Identifying Effective Biomarkers for Accurate Pancreatic Cancer Prognosis Using Statistical Machine Learning
Abstract
:1. Introduction
- (1)
- Several clinical and biochemical biomarkers for 30 PC patients belonging to three groups of POCs are reported.
- (2)
- Various statistical and exploratory data analysis techniques are applied to examine and identify the most effective panel of biomarkers for the prediction of POCs among resected PDAC patients.
- (3)
- Statistical ML models are developed and a comparative performance analysis is performed to demonstrate the combined predictive power of the panel of significant biomarkers through an improved PC prognosis accuracy.
2. Materials and Methods
2.1. Patient Grouping
2.2. Serum Samples
2.3. Biochemical Assays
2.4. Total Leukocyte Count (TLC) Determination
2.5. Quantitative Determination of Serum Immunoglobulins
2.6. Determination of Serum Procalcitonin (PCT)
2.7. Analysis of Serum Tumor Markers
2.7.1. Carbohydrate Antigen 19-9 (CA 19-9)
2.7.2. CXCL-8/IL-8
2.8. Statistical Analysis
2.8.1. Paired Sample t-Test
2.8.2. Correlation Analysis
2.8.3. Biomarker Importance Analysis
2.8.4. Statistical ML Modeling
3. Results
3.1. Patient Characteristics and Radiotherapy
3.2. Findings of Biochemical Assays
3.2.1. Biochemical and Serological Parameters
3.2.2. Estimation of Total Leukocyte Count (TLC), Levels of IgG and IgA, and Procalcitonin (PCT)
3.3. Analysis of Serum Tumor Markers
3.3.1. Carbohydrate Antigen 19-9 (CA 19-9)
3.3.2. CXCL-8/IL-8
3.4. Statistical Analysis and Modeling
3.4.1. Paired Sample t-Test of Significant Biomarkers
3.4.2. Correlations between Biomarkers and Patients’ Postoperative Complications
3.4.3. Identification of Important Biomarkers
3.4.4. Statistical Learning for PC Complication Prognosis
4. Discussion
5. Limitations and Future Research
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Patient No. | Gender | Age (Year) | Tumor Volume (cc) | Maximum Dose of RT (Dmax, Gy) | Cause of Death or Complications in ICU |
---|---|---|---|---|---|
Group A | |||||
1 | F | 65 | 60.2 | 34.0 | Septic shock |
2 | F | 61 | 68.1 | 39.0 | Sepsis |
3 | F | 67 | 68.0 | 36.0 | Sepsis and septic shock |
4 | F | 55 | 76.0 | 35.0 | Sepsis with renal and liver impairment |
5 | M | 79 | 64.0 | 31.0 | Septic shock |
