scholarly journals Broad external validation of a multivariable risk prediction model for gastrointestinal malignancy in iron deficiency anaemia

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Orouba Almilaji ◽  
Gwilym Webb ◽  
Alec Maynard ◽  
Thomas P. Chapman ◽  
Brian S. F. Shine ◽  
...  

Abstract Background Using two large datasets from Dorset, we previously reported an internally validated multivariable risk model for predicting the risk of GI malignancy in IDA—the IDIOM score. The aim of this retrospective observational study was to validate the IDIOM model using two independent external datasets. Methods The external validation datasets were collected, in a secondary care setting, by different investigators from cohorts in Oxford and Sheffield derived under different circumstances, comprising 1117 and 474 patients with confirmed IDA respectively. The data were anonymised prior to analysis. The predictive performance of the original model was evaluated by estimating measures of calibration, discrimination and clinical utility using the validation datasets. Results The discrimination of the original model using the external validation data was 70% (95% CI 65, 75) for the Oxford dataset and 70% (95% CI 61, 79) for the Sheffield dataset. The analysis of mean, weak, flexible and across the risk groups’ calibration showed no tendency for under or over-estimated risks in the combined validation data. Decision curve analysis demonstrated the clinical value of the IDIOM model with a net benefit that is higher than ‘investigate all’ and ‘investigate no-one’ strategies up to a threshold of 18% in the combined validation data, using a risk cut-off of around 1.2% to categorise patients into the very low risk group showed that none of the patients stratified in this risk group proved to have GI cancer on investigation in the validation datasets. Conclusion This external validation exercise has shown promising results for the IDIOM model in predicting the risk of underlying GI malignancy in independent IDA datasets collected in different clinical settings.

2020 ◽  
Vol 35 (Supplement_3) ◽  
Author(s):  
Simon Sawhney ◽  
Zhi Tan ◽  
Corri Black ◽  
Brenda Hemmelgarn ◽  
Angharad Marks ◽  
...  

Abstract Background and Aims There is limited evidence to inform which people should receive follow up after AKI and for what reasons. Here we report the external validation (geographical and temporal) and potential clinical utility of two complementary models for predicting different post-discharge outcomes after AKI. We used decision curve analysis, a technique that enables visualisation of the trade-off (net benefit) between identifying true positives and avoiding false positives across a range of potential risk thresholds for a risk model. Based on decision curve analysis we compared model guided approaches to follow up after AKI with alternative strategies of standardised follow up – e.g. follow up of all people with AKI, severe AKI, or a discharge eGFR<30. Method The Alberta AKI risk model predicts the risk of stage G4 CKD at one year after AKI among those with a baseline GFR>=45 and at least 90 days survival (2004-2014, n=9973). A trial is now underway using this tool at a 10% threshold to identify high risk people who may benefit from specialist nephrology follow up. The Aberdeen AKI risk model provides complementary predictions of early mortality or unplanned readmissions within 90 days of discharge (2003, n=16453), aimed at supporting non-specialists in discharge planning, with a threshold of 20-40% considered clinically appropriate in the study. For the Alberta model we externally validated using Grampian residents with hospital AKI in 2011-2013 (n=9382). For the Aberdeen model we externally validated using all people admitted to hospital in Grampian in 2012 (n=26575). Analysis code was shared between the sites to maximise reproducibility. Results Both models discriminated well in the external validation cohorts (AUC 0.855 for CKD G4, and AUC 0.774 for death and readmissions model), but as both models overpredicted risks, recalibration was performed. For both models, decision curve analysis showed that prioritisation of patients based on the presence or severity of AKI would be inferior to a model guided approach. For predicting CKD G4 progression at one year, a strategy guided by discharge eGFR<30 was similar to a model guided approach at the prespecified 10% threshold (figure 1). In contrast for early unplanned admissions and mortality, model guided approaches were superior at the prespecified 20-40% threshold (figure 2). Conclusion In conclusion, prioritising AKI follow up is complex and standardised recommendations for all people may be an inefficient and inadequate way of guiding clinical follow-up. Guidelines for AKI follow up should consider suggesting an individualised approach both with respect to purpose and prioritisation.


