddCenter for Biomedical Informatics and Information Technology, National Cancer Institute,
National Institutes of Health, 2115 E. Jefferson Street, Rockville, MD 20892
Edited by Janet D. Rowley, University of Chicago Medical Center, Chicago, IL, and approved June 11, 2009 (received for review March 20, 2009)
Pediatric de novo acute myeloid leukemia (AML) is an aggressive
malignancy with current therapy resulting in cure rates of only 60%.
To better understand the cause of the marked heterogeneity in
therapeutic response and to identify new prognostic markers and
underlie the pathogenesis of AML is needed. To approach this goal,
we examined diagnostic leukemic samples from a cohort of 111
children with de novo AML using single-nucleotide-polymorphism
that, in contrast to pediatric acute lymphoblastic leukemia (ALL), de
novo AML is characterized by a very low burden of genomic alter-
leukemia, and less than 1 nonsynonymous point mutation per leu-
kemia in the 25 genes analyzed. Even more surprising was the
observation that 34% of the leukemias lacked any identifiable copy-
number alterations, and 28% of the leukemias with recurrent trans-
locations lacked any identifiable sequence or numerical abnormali-
ties. The only exception to the presence of few mutations was acute
megakaryocytic leukemias, with the majority of these leukemias
the patient cohort, novel recurring regions of genetic alteration were
data reflect a remarkably low burden of genomic alterations within
copy number alterations ? single-nucleotide-polymorphism (SNP) ?
microarray ? candidate gene resequencing ? loss-of-heterozygosity (LOH)
their normal self-renewal, proliferation, differentiation, and apop-
totic pathways (1–3). These alterations include point mutations,
gene rearrangements, deletions, amplifications, and a diverse array
of epigenetic changes that influence gene expression. For most
leukemias the full complement of oncogenic lesions remains to be
To define the lesions in acute leukemia, we recently used
single-nucleotide-polymorphism (SNP) microarrays to perform
genome-wide DNA copy-number and loss-of-heterozygosity
(LOH) analyses on primary leukemic blasts from pediatric patients
with acute lymphoblastic leukemia (ALL) (4, 5). These studies
identified a high frequency of genetic alterations of key regulators
of B lymphoid development and cell cycle in B-progenitor ALL.
More recently, similar approaches have been used to explore the
type of copy-number alterations (CNAs) in adult myeloid malig-
nancies (6–9), although these studies have used relatively low
We have now extended these analyses to pediatric de novo acute
myeloid leukemia (AML). AML comprises 15–20% of the acute
leukemias diagnosed in this age group and remains a challenging
disease with an inferior treatment outcome compared to ALL.
Despite the introduction of new drugs and allogeneic bone marrow
transplantation, overall cure rates in most contemporary treatment
protocols remain below 60% (10–12).
Like pediatric ALL, de novo AML is a heterogeneous disease
composed of different genetic subtypes with distinct clinical fea-
tures and responses to contemporary therapies. The best charac-
terized subtypes include the core-binding factor leukemias
t(16;16)[CBF?-MYH11]), cases with rearrangements of the MLL
gene on chromosome 11q23, cases with distinct morphology in-
cluding acute promyeloctic leukemia with t(15;17)[PML-RARA]
and acute megakaryoblastic leukemia (FAB-M7), and cases with
identified in AMLs, including point mutations or CNAs of NRAS,
KRAS, FLT3, KIT, PTPN11, RUNX1, MLL, NPM1, CEBPA, and
TP53 (13–17), the full complement of cooperating lesions remains
to be defined. The identification of the complete complement of
genetic lesions within AML will not only improve our understand-
ing of the molecular pathology of acute leukemia, but should also
directly impact diagnosis and risk stratification, and may lead to the
identification of new targets against which novel therapies can be
We report the results of a study of genome-wide DNA CNAs,
LOH, and targeted gene resequencing analyses on primary leuke-
mic blasts from 111 pediatric AML patients. Our data demonstrate
that, in contrast to pediatric ALL, de novo AML is characterized
by a very low burden of genomic alterations. Despite the low
number of lesions, however, unique recurring regions of genetic
alteration were identified that harbor known, and potential new
cancer genes. Moreover, the spectrum of CNAs and sequence
mutations was found to vary significantly across the different
genetic subtypes of AML.
