Analysis of overfitting in the regularized Cox model

The Cox proportional hazards model is ubiquitous in the analysis of time-to-event data. However, when the data dimension p is comparable to the sample size $N$, maximum likelihood estimates for its regression parameters are known to be biased or break down entirely due to overfitting. This prompted the introduction of the so-called regularized Cox model. In this paper we use the replica method from statistical physics to investigate the relationship between the true and inferred regression parameters in regularized multivariate Cox regression with L2 regularization, in the regime where both p and N are large but with p/N ~ O(1). We thereby generalize a recent study from maximum likelihood to maximum a posteriori inference. We also establish a relationship between the optimal regularization parameter and p/N, allowing for straightforward overfitting corrections in time-to-event analysis

Prompt Agalsidase Alfa Therapy Initiation is Associated with Improved Renal and Cardiovascular Outcomes in a Fabry Outcome Survey Analysis

BACKGROUND: The timing of enzyme replacement therapy initiation in patients with Fabry disease is hypothesized to be critical. In this study, we used Fabry Outcome Survey data to assess the impact of prompt versus delayed initiation of treatment with agalsidase alfa on cardiovascular and renal events in patients with Fabry disease. METHODS: Available genetic data at baseline were used to define patients with mutations associated with classical versus late-onset Fabry disease. Time to cardiovascular or renal events, from treatment initiation until 120 months, was compared for patients in prompt versus delayed groups. “Prompt” was defined as treatment initiation < 24 months from symptom onset (analysis A) or diagnosis (analysis B), and “delayed” was defined as ≥ 24 months from symptom onset (analysis A) or diagnosis (analysis B). Kaplan–Meier curves and Log rank tests compared event-free probabilities and time to first event. Multivariate Cox regression estimated hazard ratios (HRs). RESULTS: Analysis by time from symptom onset included 1374 patients (172 prompt, 1202 delayed). In a multivariate Cox regression analysis, prompt versus delayed treatment initiation significantly reduced the probability of cardiovascular (HR=0.62; P< 0.001) and renal (HR=0.57; P=0.001) events. History of cardiovascular or renal events was associated with increased risk of respective events. Analysis by time from diagnosis included 2051 patients (1006 prompt, 1045 delayed). In a multivariate Cox regression analysis, prompt treatment initiation significantly reduced the probability of cardiovascular events (HR=0.83; P=0.003) after adjusting for history of cardiovascular events, sex, and age at treatment initiation. Univariate analysis showed that the probability of renal events was significantly lower in the prompt group (P=0.018); this finding was attenuated in the multivariate Cox regression analysis. CONCLUSIONS: This analysis suggests that prompt treatment initiation with agalsidase alfa provided better renal and cardiovascular outcomes than delayed treatment in patients with Fabry disease

Determinants of healthcare utilisation and predictors of outcome in colorectal cancer patients from Northern Iran

We aimed to assess healthcare utilisation (HU), its determinants, as well as its relationship with survival in colorectal cancer (CRC) patients. This study was conducted on incident CRC cases from Northern Iran. Information on HU was collected using a valid questionnaire, considering eight diagnostic and four therapeutic services. The results were categorised as good and poor HU. Multivariate logistic regression analysis was used to assess the relationship between HU and other variables. Cox regression analysis was performed to determine major predictors of survival. In total, 227 new cases of CRC were enrolled. HU could be assessed in 218 subjects (96). Living in rural areas was the strongest variable related to poor HU (adjusted OR, odds ratio=2.65; CI, confidence interval: 1.30-5.40). The median survival time was 40.5months. The 1-, 3- and 5-year survival rates were 71, 52 and 44 respectively. Cox regression analysis showed a significant lower survival rate in patients with poor HU (HR=2.3; CI: 1.46-3.64). HU was an independent predictor of survival in our CRC patients. Patients' place of residence was a significant determinant of HU. Regarding its effects on patients' outcome, HU and its determinants should be considered in designing CRC controlling programmes in our region and similar high-risk populations. © 2016 John Wiley & Sons Ltd

