REVIEW

Artificial Intelligence Applications

in Glioma With 1p/19q Co-Deletion:
A Systematic Review
Simin Zhang, PhD,1 Lijuan Yin, MD, PhD,2 Lu Ma, MD, PhD,3 and Huaiqiang Sun, PhD1*

As an important genomic marker for oligodendrogliomas, early determination of 1p/19q co-deletion status is critical for
guiding therapy and predicting prognosis in patients with glioma. The purpose of this study is to systematically review the
literature concerning the magnetic resonance imaging (MRI) with artificial intelligence (AI) methods for predicting 1p/19q
co-deletion status in glioma. PubMed, Scopus, Embase, and IEEE Xplore were searched in accordance with the Preferred
Reporting Items for systematic reviews and meta-analyses guidelines. Methodological quality of studies was assessed
according to the Quality Assessment of Diagnostic Accuracy Studies-2. Finally, 28 studies were included in the quantitative
analysis. Diagnostic test accuracy reached an area under the ROC curve of 0.71–0.98 were reported in 24 studies. The
remaining four studies with no available AUC provided an accuracy of 0.75–0. 89. The included studies varied widely in
terms of imaging sequences, input features, and modeling methods. The current review highlighted that integrating MRI
with AI technology is a potential tool for determination 1p/19q status pre-operatively and noninvasively, which can possi-
bly help clinical decision-making. However, the reliability and feasibility of this approach still need to be further validated
and improved in a real clinical setting.
Evidence Level: 2.
Technical Efficacy: 2.
J. MAGN. RESON. IMAGING 2023;58:1338–1352.

G liomas are the most common and infiltrative primary

intracranial neoplasms. In 2016, the World Health Orga-
nization (WHO) provided an update of brain tumor classifica-
tion based on histological and molecular characteristics.1
Furtherly, the latest WHO criteria (2021, 5th edition) solid-
ifies the centrality of molecular markers in the delineation of
glioma categories, generating three primary subtypes of glioma:
1) astrocytoma, IDH-mutant; 2) oligodendroglioma, IDH-
mutant, and 1p/19q co-deletion; and 3) glioblastoma, IDH-
wildtype2 (Fig. 1). Therefore, mutations in the IDH and
co-deletion of chromosomes 1p and 19q are playing vital role
in determining glioma subtypes.
As a favorable prognostic biomarker, 1p/19q co-
deletion status is a good indicator for better response to
adjuvant chemotherapy,3 and patients with 1p/19q
co-deletion have significantly longer OS/PFS times com-
pared to those with no 1p/19q co-deletion. Aside from its
diagnostic and prognostic values, 1p/19q co-deletion has
been revealed as an informative biomarker for surgical plan-
ning in low-grade glioma (LGG).4–6 A prior study suggested
1p/19q intact but not 1p/19q co-deleted LGG would bene-
fit from gross total resection.7 More specifically, studies
reported residual tumor has a more negative impact on sur-
vival in 1p/19q intact, IDH-mutated astrocytomas than on
1p/19q co-deletion, IDH-mutated oligodendrogliomas.5,8
Therefore, determination of 1p/19q co-deletion status at the
earliest possible stage, that is, even before surgery is critical
for tumor subtyping, prognostication, personalized treat-
ment, especially an informed surgical planning, which may
avoid nonmaximal resection in 1p/19q intact LGG or

View this article online at wileyonlinelibrary.com. DOI: 10.1002/jmri.28737

Received Dec 21, 2022, Accepted for publication Apr 3, 2023.

*Address reprint requests to: H.S., Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, Chengdu,
610041, China. E-mail: sunhuaiqiang@scu.edu.cn.
This work was supported by the National Natural Science Foundation of China (Grant No. 81974278).

From the 1Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, Chengdu, China; 2Department of
Pathology, West China Hospital of Sichuan University, Chengdu, China; and 3Department of Neurosurgery, West China Hospital of Sichuan University,
Chengdu, China
Additional supporting information may be found in the online version of this article

1338 © 2023 International Society for Magnetic Resonance in Medicine.

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Zhang et al.: A Review of AI Applications in Glioma With 1p/19q Co-Deletion

FIGURE 1: Sample MRI acquisition in three primary subtypes of glioma. Figure displays axial slices of three patients from our own
dataset. In the top row, MRI images from a 24-year-old female with astrocytoma (grade 2, IDH mutant and 1p/19q noncodeleted), in
the middle bottom row, images from a 37-year-old male with oligodendroglioma (grade 2, IDH-mutant and 1p/19q-codeleted), and
in the bottom row, images from a 44-year-old female with glioblastoma (grade 4, IDH-wildtype and 1p/19q noncodeleted).