approach to define the total complement of genetic lesions in
pediatric de novo AML, we performed high resolution genome-
wide analysis on leukemic blasts from diagnostic bone marrow
aspirates from 111 patients using both Affymetrix 100K and 500K
SNP microarrays (combined resolution of 615K). The leukemias
Author contributions: I.R., C.G.M., S.A.S., and J.R.D. designed research; I.R., C.G.M., M.I.,
R.C.R., J.E.R., S.C.R., and S.A.S. analyzed data; and I.R. and J.R.D. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Freely available online through the PNAS open access option.
1To whom correspondence should be addressed. E-mail: email@example.com.
This article contains supporting information online at www.pnas.org/cgi/content/full/
August 4, 2009 ?
vol. 106 ?
included a representation of the different genetic subtypes of the
pediatric de novo AML (in SI Appendix, Tables S1 and S2). Germ
line DNA was available for 65 of the patients allowing a definitive
identification of somatically acquired CNAs. Two-hundred seven
CNAs were detected across the cohort with a mean number of
CNAs/patient of 2.38 (range 0–45), with no significant difference
in the average number of gains (1.32, range 0–41) and losses (1.06,
range 0–12) (Fig. 1 and SI Appendix, Table S2). The frequency of
exception of FAB-M7, which had an average of 9.33 CNAs/patient,
with the majority consisting of gains (SI Appendix, Table S2, P ?
0.013). Excluding FAB-M7 leukemias the average number of
no association was detected between clinical outcome and the
number of gains, losses, total CNAs, or the amount of the genome
altered in either univariate or multivariate analysis.
Gene Targets of Recurrent Copy-Number Alterations. Recurrent CNAs
within a patient cohort can be used to identify alterations of
potential biological significance (driver versus passenger muta-
tions). Surprisingly, when large regions (whole chromosomes or
chromosome arms) of gains or losses were excluded the majority of
the remaining lesions were nonrecurrent, being identified in only a
single patient (SI Appendix, Table S2). Using the genomic identi-
fication of significant targets in cancer (GISTIC) algorithm (18),
only 5 significant regions of gains and 13 regions of deletion were
C). These included 1 broad lesion (gain of chromosome 22), 4 focal
lesions that were contained within broader lesions [8q24.21 (0.091
Mb), 7p21.3 (3.523 Mb), 7q36.1 (1.372 Mb), and 9q22.3 (0.943
(3 loci), 2–5 genes (3 loci), a single gene (3 loci), or lacking an
annotated gene (1 locus) (Fig. 1, Fig. 2, and SI Appendix, Table S3).
In addition, we identified 24 other recurrent lesions where the
10-0.810-110-1.4 10-2.2 10-3.8 10-7
12 genes (*CDKN2A )
13 genes (*XP A)
4 genes (*MLL)
17 genes (*CBFB)
5 genes (*MYH1 1)
False Discovery Rate
False Discovery Rate
MiscellaneousMiscellaneous Normal Normal
SNPs by chromosome
location. Cases are arranged by subgroup. Diploid regions are white. Blue represents deletion, red amplification (see color scale). Gross changes can be observed for
are plotted along the x axis with chromosomal position along the y axis. Altered regions with significance levels exceeding 0.25 (marked by vertical green line) are
DNA copy-number abnormalities in pediatric de novo AML. (A) Summary of CNA (log2ratio) from a combined 100K and 500K Affymetrix SNP array analysis
Radtke et al.PNAS ?
August 4, 2009 ?
vol. 106 ?
no. 31 ?
