Search PubMed⌕ Search

Biomedical subjects

Ruyun Jin

Publications and source records attributed to Ruyun Jin.

12 recordsLinked to original sources
PubMed2026

Next-Generation Sequencing Completion and Timeliness Using a Reflex Testing Protocol for Patients with Stage II to IV Nonsquamous Non-Small Cell Lung Cancer.

BACKGROUND: Next-generation Sequencing (NGS) is critical for providing treatment recommendations across multiple stages of non-small cell lung cancer (NSCLC). However, a substantial proportion of patients do not undergo testing. This study evaluated the completion rates and timeliness of NGS in patients with stage II to IV NSCLC at a single academic institution with a reflex NGS testing protocol. METHODS: Patients with stage II to IV nonsquamous NSCLC (ns-NSCLC) diagnosed between 2015 and 2022 were identified retrospectively. A reflex, tissue-based testing protocol was initiated in 2015 using in-house NGS. Pyrosequencing was performed if NGS failed. RESULTS: 501 patients were included: 75 (15.0%) with stage II, 82 (16.4%) with stage III, and 344 (68.6%) with stage IV ns-NSCLC. Tissue NGS was completed in 380 (75.8%) patients and 465 (92.8%) completed some tissue-based genomic testing when including pyrosequencing. Median time from biopsy to NGS was 17.0 days (range, 6-61 days). 61.0% of patients had NGS results prior to a first treatment of any type and 88.4% had tissue NGS results prior to systemic therapy. Among stage IV patients with completed NGS, median overall survival was 2.27 years for patients with NGS results prior to first treatment compared to 1.08 years for patients without NGS results prior to treatment initiation (P = .04). CONCLUSIONS: Implementation of an in-house, reflex NGS testing protocol enabled rapid genomic profiling in a high proportion of patients with stage II to IV ns-NSCLC. NGS completion prior to receiving first-line therapy was associated with improved survival compared to completion after first line treatment in stage IV patients.

Humans↗
PubMed2006

Time-related risk of the St. Jude Silzone heart valve.

OBJECTIVE: The St. Jude Medical Silzone heart valve had a silver-impregnated sewing ring designed to reduce the incidence of prosthetic valve endocarditis. Recruitment to the randomized AVERT study comparing Silzone valves with non-Silzone Control valves was stopped because of an increased risk of reoperation for paravalvular leak, but patient follow-up continues. Determining the time-related risk profile of the Silzone valve is important for helping physicians manage the approximately 28,000 patients currently alive with a Silzone valve. METHODS: Between 1998 and 2000, 403 Silzone and 404 Control patients were enrolled in AVERT. As of July 2005, there were 1819 Silzone and 1842 Control patient-years of follow-up (mean 4.5, median 5.1 years). Analysis emphasized the use and interpretation of hazard functions, since they are more meaningful than event-free percentages to currently surviving patients. To this end, instead of Cox regression, which estimates the hazard ratio, assuming it is constant over time, we employed primarily Aalen additive regression, which measures the hazard difference, and produces a plot of it over time. We assessed the risks of major paravalvular leak, endocarditis, bleeding and thrombo-embolism. RESULTS: The Silzone valve had a higher initial risk of major paravalvular leak than Control in the mitral (p=0.02) position, but not in the aortic (p=0.42) position. Analysis of this risk using additive regression, with all valve positions combined, showed that the initial risk due to Silzone lost statistical significance by 2 years and disappeared by 4 years after implant. In the mitral position, the Silzone valve had a higher initial risk of thrombo-embolism plus bleeding than Control; this risk also lost statistical significance by 2 years and subsided to zero by 4 years. The risks for death and endocarditis were similar for Slizone and Control valves. CONCLUSIONS: The additional risks of the Silzone valve, compared to Control, diminish over time and disappear by 4 years after implant. The minimum time after implant of the patients currently alive with Silzone is now well beyond 5 years; thus, these current patients now have a risk profile similar to that of patients with a standard St. Jude valve.

Aged↗
PubMed2006

Validating the Clinical Outcomes Assessment Program risk model for percutaneous coronary intervention.

BACKGROUND: The Clinical Outcomes Assessment Program (COAP) from the state of Washington recently published a risk model for hospital mortality after percutaneous coronary intervention (PCI), which was validated by a consortium of hospitals in 4 northeastern states. The Providence Health System (PHS) Cardiovascular Study Group data was used to further validate this COAP model using data from PHS hospitals in 3 western states. METHODS: All 13124 consecutive PCI procedures performed in 6 PHS hospitals from July 2001 through June 2004 were included. The c index was used to test model discrimination. The Hosmer-Lemeshow test, the le Cessie-van Houwelingen-Copas test, and the cumulative sum method were used to test model calibration. RESULTS: The patient profiles of the COAP data and the PHS data were similar. The overall mortality was 1.6% for COAP and 1.4% for PHS. The subgroup mortalities were also similar. When applying the COAP model to the PHS data, the c index (95% CI) was 0.893 (0.859-0.928), indicating excellent discrimination, and the le Cessie-van Houwelingen-Copas test and the cumulative sum method showed good global goodness of fit. CONCLUSION: The COAP model for hospital mortality was successfully validated using PHS data. With the advance of technology and changing patient profile, PCI models must be periodically checked for possible updating to reflect contemporary practice. Predictors in a PCI risk model should be objective, have standard definitions, and be easy to obtain to facilitate the transportability of the model.