less-justified surgery-related neurological deficits in 1p/19q
co-deleted glioma.
However, with current technology, identification of
1p/19q co-deletion in gliomas requires invasive surgical re-
section or biopsy followed by fluorescence in situ hybridiza-
tion.9 Nevertheless, surgical procedures may be associated
with morbidity, mortality, and high costs.10,11 Additionally,
nonrepresentative tissue samples due to intratumoural hetero-
geneity of gliomas may bring some bias in determining gene
mutation status.12 Thus, there is a growing interest in devel-
oping noninvasive alternatives that can provide molecular and
genetic information.
Magnetic resonance imaging (MRI) has been proposed
as a potential candidate due to its noninvasive nature and
wide clinical applicability. Studies suggested that 1p/19q co-
deletion was associated with specific imaging characteristics,
such as indistinct border, heterogeneous signal intensity, para-
magnetic susceptibility effect and calcification.13 Recently,
studies have also reported the “T2-FLAIR mismatch sign,”
which represents a highly specific imaging biomarker for the
IDH-mutant, 1p/19q non-co-deletion molecular sub-
type.14,15 These investigations encourage prospective evalua-
tion of molecular alterations and MRI characteristics of
glioma. Nonetheless, these image features are qualitative and,
as a result, subjective, with interobserver variability in diagno-
sis. Therefore, the accuracy of visual features has not yet been
sufficiently established to completely avoid histopathological
evaluation following neurosurgical intervention.
Artificial intelligence (AI) is emerging as a solution to
the limitations of conventional visual assessment, which may
help identify features that hidden to the naked eye and associ-
ate them with outcomes. Machine learning (ML), a sub-
category of AI, focused on developing algorithms that can
identify patterns within data without explicit specification.
ML used artificial feature engineering (extraction of hand-
crafted radiomics feature, reduction and selection of features)
followed by utilization of ML algorithms for task predic-
tion.16 This pipeline is simplified and, at the same time,
enhanced by using deep learning (DL). Unlike ML, DL fol-
lows the neural network architectures approach, which pro-
vides automatic learning of features and their representation
in a hierarchical manner at various levels. Additionally, by
employing a hierarchy of nonlinear transforms, DL can model
very complex data patterns, making it more suitable for learn-
ing complicated patterns and subtle differences in data, par-
ticularly the image data of human brain.17 The introduction
of AI to neuro-oncology imaging has been met with great
enthusiasm from clinicians. Currently, extensive research

November 2023 1339


Journal of Magnetic Resonance Imaging
articles using AI in neuro-oncology have been published,
which mainly focus on the following tasks: 1) brain tumor
segmentation18; 2) predictive tasks (tumor type, grade, genet-
ics, and molecular marker identification)19,20; 3) survival pre-
diction.21 With regard to the utilization of AI in genetic
status prediction, various studies have reported promising
results on prediction of 1p/19q co-deletion.
We believe that it is of utmost importance to evaluate
the published research on the prediction 1p/19q co-deletion
of glioma of AI applications due to the growing significance
of understanding the pathophysiology of glioma with 1p/19q
co-deletion and the rising dependence on AI for prediction.
In this article, we will review the articles concerning the com-
bination of MRI with AI to predict glioma 1p/19q co-
deletion status and discusses the special considerations in
neuro-oncology, with the hope of yielding more actionable
change to clinical workflows.
Methods
Article Search Strategy
A search was conducted across several databases (PubMed,
Scopus, Embase, and IEEE Xplore) to identify all relevant
publications. Our review included studies published before
August 2022. The search strategy used to find AI studies were
(“radiomics” OR “radiogenomics” OR “machine learning”
OR “support vector machine” OR “random forest” OR
“deep learning” OR “deep neural network” OR “deep belief
network” OR “convolutional neural network” OR “CNN”
OR “artificial intelligence” OR “AI” OR “computer aided
diagnosis”) AND (“astrocytoma” OR “glioma” OR
FIGURE 2: PRISMA flowchart of systematic literature search.
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“oligodendroglioma” OR “LGG” OR “glioblastoma” OR
“GBM”) AND (“1p/19q” OR “phenotyping” OR “molecu-
lar subtypes” OR “genotype”) AND (“magnetic resonance
imaging” OR “MRI”).
Eligibility Criteria
According to the scope of the review, we considered AI inves-
tigations aimed at 1p/19q co-deletion prediction in glioma.
The imaging modalities we considered were MRI and
PET/MRI. Studies were excluded under the following cir-
cumstances: 1) articles that are not written in English; 2) the
type of articles are review, meta-analysis, case reports, edito-
rials or letters, comments, guidelines, and conference proceed-
ings; 3) animal studies; 4) research articles focused on
methodological aspects; 5) lack of validation in a clinical set-
ting; 6) lack of model evaluation metrics (i.e. sensitivity, spec-
ificity, accuracy, and/or AUC) on validation cohorts.
Based on the eligibility criteria, the titles and abstracts
of articles were screened to evaluate their suitability for inclu-
sion in this review by two reviewers (Z.S.M and Y. L.J), and
disagreements were resolved by discussion. The PRISMA
flowchart of study is shown in Fig. 2.
Data Extraction
The extracted data from the included studies were number of
patients, glioma grade, type of dataset, MRI sequences, tumor
segmentation method, type of feature, software for feature
extraction, feature selection method, AI method for classifica-
tion, model performance on validation set (a held-out test set
or external cohort was treated as validation).
Volume 58, No. 5