S4). Together, these 41 recurrent focal lesions contained a total of
1,158 genes (290 from GISTIC peaks, 868 from other MARs), of
which only 30 (2.6%) were contained within the Cancer Gene
Census listing (http://www.sanger.ac.uk/genetics/CGP/Census/)
(19), suggesting that new AML cancer genes are likely to exist
genes have been previously implicated in AML as targets of
translocations or sequence mutation including CBFB, CDKN2A,
ELL, ERG, ETV6, FLI1, GMPS, JAK3, LYL1, MLF1, MLL,
MLLT1, MLLT4, MYH11, MYST4, NPM1, NSD1, PBX1, RUNX1,
SH3GL1, and WT1. A number of other cancer consensus genes
were contained within nonrecurrent CNAs suggesting that a subset
leukemic cell and thus constitute driver mutations (SI Appendix,
Tables S5 and S6).
When broad and focal CNAs were combined the most common
affected region was on chromosome 8, band q24, which showed a
S6). Focal gains were identified in 4 patients, and in an additional
11 patients an increase in copy number was observed either as a
result of a larger region of chromosomal gains (1 case), or as the
alteration was detected across the different AML genetic subtypes.
in a forward genetic screen to identify genes that are required for
retinoic acid (RA)-induced myeloid cell differentiation (20, 21).
Retroviral integration into this locus disrupted RA-induced differ-
entiation. The region contains a putative gene referred to as
CCDC26, and a highly conserved large intervening noncoding
RNA of unknown function (22). Which of these transcripts nor-
mally functions in myeloid differentiation, and whether the iden-
tified copy-number changes alter their expression and function
remain to be determined.
The MARs in 8 other recurrent CNAs were each limited to a
single gene in at least 1 patient, thus identifying the gene as a target
of the lesion (SI Appendix, Table S6). These included monoallelic
deletions involving RUNX1T1 (ETO), a known target of the AML-
associated t(8;21) translocations, MLL involved in 11q23 translo-
cations, FAM20C, which is expressed in hematopoietic cells and is
the target of mutations in Raine’s syndrome (23) a lethal osteo-
sclerotic bone disease, and the putative tumor suppressors TUSC1
(24) and BCOR (25), and amplifications of ABCC4, encoding a
multidrug resistance membrane protein (26), MLLT4, a target of
the AML-associated t(6;11) translocations (27), and PRDM5 (28),
a putative tumor suppressor. The CNAs of RUNX1T1 were ob-
served in three t(8;21) leukemias, whereas the MLLT4 alteration
with a complex karyotype that did not include a detectable struc-
tural alteration of 6q (SI Appendix, Fig. S1).
In addition to RUNX1T1 and MLLT4, 7 other genes that are the
targets of AML-associated chromosomal translocations were af-
fected by recurrent CNAs, including MYH11, CBF?, MLL, NSD1,
MLF1, ERG, and MYST4 (SI Appendix, Tables S3 and S4). Prior
studies have demonstrated that focal micro deletions and amplifi-
cations can occur near the breakpoints of chromosomal transloca-
tions (4, 29). Consistent with these observations, the CNAs of
the CNAs of MLL were seen in a subset of cases with MLL
translocations (SI Appendix, Fig. S1 and S2). On the basis of these
observations, we examined whether any other recurrent CNAs of
genes were the result of cryptic translocations. Our analysis iden-
(SI Appendix, Fig. S2) and 2 cases that expressed the t(6;11)-
encoded MLL-MLLT4(AF6) chimeric transcript, with associated
CNAs involving both genes (SI Appendix, Fig. S2). These data
indicated that at least 14% of the cytogenetically normal or
miscellaneous karyotype subgroups within this cohort contained a
cryptic translocation. Whether the CNAs involving MLF1, ERG,
and MYST4 are also the result of cryptic translocations remains to
Copy Neutral Loss of Heterozygosity. The genotypes generated by the
Affymetrix SNP array platform enable the detection of regions of
somatic copy neutral-loss of heterozygosity (CN-LOH), which may
identify reduplication of mutated or aberrantly methylated genes
that contribute to tumorigenesis. Prior publications have identified
CN-LOH of 11p (involving WT1), 13q (FLT3), and 19q (CEPBA)
in AML (30, 31), and have suggested that CN-LOH is the most
frequent lesion in myeloid malignancies, occurring in up to 48% of
SNP genotypes of the tumor to the patient’s own constitutional
somatic CN-LOH from inherited homozygosity. We initially per-
formed paired CN-LOH analysis for 60 patients with matched
constitutional and leukemia cell DNA and identified only 6 leuke-
mias that contained somatic CN-LOH that were defined by 3 or
more contiguous SNPs (SI Appendix, Fig. S3 and Table S7). These
chromosome 8, with exons labeled by lowercase e, and an alternative transcript initiating from exon e1a. The vertical blue lines show the location of the SNPs on
transcription. The vertical red arrow marks the integration site found in a retroviral integration screen of retinoic acid resistant myeloid cell lines (20). The green box
to have focal amplification of this locus.
