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RET variants and haplotype analysis in a cohort of Czech patients with Hirschsprung disease.
[hirschsprung disease]
Hirschsprung
disease
(
HSCR
)
is
a
congenital
aganglionosis
of
myenteric
and
submucosal
plexuses
in
variable
length
of
the
intestine
.
This
study
investigated
the
influence
and
a
possible
modifying
function
of
RET
proto-oncogene
's
single
nucleotide
polymorphisms
(
SNPs
)
and
haplotypes
in
the
development
and
phenotype
of
the
disease
in
Czech
patients
.
Genotyping
of
14
SNPs
was
performed
using
TaqMan
Genotyping
Assays
and
direct
sequencing
.
The
frequencies
of
SNPs
and
generated
haplotypes
were
statistically
evaluated
using
chi
-square
test
and
the
association
with
the
risk
of
HSCR
was
estimated
by
odds
ratio
.
SNP
analysis
revealed
significant
differences
in
frequencies
of
11
polymorphic
RET
variants
between
162
HSCR
patients
and
205
unaffected
controls
.
Particularly
variant
alleles
of
rs
1864410
,
rs
2435357
,
rs
2506004
(
intron
1
)
,
rs
1800858
(
exon
2
)
,
rs
1800861
(
exon
13
)
,
and
rs
2565200
(
intron
19
)
were
strongly
associated
with
increased
risk
of
HSCR
(
p
<
0
.
00000
)
and
were
over-represented
in
males
vs
.
females
.
Conversely
,
variant
alleles
of
rs
1800860
,
rs
1799939
and
rs
1800863
(
exons
7
,
11
,
15
)
had
a
protective
role
.
The
haploblock
comprising
variants
in
intron
1
and
exon
2
was
constructed
.
It
represented
a
high
risk
of
HSCR
,
however
,
the
influence
of
other
variants
was
also
found
after
pruning
from
effect
of
this
haploblock
.
Clustering
patients
according
to
genotype
status
in
haploblock
revealed
a
strong
co
-segregation
with
several
SNPs
and
pointed
out
the
differences
between
long
and
short
form
of
HSCR
.
This
study
involved
a
large
number
of
SNPs
along
the
entire
RET
proto-oncogene
with
demonstration
of
their
risk
/
protective
role
also
in
haplotype
and
diplotype
analysis
in
the
Czech
population
.
The
influence
of
some
variant
alleles
on
the
aggressiveness
of
the
disease
and
their
role
in
gender
manifestation
differences
was
found
.
These
data
contribute
to
worldwide
knowledge
of
the
genetics
of
HSCR
.
Diseases
Validation
Diseases presenting
"single nucleotide polymorphisms"
symptom
adrenomyeloneuropathy
alpha-thalassemia
benign recurrent intrahepatic cholestasis
congenital adrenal hyperplasia
dentin dysplasia
esophageal adenocarcinoma
esophageal carcinoma
esophageal squamous cell carcinoma
familial hypocalciuric hypercalcemia
hirschsprung disease
neonatal adrenoleukodystrophy
oculocutaneous albinism
oligodontia
pendred syndrome
primary effusion lymphoma
scrub typhus
triple a syndrome
waldenström macroglobulinemia
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