Zhang et al.: A Review of AI Applications in Glioma With 1p/19q Co-Deletion
Quality Assessment
The quality assessments were performed based on Quality
Assessment of Diagnostic Accuracy Studies-2 (QUADAS-
2).22,23 The entire processes of evaluation and questionnaire
filling were double-checked independently by Z.S.M and
Y. L. J and disagreement was resolved by consensus.
Results
We identified 404 articles from the initial search. After pre-
liminary screening and full text review, most studies were
excluded for a number of reasons outlined (Fig. 2). Finally,
28 studies met all eligibility criteria were involved.
Quality assessment results are summarized in Table S1,
five studies were considered as an unclear risk of bias in
patients selection domain as a lack of specification of consecu-
tive patient selection, four studies were categorized as unclear
risk of bias in reference standard domain as lack of descrip-
tion the reference standard and how it was conducted and
interpreted.
Study Characteristics
All studies used retrospectively collected data. Twenty studies
drew patients from multiple institutions, commonly using the
TCIA database. The sample size ranged from 42 to 1748.
Most studies focused on WHO 2–4 glioma or WHO 2–3,
with one study including only WHO 2 glioma24 and one
study including only WHO 4 glioma.25 For the target condi-
tion, 10 studies focused on IDH mutation combined 1p/19q
co-deletion, while 18 studies on 1p/19q co-deletion only.
Imaging Acquisition
Imaging methods including scanner types and sequence
parameters can affect feature calculations. In total, 24 studies
used conventional MRI sequences, including T1-weighted
imaging (T1WI), contrast-enhanced T1-weighted imaging
(T1CE), followed by a frequent addition of T2-weighted
imaging (T2WI) and fluid-attenuated inversion recovery
(FLAIR). The use of diffusion-weighted imaging (DWI) was
presented in three publications, and the dynamic susceptibil-
ity contrast perfusion MR imaging (DSC) was investigated in
one publication (see Table 1 and Fig. 3a).
Glioma Segmentation
Segmentation is a crucial initial step in neuro-oncology imag-
ing analysis. Method of segmentation can be manual, semi-
automatic, or fully automated. Manual segmentation involves
comprehensively labeling the structure in each slice, which is
a time-consuming task with relatively low inter- and intra-
individual reliability. Semi-automatic is a combination of
manual guidance and region growing algorithms. While, the
automated method does not require any human involvement
and is more suitable for processing large data sets. In the cur-
rent review, 15 studies adopted manual segmentation,
November 2023
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4 adopted semi-automatic segmentation, 7 studies adopted
automated segmentation, 2 studies developed multitask CNN
that can predict 1p/19q status simultaneously segmented
tumor (Fig. 3b).
Feature
Totally, 17 of included studies extracted radiomics features
such as tumor shape, intensity and texture, among which,
5 studies combined with Visually Accessible Rembrandt
Imaging (VASARI) features and/or clinical characteristics
(Fig. 3c). Of the remaining 11 studies adopted DL features
utilizing 2D/2.5D/3D image patches as input (Fig. 3c).
As for radiomics-based ML, the software for feature
extraction were Pyradiomics (n = 5), Matlab with extention
(n = 3), 3D Slicer (n = 1), PREDICT toolbox (n = 1),
RadiomiX (n = 1), GLISTRboost (n = 1). Since the high
dimensionality and complexity of MRI data obtained through
different sequences, feature dimensionality reduction, and
selection were critical steps in the discovery of predictors from
high-dimensional input. The used dimensionality reduction
and selection techniques of the included studies were as fol-
lows: least absolute shrinkage and selection operator (LASSO)
(n = 2), PCA (n = 2), variance threshold (n = 2), Spearman
correlation coefficient (n = 2), Bootstrap resampling (n = 1),
ANOVA F-test (n = 1).
AI Method
Seventeen studies utilized radiomics-based traditional ML for
1p/19q status perdition, the classification algorithms includ-
ing Random Forest (RF) (n = 6), support vector machine
(SVM) (n = 4), logistic regression (LR) (n = 3), Xtreme gra-
dient boosting (XGBoost) (n = 2), Ensemble Bagged Trees
(EBT) (n = 1), neural network (n = 1). Eleven studies uti-
lized DL method, including autoencoder (n = 2), CNN
(n = 7), recurrent neural network (RNN) (n = 1), and gen-
erative adversarial network (GAN) (n = 1). Notably, several
studies used more than one AI method (see Table 1 and
Fig. 3d).
As for model development and evaluation, the methods
employed are as follows: k-fold cross validation
(CV) (n = 13), hold out (n = 6), Bootstrap (n = 5), leave
one out CV (n = 1), hold-out and inner K-fold CV (n = 1).
Additionally, 11 studies provided external validation cohorts
to assess model performance (Fig. 3e,f).
Model Performance
The proposed models were assessed based on their presented
area under the curve (AUC). An AUC was available in 24 of
the included studies, with AUC ranging from 0.71 to 0.98.
The remaining four studies provided accuracy (ACC) for
model performance (0.75–0.89). Table 1 summarized the
study characteristics, AI method and the performance of the
AI in terms of AUC or accuracy on the validation set. While
1341
 TABLE 1. Participant Demographics, Study Characteristics, and AI Performance of the Included Studies