Amplification of CCDC26 in pediatric AML. The genomic organization of CCDC26 is illustrated relative to the telomere (tel) and centromere (cent) of
www.pnas.org?cgi?doi?10.1073?pnas.0903142106Radtke et al.
leukemias included 5 cases with large regions of CN-LOH (chro-
a single case with a focal region of CN-LOH on chromosome 8q11
that contained no genes.
We next performed unpaired CN-LOH analysis for the 51
patients that lacked constitutional DNA by using the 60 constitu-
tional DNA samples from our AML cohort as a reference pool to
this approach can fail to exclude private regions of inherited LOH,
we decided to limit our calls to regions of CN-LOH that were ?20
Mb, thus significantly improving the accuracy of identifying true
analyses were combined, we identified somatic CN-LOH in only
13% of the entire cohort, including chromosome 13 (n ? 4), 11p
(n ? 3), 9p (n ? 2), and 6p, 8q, 15q, 17q, and chromosome 21 (1
patient each). The 4 leukemias with chromosome 13 CN-LOH had
homozygous FLT3-ITD mutations (see below), and the two leuke-
mias with 9p CN-LOH had homozygous deletions of CDKN2A/B
that were included in the regions of LOH. Thus, somatically
acquired CN-LOH occurs in 13% of de novo AML, with many of
the identified lesions targeting genes previously shown to be
involved in the pathogenesis of AML.
gain further insights into the complement of oncogenic lesions in
(AML-associated cancer genes, including NRAS, KRAS, PTPN11,
FLT3, KIT, RUNX1, CEBPA, ETV6, NPM1, TP53, CDKN2A/B,
GATA1, and MLL), along with a subset of the genes targeted by
CNAs in this cohort (CCDC26, FAM20C, TUSC1, ERG, IKZF1,
PAXIP1, PTEN, FBXW7, BTG1, XRCC2, BRAF, and LYL1).
Surprisingly, nonsynonymous somatic sequence mutations were
only identified in the AML-associated cancer genes (Fig. 3 and see
SI Appendix, SI Text).
Forty-seven leukemias contained somatic activating mutations
of genes within the RAS-signaling pathway or upstream receptor
tyrosine kinases (NRAS, n ? 26; KRAS, n ? 2; PTPN11, n ? 3;
FLT3-ITD, n ? 15; and KIT, n ? 5). Consistent with previously
published data, mutations of NRAS were frequent in the core
binding factor (44%) and MLL rearranged AMLs (24%) (33), but
were uncommon in other AML subtypes (12%) (P ? 0.015) (Fig.
3 and SI Appendix, Table S2). By contrast, mutations in FLT3 were
only found in acute promyelocytic leukemia and in patients with a
normal or miscellaneous karyotype (Fig. 3, P ? 0.0015). The
mutations in these genes were heterozygous with the exception of
4 leukemias that contained homozygous FLT3 mutations associ-
ated with chromosome 13 CN-LOH. Although mutations in these
genes are usually mutually exclusive (33), two t(8;21) containing
AMLs had mutation in both NRAS and KIT (Fig. 3).
