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Identification of a novel, recurrent HEY1-NCOA2 fusion in mesenchymal chondrosarcoma based on a genome-wide screen of exon-level expression data.
[dedifferentiated liposarcoma]
Cancer
gene
fusions
that
encode
a
chimeric
protein
are
often
characterized
by
an
intragenic
discontinuity
in
the
RNA
\
expression
levels
of
the
exons
that
are
5
'
or
3
'
to
the
fusion
point
in
one
or
both
of
the
fusion
partners
due
to
differences
in
the
levels
of
activation
of
their
respective
promoters
.
Based
on
this
,
we
developed
an
unbiased
,
genome-
wide
bioinformatic
screen
for
gene
fusions
using
Affymetrix
Exon
array
expression
data
.
Using
a
training
set
of
46
samples
with
different
known
gene
fusions
,
we
developed
a
data
analysis
pipeline
,
the
"
Fusion
Score
(
FS
)
model
"
,
to
score
and
rank
genes
for
intragenic
changes
in
expression
.
In
a
separate
discovery
set
of
41
tumor
samples
with
possible
unknown
gene
fusions
,
the
FS
model
generated
a
list
of
552
candidate
genes
.
The
transcription
factor
gene
NCOA
2
was
one
of
the
candidates
identified
in
a
mesenchymal
chondrosarcoma
.
A
novel
HEY
1
-
NCOA
2
fusion
was
identified
by
5
'
RACE
,
representing
an
in
-frame
fusion
of
HEY
1
exon
4
to
NCOA
2
exon
13
.
RT-PCR
or
FISH
evidence
of
this
HEY
1
-
NCOA
2
fusion
was
present
in
all
additional
mesenchymal
chondrosarcomas
tested
with
a
definitive
histologic
diagnosis
and
adequate
material
for
analysis
(
n
=
9
)
but
was
absent
in
15
samples
of
other
subtypes
of
chondrosarcomas
.
We
also
identified
a
NUP
107
-
LGR
5
fusion
in
a
dedifferentiated
liposarcoma
but
analysis
of
17
additional
samples
did
not
confirm
it
as
a
recurrent
event
in
this
sarcoma
type
.
The
novel
HEY
1
-
NCOA
2
fusion
appears
to
be
the
defining
and
diagnostic
gene
fusion
in
mesenchymal
chondrosarcomas
.
Diseases
Validation
Diseases presenting
"cancer"
symptom
achondroplasia
acute rheumatic fever
adrenal incidentaloma
alpha-thalassemia
benign recurrent intrahepatic cholestasis
cadasil
canavan disease
carcinoma of the gallbladder
cholangiocarcinoma
coats disease
congenital adrenal hyperplasia
congenital diaphragmatic hernia
cowden syndrome
cushing syndrome
cutaneous mastocytosis
dedifferentiated liposarcoma
dystrophic epidermolysis bullosa
epidermolysis bullosa simplex
erdheim-chester disease
erythropoietic protoporphyria
esophageal adenocarcinoma
esophageal carcinoma
esophageal squamous cell carcinoma
familial hypocalciuric hypercalcemia
familial mediterranean fever
gm1 gangliosidosis
heparin-induced thrombocytopenia
hereditary cerebral hemorrhage with amyloidosis
hirschsprung disease
hodgkin lymphoma, classical
inclusion body myositis
junctional epidermolysis bullosa
kabuki syndrome
kallmann syndrome
kindler syndrome
lamellar ichthyosis
liposarcoma
locked-in syndrome
lymphangioleiomyomatosis
monosomy 21
neuralgic amyotrophy
oculocutaneous albinism
oligodontia
oral submucous fibrosis
papillon-lefèvre syndrome
pendred syndrome
pleomorphic liposarcoma
primary effusion lymphoma
proteus syndrome
pyomyositis
pyruvate dehydrogenase deficiency
severe combined immunodeficiency
sneddon syndrome
systemic capillary leak syndrome
triple a syndrome
von hippel-lindau disease
waldenström macroglobulinemia
well-differentiated liposarcoma
werner syndrome
wiskott-aldrich syndrome
wolf-hirschhorn syndrome
x-linked adrenoleukodystrophy
This symptom has already been validated