1342
Patients, Glioma MRI Externally Feature Model
Study N Grade Sequences Data AI Methods D&E Validated Segmentation Software Input Selection Performance
Radiomics-based machine learning
Zhou et al 165 2, 3 T1, T2, TCIA LR Bootstrap No Manual Matlab Radiomics; Bootstrap AUC = 0.96
(2017)26 T1C, VASARI resampling
FLAIR
Han et al 277 2, 3 T2 In-house RF K-fold No Manual NA Radiomics; Variance AUC = 0.76
(2018)27 clinical threshold
Journal of Magnetic Resonance Imaging

Lu et al 87 2, 3, 4 T1, T2, TCIA SVM K-fold No Semiautomatic Matlab Radiomics t-test AUC = 0.92
(2018)28 T1C,
FLAIR
Shofty et al 47 2 T2, T1C, In-house EBT K-fold No Manual Matlab Radiomics PCA AUC = 0.87
(2018)29 FLAIR
Kim et al 167 2, 3, 4 T1, T2, TCIA RF Hold-out No Manual Pyradiomics Radiomics PCA AUC = 0.71
(2018)30 T1C,
FLAIR
van der 413 2, 3 T1C, T2 In- SVM K-fold Yes Manual PREDICT Radiomics; Not applied AUC = 0.72
Voort et al house, clinical
(2019)31 TCIA
Zhou et al 281 2, 3, 4 T1C, HUP, RF Bootstrap Yes Manual MATLAB Radiomics; Not applied AUC = 0.72
(2019)32 FLAIR BWH, clinical
MGH,
TCIA
Kong et al 96 2, 3 T1C, T2 In-house RF Hold-out No Manual Pyradiomics Radiomics LASSO AUC = 0.89
(2020)33
Kocak et al 107 2, 3 T1C, T2 TCIA Neural K-fold No Semiautomatic LIFEx Radiomics ReliefF AUC = 0.87
(2020)34 network
Rathore et al 159 2, 3 T1, T2 TCIA SVM Leave- No Semiautomatic NA Radiomics Not applied AUC = 0.86
(2020)35 one-
out

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 TABLE 1. Continued

Patients, Glioma MRI Externally Feature Model

Study N Grade Sequences Data AI Methods D&E Validated Segmentation Software Input Selection Performance

November 2023
Casale et al 209 2, 3 T1C, T2 TCIA RF Hold- Yes Manual RadiomiX Radiomics Spearman AUC = 0.87
(2021)36 out; correlation
inner coefficient
K-fold
Fan et al 157 2 T1, T2, CGGA SVM Nested No Manual Matlab Radiomics Elastic Net AUC = 0.81
(2021)24 T1C K-fold
Kha 159 2, 3 T2 TCIA XGBoost K-fold Yes Manual 3D Slicer Radiomics Spearmans AUC = 0.87
et al Correlation
(2021)37 Coefficient
Sun et al 335 2, 3 T1, T2, In-house RF Hold- No Manual Pyradiomics Radiomics; Boruta AUC = 0.76
(2021)38 T1C, out; VASARI;
FLAIR inner clinical
DWI K-fold
Yan et al 357 2, 3, 4 T1, T2, In-house LR Hold- No Manual Pyradiomics Radiomic Variance AUC = 0.82
(2021)39 T1C, out; threshold;
FLAIR inner LASSO
DWI K-fold
Lam et al 106 2, 3 T1C, T2, TCIA XGBoost K-fold Yes Automatic GLISTRboost Radiomics Not applied AUC = 0.78
(2022)40 FLAIR
Li (2022)41 212 2, 3, 4 T1, T2, TCIA LR Hold-out No Automatic Pyradiomics Radiomics ANOVA F- AUC = 0.86
T1C, test
FLAIR
Deep learning
Akkus et al 159 2, 3 T1C, T2 In-house CNN K-fold No Semiautomatic NA Image NA ACC = 0.88
(2017)42 patch
(2D)
Chang et al 259 2, 3, 4 T1, T2, TCIA CNN K-fold No Automatic NA Image NA AUC = 0.88
(2018)43 T1C, patch
FLAIR (2D)
Zhang et al.: A Review of AI Applications in Glioma With 1p/19q Co-Deletion

