Domain Mapping and Deep Learning from Multiple MRI Clinical Datasets for Prediction of Molecular Subtypes in Low Grade Gliomas

Brain tumors, such as low grade gliomas (LGG), are molecularly classified which require the surgical collection of tissue samples. The pre-surgical or non-operative identification of LGG molecular type could improve patient counseling and treatment decisions. However, radiographic approaches to LGG molecular classification are currently lacking, as clinicians are unable to reliably predict LGG molecular type using magnetic resonance imaging (MRI) studies. Machine learning approaches may improve the prediction of LGG molecular classification through MRI, however, the development of these techniques requires large annotated data sets. Merging clinical data from different hospitals to increase case numbers is needed, but the use of different scanners and settings can affect the results and simply combining them into a large dataset often have a significant negative impact on performance. This calls for efficient domain adaption methods. Despite some previous studies on domain adaptations, mapping MR images from different datasets to a common domain without affecting subtitle molecular-biomarker information has not been reported yet. In this paper, we propose an effective domain adaptation method based on Cycle Generative Adversarial Network (CycleGAN). The dataset is further enlarged by augmenting more MRIs using another GAN approach. Further, to tackle the issue of brain tumor segmentation that requires time and anatomical expertise to put exact boundary around the tumor, we have used a tight bounding box as a strategy. Finally, an efficient deep feature learning method, multi-stream convolutional autoencoder (CAE) and feature fusion, is proposed for the prediction of molecular subtypes (1p/19q-codeletion and IDH mutation). The experiments were conducted on a total of 161 patients consisting of FLAIR and T1 weighted with contrast enhanced (T1ce) MRIs from two different institutions in the USA and France. The proposed scheme is shown to achieve the test accuracy of 74 . 81 % on 1p/19q codeletion and 81 . 19 % on IDH mutation, with marked improvement over the results obtained without domain mapping. This approach is also shown to have comparable performance to several state-of-the-art methods.

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Classification of Brain Tumor IDH Status using MRI and Deep Learning

10.1101/757344 ◽

2019 ◽

Author(s):

Sahil Nalawade ◽

Gowtham Murugesan ◽

Maryam Vejdani-Jahromi ◽

Ryan A. Fisicaro ◽

Chandan Ganesh Bangalore Yogananda ◽

...

Keyword(s):

Deep Learning ◽

Classification Accuracy ◽

Test Accuracy ◽

Low Grade ◽

Idh Mutation ◽

Validation Data ◽

Mutation Status ◽

Radiologic Imaging ◽

Address Data

AbstractIsocitrate dehydrogenase (IDH) mutation status is an important marker in glioma diagnosis and therapy. We propose a novel automated pipeline for predicting IDH status noninvasively using deep learning and T2-weighted (T2w) MR images with minimal preprocessing (N4 bias correction and normalization to zero mean and unit variance). T2w MRI and genomic data were obtained from The Cancer Imaging Archive dataset (TCIA) for 260 subjects (120 High grade and 140 Low grade gliomas). A fully automated 2D densely connected model was trained to classify IDH mutation status on 208 subjects and tested on another held-out set of 52 subjects, using 5-fold cross validation. Data leakage was avoided by ensuring subject separation during the slice-wise randomization. Mean classification accuracy of 90.5% was achieved for each axial slice in predicting the three classes of no tumor, IDH mutated and IDH wild-type. Test accuracy of 83.8% was achieved in predicting IDH mutation status for individual subjects on the test dataset of 52 subjects. We demonstrate a deep learning method to predict IDH mutation status using T2w MRI alone. Radiologic imaging studies using deep learning methods must address data leakage (subject duplication) in the randomization process to avoid upward bias in the reported classification accuracy.

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P10.21 2-hydroxyglutarate as a biomarker for IDH mutation in low grade gliomas

Neuro-Oncology ◽

10.1093/neuonc/nox036.339 ◽

2017 ◽

Vol 19 (suppl_3) ◽

pp. iii89-iii90

Author(s):

R. Nejad ◽

H. Sim ◽

K. Aldape ◽

W. Mason ◽

M. Bernstein ◽

...