6 | M | 65 | 45.0 | 32.0 | Sepsis |
7 | F | 68 | 69.6 | 39.0 | Sepsis and septic shock |
8 | M | 63 | 70.0 | 39.0 | Sepsis |
9 | F | 64 | 57.0 | 37.0 | Septic shock |
10 | M | 57 | 60.2 | 38.0 | Sepsis * |
Group B | |||||
1 | F | 50 | 66.0 | 34.0 | Recurrence |
2 | F | 40 | 62.5 | 32.0 | Recurrence |
3 | M | 57 | 68.1 | 40.0 | Recurrence |
4 | M | 53 | 67.5 | 38.0 | Recurrence |
5 | M | 53 | 43.2 | 38.0 | Recurrence |
6 | M | 41 | 57.2 | 34.0 | Recurrence |
7 | M | 40 | 45.0 | 38.0 | Recurrence |
8 | M | 53 | 50.0 | 36.0 | Recurrence |
9 | M | 51 | 57.1 | 40.0 | Recurrence |
10 | M | 62 | 56.0 | 40.0 | Recurrence |
Group C | |||||
1 | F | 52 | 62.0 | 43.0 | Unknown |
2 | M | 51 | 40.0 | 38.0 | Unknown |
3 | F | 50 | 76.0 | 39.0 | Unknown |
4 | M | 65 | 76.0 | 38.0 | Unknown |
5 | M | 62 | 56.0 | 36.0 | Unknown |
6 | F | 52 | 62.0 | 38.0 | Unknown |
7 | F | 51 | 40.0 | 43.0 | Unknown |
8 | M | 50 | 76.0 | 36.0 | Unknown |
9 | M | 65 | 76.0 | 38.0 | Unknown |
10 | M | 62 | 56.0 | 39.0 | Unknown |
Biochemical Test | Preoperative Findings | Postoperative Findings | Healthy Controls | ||
---|---|---|---|---|---|
Sepsis (Group A: 10) | Recurrence (Group B: 10) | Unknown Complications (Group C: 10) | |||
TBIL (mg/dL) | 2.3 ± 0.5 ** | 0.87 ± 0.1 * | 0.84 ± 0.1 * | 0.86 ± 0.1 * | 0.72 ± 0.1 |
DBIL (mg/dL) | 0.78 ± 0.08 ** | 0.16 ± 0.01 * | 0.15 ± 0.05 * | 0.16 ± 0.05 * | 0.13 ± 0.01 |
ALT (U/L) | 106.0 ± 8.5 ** | 26.0 ± 1.2 * | 21.0 ± 0.9 * | 15.0 ± 0.9 * | 19.0 ± 1.0 |
ALB (g/L) | 4.14 ± 0.3 ** | 3.5 ± 0.2 ** | 4.35 ± 0.3 * | 4.35 ± 0.3 * | 4.7 ± 0.5 |
TLC (×103/mm3) | 5.99 ± 0.085 ns | 17.12 ± 0.15 ** | 4.2 ± 0.331 * | 4.0 ± 0.331 * | 5.8 ± 0.04 |
IgG (g/L) | 8.01 ± 0.6 ns | 5.96 ± 0.44 ** | 8.76 ± 0.7 ns | 8.01 ± 0.7 ns | 8.57 ± 0.76 |
IgA (×102 g/L) | 9.41 ± 0.8 ** | 7.8 ± 0.6 ** | 7.81 ± 0.7 ** | 7.71 ± 0.7 ** | 31.2 ± 2.5 |
PCT (ng/mL) | 0.00 | 6.9 ± 0.8 ** | 0.072 ± 0.01 * | 0.070 ± 0.001 * | 0.01 |
Patient No. | Preoperative CA19-9 (U/mL) | Postoperative CA19-9 (U/mL) | Preoperative CXCL-8 (pg/mL) | Postoperative CXCL-8 (pg/mL) |
---|---|---|---|---|
Group A | ||||
1 | 196.0 ± 29.0 ** | 23.5 ± 2.0 ** | 182.0 ± 13.0 ** | 336.0 ± 35.0 ** |
2 | 429.0 ± 39.0 ** | 37.0 ± 2.0 ** | 319.0 ± 40.0 ** | 912.0 ± 82.0 ** |
3 | 267.0 ± 18.0 ** | 12.0 ± 1.1 ** | 215.0 ±17.0 ** | 467.0 ± 48.0 ** |