2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jianfeng Zheng ◽  
Jialu Guo ◽  
Linling Zhu ◽  
Ying Zhou ◽  
Jinyi Tong

Abstract Background Not only glycolysis but also lncRNAs play a significant role in the growth, proliferation, invasion and metastasis of of ovarian cancer (OC). However, researches about glycolysis -related lncRNAs (GRLs) remain unclear in OC. Herein, we first constructed a GRL-based risk model for patients with OC. Methods The processed RNA sequencing (RNA-seq) profiles with clinicopathological data were downloaded from TCGA and glycolysis-related genes (GRGs) were obtained from MSigDB. Pearson correlation coefficient between glycolysis-related genes (GRGs) and annotated lncRNAs (|r| > 0.4 and p < 0.05) were calculated to identify GRLs. After screening prognostic GRLs, a risk model based on five GRLs was constructed using Univariate and Cox regression. The identified risk model was validated by two validation sets. Further, the differences in clinicopathology, biological function, hypoxia score, immune microenvironment, immune checkpoint, immune checkpoint blockade, chemotherapy drug sensitivity, N6-methyladenosine (m6A) regulators, and ferroptosis-related genes between risk groups were explored by abundant algorithms. Finally, we established networks based on co-expression, ceRNA, cis and trans interaction. Results A total of 535 GRLs were gained and 35 GRLs with significant prognostic value were identified. The prognostic signature containing five GRLs was constructed and validated and can predict prognosis. The nomogram proved the accuracy of the model for predicting prognosis. After computing hypoxia score of each sample by ssGSEA, we found patients with higher risk scores exhibited higher hypoxia score and high hypoxia score was a risk factor. It was revealed that a total of 21 microenvironment cells (such as Central memory CD4 T cell, Neutrophil, Regulatory T cell and so on) and Stromal score had significant differences between the two groups. Four immune checkpoint genes (CD274, LAG3, VTCN1, and CD47) showed disparate expression levels in the two groups. Besides, 16 m6A regulators and 126 ferroptosis-related genes were expressed higher in the low-risk group. GSEA revealed that the risk groups were associated with tumor-related pathways. The two risk groups were confirmed to be sensitive to several chemotherapeutic agents and patients in the low-risk group were more sensitive to ICB therapy. The networks based on co-expression, ceRNA, cis and trans interaction provided insights into the regulatory mechanisms of GRLs. Conclusions Our identified and validated risk model based on five GRLs is an independent prognostic factor for OC patients. Through comprehensive analyses, findings of our study uncovered potential biomarker and therapeutic target for the risk model based on the GRLs.


2020 ◽  
Vol 40 (8) ◽  
Author(s):  
Kaifei Zhao ◽  
Lin Xu ◽  
Feng Li ◽  
Jin Ao ◽  
Guojun Jiang ◽  
...  

Abstract Background: Due to the heterogeneity of hepatocellular carcinoma (HCC), hepatocelluarin-associated differentially expressed genes were analyzed by bioinformatics methods to screen the molecular markers for HCC prognosis and potential molecular targets for immunotherapy. Methods: RNA-seq data and clinical follow-up data of HCC were downloaded from The Cancer Genome Atlas (TCGA) database. Multivariate Cox analysis and Lasso regression were used to identify robust immunity-related genes. Finally, a risk prognosis model of immune gene pairs was established and verified by clinical features, test set and Gene Expression Omnibus (GEO) external validation set. Results: A total of 536 immune-related gene (IRGs) were significantly associated with the prognosis of patients with HCC. Ten robust IRGs were finally obtained and a prognostic risk prediction model was constructed by feature selection of Lasso. The risk score of each sample is calculated based on the risk model and is divided into high risk group (Risk-H) and low risk group (Risk-L). Risk models enable risk stratification of samples in training sets, test sets, external validation sets, staging and subtypes. The area under the curve (AUC) in the training set and the test set were all &gt;0.67, and there were significant overall suvival (OS) differences between the Risk-H and Risk-L samples. Compared with the published four models, the traditional clinical features of Grade, Stage and Gender, the model performed better on the risk prediction of HCC prognosis. Conclusion: The present study constructed 10-gene signature as a novel prognostic marker for predicting survival in patients with HCC.