Keyword(s):

Low Grade ◽

Idh Mutation ◽

Low Grade Gliomas

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IDH mutation and 1p19q codeletion distinguish two radiological patterns of diffuse low-grade gliomas

Journal of Neuro-Oncology ◽

10.1007/s11060-017-2421-0 ◽

2017 ◽

Vol 133 (1) ◽

pp. 37-45 ◽

Cited By ~ 29

Author(s):

Amélie Darlix ◽

Jérémy Deverdun ◽

Nicolas Menjot de Champfleur ◽

Florence Castan ◽

Sonia Zouaoui ◽

...

Keyword(s):

Low Grade ◽

Idh Mutation ◽

Low Grade Gliomas ◽

1P19q Codeletion ◽

Radiological Patterns

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Pharmacoresistant seizures and IDH mutation in low grade gliomas

Neuro-Oncology Advances ◽

10.1093/noajnl/vdab146 ◽

2021 ◽

Author(s):

Carlos Eduardo Correia ◽

Yoshie Umemura ◽

Jessica R Flynn ◽

Anne S Reiner ◽

Edward K Avila

Keyword(s):

Tumor Resection ◽

Incidence Rates ◽

P Value ◽

Low Grade ◽

Idh Mutation ◽

Wild Type ◽

Mutation Status ◽

Low Grade Gliomas ◽

Idh1 R132h ◽

Idh Mutations

Abstract Purpose Many low-grade gliomas (LGG) harbor isocitrate dehydrogenase (IDH) mutations. Although IDH mutation is known to be epileptogenic, the rate of refractory seizures in LGG with IDH mutation vs wild-type had not been previously compared. We therefore compared seizure pharmacoresistance in IDH-mutated and wild-type LGGs. Methods Single-institution retrospective study of patients with histologic proven LGG, known IDH mutation status, seizures, and ≥ 2 neurology clinic encounters. Seizure history was followed until histological high-grade transformation or death. Seizures requiring ≥ 2 changes in anti-epileptic drugs were considered pharmacoresistant. Incidence rates of pharmacoresistant seizures were estimated using competing risks methodology. Results Of 135 patients, 25 patients (19%) had LGGs classified as IDH wild-type. Of those with IDH mutation, 104 (94.5%) were IDH1 R132H; only six were IDH2 R172K. 120 patients (89%) had tumor resection and 14 (10%) had biopsy. Initial post-surgical management included observation (64%), concurrent chemoradiation (23%), chemotherapy alone (9%), and radiotherapy alone (4%). Seizures became pharmacoresistant in 24 IDH-mutated patients (22%) and in 3 IDH wild-type patients (12%). The 4-year cumulative incidence of intractable seizures was 17.6% (95% CI: 10.6%-25.9%) in IDH-mutated and 11% (95% CI: 1.3%-32.6%) in IDH wild-type LGG (Gray’s P-value= 0.26). Conclusions 22% of the IDH-mutated patients developed pharmacoresistant seizures, compared to 12% of the IDH wild-type tumors.The likelihood of developing pharmacoresistant seizures in patients with LGG-related epilepsy is independent to IDH mutation status, however, IDH-mutated tumors were approximately twice as likely to experience LGG-related pharmacoresistant seizures.

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Prognostic significance of IDH mutation in adult low-grade gliomas: a meta-analysis

Journal of Neuro-Oncology ◽

10.1007/s11060-013-1107-5 ◽

2013 ◽

Vol 113 (2) ◽

pp. 277-284 ◽

Cited By ~ 37

Author(s):

Hairui Sun ◽

Lianhu Yin ◽

Showwei Li ◽

Song Han ◽

Guangrong Song ◽

...