Mutations in CEBPA, RUNX1, ETV6, and MLL partial tandem
duplications (MLL-PTD) were also common (Fig. 3 and SI Appen-
dix, Table S2) and were more frequent in AMLs with either a
normal or miscellaneous karyotype. For patients with matched
constitutional DNA, we were able to show that each mutation was
somatic except for CEBPA, which was germ line in 3 of 6 patients
previously identified in rare pedigrees of familial AML (34). Point
rare in this patient cohort (Fig. 3 and SI Appendix, Table S2).
Importantly, 42% of patients had no point mutations in the 25
genes analyzed, 38% had only 1 gene mutated, 13% had 2 genes
with a higher number of lesions observed in the cases with normal
or miscellaneous karyotypes as compared to the other subtypes
(1.36 sequence mutations/patients in normal or miscellaneous
karyotypes versus 0.54/patient in other subtypes, P ? 0.0001).
Integration of the CNA/CN-LOH analysis and candidate gene
resequencing revealed several important findings (Fig. 3 and SI
Appendix, Table S2). First, 28% of leukemias with recurrent trans-
a single patient, with the patients grouped into the 7 genetic AML subtypes, which are color coded as illustrated. The rows depict the presence of mutations from
by the color of the box as shown. The presence of copy-number alterations is shown in the Bottom 2 rows with amplifications in red, and deletions in green, and the
intensity of the color corresponding to the number of copy-number alterations according to the scale shown at bottom right.
Integrated analysis of copy-number alterations, CN-LOH, and point mutations. Each column illustrates the results of the integrated mutational analysis for
Radtke et al. PNAS ?
August 4, 2009 ?
vol. 106 ?
no. 31 ?
locations lacked any identifiable sequence or numerical abnormal-
ities. Second, although the FAB-M7 leukemias had the highest
number of CNAs per case, they rarely contained point mutations,
with only a single patient having a GATA1 mutation. Third, the
leukemic cells from AML patients with normal or miscellaneous
karyotypes each contained 1 or more alterations, with over 40% of
these leukemias containing both CNAs and sequence mutations.
These data demonstrate that genomewide copy-number alteration
and target gene resequencing complement routine cytogenetic
analysis and identify new genetic lesions in more than half of
pediatric de novo AMLs (Fig. 3). However, although new lesions
are identified, the total burden of genomic alterations is low, with
S2). This is in stark contrast to results from pediatric ALL where 77%
of cases have ?5 lesions excluding point mutations (4, 5).
Our analyses of CNAs, CN-LOH, and sequence mutations in
pediatric de novo AML identified remarkably few somatic
genetic alterations within the leukemia cells. We identified a
mean of only 2.38 somatic CNAs per leukemia and less than 1
nonsynonymous point mutation per leukemia in the 25 genes
analyzed. Moreover, somatic CN-LOH was observed in only
13% of patients. Even more surprising was the observation that
34% of the leukemias lacked any identifiable CNAs, and 28% of
the leukemias with recurrent translocation lacked any identifi-
able sequence or numerical abnormalities. The only exception to
the presence of few mutations was acute megakaryocytic leu-
kemias, with the majority of these leukemias being characterized
by a high number of CNAs but rare point mutations.