2021 ◽  
Author(s):  
Hui Xiong ◽  
Weiting Kang ◽  
Qi Zhang

Abstract Background: This study aimed to explore N6-methyladenosine (m6A) methylation-related immune biomarkers and their clinical value in clear cell renal cell carcinoma (ccRCC).Methods: The RNA-seq data and clinical phenotype of ccRCC were downloaded from TCGA database. Immune-related genes list was downloaded from InnateDB database. Correlation analysis, survival analysis, univariate and multivariate Cox regression analysis were used to investigate the prognostic independent m6A-related immune genes, followed by prognosis risk model establishment. Patients were divided into high/low risk groups, followed by survival analysis, clinical factors, immune checkpoint genes and gene set variation analysis in high-risk vs. low-risk group. Results: Five prognostic independent m6A-related immune genes (PKHD1, IGF2BP3, RORA, FRK and MZF1) were identified. Low expression of PKHD1, RORA and FRK were associated with poor survival, while high expression of IGF2BP3 and MZF1 were associated with poor survival for ccRCC patients. Their expression showed correlations with multiple m6A genes. The risk model could stratify ccRCC patients into high/low risk group, and patients with high-risk were associated with short survival time. High-risk group had an high proportion of patients in tumor stage Ⅲ-Ⅳ and patients with pathologic T3-T4 tumors, lymph node metastasis (N1) and distant metastasis (M1). Ten immune checkpoint genes were differentially expressed in high/low risk groups, such as PD1 and CTLA-4. The risk group could be an independent prognostic factor (HR=1.69, 95% CI 1.07-2.68, P=0.0246). Conclusion: In this study, we developed a five genes risk model, which had independent prognostic value and associated with tumor stage, pathologic T/N/M and immune checkpoint expression in ccRCC.


Author(s):  
Junfan Pan ◽  
Zhidong Huang ◽  
Yiquan Xu

Long non-coding RNAs (lncRNAs), which are involved in the regulation of RNA methylation, can be used to evaluate tumor prognosis. lncRNAs are closely related to the prognosis of patients with lung adenocarcinoma (LUAD); thus, it is crucial to identify RNA methylation-associated lncRNAs with definitive prognostic value. We used Pearson correlation analysis to construct a 5-Methylcytosine (m5C)-related lncRNAs–mRNAs coexpression network. Univariate and multivariate Cox proportional risk analyses were then used to determine a risk model for m5C-associated lncRNAs with prognostic value. The risk model was verified using Kaplan–Meier analysis, univariate and multivariate Cox regression analysis, and receiver operating characteristic curve analysis. We used principal component analysis and gene set enrichment analysis functional annotation to analyze the risk model. We also verified the expression level of m5C-related lncRNAs in vitro. The association between the risk model and tumor-infiltrating immune cells was assessed using the CIBERSORT tool and the TIMER database. Based on these analyses, a total of 14 m5C-related lncRNAs with prognostic value were selected to build the risk model. Patients were divided into high- and low-risk groups according to the median risk score. The prognosis of the high-risk group was worse than that of the low-risk group, suggesting the good sensitivity and specificity of the constructed risk model. In addition, 5 types of immune cells were significantly different in the high-and low-risk groups, and 6 types of immune cells were negatively correlated with the risk score. These results suggested that the risk model based on 14 m5C-related lncRNAs with prognostic value might be a promising prognostic tool for LUAD and might facilitate the management of patients with LUAD.


2021 ◽  
Vol 12 ◽  
Author(s):  
JingJing Zhang ◽  
Pengcheng He ◽  
Xiaoning Wang ◽  
Suhua Wei ◽  
Le Ma ◽  
...  

