Table 5.
Diagnostic and predictive models built using genetic variables.
| AI methods used | Authors [ref.] | Stage of endometriosis | Type of endometriosis | Sample size | Inputs used | Method accuracy |
|---|---|---|---|---|---|---|
| Deep Machine Learning Algorithm | Li et al.52 | All four stages of endometriosisa | Not specified | 213 patients (142 endometriosis, 71 controls) | SCAF11, KIF3A, KRAS, MDM2 |
SE = 100% SP = 61.1% |
| GenomeForest | Akter et al.53 | All four stages of endometriosisa | Not specified | Transcriptomics dataset: 16 endometriosis, 22 controls; methylomics dataset: 44 endometriosis, 36 controls | Genes in transcriptomics data and genomic regions in methylated data. 11 687 protein-coding genes (14 154 genes total) |
For transcriptomics data: SE = 93.8% SP = 100% For methylomics data: SE = 92.9% SP = 88.6% |
| Random-Forest-based Machine Learning Classification Analysis | Perrotta et al.54 | All four stages of endometriosisa | Not specified | 59 patients (35 endometriosis, 24 controls) | Operational taxonomic unit and community state types in vaginal microbiome |
SE = NR SP = NR |
| Decision Tree | Akter et al.55 | All four stages of endometriosisa | Not specified | Transcriptomics dataset: 38 samples (16 endometriosis, 22 controls); methylomics dataset: 77 samples (42 endometriosis, 35 controls) | Transcriptomics: 14 154 genes; methylomics: 2 577 382 methylated regions |
For transcriptomics: SE = 81.3% SP = 95.5% For methylomics: SE = 76.2% SP = 80% |
| Partial Least Squares Discrimination Analysis | Akter et al.55 | All four stages of endometriosisa | Not specified | Transcriptomics dataset: 38 samples (16 endometriosis, 22 controls); methylomics dataset: 77 samples (42 endometriosis, 35 controls) | Transcriptomics: 14 154 genes; methylomics: 2 577 382 methylated regions |
For transcriptomics: SE = 86.4% SP = 56.3% For methylomics: SE = 60% SP = 76.2% |
| Support Vector Machines | Akter et al.55 | All four stages of endometriosisa | Not specified | Transcriptomics dataset: 38 samples (16 endometriosis, 22 controls); methylomics dataset: 77 samples (42 endometriosis, 35 controls) | Transcriptomics: 14 154 genes; methylomics: 2 577 382 methylated regions |
For transcriptomics: SE = 63.6% SP = 43.8% For methylomics: SE = 40% SP = 61.9% |
| Random Forest | Akter et al.55 | All four stages of endometriosisa | Not specified | Transcriptomics dataset: 38 samples (16 endometriosis, 22 controls); methylomics dataset: 77 samples (42 endometriosis, 35 controls) | Transcriptomics: 14 154 genes; methylomics: 2 577 382 methylated regions |
For transcriptomics: SE = 45.5% SP = 43.8% For methylomics: SE = 31.4% SP = 52.4% |
| Margin Tree Classification | Tamaresis et al.56 | All four stages of endometriosisa | Not specified | 148 endometrial samples (77 endometriosis, 37 without endometriosis but other uterine/pelvic pathology, 34 controls) | FOSB, FOS, EGR1, JUNB, MTSS1L, CTSW, TGFB1, SOC3, IL32, FKBP8, ISYNA1, CCL3, GNLY, MAP3K11, C1QA, NOTCH3, CYR61, NPTXR, FBN1, PNRC2, ITGA6, DHFR, SLC39A6, MYO10, HSP90B1, SMC3, PKP4, PALLD, DIO2 |
SE = NR SP = NR |
NR not reported, SCAF11 SR-related CTD-associated factor 11, KIF3A kinesin family member 3A, KRAS Kirsten rat sarcoma viral oncogene homolog, MDM2 mouse double minute 2 homolog, FOSB Fbj murine osteosarcoma oncogene B, EGR1 early growth response 1, JUNB JunB proto-oncogene, MTSS1L metastasis suppressor 1-like, CTSW cathepsin W, TGFB1 transforming growth factor beta 1, SOC3 suppressor of cytokine signaling 3, IL32 interleukin 32, FKBP8 FKBP prolyl isomerase 8, ISYNA1 inositol-3-phosphate synthase 1, CCL3 chemokine ligand 3, GNLY granulysin, MAP3K11 mitogen-activated protein kinase kinase kinase 11, C1QA complement C1q A chain, NOTCH3 notch receptor 3, CYR61 cysteine-rich angiogenic inducer 61, NPTXR neuronal pentraxin receptor, FBN1 fibrillin 1, PNRC2 protein rich nuclear receptor coactivator 2, ITGA6 integrin subunit alpha 6, DHFR dihydrofolate reductase, SLC39A6 Dolutegravir carrier family 39 member 6, MYO10 myosin X, HSP90B1 heat shock protein 90 beta family member 1, SMC3 structural maintenance of chromosomes 3, PKP4 plakophillin 4, PALLD Palladin, cytoskeletal associated protein, DIO2 iodothyronine deiodinase 2, SE sensitivity, SP specificity.
aMinimal, mild, moderate and severe stages of endometriosis were included.