Department of Biochemistry, Konkuk University School of Medicine, Seoul, Korea
Copyright © 2019 by the Korean Cancer Association
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Cohort |
Drug sensitivity |
Cancer cell lines | Centre | Platform | ||
---|---|---|---|---|---|---|
S | R | |||||
Intrinsic drug resistance | CCLE–PTXa) | 239a) | 240 | 240 Human cancer cell lines | Broad Institute | Affymetrix HG U133 Plus 2.0 Array |
CGP–PTX, DTXa) (E-MTAB-783) | 143 | 143 | 388 Human cancer cell lines | Wellcome Sanger Institute | Affymetrix HG U133A | |
244 | 244 | |||||
Aqucired drug resistance | GSE36135 (Domingo-Domenech et al. [4]) | 6 | 6 | Parental docetaxel-sensitive prostate cancer cell lines (DU145 and 22Rv1) and selected docetaxel-resistant cells (DU145-DR and 22Rv1-DR) | Mount Sinai School of Medicine | Affymetrix HG U133 Plus 2.0 Array |
GSE28784 (Zwart and Rechache [5]) | 3 | 6 | Docetaxel and paclitaxel resistant MDA-MB-231 (breast cancer) cells | Georgetown University | Affymetrix HG U133A Array | |
GSE12791 (Luo et al. [7]) | 8 | 8 | Parental paclitaxel-sensitive breast cancer cell lines (MDA-MB-231) and paclitaxel resistant cells (MDA-PR) | Denovo Biopharma | Affymetrix HG U133A Array | |
GSE33455 (Marin-Aguilera et al. [8]) | 6 | 6 | Parental docetaxel-sensitive prostate cancer cell lines (DU145 and PC3) and selected docetaxel-resistant cells (DU145-DR and PC3-DR) | Fundació Clínic per a la Recerca Biomèdica | Affymetrix HG U133 Plus 2.0 Array | |
GSE23779 (Landen et al. [6]) | 3 | 3 | Parental ovarian cancer cell lines (SKOV3ip1) and paclitaxel-resistant SKOV3TRip2 | University of Alabama at Birmingham | Illumina Human Ref-8 v2.0 |
S, sensitive; R, resistant; CCLE, Cancer Cell Line Encyclopedia; PTX, paclitaxel; CGP, Cancer Genome Project; DTX, docetaxel.
a) The resistant/sensitive phenotypes to taxane were classified as follows: cell lines in the below median IC50 or area under curve (referred to as ActArea in CCLE) values were classified as sensitive and those above median IC50 or area under curve values were classified as resistance.
GSE36135 (Domingo-Domenech et al. [4]) | GSE28784 (Zwart and Rechache [5]) | GSE23779 (Landen et al. [6]) | |
---|---|---|---|
AUROC | 1.000 | 1.000 | 1.000 |
AUPRC | 1.000 | 1.000 | 1.000 |
Brier | 0.022 | 0 | 0.001 |
Cross study validation | Blind study validation | |
---|---|---|
AUROC | 1.000 (1.000-1.000) | 0.940 (0.841-1.000) |
AUPRC | 1.000 | 0.940 |
Brier score | 0.007 | 0.127 |
Confusion matrix metrics | ||
Sensitivity (Recall/TPR) | 1.000 | 0.900 |
Specificity | 1.000 | 0.800 |
Precision (PPV) | 1.000 | 0.818 |
Likelihood ratio positive (LR+) | Inf | 4.500 |
Likelihood ratio negative (LR–) | 0.000 | 0.125 |
F1 | 1.000 | 0.857 |
Cohort | GSE3613 (Domingo-Domenech et al. [4]), GSE28784 (Zwart and Rechache [5]), GSE23779 (Landen et al. [6]) | GSE33455 (Marin-Aguilera et al. [8]), GSE12791 (Luo et al. [7]) |
CCLE-PTX | CGP-PTX | CGP-DTX | |
---|---|---|---|
AUROC | 0.739 (0.695-0.783) | 0.660 (0.597-0.722) | 0.692 (0.645-0.738) |
AUPRC | 0.735 | 0.679 | 0.708 |
BRIER | 0.208 | 0.23 | 0.221 |
Cross study validation | Blind study validation | |
---|---|---|
AUROC | 0.703 (0.674, 0.731) | 0.688 (0.539, 0.837) |
AUPRC | 0.712 | 0.735 |
Brier score | 0.218 | 0.226 |
Confusion matrix metrics | ||
Sensitivity (Recall/TPR) | 0.617 | 0.680 |
Specificity | 0.671 | 0.640 |
Precision (PPV) | 0.653 | 0.654 |
Likelihood ratio positive (LR+) | 1.876 | 1.889 |
Likelihood ratio negative (LR–) | 0.571 | 0.500 |
F1 | 0.634 | 0.667 |
Cohort | CCLE-PTX CGP-PTX CGP-DTX | GSE3613 (Domingo-Domenech et al. [4]), GSE28784 (Zwart and Rechache [5]), GSE23779 (Landen et al. [6]), GSE33455 (Marin-Aguilera et al. [8]), GSE12791 (Luo et al. [7]) |
Values in parentheses are 95% confidence intervals. ITR, intrinsic taxane resistance; ATR, acquired taxane resistance; AUROC, area under the receiver operating curve; AUPRC, area under the precision-recall curve; TPR, true positive rate; PPV, positive predictive value; CCLE, Cancer Cell Line Encyclopedia; PTX, paclitaxel; CGP, Cancer Genome Project; DTX, docetaxel.