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 1344
TABLE 1. Continued

Patients, Glioma MRI Externally Feature Model

Study N Grade Sequences Data AI Methods D&E Validated Segmentation Software Input Selection Performance
Choi et al 463 2, 3, 4 DSC In-house RNN Bootstrap No Automatic NA Time series NA AUC = 0.89
(2019)44 perfusion + LSTM
MRI
Ali et al 161 2 T1C, In-house GAN K-fold Yes End to end NA Image NA ACC = 0.75
(2020)45 FLAIR (two patch
Journal of Magnetic Resonance Imaging

sites) (2D)
Tang et al 120 4 T1C, DWI In-house CNN K-fold NO Manual NA Image NA ACC = 0.88
(2020)25 patch
(3D)
Decuyper 628 2, 3, 4 T1, T2, TCIA, CNN Bootstrap Yes Automatic NA Image NA AUC = 0.82
et al T1C, BraTS; patch
(2021)46 FLAIR in- (3D)
house
Tupe- 375 3, 4 T1C, T2, TCIA, Autoencoder NA No Automatic NA Image NA AUC = 0.87
Waghmare FLAIR in- patch
et al house (3D)
(2021)47
Ning et al 431 2, 3, 4 T1C, TCIA, Autoencoder NA Yes Manual NA Image NA AUC = 0.90
(2021)48 FLAIR in- patch
house (2.5D)
van der 1748 2, 3, 4 T1C, T2, TCIA, CNN Bootstrap Yes End to end NA Image NA AUC = 0.85
Voort et al FLAIR in- patch
(2022)49 house (3D)
Cluceru et al 531 2, 3, 4 T1C, T2, TCIA, CNN NA Yes Automatic NA Image NA ACC = 0.89
(2022)50 FLAIR, in- patch
DWI house (3D)

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Zhang et al.: A Review of AI Applications in Glioma With 1p/19q Co-Deletion

Fig. 4 provides the associated forest plot for studies assessing

Performance

FLAIR = fluid attenuated inversion recovery; VASARI = visually accessible rembrandt images; LR = logistic regression; RF = random forest; EBT = Ensemble Bagged Trees;
network; DSC = dynamic susceptibility contrast perfusions weighted imaging; T1 = T1-weighted images; T1C = T1-weighted postcontrast images; T2 = T2-weighted images;
DWI = diffusion-weighted images; BraTS = brain tumor segmentation challenge; CNN = convolutional neural network; GAN = generative adversarial network; RNN = recurrent neural
AUC = 0.98
1p/19q co-deletion.
Model
Studies With Code
Seven studies published the analysis code they used, including
six radiomics studies and one DL study. All of the code is
Selection

hosted on Github (https://github.com/). Most of the code is

Feature

NA

written in Python, and most of the ML functions in it are

implemented using methods from the popular machine learn-
ing library scikit-learn. Some of the code also uses the
imbalanced-learn library to deal with data imbalance. It is
patch
(3D)
Image
Input

worth noting that the completeness of the code provided var-

ies from study to study, with some studies publishing code
that contains only the key steps in their analysis process. The
ease of use of these codes also varies, and the easiest one is
Software

PREDICT (https://github.com/Svdvoort/PREDICT), which

NA

puts all the information that needs to be configured into one

file, and one only needs to modify this file when applying the
code to a custom dataset. Given the difficulty of setting up a
Validated Segmentation

DL environment, PrognosAIs_glioma (https://github.com/

Manual

Svdvoort/PrognosAIs_glioma) provides a docker file to deploy

its preprocessing pipeline and the classification model in a vir-
tualized container (see Table 2 for more details).
Externally

CGGA = Chinese Glioma Genome Atlas; D&E = model development and evaluation; ACC = accuracy.

Discussion
Yes

According to the current systematic review, the status of

1p/19q co-deletion of gliomas can be predicted from nonin-
vasive medical imaging data using AI approaches with an
D&E
NA

AUC ranging from 0.71 to 0.98. The implementation of this

approach will help clinicians choose the best treatment plan
for glioma patients, particularly in planning the extent of re-
AI Methods

section prior to surgery. As shown in Fig. 5, there are cur-

CNN

rently two mainstream ways to implement AI in the field of

image-based prediction/classification: conventional ML
methods based on artificial feature engineering, such as radi-
house
TCIA,
Data

in-

omics and DL methods. Although differing in terms of fea-

ture extraction and model development, radiomics and DL
still share some common scientific and technical concerns,
Grade Sequences

FLAIR
T1, T2,

such as data collection and lesion segmentation.

T1C,
MRI

Imaging Modalities
The evaluation of the importance of different imaging modal-
Patients, Glioma

ities for the molecular prediction of glioma patients has

2, 3

always been one of the popular concerns. Given its availabil-

ity in most institutions, conventional MRI modalities
(T1WI, T2WI, T1CE, and FLAIR) are mostly used for gli-
555
N
TABLE 1. Continued

oma diagnosis. Based on our review, AI models based on rou-

tine MRI sequences achieved performance for predicting
1p/19q status with AUC ranging from 0.71 to 0.96. Other
(2022)51

advanced MRI modalities, like diffusion MRI (DWI) and

Yan et al

perfusion MRI (PWI), are also promising to capture more

Study

information that contributed to the prediction of 1p/19q sta-

tus. Compared with conventional MRI, the advantage of

November 2023 1345

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Journal of Magnetic Resonance Imaging

FIGURE 3: Summary of MRI sequences (a), tumor segmentation methods (b), types of imaging features (c), AI methods (d), model
development and evaluation methods (e), external validation (f) used by studies (n = 28) investigating AI models for predicting
1p/19q co-deletion in glioma. VASARI = visually accessible rembrandt imaging; GAN = generative adversarial network;
CNN = convolutional neural network; RNN = recurrent neural network; ML = machine learning.