Background: RNA-binding proteins (RBPs) act as important regulators in the progression of tumors. However, their role in the tumorigenesis and prognostic assessment in multiple myeloma (MM), a B-cell hematological cancer, remains elusive. Thus, the current study was designed to explore a novel prognostic B-cell-specific RBP signature and the underlying molecular mechanisms.Methods: Data used in the current study were obtained from the Gene Expression Omnibus (GEO) database. Significantly upregulated RBPs in B cells were defined as B cell-specific RBPs. The biological functions of B-cell-specific RBPs were analyzed by the cluster Profiler package. Univariate and multivariate regressions were performed to identify robust prognostic B-cell specific RBP signatures, followed by the construction of the risk classification model. Gene set enrichment analysis (GSEA)-identified pathways were enriched in stratified groups. The microenvironment of the low- and high-risk groups was analyzed by single-sample GSEA (ssGSEA). Moreover, the correlations among the risk score and differentially expressed immune checkpoints or differentially distributed immune cells were calculated. The drug sensitivity of the low- and high-risk groups was assessed via Genomics of Drug Sensitivity in Cancer by the pRRophetic algorithm. In addition, we utilized a GEO dataset involving patients with MM receiving bortezomib therapy to estimate the treatment response between different groups.Results: A total of 56 B-cell-specific RBPs were identified, which were mainly enriched in ribonucleoprotein complex biogenesis and the ribosome pathway. ADAR, FASTKD1 and SNRPD3 were identified as prognostic B-cell specific RBP signatures in MM. The risk model was constructed based on ADAR, FASTKD1 and SNRPD3. Receiver operating characteristic (ROC) curves revealed the good predictive capacity of the risk model. A nomogram based on the risk score and other independent prognostic factors exhibited excellent performance in predicting the overall survival of MM patients. GSEA showed enrichment of the Notch signaling pathway and mRNA cis-splicing via spliceosomes in the high-risk group. Moreover, we found that the infiltration of diverse immune cell subtypes and the expression of CD274, CD276, CTLA4 and VTCN1 were significantly different between the two groups. In addition, the IC50 values of 11 drugs were higher in the low-risk group. Patients in the low-risk group exhibited a higher complete response rate to bortezomib therapy.Conclusion: Our study identified novel prognostic B-cell-specific RBP biomarkers in MM and constructed a unique risk model for predicting MM outcomes. Moreover, we explored the immune-related mechanisms of B cell-specific RBPs in regulating MM. Our findings could pave the way for developing novel therapeutic strategies to improve the prognosis of MM patients.


2021 ◽  
Author(s):  
Fang Wen ◽  
Xiaoxue Chen ◽  
Wenjie Huang ◽  
Shuai Ruan ◽  
Suping Gu ◽  
...  

Abstract Background: The diagnosis rate and mortality of gastric cancer (GC) are among the highest in the global, so it is of great significance to predict the survival time of GC patients. Ferroptosis and iron-metabolism make a critical impact on tumor development and are closely linked to the treatment of cancer and the prognosis of patients. However, the predictive value of the genes involved in ferroptosis and iron-metabolism in GC and their effects on immune microenvironment remain to be further clarified.Methods: In this study, the RNA sequence information and general clinical indicators of GC patients were acquired from the public databases. We first systematically screen out 134 DEGs and 13 PRGs related to ferroptosis and iron-metabolism. Then, we identified six PRDEGs (GLS2, MTF1, SLC1A5, SP1, NOX4, and ZFP36) based on the LASSO-penalized Cox regression analysis. The 6-gene prognostic risk model was established in the TCGA cohort and the GC patients were separated into the high- and the low-risk groups through the risk score median value. GEO cohort was used for verification. The expression of PRDEGs was verified by quantitative QPCR.Results: Our study demonstrated that patients in the low-risk group had a higher survival probability compared with those in high-risk group. In addition, univariate and multivariate Cox regression analyses confirmed that the risk score was an independent prediction parameter. The ROC curve analysis and nomogram manifested that the risk model had the high predictive ability and was more sensitive than general clinical features. Furthermore, compared with the high-risk group, the low-risk group had higher TMB and a longer 5-year survival period. In the immune microenvironment of GC, there were also differences in immune function and highly infiltrated immune cells between the two risk groups.Conclusions: The prognostic risk model based on the six genes associated with ferroptosis and iron-metabolism has a good performance for predicting the prognosis of patients with GC. The treatment of cancer by inducing tumor ferroptosis or mediating tumor iron-metabolism, especially combined with immunotherapy, provides a new possibility for individualized treatment of GC patients.


Stroke ◽  
2021 ◽  
Author(s):  
Michiel H.F. Poorthuis ◽  
Reinier A.R. Herings ◽  
Kirsten Dansey ◽  
Johanna A.A. Damen ◽  
Jacoba P. Greving ◽  
...  

