CT Radiomics and Whole Genome Sequencing in Patients with Pancreatic Ductal Adenocarcinoma: Predictive Radiogenomics Modeling
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Image Acquisition
2.2. Image Segmentation, Radiomic Feature Extraction and Genomic Data
2.3. Statistical Analysis and Modelling
2.3.1. Feature Selection
2.3.2. Model Building
3. Results
3.1. Baseline Characteristics of the Study Cohort
3.2. Whole Genome Sequencing
3.3. Method 1
3.4. Method 2
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Characteristics | n = 47 |
---|---|
Age (mean ± SD; range) | 63.7 ± 10.7 (42–86) |
Sex | |
Females | 21 (45%) |
Male | 26 (55%) |
Current or former smoker | 21 (45%) |
Race | |
Asian | 6 (13%) |
Non-Asian | 41 (87%) |
Tumor Grade | |
G1 | 8 (17%) |
G2 | 26 (55%) |
G3 | 12 (26%) |
G4 | 1 (2%) |
TNM | |
T2 | 5 (11%) |
T3-4 | 42 (89%) |
N1 | 37 (78%) |
M1 | 8 (17%) |
Treatment | |
Surgery | 47 (100%) |
Whipple’s procedure | 41 (87%) |
Distal Pancreatectomy | 6 (13%) |
Adjuvant Chemotherapy | 42 (89%) |
Genes | Prevalence of Mutations N (%) |
---|---|
Significantly mutated genes | |
KRAS | 38 (81) |
TP53 | 32 (68) |
SMAD4 | 12 (26) |
CDKN2A | 9 (19) |
ARID1A | 2 (4) |
TGFBR2 | 1 (2) |
NF1 | 1 (2) |
Oncogenes | |
BRAF | 1 (2) |
EGFR | 1 (2) |
ERBB2 | 1 (2) |
FGFR1 | 1 (2) |
GNAS | 1 (2) |
MET | 1 (2) |
PAK4 | 1 (2) |
DNA damage repair genes | |
BRCA2 | 1 (2) |
ATM | 1 (2) |
Tumor suppressor genes | |
RNF43 | 2 (4) |
ACVR2A | 2 (4) |
SMAD3 | 1 (2) |
TSC2 | 1 (2) |
Chromatin modification genes | |
KDM6A | 1 (2) |
KMT2C | 3 (6) |
PBRM1 | 1 (2) |
SMARCA2 | 1 (2) |
SMARCA4 | 1 (2) |
Feature | KRAS | TP53 | SMAD4 | CDKN2A |
---|---|---|---|---|
HU_Skewness | 918 | 981 | ||
HU_Q3 | 860 | |||
GLZLM_LZLGE | 690 | |||
GLRLM_LRLGE | 664 | |||
GLRLM_SRHGE | 578 | |||
GLRLM_LGRE | 514 | |||
NGLDM_Contrast | 470 | |||
GLZLM_SZHGE | 782 | |||
NGLDM_Coarseness | 752 | 423 | 584 | |
GLCM_Energy | 617 | |||
GLZLM_ZLNU | 502 | |||
PARAMS_ZSpatialResampling | 353 | |||
HU_max | 351 | |||
GLZLM_SZLGE | 743 | 397 | ||
HU_peakSphere1mL | 633 | |||
HUmin | 541 | 465 | ||
GLZLM_GLNU | 528 | 561 | ||
HU_Q1 | 491 | 580 | ||
SHAPE_Volume | 396 | |||
GLCM_Correlation | 526 | |||
SHAPE_Sphericity | 461 |
KRAS | TP53 | SMAD4 | CDKN2A | |
---|---|---|---|---|
Model 1 | ||||
NPV | 0.00 (0.00, 1.00) | 0.50 (0.00, 1.00) | 0.75 (0.44, 1.00) | 0.80 (0.56, 1.00) |
PPV | 0.86 (0.56, 1.00) | 0.75 (0.43, 1.00) | 0.00 (0.00, 0.50) | 0.00 (0.00, 0.50) |