These data reflect a very low burden of genomic alterations in
pediatric de novo AML, which is in stark contrast to most other
cancers. Recent studies using similar approaches in pediatric ALL,
and adult cancers [lung (35), pancreatic (36), glioblastoma multi-
forme (37, 38), breast and colon (39, 40)], have demonstrated a
much higher number of CNAs and point mutations, with the
majority of these cancers containing a very large number of
mutations. Although the possibility exists that AMLs may contain
small regions of CNAs that are below the resolution of detection
using the combined 100K and 500K SNP platforms, this appears
unlikely on the basis of the absence of smaller lesions in pediatric
and adult AMLs analyzed using the higher resolution Affymetrix
cancer cells arise either from inherent genomic instability or as the
result of a single mutational crisis. Although we have performed
have sequenced only a limited number of potential cancer genes,
mutational rate. Moreover, our data raise the possibility that the
development of AML may require fewer genetic alterations than
may need to be altered in hematopoietic stem cells, multipotential
progenitors, or committed myeloid progenitors to convert them
from a normal cell into an acute myeloid leukemic cell. An
alternative but not mutually exclusive possibility is that epigenetic
changes may play a more predominant role in AML, working in
concert with genetic alterations to alter a wider range of biological
processes to induce overt leukemia. Detailed genomewide epige-
netic analysis and whole genome resequencing will ultimately be
required to determine the range of mutations and epigenetic
changes required for the development of AML. However, the
recent sequence of all coding exons in the DNA of an AML
patient’s leukemia cells revealed only 10 somatically acquired
nonsynonymous mutations in the coding region of annotated genes
(41), suggesting that even with single base pair resolution few
mutations may be the rule in AML.
case, the recurrent lesions targeted 30 genes known to be involved
in cancer, including 21 that have been previously implicated in
AML. In addition, many of the recurrent lesions lacked any cancer
consensus genes, suggesting that new AML cancer genes exist
genes, thereby directly implicating the target genes in AML patho-
genesis. The top-ranked recurrent lesion in this category targeted
a MAR that contained a putative gene CCDC26, along with a
recently described ?10-kb highly conserved noncoding RNA (lin-
cRNA-CCDC26) that resides within an intron of CCDC26 (22).
Interestingly, the lincRNA-CCDC26 resides within 1 kb of the
retroviral integration site that disrupted myeloid differentiation
(20). Moreover, multiple transcripts are encoded within this locus
and some are normally downregulated during myeloid cell differ-
entiation (20, 21). Exactly how the AML-associated CNAs affect
expression of these transcriptional units and whether their alter-
ations contribute to the development of AML remains to be
determined. Nevertheless, the locus is a good candidate to contain
Acute Myeloid Leukemia
Acute Lymphoblastic Leukemia
+ 615K SNP analysis
+ 615K SNP analysis
+ 615K SNP array
+ sequence mutation analysis
on cytogenetics, cytogenetics plus CNAs using 615K SNP arrays, or cytogenetics, 615K SNP arrays, and targeted gene resequencing of 25 candidate genes in A
AML (n ? 111 cases) and B ALL (n ? 212, cases from refs. 4, 5).
Spectrum of number of lesions per case in pediatric AML and ALL. Percentage of cases containing zero (normal), 1, 2, 3, 4, 5, or ?5 alterations based
www.pnas.org?cgi?doi?10.1073?pnas.0903142106 Radtke et al.
gene(s) whose alterations may contribute to the development of Download full-text
suppressors TUSC1, BCOR, and PRDM5, ABCC4, which encodes
a multidrug resistance membrane protein, and FAM20C, a gene
of these genes contribute to the AML pathogenesis will require
direct functional studies on the biological role of the encoded gene
products in normal and leukemic hematopoiesis.
The limited number of recurrent lesions and the low frequency
of individual recurrent lesions across the cohort are notable and
likely reflect the marked heterogeneity among the AML cases that
of de novo AML were included. Each subtype might arise from a
different combination of genetic lesions, with the complement of
lesions being heavily influenced by the initiating event (a chromo-
somal translocation in many pediatric de novo AMLs). Our inte-
grated analysis of cytogenetics, CNAs, and sequence mutations is
consistent with this interpretation, with marked difference in the
spectrum of changes observed across the AML genetic subtypes.
number of leukemias for each individual known genetic subtype of
de novo AML should yield valuable information on the spectrum
the limited number of CNAs and point mutations found in de novo
pediatric AML, will also be observed in other subtypes of AML
including myelodysplasia-related AML, and secondary AML that
results from prior chemotherapy and/or radiation therapy.
at St. Jude Children’s Research Hospital (SJCRH) were studied. Written informed
consent and institutional-review-board approval was obtained for each patient.