Background and Purpose: The net benefit of carotid endarterectomy (CEA) is determined partly by the risk of procedural stroke or death. Current guidelines recommend CEA if 30-day risks are <6% for symptomatic stenosis and <3% for asymptomatic stenosis. We aimed to identify prediction models for procedural stroke or death after CEA and to externally validate these models in a large registry of patients from the United States. Methods: We conducted a systematic search in MEDLINE and EMBASE for prediction models of procedural outcomes after CEA. We validated these models with data from patients who underwent CEA in the American College of Surgeons National Surgical Quality Improvement Program (2011–2017). We assessed discrimination using C statistics and calibration graphically. We determined the number of patients with predicted risks that exceeded recommended thresholds of procedural risks to perform CEA. Results: After screening 788 reports, 15 studies describing 17 prediction models were included. Nine were developed in populations including both asymptomatic and symptomatic patients, 2 in symptomatic and 5 in asymptomatic populations. In the external validation cohort of 26 293 patients who underwent CEA, 702 (2.7%) developed a stroke or died within 30-days. C statistics varied between 0.52 and 0.64 using all patients, between 0.51 and 0.59 using symptomatic patients, and between 0.49 to 0.58 using asymptomatic patients. The Ontario Carotid Endarterectomy Registry model that included symptomatic status, diabetes, heart failure, and contralateral occlusion as predictors, had C statistic of 0.64 and the best concordance between predicted and observed risks. This model identified 4.5% of symptomatic and 2.1% of asymptomatic patients with procedural risks that exceeded recommended thresholds. Conclusions: Of the 17 externally validated prediction models, the Ontario Carotid Endarterectomy Registry risk model had most reliable predictions of procedural stroke or death after CEA and can inform patients about procedural hazards and help focus CEA toward patients who would benefit most from it.


2021 ◽  
Vol 28 (3) ◽  
pp. 2029-2039
Author(s):  
Camille Tessier ◽  
Thomas Allard ◽  
Jean-Samuel Boudreault ◽  
Rayan Kaedbey ◽  
Vincent Éthier ◽  
...  

Background—smoldering multiple myeloma (SMM) risk of progression to multiple myeloma (MM) is highly heterogeneous and several models have been suggested to predict this risk. Lakshman et al. recently proposed a model based on three biomarkers: bone marrow plasma cell (BMPC) percentage > 20%, free light chain ratio (FLCr) > 20 and serum M protein > 20 g/L. The goal of our study was to test this “20/20/20” model in our population and to determine if similar results could be obtained in another cohort of SMM patients. Method—we conducted a retrospective, single center study with 89 patients diagnosed with SMM between January 2008 and December 2019. Results—all three tested biomarkers were associated with an increased risk of progression: BMPC percentage ≥ 20% (hazard ratio [HR]: 4.28 [95%C.I., 1.90–9.61]; p < 0.001), serum M protein ≥ 20 g/L (HR: 4.20 [95%C.I., 1.90–15.53]; p = 0.032) and FLCr ≥ 20 (HR: 3.25 [95%C.I., 1.09–9.71]; p = 0.035). The estimated median time to progression (TTP) was not reached for the low and intermediate risk groups and was 29.1 months (95%C.I., 3.9–54.4) in the high-risk group (p = 0.006). Conclusions—the 20/20/20 risk stratification model adequately predicted progression in our population and is easy to use in various clinical settings.


2011 ◽  
Vol 19 (4) ◽  
pp. 874-884 ◽  
Author(s):  
Maria F Hughes ◽  
Olli Saarela ◽  
Stefan Blankenberg ◽  
Tanja Zeller ◽  
Aki S Havulinna ◽  
...  

Aims: We assessed whether a cardiovascular risk model based on classic risk factors (e.g. cholesterol, blood pressure) could refine disease prediction if it included novel biomarkers (C-reactive protein, N-terminal pro-B-type natriuretic peptide, troponin I) using a decision curve approach which can incorporate clinical consequences. Methods and results: We evaluated whether a model including biomarkers and classic risk factors could improve prediction of 10 year risk of cardiovascular disease (CVD; chronic heart disease and ischaemic stroke) against a classic risk factor model using a decision curve approach in two prospective MORGAM cohorts. This included 7739 men and women with 457 CVD cases from the FINRISK97 cohort; and 2524 men with 259 CVD cases from PRIME Belfast. The biomarker model improved disease prediction in FINRISK across the high-risk group (20⊟40%) but not in the intermediate risk group, at the 23% risk threshold net benefit was 0.0033 (95% CI 0.0013−0.0052). However, in PRIME Belfast the net benefit of decisions guided by the decision curve was improved across intermediate risk thresholds (10⊟20%). At pt = 10% in PRIME, the net benefit was 0.0059 (95% CI 0.0007⊟0.0112) with a net increase in 6 true positive cases per 1000 people screened and net decrease of 53 false positive cases per 1000 potentially leading to 5% fewer treatments in patients not destined for an event. Conclusion: The biomarker model improves 10-year CVD prediction at intermediate and high-risk thresholds and in particular, could be clinically useful at advising middle-aged European males of their CVD risk.


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