Sensitivity | 0.88 (0.57, 1.00) | 0.80 (0.44, 1.00) | 0.00 (0.00, 0.67) | 0.00 (0.00, 0.50) |
Specificity | 0.00 (0.00, 1.00) | 0.50 (0.00, 1.00) | 0.86 (0.50, 1.00) | 0.89 (0.56, 1.00) |
Youden Index | 0.50 (0.31, 0.94) | 0.62 (0.31, 0.94) | 0.44 (0.28, 0.72) | 0.50 (0.28, 0.69) |
Model 2 | ||||
NPV | 0.33 (0.00, 1.00) | 0.50 (0.00, 1.00) | 0.75 (0.50, 1.00) | 0.80 (0.56, 1.00) |
PPV | 0.88 (0.62, 1.00) | 0.78 (0.43, 1.00) | 0.00 (0.00, 1.00) | 0.00 (0.00, 1.00) |
Sensitivity | 0.88 (0.62, 1.00) | 0.83 (0.50, 1.00) | 0.00 (0.00, 0.50) | 0.00 (0.00, 0.50) |
Specificity | 0.25 (0.00, 1.00) | 0.50 (0.00, 1.00) | 0.89 (0.57, 1.00) | 0.89 (0.56, 1.00) |
Youden Index | 0.56 (0.33, 0.97) | 0.67 (0.33, 0.94) | 0.50 (0.31, 0.69) | 0.50 (0.31, 0.75) |
Feature | KRAS Mutations N (%) | TP53 | SMAD4 | CDKN2A |
---|---|---|---|---|
HUSkewness | x | x | ||
HU_Q3 | x | |||
GLZLM_LZLGE | x | |||
GLRLM_LRLGE | x | |||
NGLDM_Contrast | x | |||
GLZLM_SZHGE | x | |||
NGLDM_Coarseness | x | x | x | |
GLCM_Energy | x | |||
GLZLM_ZLNU | x | |||
GLZLM_SZLGE | x | x | ||
HUpeakSphere1mL | x | x | ||
GLZLM_GLNU | x | x | ||
HU_Q1 | x | |||
GLCM_Correlation | x | |||
SHAPE_Sphericity | x |
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Hinzpeter, R.; Kulanthaivelu, R.; Kohan, A.; Avery, L.; Pham, N.-A.; Ortega, C.; Metser, U.; Haider, M.; Veit-Haibach, P. CT Radiomics and Whole Genome Sequencing in Patients with Pancreatic Ductal Adenocarcinoma: Predictive Radiogenomics Modeling. Cancers 2022, 14, 6224. https://doi.org/10.3390/cancers14246224
Hinzpeter R, Kulanthaivelu R, Kohan A, Avery L, Pham N-A, Ortega C, Metser U, Haider M, Veit-Haibach P. CT Radiomics and Whole Genome Sequencing in Patients with Pancreatic Ductal Adenocarcinoma: Predictive Radiogenomics Modeling. Cancers. 2022; 14(24):6224. https://doi.org/10.3390/cancers14246224
Chicago/Turabian StyleHinzpeter, Ricarda, Roshini Kulanthaivelu, Andres Kohan, Lisa Avery, Nhu-An Pham, Claudia Ortega, Ur Metser, Masoom Haider, and Patrick Veit-Haibach. 2022. "CT Radiomics and Whole Genome Sequencing in Patients with Pancreatic Ductal Adenocarcinoma: Predictive Radiogenomics Modeling" Cancers 14, no. 24: 6224. https://doi.org/10.3390/cancers14246224
APA StyleHinzpeter, R., Kulanthaivelu, R., Kohan, A., Avery, L., Pham, N. -A., Ortega, C., Metser, U., Haider, M., & Veit-Haibach, P. (2022). CT Radiomics and Whole Genome Sequencing in Patients with Pancreatic Ductal Adenocarcinoma: Predictive Radiogenomics Modeling. Cancers, 14(24), 6224. https://doi.org/10.3390/cancers14246224