Cohort | Drug sensitivity |
Cancer cell lines | Centre | Platform | ||
---|---|---|---|---|---|---|
S | R | |||||
Intrinsic drug resistance | CCLE–PTX |
239 |
240 | 240 Human cancer cell lines | Broad Institute | Affymetrix HG U133 Plus 2.0 Array |
CGP–PTX, DTX |
143 | 143 | 388 Human cancer cell lines | Wellcome Sanger Institute | Affymetrix HG U133A | |
244 | 244 | |||||
Aqucired drug resistance | GSE36135 (Domingo-Domenech et al. [4]) | 6 | 6 | Parental docetaxel-sensitive prostate cancer cell lines (DU145 and 22Rv1) and selected docetaxel-resistant cells (DU145-DR and 22Rv1-DR) | Mount Sinai School of Medicine | Affymetrix HG U133 Plus 2.0 Array |
GSE28784 (Zwart and Rechache [5]) | 3 | 6 | Docetaxel and paclitaxel resistant MDA-MB-231 (breast cancer) cells | Georgetown University | Affymetrix HG U133A Array | |
GSE12791 (Luo et al. [7]) | 8 | 8 | Parental paclitaxel-sensitive breast cancer cell lines (MDA-MB-231) and paclitaxel resistant cells (MDA-PR) | Denovo Biopharma | Affymetrix HG U133A Array | |
GSE33455 (Marin-Aguilera et al. [8]) | 6 | 6 | Parental docetaxel-sensitive prostate cancer cell lines (DU145 and PC3) and selected docetaxel-resistant cells (DU145-DR and PC3-DR) | Fundació Clínic per a la Recerca Biomèdica | Affymetrix HG U133 Plus 2.0 Array | |
GSE23779 (Landen et al. [6]) | 3 | 3 | Parental ovarian cancer cell lines (SKOV3ip1) and paclitaxel-resistant SKOV3TRip2 | University of Alabama at Birmingham | Illumina Human Ref-8 v2.0 |
GSE36135 (Domingo-Domenech et al. [4]) | GSE28784 (Zwart and Rechache [5]) | GSE23779 (Landen et al. [6]) | |
---|---|---|---|
AUROC | 1.000 | 1.000 | 1.000 |
AUPRC | 1.000 | 1.000 | 1.000 |
Brier | 0.022 | 0 | 0.001 |
Cross study validation | Blind study validation | |
---|---|---|
AUROC | 1.000 (1.000-1.000) | 0.940 (0.841-1.000) |
AUPRC | 1.000 | 0.940 |
Brier score | 0.007 | 0.127 |
Confusion matrix metrics | ||
Sensitivity (Recall/TPR) | 1.000 | 0.900 |
Specificity | 1.000 | 0.800 |
Precision (PPV) | 1.000 | 0.818 |
Likelihood ratio positive (LR+) | Inf | 4.500 |
Likelihood ratio negative (LR–) | 0.000 | 0.125 |
F1 | 1.000 | 0.857 |
Cohort | GSE3613 (Domingo-Domenech et al. [4]), GSE28784 (Zwart and Rechache [5]), GSE23779 (Landen et al. [6]) | GSE33455 (Marin-Aguilera et al. [8]), GSE12791 (Luo et al. [7]) |
CCLE-PTX | CGP-PTX | CGP-DTX | |
---|---|---|---|
AUROC | 0.739 (0.695-0.783) | 0.660 (0.597-0.722) | 0.692 (0.645-0.738) |
AUPRC | 0.735 | 0.679 | 0.708 |
BRIER | 0.208 | 0.23 | 0.221 |
Cross study validation | Blind study validation | |
---|---|---|
AUROC | 0.703 (0.674, 0.731) | 0.688 (0.539, 0.837) |
AUPRC | 0.712 | 0.735 |
Brier score | 0.218 | 0.226 |
Confusion matrix metrics | ||
Sensitivity (Recall/TPR) | 0.617 | 0.680 |
Specificity | 0.671 | 0.640 |
Precision (PPV) | 0.653 | 0.654 |
Likelihood ratio positive (LR+) | 1.876 | 1.889 |
Likelihood ratio negative (LR–) | 0.571 | 0.500 |
F1 | 0.634 | 0.667 |
Cohort | CCLE-PTX CGP-PTX CGP-DTX | GSE3613 (Domingo-Domenech et al. [4]), GSE28784 (Zwart and Rechache [5]), GSE23779 (Landen et al. [6]), GSE33455 (Marin-Aguilera et al. [8]), GSE12791 (Luo et al. [7]) |
S, sensitive; R, resistant; CCLE, Cancer Cell Line Encyclopedia; PTX, paclitaxel; CGP, Cancer Genome Project; DTX, docetaxel. The resistant/sensitive phenotypes to taxane were classified as follows: cell lines in the below median IC50 or area under curve (referred to as ActArea in CCLE) values were classified as sensitive and those above median IC50 or area under curve values were classified as resistance.
AUROC, area under the receiver operating curve; AUPRC, area under the precision-recall curve.
Values in parentheses are 95% confidence intervals. ATR, acquired taxane resistance; AUROC, area under the receiver operating curve; AUPRC, area under the precision-recall curve; TPR, true positive rate; PPV, positive predictive value.
Values in parentheses are 95% confidence intervals. ITR, intrinsic taxane resistance; CCLE, Cancer Cell Line Encyclopedia; PTX, paclitaxel; CGP, Cancer Genome Project; DTX, docetaxel; AUROC, area under the receiver operating curve; AUPRC, area under the precision-recall curve.
Values in parentheses are 95% confidence intervals. ITR, intrinsic taxane resistance; ATR, acquired taxane resistance; AUROC, area under the receiver operating curve; AUPRC, area under the precision-recall curve; TPR, true positive rate; PPV, positive predictive value; CCLE, Cancer Cell Line Encyclopedia; PTX, paclitaxel; CGP, Cancer Genome Project; DTX, docetaxel.