DWI is the assessment of high cellularity areas, which can
help identify tissue microstructure and depict neoplastic infil-
tration in region of brain that appear normal on conventional
MRI. Sun et al38 reported that the AUC of the radiomics
model without ADC sequence in the testing cohort were
0.65 for IDH mutation combined 1p/19q co-deletion, while
after incorporating the ADC information into the radiomics
model, the AUC of prediction model increased to 0.76.
Recent study suggested that the IDH genotype can be predi-
cated using relative cerebral blood volume (rCBV) mapping
obtained from DSC perfusion MRI,52 which has highlighted
its potential value used to investigate glioma angiogenesis.
Further, Choi et al44 assessed feasibility of multidimensional
time-series from DSC perfusion MRI in prediction of 1p/19q
status. The results demonstrate excellent performance with
both interpretability and reproducibility on the test set
(AUC = 0.95). From the published literature, it is evident
that advanced sequences have the potential to enhance predic-
tive ability. However, it remains to be further investigated
whether the model should be constructed by combining tra-
ditional and advanced sequences or by choosing one of them.
More sequences may increase the redundant features in the
prediction model and reduce its diagnostic specificity. On the
other hand, the lack of broad clinical dissemination of
advanced MRI sequences in most hospital imaging protocols
and the expertise needed for data postprocessing and interpre-
tation make this approach difficult to be widely implemented
in clinical practice.
Lesion Segmentation
Accurate segmentation of lesion regions is crucial for radi-
omics studies. Although DL methods have the ability to
extract useful features directly from images, most DL-based
studies (9/11 in the current review) still perform lesions seg-
mentation due to the limitation of sample size. And the pat-
ches that contain lesion were used as the input for deep
network training, allowing the network to focus on the lesion
regions without the interference of normal regions and back-
ground. The irregular morphology, complex tissue compo-
nents (often including tumor parenchyma, necrosis,
peritumour edema), ambiguous boundaries as well as variable
location make accurate segmentation of glioma very challeng-
ing. Glioma was segmented manually by clinicians in 15 of
included studies, however, this process is time-consuming
with high inter-observer variability. Semi-automatic segmen-
tation is a combination of manual interventions and algo-
rithms. It usually requires a manual initialization to guide the
algorithm and post correction by experienced physicians. This
method can save part of the labor and was used in 4 of the
involved studies. In contrast, fully automated methods do not

1346 Volume 58, No. 5


Zhang et al.: A Review of AI Applications in Glioma With 1p/19q Co-Deletion
FIGURE 4: 1p/19q status forest plot of included studies with an AUC.
require human involvement and are more suitable for han-
dling large data sets. Currently, automatic methods are
increasingly employed, and the field has been growing in part
spurred on by the Brain Tumor Segmentation (BraTS) chal-
lenges, which aiming to automatically segment the gliomas.
Li et al41 employed a conventional computer vision method,
named GLISTRboost, to obtain the glioma masks automati-
cally. This algorithm achieved 88.5% dice score on BraTS
2015 dataset.53 However, compared with computer vision
methods, recently proposed DL-based methods are more
robust in segmenting targets with large variations. Chang
et al43 implemented a fully CNN with residual connections
to perform whole-tumor segmentation which was the top-
performing algorithm as evaluated in the 2016 international
Multimodal BraTS Challenge with a dice score of 0.87.54
Additionally, in our included studies, Choi et al44 used cas-
cade CNN to segment whole tumors into three sub-regions:
the enhancing and nonenhancing tumor core and the peri-
tumoral edema. The cascaded CNN architecture proposed by
Wang et al,55 achieving a dice score of 0.90 for whole tumor
on BraTS 2017 dataset. Recently, deep neural network with
U-Net architecture showed state-of-the-art performance in
brain tumor segmentation. U-Net is an encoder-decoder net-
work that combines semantic and spatial information through
the use of skip connections from the encoder to the decoder,
resulting satisfactory performance in both gross and fine
structure segmentation. Decuyper et al46 applied a 3D U-Net
similar to the architecture proposed by Isensee et al,18 which
achieved a dice score of 90% on BraTS 2019 dataset.
November 2023
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Notably, this segmentation architecture demonstrated only a
slight degradation in performance when only T1CE and
FLAIR or T1CE and T2WI scans are available compared to
simultaneous input of all four modalities. This is particularly
useful as not all four modalities are available for all patients in
clinical practice. Since U-net architecture showed excellent
segmentation performance, a series of improved variants
based on original U-net were developed. For example,
Yogananda et al56 developed a 3D-Dense-UNets, which can
perform 1p/19q co-deletion status classification and simulta-
neous single-label tumor segmentation. The whole tumor seg-
mentation mean dice score was 0.80 on TCIA dataset.
Classification Model Development
The classical ML algorithms, like RF, SVM, LR and
XGBoost are mostly chosen in radiomics style studies. During
2018–2019, most of studies trained a single ML algorithm in
their workflow. For example, Lu et al28 used and quadratic
SVM and achieved 80% accuracy in prediction 1p/19q co-
deletion in IDH mutation low-grade glioma on the indepen-
dent validation cohort containing only five patients. Han
et al27 used RF and achieved an AUC of 0.76 on the valida-
tion cohort, which contains 93 subjects. Recently, there has
been a clear trend to blend or stack multiple ML algorithms
with different advantages to achieve improved and robust pre-
dictive performance. In the work of Li et al41 and Kocak
et al,34 they employed various state-of-the-art ML algorithms
to predict the 1p/19q status and compared the performance
of each algorithm. Overall, most existing radiomics studies
1347
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Journal of Magnetic Resonance Imaging

