npj Precision Oncology,
Год журнала:
2025,
Номер
9(1)
Опубликована: Март 24, 2025
Circulating
tumor
DNA
(ctDNA)
has
emerged
as
a
dynamic
biomarker
in
cancer,
evidenced
by
its
increasing
integration
into
clinical
practice.
Carrying
specific
characteristics,
ctDNA
can
be
used
to
inform
treatment
selection,
monitor
response,
and
identify
drug
resistance.
In
this
review,
we
provide
comprehensive,
up-to-date
summary
of
monitoring
response
with
focus
on
lung,
colorectal,
breast
cancers,
discuss
current
challenges
future
directions.
International Journal of Health Sciences,
Год журнала:
2022,
Номер
unknown, С. 9364 - 9375
Опубликована: Июль 18, 2022
In
general,
the
various
medical
systems
currently
available
provide
insights
into
changes
in
tumor
genome
of
patients
with
sequencing.
Most
DNA
sequencing
can
also
be
referred
to
as
genetic
specification
or
testing.
The
sequence
results
help
clinical
decision-making
develop
a
personalized
cancer
treatment
plan
based
on
molecular
characteristics
rather
than
one-size-fits-all
approach.
plays
major
role
research.
this
paper,
an
improved
method
machine
learning
was
proposed
analyze
and
patterns
human
gene.
This
analyzes
circulatory
problems
different
types
for
analysis
public
domain.
It
constantly
monitors
large
data
sets
sequences
calculate
size
location.
allows
doctor
get
accurate
report
type
it
cause
patient.
Analysis
these
datasets
gene
reveals
that
makeup
each
patient
is
no
two
cancers
are
same.
Proceedings of the National Academy of Sciences,
Год журнала:
2022,
Номер
119(44)
Опубликована: Окт. 26, 2022
Cell-free
DNA
(cfDNA)
fragmentation
patterns
contain
important
molecular
information
linked
to
tissues
of
origin.
We
explored
the
possibility
using
predict
cytosine-phosphate-guanine
(CpG)
methylation
cfDNA,
obviating
use
bisulfite
treatment
and
associated
risks
degradation.
This
study
investigated
cfDNA
cleavage
profile
surrounding
a
CpG
(i.e.,
within
an
11-nucleotide
[nt]
window)
analyze
methylation.
The
proportion
across
positions
window
appeared
nonrandom
exhibited
correlation
with
status.
mean
was
∼twofold
higher
at
cytosine
methylated
CpGs
than
unmethylated
ones
in
healthy
controls.
In
contrast,
rapidly
decreased
1-nt
position
immediately
preceding
CpGs.
Such
differential
cleavages
resulted
characteristic
change
relative
presentations
CGN
NCG
motifs
5′
ends,
where
N
represented
any
nucleotide.
CGN/NCG
motif
ratios
were
correlated
levels
tissue-specific
(e.g.,
placenta
or
liver)
(Pearson’s
absolute
r
>
0.86).
profiles
thus
informative
for
tissue-of-origin
analyses.
Using
CG-containing
end
motifs,
we
achieved
area
under
receiver
operating
curve
(AUC)
0.98
differentiating
patients
without
hepatocellular
carcinoma
enhanced
positive
predictive
value
nasopharyngeal
screening
(from
19.6
26.8%).
Furthermore,
elucidated
feasibility
deduce
single
resolution
deep
learning
algorithm
AUC
0.93.
FRAGmentomics-based
Methylation
Analysis
(FRAGMA)
presents
many
possibilities
noninvasive
prenatal,
cancer,
organ
transplantation
assessment.
New England Journal of Medicine,
Год журнала:
2024,
Номер
390(22), С. 2047 - 2060
Опубликована: Июнь 12, 2024
The
risk
of
second
tumors
after
chimeric
antigen
receptor
(CAR)
T-cell
therapy,
especially
the
neoplasms
related
to
viral
vector
integration,
is
an
emerging
concern.
Trends in Genetics,
Год журнала:
2023,
Номер
39(4), С. 285 - 307
Опубликована: Фев. 13, 2023
Liquid
biopsies
(LBs),
particularly
using
circulating
tumor
DNA
(ctDNA),
are
expected
to
revolutionize
precision
oncology
and
blood-based
cancer
screening.
Recent
technological
improvements,
in
combination
with
the
ever-growing
understanding
of
cell-free
(cfDNA)
biology,
enabling
detection
tumor-specific
changes
extremely
high
resolution
new
analysis
concepts
beyond
genetic
alterations,
including
methylomics,
fragmentomics,
nucleosomics.
The
interrogation
a
large
number
markers
complexity
data
render
traditional
correlation
methods
insufficient.
In
this
regard,
machine
learning
(ML)
algorithms
increasingly
being
used
decipher
disease-
tissue-specific
signals
from
cfDNA.
Here,
we
review
recent
insights
into
biological
ctDNA
features
how
these
incorporated
sophisticated
ML
applications.
Nature Communications,
Год журнала:
2023,
Номер
14(1)
Опубликована: Янв. 18, 2023
Plasma
cell-free
DNA
(cfDNA)
are
small
molecules
generated
through
a
non-random
fragmentation
procedure.
Despite
commendable
translational
values
in
cancer
liquid
biopsy,
however,
the
biology
of
cfDNA,
especially
principles
cfDNA
fragmentation,
remains
largely
elusive.
Through
orientation-aware
analyses
patterns
against
nucleosome
structure
and
integration
with
multidimensional
functional
genomics
data,
here
we
report
methylation
-
nuclease
preference
cutting
end
size
distribution
axis,
demonstrating
role
as
molecular
regulator
fragmentation.
Hence,
low-level
could
increase
accessibility
alter
activities
nucleases
during
which
further
leads
to
variation
sites
cfDNA.
We
develop
ending
preference-based
metric
for
diagnosis,
whose
performance
has
been
validated
by
multiple
pan-cancer
datasets.
Our
work
sheds
light
on
basis
towards
broader
applications
biopsy.
Cancer Cell,
Год журнала:
2024,
Номер
42(2), С. 225 - 237.e5
Опубликована: Янв. 25, 2024
Small
cell
lung
cancer
(SCLC)
is
an
aggressive
malignancy
composed
of
distinct
transcriptional
subtypes,
but
implementing
subtyping
in
the
clinic
has
remained
challenging,
particularly
due
to
limited
tissue
availability.
Given
known
epigenetic
regulation
critical
SCLC
programs,
we
hypothesized
that
subtype-specific
patterns
DNA
methylation
could
be
detected
tumor
or
blood
from
patients.
Using
genomic-wide
reduced-representation
bisulfite
sequencing
(RRBS)
two
cohorts
totaling
179
patients
and
using
machine
learning
approaches,
report
a
highly
accurate
methylation-based
classifier
(SCLC-DMC)
can
distinguish
subtypes.
We
further
adjust
for
circulating-free
(cfDNA)
subtype
plasma.
cfDNA
(cfDMC),
demonstrate
phenotypes
evolve
during
disease
progression,
highlighting
need
longitudinal
tracking
clinical
treatment.
These
data
establish
used
identify
subtypes
might
guide
precision
therapy.