Circular RNAs in Clear Cell Renal Cell Carcinoma: Their Microarray-Based Identification, Analytical Validation, and Potential Use in a Clinico-Genomic Model to Improve Prognostic Accuracy

Circular RNAs (circRNAs) may act as novel cancer biomarkers. However, a genome-wide evaluation of circRNAs in clear cell renal cell carcinoma (ccRCC) has yet to be conducted. Therefore, the objective of this study was to identify and validate circRNAs in ccRCC tissue with a focus to evaluate their potential as prognostic biomarkers. A genome-wide identification of circRNAs in total RNA extracted from ccRCC tissue samples was performed using microarray analysis. Three relevant differentially expressed circRNAs were selected (circEGLN3, circNOX4, and circRHOBTB3), their circular nature was experimentally confirmed, and their expression-along with that of their linear counterparts-was measured in 99 malignant and 85 adjacent normal tissue samples using specifically established RT-qPCR assays. The capacity of circRNAs to discriminate between malignant and adjacent normal tissue samples and their prognostic potential (with the endpoints cancer-specific, recurrence-free, and overall survival) after surgery were estimated by C-statistics, Kaplan-Meier method, univariate and multivariate Cox regression analysis, decision curve analysis, and Akaike and Bayesian information criteria. CircEGLN3 discriminated malignant from normal tissue with 97% accuracy. We generated a prognostic for the three endpoints by multivariate Cox regression analysis that included circEGLN3, circRHOBT3 and linRHOBTB3. The predictive outcome accuracy of the clinical models based on clinicopathological factors was improved in combination with this circRNA-based signature. Bootstrapping as well as Akaike and Bayesian information criteria confirmed the statistical significance and robustness of the combined models. Limitations of this study include its retrospective nature and the lack of external validation. The study demonstrated the promising potential of circRNAs as diagnostic and particularly prognostic biomarkers in ccRCC patients

A new method to analyse the pace of child development: Cox regression validated by a bootstrap resampling procedure

<p>Abstract</p> <p>Background</p> <p>Various perinatal factors influencing neuromotor development are known from cross sectional studies. Factors influencing the age at which distinct abilities are acquired are uncertain. We hypothesized that the Cox regression model might identify these factors.</p> <p>Methods</p> <p>Neonates treated at Aachen University Hospital in 2000/2001 were identified retrospectively (n = 796). Outcome data, based on a structured interview, were available from 466 children, as were perinatal data. Factors possibly related to outcome were identified by bootstrap selection and then included into a multivariate Cox regression model. To evaluate if the parental assessment might change with the time elapsed since birth we studied five age cohorts of 163 normally developed children.</p> <p>Results</p> <p>Birth weight, gestational age, congenital cardiac disease and periventricular leukomalacia were related to outcome in the multivariate analysis (p < 0.05). Analysis of the control cohorts revealed that the parents' assessment of the ability of bladder control is modified by the time elapsed since birth.</p> <p>Conclusions</p> <p>Combined application of the bootstrap resampling procedure and multivariate Cox regression analysis effectively identifies perinatal factors influencing the age at which distinct abilities are acquired. These were similar as known from previous cross sectional studies. Retrospective data acquistion may lead to a bias because the parental memories change with time. This recommends applying this statistical approach in larger prospective trials.</p

The predictive role of NLR and PLR for solid non-AIDS defining cancer incidence in HIV-infected subjects: a MASTER cohort study

Patients’ characteristics according to lost to follow-up at 3-years. Table S2. Distribution of non-AIDS defining cancer. Table S3. Multivariate analysis: time dependent Cox regression model. Variables included in the full model. (DOCX 20 kb

Polusi Udara dalam Ruangan dan Kejadian Kardiometabolik di Indonesia: Analisis Data Indonesian Family Life Survey (IFLS)