No commercial entity was involved in the conduct of the study, the analysis or
the completeness and accuracy of the data and analysis.
Genomic Analyses. DNA extracted from leukemic cells obtained at diagnosis and
Data from all 4 arrays were combined before analysis for the presence of CNAs,
resulting in an average intermarker distance of less than 5 kb. SNP array analysis
of copy-number alterations and LOH was performed as previously reported (4)
and is described in SI. A subset of the identified copy-number alterations was
PCR. The primary SNP data are available upon request. Identifiers for each case
are listed in SI Appendix, Table S1.
Genomic Resequencing of Candidate AML Cancer Genes. Genomic sequencing of
exons and adjacent splice sites was performed on the genes listed in the text. A
detailed description of the sequencing methods are in SI.
21765 from the National Cancer Institute, a Leukemia and Lymphoma Society
Specialized Center of Research Grant (LLS7015, to J.R.D.), a grant from the
National Health and Medical Research Council of Australia (C.G.M.), and the
American Lebanese Syrian Associated Charities of St. Jude Children’s Research
Hospital. We thank Claire Boltz, Letha Phillips, and James Dalton for technical
1. Kelly LM, Gilliland DG (2002) Genetics of myeloid leukemias. Annu Rev Genomics Hum
2. Reya T, Morrison SJ, Clarke MF, Weissman IL (2001) Stem cells, cancer, and cancer stem
cells. Nature 414:105–111.
3. Schimmer AD (2006) Induction of apoptosis in lymphoid and myeloid leukemia. Curr
Oncol Rep 8:430–436.
4. Mullighan CG, et al. (2007) Genome-wide analysis of genetic alterations in acute
lymphoblastic leukaemia. Nature 446:758–764.
5. Mullighan CG, et al. (2008) BCR-ABL1 lymphoblastic leukaemia is characterized by the
deletion of Ikaros. Nature 453:110–114.
6. Dunbar AJ, et al. (2008) 250K single nucleotide polymorphism array karyotyping
identifies acquired uniparental disomy and homozygous mutations, including novel
missense substitutions of c-Cbl, in myeloid malignancies. Cancer Res 68:10349–10357.
arrays in MDS, MDS/MPD, and MDS-derived AML. Blood 111:1534–1542.
8. Raghavan M, et al. (2005) Genome-wide single nucleotide polymorphism analysis
reveals frequent partial uniparental disomy due to somatic recombination in acute
myeloid leukemias. Cancer Res 65:375–378.
9. Rucker FG, et al. (2006) Disclosure of candidate genes in acute myeloid leukemia with
complex karyotypes using microarray-based molecular characterization. J Clin Oncol
10. Ravindranath Y, et al. (2005) Pediatric Oncology Group (POG) studies of acute myeloid
leukemia (AML): A review of four consecutive childhood AML trials conducted be-
tween 1981 and 2000. Leukemia 19:2101–2116.
11. Ribeiro RC, et al. (2005) Successive clinical trials for childhood acute myeloid leukemia
at St Jude Children’s Research Hospital, from 1980 to 2000. Leukemia 19:2125–2129.
12. Rubnitz JE, et al. (2007) Prognostic factors and outcome of recurrence in childhood
acute myeloid leukemia. Cancer 109:157–163.
13. Bacher U, Haferlach T, Schoch C, Kern W, Schnittger S (2006) Implications of NRAS
mutations in AML: A study of 2502 patients. Blood 107:3847–3853.
14. Frohling S, et al. (2004) CEBPA mutations in younger adults with acute myeloid
leukemia and normal cytogenetics: Prognostic relevance and analysis of cooperating
mutations. J Clin Oncol 22:624–633.
15. Loh ML, et al. (2004) PTPN11 mutations in pediatric patients with acute myeloid
leukemia: Results from the Children’s Cancer Group. Leukemia 18:1831–1834.
16. Renneville A, et al. (2008) Cooperating gene mutations in acute myeloid leukemia: A
review of the literature. Leukemia 22:915–931.