TABLE 2. Studies With Code

Study Main How to

Study URL Language Type Input Dependencies Functionalities Re-use
Zhou et al https://github. MATLAB Radiomics Image NA Feature Additional
(2017)26 com/ and extraction; coding is
mvallieres/ mask feature needed to
radiomics processing; call the
model functions
development
van der https://github. Python Radiomics Image scikit-learn Feature Modify the
Voort com/ and extraction; configure
et al Svdvoort/ mask model file
(2019)31 PREDICT development
Kha e al https://github. Python Radiomics Tabular scikit-learn Model Change the
(2021)37 com/ data development path
khanhlee/ specified
LGG- in the
radiomics source
code
Casale https://github. Python Radiomics Tabular scikit-learn Feature selection Change the
et al com/ data imbalanced- model path
(2021)36 roberto- learn development specified
casale/LGG- in source
1p-19q- code
deletion
Yan et al https://github. Python R Radiomics Tabular brnn Feature selection; Change the
(2021)39 com/zhang- data model path
AI-MI/ development specified
glioma- in the
genotype- source
radiomics code
Li et al https://github. Python Radiomics Image pyradiomics Feature Change the
(2022)41 com/ and scikit-learn extraction; path
Yingping- mask imbalanced- feature specified
LI/ learn processing; in the
Radiomics model setting file
development
visualization
van der https://github. Python Deep Image tensorflow Image Build the
Voort com/ learning preprocessing; Docker
et al Svdvoort/ model and
(2022)49 PrognosAIs_ development organize
glioma the data as
requisted

identify ML algorithms mainly based on the researcher’s pref-
erence or the popularity of the algorithm. However, choosing
the most appropriate ML pipeline for a given problem tends
to be complicated, requiring the researcher to have expertise
in both the ML algorithm and the target problem.57 To over-
come these challenges, a relatively new system called
“automated machine learning (autoML)” has been devel-
oped to automate key steps of ML and to maximize the
performance of ML models.58 As a new research direction,
autoML has been successfully applied to H3K27M
prediction and IDH combined with MGMT status
prediction.59,60 However, fewer studies have applied

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 15222586, 2023, 5, Downloaded from https://onlinelibrary.wiley.com/doi/10.1002/jmri.28737 by Manager Information Resources Bond University Library, Wiley Online Library on [14/12/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Zhang et al.: A Review of AI Applications in Glioma With 1p/19q Co-Deletion

FIGURE 5: Characteristic workflow for developing ML glioma 1p/19q status prediction models.

AutoML to 1p/19q status prediction. Thus, further studies
that focus on the feasibility of this approach for 1p/19q
status prediction are warranted.
Due to its better feasibility and interpretability on task
datasets with limited sample size, radiomics continues to be the
preferred tool for predicting clinical target based on imaging
features. However, artificially engineered features from radi-
omics method may be a bottle neck limiting the performance
of ML model, with their limited ability to represent complex
data. In addition, radiomics features are susceptible to varia-
tions in imaging devices and imaging parameters, limiting the
value of radiomics models for application in real-world clinical
settings. The newly proposed DL method uses a neural net-
work with a large number of hidden layers to automatically
learn representations that are related to the task directly from
raw images, overcoming the limitations of radiomics in feature
extraction. Akkus et al42 used a multiscale 2D CNN on three
slices centered at the tumor “equator” and achieved an accu-
racy of 88% on the test set. Further, Chang et al43 used a com-
bination of ResNet and principal component analysis (PCA) to
predict 1p/19q status, achieving an AUC of 0.88 on their in-
house data. It is worth noting that the above models are all
trained on labelled data. In addition, Tupe-Waghmare et al47
built a semi-supervised model that can incorporate unlabeled
glioma data and learn to predict 1p/19q status. This model
combined auto-encoder with multitask CNN, which achieved
an AUC of 0.82. While still in their pioneer stage, the DL
approaches are promising tools for gaining insight into the

FIGURE 6: Challenges for clinical implementation of ML glioma 1p/19q status prediction models.

