| Literature DB >> 33281864 |
Hongxiang Lu1,2, Dalin Wen1, Jianhui Sun1, Juan Du1, Liang Qiao3, Huacai Zhang1, Ling Zeng1, Lianyang Zhang1, Jianxin Jiang1, Anqiang Zhang1.
Abstract
BACKGROUND: Increasing genetic variants associated with sepsis have been identified by candidate-gene and genome-wide association studies, but single variants conferred minimal alterations in risk prediction. Our aim is to evaluate whether a weighted genetic risk score (wGRS) that aggregates information from multiple variants could improve risk discrimination of traumatic sepsis.Entities:
Keywords: genetic variants; prediction; sepsis; trauma; weighted genetic risk score
Year: 2020 PMID: 33281864 PMCID: PMC7689156 DOI: 10.3389/fgene.2020.545564
Source DB: PubMed Journal: Front Genet ISSN: 1664-8021 Impact factor: 4.599
Seventeen selected genetic variants with MDA > 1 by random forest algorithm.
| rs2297518 | G | NOS2 | 3.73 | 0.43 | 1.53 (1.12–2.10) | 0.01 |
| rs62375529 | C | FER | 2.89 | 0.29 | 1.34 (0.87–2.05) | 0.19 |
| rs760477 | A | TONSL | 2.70 | 0.03 | 1.03 (0.83–1.28) | 0.97 |
| rs10865710 | G | PPARG | 2.64 | 0.27 | 1.32 (1.06–1.63) | 0.01 |
| rs4957796 | C | FER | 2.25 | 0.29 | 1.34 (0.87–2.05) | 0.19 |
| rs1799983 | T | NOS3 | 2.08 | 0.22 | 1.24 (0.93–1.70) | 0.18 |
| rs11465996 | G | MD2 | 1.81 | 0.17 | 1.18 (0.92–1.52) | 0.19 |
| rs4919510 | C | SEMA4G | 1.56 | 0.05 | 1.05 (0.85–1.31) | 0.63 |
| rs2071746 | T | HMOX1 | 1.53 | 0.07 | 1.07 (0.87–1.31) | 0.53 |
| rs2069912 | C | PROC | 1.49 | 0.06 | 1.07 (0.86–1.32) | 0.56 |
| rs4073 | T | CXCL8 | 1.49 | 0.11 | 1.11 (0.90–1.38) | 0.33 |
| rs740598 | G | HSPA12A | 1.46 | 0.22 | 1.25 (1.01–1.53) | 0.04 |
| rs820336 | G | MYLK | 1.42 | 0.06 | 1.07 (0.62–1.85) | 0.82 |
| rs7851696 | T | FCN2 | 1.32 | 0.14 | 1.15 (0.88–1.49) | 0.31 |
| rs352162 | T | TLR9 | 1.30 | 0.12 | 1.13 (0.91–1.41) | 0.27 |
| rs5743867 | C | TOLLIP | 1.07 | 0.17 | 1.18 (0.95–1.46) | 0.12 |
| rs2243250 | C | IL4 | 1.03 | 0.08 | 1.08 (0.83–1.40) | 0.57 |
FIGURE 1Random forest model including 17 variants previously associated with sepsis. The first 64 variables with the highest mean decrease accuracy are plotted. Seventeen sepsis-associated variants were shown to induce a positive change in mean decrease accuracy. These variants were thus considered to have a relevant influence on the model and were chosen for inclusion in the wGRS.
FIGURE 2Distributions of the wGRS among sepsis cases and controls. (A) The percentage of wGRS of 17 variants displaying a significant difference among cases and controls. (B) The distributions of wGRS of 17 variants among cases and controls.
Cumulative effects of wGRS on the risk of sepsis.
| (0.70–1.80) (≤ Q25) | 237 | 20.28 ± 6.33 | 42 (17.72%) | 1.00 (reference) | ||
| (1.80–2.20) (Q25∼Q50) | 225 | 21.26 ± 6.86 | 54 (24.00%) | 1.47 (0.93–2.30) | 0.10 | |
| (2.20–2.50) (Q50∼Q75) | 216 | 21.11 ± 7.57 | 62 (28.70%) | 1.87 (1.20–2.92) | 6.00 × 10–3 | |
| (2.50–3.70) (> Q75) | 205 | 21.22 ± 8.04 | 83 (40.48%) | 3.16 (2.05–4.88) | 1.20 × 10–7 | 6.81 × 10–8 |
Associations of wGRS with the severity and organ failure after trauma.
| (0.70–1.80) (≤ Q25) | 237 | 3.05 ± 2.39 | 7.12 ± 5.23 |
| (1.80–2.20) (Q25∼Q50) | 225 | 3.46 ± 2.65 | 8.38 ± 6.40 |
| (2.20–2.50) (Q50∼Q75) | 216 | 3.62 ± 3.15 | 8.65 ± 6.61 |
| (2.50–3.70) (> Q75) | 205 | 3.98 ± 2.81 | 9.41 ± 5.86 |
FIGURE 3Model comparisons and clinical usefulness of the nomogram. (A) The nomogram incorporating ISS and wGRS was constructed for the prediction of sepsis after trauma. (B) ROC curves of three models for sepsis risk. The area under the ROC curves (AUCs) are based on logistic regression models of only clinical risk factor (ISS), only genetic factor (wGRS), and both clinical risk factor and genetic factor (ISS + wGRS). (C) DCA for the nomogram. The net benefit was plotted vs. the threshold probability. The red line represents the nomogram. The gray and black lines represent the hypothesis that all patients and no patients had sepsis, respectively.
Reclassification of predicted risk with the addition of wGRS using NRI.
| 0–5% | 0 | 0 | 0 | 0 | 0 | 74 (11.53%) | 217 (33.80%) | 22.27% |
| 5–10% | 0 | 0 | 0 | 0 | 0 | |||
| 10–15% | 0 | 0 | 0 | 0 | 0 | |||
| 15–20% | 0 | 42 | 154 | 162 | 74 | |||
| ≥20% | 0 | 0 | 2 | 19 | 189 | |||
| 0–5% | 0 | 0 | 0 | 0 | 0 | 26 (10.79%) | 19 (7.88%) | 2.91% |
| 5–10% | 0 | 0 | 0 | 0 | 0 | |||
| 10–15% | 0 | 0 | 0 | 0 | 0 | |||
| 15–20% | 0 | 1 | 11 | 22 | 26 | |||
| ≥ 20% | 0 | 0 | 3 | 4 | 174 | |||
| NRI(95%CI) | 25.18% (17.84–32.51%) | |||||||
| P | 6.00 × 10–5 | |||||||