17. Zwaan CM, et al. (2003) FLT3 internal tandem duplication in 234 children with acute
myeloid leukemia: Prognostic significance and relation to cellular drug resistance.
Methodology and application to glioma. Proc Natl Acad Sci USA 104:20007–20012.
19. Futreal PA, et al. (2004) A census of human cancer genes. Nat Rev Cancer 4:177–183.
20. Yin W, Rossin A, Clifford JL, Gronemeyer H (2006) Co-resistance to retinoic acid and
TRAIL by insertion mutagenesis into RAM. Oncogene 25:3735–3744.
21. Hirano T, et al. (2008) Genes encoded within 8q24 on the amplicon of a large
extrachromosomal element are selectively repressed during the terminal differentia-
tion of HL-60 cells. Mutat Res 640:97–106.
large non-coding RNAs in mammals. Nature 458:223–227.
23. Simpson MA, et al. (2007) Mutations in FAM20C are associated with lethal osteoscle-
rotic bone dysplasia (Raine syndrome), highlighting a crucial molecule in bone devel-
opment. Am J Hum Genet 81:906–912.
24. Shan Z, Parker T, Wiest JS (2004) Identifying novel homozygous deletions by micro-
satellite analysis and characterization of tumor suppressor candidate 1 gene, TUSC1,
on chromosome 9p in human lung cancer. Oncogene 23:6612–6620.
25. Huynh KD, Fischle W, Verdin E, Bardwell VJ (2000) BCoR, a novel corepressor involved
in BCL-6 repression. Genes Dev 14:1810–1823.
26. Rius M, Hummel-Eisenbeiss J, Keppler D (2008) ATP-dependent transport of leukotri-
enes B4 and C4 by the multidrug resistance protein ABCC4 (MRP4). J Pharmacol Exp
27. Taki T, et al. (1996) Fusion of the MLL gene with two different genes, AF-6 and
AF-5alpha, by a complex translocation involving chromosomes 5, 6, 8 and 11 in infant
leukemia. Oncogene 13:2121–2130.
28. Deng Q, Huang S (2004) PRDM5 is silenced in human cancers and has growth suppres-
sive activities. Oncogene 23:4903–4910.
29. Zhang Y, Rowley JD (2006) Chromatin structural elements and chromosomal translo-
cations in leukemia. DNA Repair (Amst) 5:1282–1297.
30. Gupta M, et al. (2008) Novel regions of acquired uniparental disomy discovered in
acute myeloid leukemia. Genes Chromosomes Cancer 47:729–739.
31. Serrano E, et al. (2008) Uniparental disomy may be associated with microsatellite
high-density oligonucleotide SNP arrays. PLoS Comput Biol 2:e41.
33. Nanri T, et al. (2005) Mutations in the receptor tyrosine kinase pathway are associated
with clinical outcome in patients with acute myeloblastic leukemia harboring
t(8;21)(q22;q22). Leukemia 19:1361–1366.
34. Owen C, Barnett M, Fitzgibbon J (2008) Familial myelodysplasia and acute myeloid
leukaemia: A review. Br J Haematol 140:123–132.
35. Weir BA, et al. (2007) Characterizing the cancer genome in lung adenocarcinoma.
36. Jones S, et al. (2008) Core signaling pathways in human pancreatic cancers revealed by
global genomic analyses. Science 321:1801–1806.
37. Anonymous (2008) Comprehensive genomic characterization defines human glioblas-
toma genes and core pathways. Nature 455:1061–1068.
38. Parsons DW, et al. (2008) An integrated genomic analysis of human glioblastoma
multiforme. Science 321:1807–1812.
39. Leary RJ, et al. (2008) Integrated analysis of homozygous deletions, focal amplifica-
cancers. Science 314:268–274.
41. Ley TJ, et al. (2008) DNA sequencing of a cytogenetically normal acute myeloid
leukaemia genome. Nature 456:66–72.
Radtke et al.PNAS ?
August 4, 2009 ?
vol. 106 ?
no. 31 ?