November 2023 1349


Journal of Magnetic Resonance Imaging
relationships between complex data and avoiding the limita-
tions of artificial feature engineering.
Challenges
The small-sample high-dimensional problem is a challenge
faced by almost all medical AI research and it is no exception
in 1p/19q status prediction. DL is more data-intensive than
radiomics as tens of thousands of weights in the deep neural
network need to be determined during training. In our
included radiomics studies, the sample size ranged from 47 to
413. As for DL, the sample size ranged from 120 to 1748. If
the feature dimension is high and the training data is insuffi-
cient, there will be a great risk of obtaining an overfit model,
which works perfectly on the training set but significantly
degrades on the test set.61 The best solution to overfitting is
of course collecting more data. However, in field of neuro-
oncology, large dataset with both radiological and pathologi-
cal data are often not easy to obtain as data acquisition is
costly and pooling data from multiple institutions is often
restricted due to privacy protection policies. Alternatively,
data augmentation is proposed to alleviate data insufficiency
and improve the robustness of predictions by adding trans-
formed copies of already existing data. There are seven studies
utilized data augmentation, generating equivalent data based
on limited real data according to various transforms (flipping,
rotating, cropping and scaling). Transfer learning is another
way to mitigate small sample size problem. Two stages of
model training are involved in transfer learning. The model
was pretrained on a large-scale benchmark dataset and then
fine-tuned on a small but study-specific dataset. Yogananda
et al56 applied transfer learning in 1p/19q status prediction,
using the network “T2-net” previously trained on dataset
regarding IDH classification. The model achieves good per-
formance (AUC = 0.95) with substantially less training data.
Generalizability of the AI models is one of the major
challenges hindering their board clinical applicability. Devel-
oping an AI model on one dataset and evaluating it on
dataset from other institutions (external validation) is the best
strategy to assess the performance, robustness, and depend-
ability of AI models. Unfortunately, this approach is not
prevalent in most of medical AI studies. So far, only about
6% of published medical AI studies used external valida-
tion.62 In our review of 1p/19q prediction, only 11 studies
validated their models on external datasets. Furthermore,
given that studies based on highly curated datasets (including
BraTS or TCIA) have shown consistently high classification
accuracy, performances of models trained on these datasets
may not be reproducible in real-world scenario. Future works
should validate their model externally using large, less-curated
datasets to evaluate the model’s generalizability on real-world
data and the potential for broad clinical deployment.
1350
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Multicenter study is the current trend in AI research,
which can, on the one hand, attenuate the risk of over-
fitting and, at the same time, due to the inherent variabil-
ity of the data, make the cohort more representative and
thus lead to more robust inference of the model. TCIA
dataset are mostly used dataset in glioma AI studies, which
including patients collected from different institutions with
different imaging devices or imaging protocols. Thus, the
nonbiological batch effects might be introduced.63 Data
harmonization may be helpful for standardizing the vari-
able images for analysis. This process can mitigate spurious
effects on the scientific conclusions incorporated due to
undesired sources of variation, such as batch effects, intrin-
sic factors within the subjects, and scanning sites. Remark-
ably, only Li et al41 applied both Z-score and ComBat for
normalization. Thus, for reducing the variability of the
image properties, standard imaging protocols, consistent
image processing together with appropriate harmonization
method are warranted in the future study. Figure 6 shows
challenges for clinical implementation of ML glioma
1p/19q status prediction models.
In summary, the current review corporates two categories
of models: traditional ML and DL models. As for traditional
ML, it cannot work with raw image data directly and must rely
on expert design techniques to extract and construct informative
features (namely “feature engineering”),64 the process is strongly
related to the data acquisition. The protocol and scanners
change between different institutions, which may be limiting
factors in the development of a robust ML model. As regard to
DL models, image features can be “learned” implicitly through
the iterative process of optimizing prediction performance, it
takes images as input eliminating the steps of feature engineering
and selection, hence potentially mitigating human bias.65 How-
ever, DL is not without drawbacks, it depends on tremendous
volume of high quality, well-annotated data to train a reliable
model,66 such data are difficult to aggregate in large part because
of regulatory and privacy concerns across institutions. Thus,
data-sharing and federated learning may be future directions for
overcoming current barriers for supporting clinical implementa-
tion of DL models.
Conclusions
Current evidence shows promising results for various AI
methodologies for 1P/19q status classification, which could
be beneficial for personalized treatment. However, till now,
there is no agreement about the radiomics pipeline, and the
prior studies are very heterogeneous regarding the segmenta-
tion methods, the number and category of extracted features,
MRI sequences, and AI technique. In addition, only 11 stud-
ies have implemented their model on external datasets. All of
the studies were retrospective in design. Before the clinical
Volume 58, No. 5

Zhang et al.: A Review of AI Applications in Glioma With 1p/19q Co-Deletion
implementation of glioma 1p/19q prediction by AI, more
standardized research is needed.
Conflicts of Interest
The authors declare no potential conflicts of interest.
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Volume 58, No. 5