Indoor air pollution and cardiometabolic diseases in Indonesia: an Indonesian Family Life Survey (IFLS) analysis PurposeThe purpose of this study was to determine the relationship between indoor air pollution due to the use of firewood with cardiometabolic disease.MethodsThis research was a prospective cohort study conducted by comparing secondary data of the Indonesian Family Life Survey (IFLS) 2 to IFLS 5. Bivariate analysis used logistic regression and simple Cox regression tests. Multivariate analysis used Cox regression tests.ResultsResults showed exposure to air pollution due to the use of firewood accelerated the incidence of diabetes mellitus by 1.32 times, after controlling for the variables of smoking status, education level, body mass index, waist circumference, and domicile areas. The use of firewood was not correlated to the rate of onset of cardiovascular disease such as CHD and stroke.ConclusionThis research recommends LPG as a replacement fuel

Urinary proteomics for prediction of mortality in patients with type 2 diabetes and microalbuminuria

Background: The urinary proteomic classifier CKD273 has shown promise for prediction of progressive diabetic nephropathy (DN). Whether it is also a determinant of mortality and cardiovascular disease in patients with microalbuminuria (MA) is unknown. Methods: Urine samples were obtained from 155 patients with type 2 diabetes and confirmed microalbuminuria. Proteomic analysis was undertaken using capillary electrophoresis coupled to mass spectrometry to determine the CKD273 classifier score. A previously defined CKD273 threshold of 0.343 for identification of DN was used to categorise the cohort in Kaplan–Meier and Cox regression models with all-cause mortality as the primary endpoint. Outcomes were traced through national health registers after 6 years. Results: CKD273 correlated with urine albumin excretion rate (UAER) (r = 0.481, p = &lt;0.001), age (r = 0.238, p = 0.003), coronary artery calcium (CAC) score (r = 0.236, p = 0.003), N-terminal pro-brain natriuretic peptide (NT-proBNP) (r = 0.190, p = 0.018) and estimated glomerular filtration rate (eGFR) (r = 0.265, p = 0.001). On multivariate analysis only UAER (β = 0.402, p &lt; 0.001) and eGFR (β = − 0.184, p = 0.039) were statistically significant determinants of CKD273. Twenty participants died during follow-up. CKD273 was a determinant of mortality (log rank [Mantel-Cox] p = 0.004), and retained significance (p = 0.048) after adjustment for age, sex, blood pressure, NT-proBNP and CAC score in a Cox regression model. Conclusion: A multidimensional biomarker can provide information on outcomes associated with its primary diagnostic purpose. Here we demonstrate that the urinary proteomic classifier CKD273 is associated with mortality in individuals with type 2 diabetes and MA even when adjusted for other established cardiovascular and renal biomarkers

Ventriculoperitoneal Shunt Outcomes among Infants

Ventriculoperitoneal shunts (VPSs) are used for the treatment of hydrocephalus. Here we analyzed the outcomes of VPS placements in 24 infants to determine the risk factors for shunt failure. The infants had undergone the initial VPS operation in our hospital between March 2005 and December 2013. They were observed until the end of January 2014. We obtained Kaplan-Meier curves and performed a multivariate Cox regression analysis of shunt failure. Of the 24 cases, the median (range) values for gestational age, birth weight, and birth head circumference (HC) were 37 (27-39) wks, 2,736 (686-3,788) g, and 35.3 (23.0-45.3) cm, respectively. The total number of shunt procedures was 45. Shunt failure rates were 0.51/shunt and 0.0053/shunt/year. Shunt infection rates were 0.13/shunt and 0.0014/shunt/year. The Kaplan-Meier analysis revealed an increased risk for shunt failure in infants ＜1 month old or in the HC ＞90ｵtile. The Cox regression analysis yielded hazard ratios (HRs) of 2.93 (95ｵ confidence interval (CI), 0.96-10.95, p＝0.059) for age ＜1 month, and 4.46 (95ｵCI:1.20-28.91,p＝0.023) for the HC ＞90ｵtile. The multivariate Cox regression analysis showed adjusted HRs of 17.56 (95ｵCI:2.69-202.8, p＝0.001) for age ＜1 month, and 2.95 (95ｵCI:0.52-24.84, p＝0.228) for the HC ＞90ｵtile. Our findings thus revealed that the risk factors for shunt failure in infants include age ＜1 month at the initial VPS placement