4 | 53.0 ± 6.0 ** | 22.0 ± 1.0 ** | 42.1 ±37.0 ** | 189.0 ± 17.0 ** |
5 | 193.0 ± 17.0 ** | 55.0 ± 4.0 ** | 187.0 ± 15.0 ** | 602.0 ± 55.0 ** |
6 | 19.8 ± 1.8 ** | 2.5 ± 1.0 ** | 20.3 ± 1.0 ** | 214.0 ± 22.0 ** |
7 | 58.0 ± 5.0 ** | 1.2 ± 0.1 ** | 22.0 ± 1.0 ** | 168.0 ± 15.0 ** |
8 | 6.47 ± 0.3 ** | 1.3 ± 0.1 ** | 24.0 ± 1.0 ** | 210.0 ± 17.0 ** |
9 | 231.0 ± 15.0 ** | 1.2 ± 0.1 ** | 22.0 ± 1.0 ** | 211.5 ± 17.0 ** |
10 | 85.0 ± 8.0 ** | 12.7 ± 1.0 ** | 42.1 ± 6.0 ** | 26.5 ± 2.0 ** |
Mean ± SD | 153.83 ± 13.9 ** | 24.3 ± 1.2 ** | 107.5 ± 11.0 ** | 333.6 ± 29.0 ** |
Group B | ||||
1 | 421.0 ± 55.0 ** | 266.0 ± 18.0 ** | 396.0 ± 36.0 ** | 191.0 ± 18.0 ** |
2 | 891.0 ± 111.0 ** | 211.0 ± 15.0 ** | 759.0 ± 81.0 ** | 98.0 ± 6.0 ** |
3 | 613.0 ± 29.0 ** | 178.0 ± 16.0 ** | 606.0 ± 50.0 ** | 981.0 ± 96.0 ** |
4 | 1444.0 ± 112.0 * | 325.0 ± 26.0 ** | 1384.0 ± 112.0 ** | 298.0 ± 22.0 ** |
5 | 491.0 ± 40.0 ** | 98.0 ± 8.0 ** | 405.0 ± 36.0 ** | 281.0 ± 21.0 ** |
6 | 412.0 ± 36.0 ** | 257.0 ± 16.0 ** | 365.0 ± 11.0 ** | 79.0 ± 8.0 ** |
7 | 1012.0 ± 98.0 ** | 277.0 ± 17.0 ** | 891.0 ± 66.0 ** | 704.0 ± 60.0 ** |
8 | 112.0 ± 10.0 ** | 2.7 ± 0.1 ** | 26.3 ± 2.0 ** | 96.2 ± 6.0 ** |
9 | 512.0 ± 53.0 ** | 203.0 ± 19.0 ** | 349.0 ± 28.0 ** | 462.0 ± 12.0 ** |
10 | 1577.0 ± 150.0 * | 421.0 ± 36.0 ** | 1448.0 ± 132.0 * | 1081.0 ± 95.0 ** |
Mean ± SD | 748.5 ± 59.4 ** | 233.7 ± 17.22 ** | 659.5 ± 55.4 ** | 427.1 ± 34.4 ** |
Group C | ||||
1 | 80.0 ± 17.0 ** | 17.0 ± 1.5 ** | 65.0 ± 6.0 * | 85.0 ± 7.0 * |
2 | 84.0 ± 6.5 ** | 3.5 ± 0.5 ** | 56.0 ± 4.0 * | 32.5 ± 3.0 * |
3 | 23.6 ± 3.0 ** | 5.7 ± 0.2 ** | 31.0 ± 1.0 * | 66.0 ± 2.9 * |
4 | 3.34 ± 0.5 ** | 1.2 ± 0.6 ** | 25.3 ± 1.0 * | 35.8 ± 1.0 * |
5 | 65.7 ± 5.0 ** | 1.3 ± 0.1 ** | 29.0 ± 2.0 * | 78.0 ± 7.0 * |
6 | 75.0 ± 17.0 ** | 19.0 ± 1.5 ** | 69.0 ± 6.0 * | 85.0 ± 7.0 * |
7 | 89.0 ± 6.5 ** | 3.5 ± 0.5 ** | 59.0 ± 4.0 * | 32.5 ±3.0 * |
8 | 23.6 ± 3.0 ** | 5.7 ± 0.2 ** | 19.5 ± 1.0 * | 86.0 ± 2.9 * |
9 | 3.34 ± 0.5 ** | 1.2 ± 0.6 ** | 21.3 ± 1.0 * | 42.3 ± 1.0 * |
10 | 75.7 ± 5.0 ** | 1.3 ± 0.1 ** | 25.0 ± 2.0 * | 72.0 ± 7.0 * |
Mean ± SD | 52.2 ± 5.9 ** | 5.39 ± 0.58 ** | 39.95 ± 2.8 * | 61.6 ± 4.18 * |
Healthy controls | ||||
1 | 11.0 ± 1.0 | - | 23.0 ± 2.0 | - |
2 | 18.0 ± 1.0 | - | 21.8 ± 2.0 | - |