Keyword(s):

Meta Analysis ◽

Prognostic Significance ◽

Low Grade ◽

Idh Mutation ◽

Low Grade Gliomas

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Isocitrate dehydrogenase status and molecular subclasses of glioma and glioblastoma

Neurosurgical FOCUS ◽

10.3171/2014.9.focus14505 ◽

2014 ◽

Vol 37 (6) ◽

pp. E13 ◽

Cited By ~ 24

Author(s):

Sameer Agnihotri ◽

Kenneth D. Aldape ◽

Gelareh Zadeh

Keyword(s):

Molecular Subtypes ◽

Genetic Alterations ◽

Metabolic Enzyme ◽

Low Grade ◽

Lower Grade ◽

Low Grade Gliomas ◽

Fundamental Understanding ◽

Diffuse Gliomas ◽

Idh1 Mutations ◽

Secondary Glioblastomas

Diffuse gliomas and secondary glioblastomas (GBMs) that develop from low-grade gliomas are a common and incurable class of brain tumor. Mutations in the metabolic enzyme glioblastomas (IDH1) represent a distinguishing feature of low-grade gliomas and secondary GBMs. IDH1 mutations are one of the most common and earliest detectable genetic alterations in low-grade diffuse gliomas, and evidence supports this mutation as a driver of gliomagenesis. Here, the authors highlight the biological consequences of IDH1 mutations in gliomas, the clinical and therapeutic/diagnostic implications, and the molecular subtypes of these tumors. They also explore, in brief, the non-IDH1–mutated gliomas, including primary GBMs, and the molecular subtypes and drivers of these tumors. A fundamental understanding of the diversity of GBMs and lower-grade gliomas will ultimately allow for more effective treatments and predictors of survival.

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IDH mutation status trumps the Pignatti risk score as a prognostic marker in low-grade gliomas

Journal of Neuro-Oncology ◽

10.1007/s11060-017-2570-1 ◽

2017 ◽

Vol 135 (2) ◽

pp. 273-284 ◽

Cited By ~ 8

Author(s):

Olatz Etxaniz ◽

Cristina Carrato ◽

Itziar de Aguirre ◽

Cristina Queralt ◽

Ana Muñoz ◽

...

Keyword(s):

Prognostic Marker ◽

Risk Score ◽

Low Grade ◽

Idh Mutation ◽

Mutation Status ◽

Low Grade Gliomas

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SURG-11. TUMOR RECURRENCE PATTERNS AFTER SURGICAL RESECTION OF INTRACRANIAL LOW-GRADE GLIOMAS

Neuro-Oncology ◽

10.1093/neuonc/noab196.781 ◽

2021 ◽

Vol 23 (Supplement_6) ◽

pp. vi197-vi197

Author(s):

Yoshihiro Muragaki ◽

Yasukazu Fukuya ◽

Soko Ikuta ◽

Masayuki NItta ◽

Taiichi Saito ◽

...

Keyword(s):

Tumor Recurrence ◽

Negative Impact ◽

Extent Of Resection ◽

Low Grade ◽

Radiological Progression ◽

Low Grade Gliomas ◽

Primary Surgery ◽

Non Local ◽

Recurrence Patterns

Abstract INTRODUCTION Tumor recurrence patterns after resection of intracranial low-grade gliomas (LGG) generally remain obscured. The objective of the present retrospective study was their multifaceted analysis, evaluation of associated factors, and assessment of impact on prognosis. METHODS Study group comprised 81 consecutive adult patients (46 men and 35 women; median age, 37 years) with recurrent diffuse astrocytomas (DA; 51 cases) and oligodendrogliomas (OD; 30 cases). The median length of follow-up after primary surgery was 6.7 years. RESULTS Early (within 2 years after primary surgery) and non-early ( > 2 years after primary surgery) recurrence was noted in 23 (28%) and 58 (72%) cases, respectively. Fast (≤ 6 months) and slow ( > 6 months) radiological progression of relapse was noted in 31 (38%) and 48 (59%) cases, respectively. Tumor recurrence was local and non-local in 71 (88%) and 10 (12%) cases, respectively. Recurrence patterns have differed in OD, IDH1-mutant DA, and IDH wild-type DA. Early onset, fast radiological progression, and non-local site of relapse had statistically significant negative impact on overall survival of patients and were often associated with malignant transformation of the tumor (38 cases). However, in subgroup with extent of resection ≥ 90% (56 cases) no differences in recurrence characteristics were found between 3 molecularly defined groups of LGG. Follow-up MRI also showed same results. CONCLUSIONS Recurrence patterns after resection of LGG show significant variability, differ in distinct molecularly defined types of tumors, and demonstrate definitive impact on prognosis. Aggressive resection at the time of primary surgery may result in more favorable characteristics of recurrence at the time of its development.

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