3 | 12.3 ± 1.0 | - | 22.0 ± 2.0 | - |
4 | 21.2 ± 1.2 | - | 21.5 ± 1.5 | - |
Mean ± SD | 15.6 ± 2.0 | - | 22.07 ± 1.9 | - |
Sample Parameters | t-Value | p-Value | Cohen-d | |
---|---|---|---|---|
CA19-9_post | G2 vs. G3 | 5.91106 | 0.00023 | 2.64 |
G1 vs. G2 | −5.448325 | 0.00041 | 2.48 | |
G1 vs. G3 | 1.686535 | 0.125969 | 0.804603 | |
CXCL-8_post | G2 vs. G3 | 3.076225 | 0.01322 | 1.387486 |
G1 vs. G2 | −0.564692 | 0.58608 | 0.291199 | |
G1 vs. G3 | 3.236429 | 0.010217 | 1.470414 | |
PCT_post | G2 vs. G3 | 0.631454 | 0.543447 | 0.059925 |
G1 vs. G2 | 10.414405 | 0.00003 | 4.701717 | |
G1 vs. G3 | 10.433683 | 0.000003 | 4.702802 |
Model | Accuracy | Precision | Recall | F-Score | AUC-ROC Score |
---|---|---|---|---|---|
GNB | 100 | 100 | 100 | 100 | 100 |
MLR | 100 | 100 | 100 | 100 | 100 |
RC | 100 | 100 | 100 | 100 | 100 |
GPC | 100 | 100 | 100 | 100 | 100 |
KNN | 100 | 100 | 100 | 100 | 100 |
DT | 100 | 100 | 100 | 100 | 100 |
Model | Accuracy | Precision | Recall | F-Score | AUC-ROC Score |
---|---|---|---|---|---|
GNB | 66.67 | 66.67 | 66.67 | 66.67 | 50 |
MLR | 66.67 | 66.67 | 66.67 | 66.67 | 50 |
RC | 66.67 | 66.67 | 66.67 | 66.67 | 50 |
GPC | 83.33 | 83.33 | 83.33 | 83.33 | 75 |
KNN | 83.33 | 83.33 | 83.33 | 83.33 | 75 |
DT | 83.33 | 83.33 | 83.33 | 83.33 | 75 |
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Share and Cite
Abu-Khudir, R.; Hafsa, N.; Badr, B.E. Identifying Effective Biomarkers for Accurate Pancreatic Cancer Prognosis Using Statistical Machine Learning. Diagnostics 2023, 13, 3091. https://doi.org/10.3390/diagnostics13193091
Abu-Khudir R, Hafsa N, Badr BE. Identifying Effective Biomarkers for Accurate Pancreatic Cancer Prognosis Using Statistical Machine Learning. Diagnostics. 2023; 13(19):3091. https://doi.org/10.3390/diagnostics13193091
Chicago/Turabian StyleAbu-Khudir, Rasha, Noor Hafsa, and Badr E. Badr. 2023. "Identifying Effective Biomarkers for Accurate Pancreatic Cancer Prognosis Using Statistical Machine Learning" Diagnostics 13, no. 19: 3091. https://doi.org/10.3390/diagnostics13193091
APA StyleAbu-Khudir, R., Hafsa, N., & Badr, B. E. (2023). Identifying Effective Biomarkers for Accurate Pancreatic Cancer Prognosis Using Statistical Machine Learning. Diagnostics, 13(19), 3091. https://doi.org/10.3390/diagnostics13193091