Adult↗
PubMed2006

Homograft implantation techniques in the aortic position: to preserve or replace the aortic root?

BACKGROUND: One determinant of durability of the homograft in the aortic position is the implantation technique. This study uses meta-analytical techniques to evaluate the differences in early and long-term outcomes of patients undergoing aortic homograft implantation with either a root replacement or a root preserving technique. METHODS: A systematic review of the literature (1965-2005) reporting results after homograft implantation in the aortic position with emphasis in the implantation technique was performed. Random and fixed-effects models were used. Cumulative and influential meta-analysis, graphic exploration, and sensitivity analysis were carried out to explain the heterogeneity between studies and to investigate potential publication bias. RESULTS: Eleven studies were included. None of the studies was randomized. There was no significant difference in early mortality between root replacement and root preserving groups (odds ratio = 2.57 with 95% confidence interval [CI] 0.68-9.72 in random-effects model) and the root replacement group had a significantly lower rate of reoperation during long-term follow-up (hazard ratio = 0.55 with 95% CI 0.38-0.80 in random-effects model). Subgroup analysis focusing on patients having the subcoronary technique for homograft implantation showed similar results. Significant heterogeneity between studies can be detected. No publication bias was found. CONCLUSIONS: There was no significant difference in early mortality between root replacement and root preserving groups. However, the root replacement technique group had a significantly lower rate of reoperation during long-term follow-up. Excluding outliers identified in a funnel plot reduced the heterogeneity and reached a similar conclusion.

Aortic Valve↗
PubMed2006

Prosthetic heart valves: Objective Performance Criteria versus randomized clinical trial.

The current Food and Drug Administration (FDA) heart valve guidance document uses an objective performance criteria (OPC) methodology to evaluate the clinical performance of prosthetic heart valves. OPC are essentially historical controls, but they have turned out to be an adequate, and perhaps optimal, study design in this situation. Heart valves have a simple open-and-close mechanism, device effectiveness is easy to document, and the common complications (thromboembolism, thrombosis, bleeding, leak, and infection) are well known and easily detected. Thus, randomized clinical trials (RCTs) have not been deemed necessary for the regulatory approval of prosthetic heart valves. The OPC are derived from the average complication rates of all approved heart valves. Studies based on OPC have been shown to work well; many different valve models have gained FDA market approval based on this methodology. Although heart valve RCTs are not required by the FDA, they have been done to compare valves or treatment regimens after approval. Recently, the Artificial Valve Endocarditis Reduction Trial (AVERT) was designed to compare a new Silzone sewing ring, designed to reduce infection, with the Standard sewing ring on a St. Jude Medical heart valve. This was the largest heart valve RCT ever proposed (4,400 valve patients, followed for as long as 4 years), but it was stopped prematurely because of a high leak rate associated with the Silzone valve. Examining the results showed that a much smaller, OPC-based study with 800 patient-years would have been sufficient to disclose this complication of the Silzone valve.

Bayes Theorem↗
PubMed2005

Aborted off-pump coronary artery bypass patients have much worse outcomes than on-pump or successful off-pump patients.

BACKGROUND: Off-pump coronary artery bypass graft (CABG) surgery is purported to reduce perioperative mortality and morbidity compared with on-pump coronary bypass graft surgery. However, the outcomes of patients for whom an off-pump strategy must be changed to an on-pump procedure during surgery have not been extensively studied. METHODS AND RESULTS: The Merged Cardiac Registry (Health Data Research, Inc) contains 70 514 isolated CABG performed from January 1998 to March 2004 in 40 facilities. Among them, 62 634 patients begun and completed on-pump bypass (CPB); 7880 patients begun off-pump, of which 7424 (94.2%) completed off-pump coronary artery bypass (OPCAB), whereas 456 (5.8%) were converted to on-pump (CONVERT). CONVERT patients were more severely ill. The observed mortality of CONVERT, CPB, and OPCAB was 9.9%, 3.0%, and 1.6%, respectively, and the observed-to-predicted ratio was 2.77, 1.20, and 0.74, respectively. CONVERT also had more morbidity than either OPCAB or CPB. Finally, a risk model was created to identify patients who might be at risk for conversion from off-pump to on-pump CABG. CONCLUSIONS: Patients who are intended for an off-pump strategy and then require conversion to on-pump have significantly higher operative mortality and morbidity than either completed OPCAB or CPB patients. In addition, the operative mortality and morbidity are far in excess of that predicted preoperatively. Based on these results, strong consideration should be given for a planned strategy of CPB for those patients with preoperative hemodynamic instability requiring a salvage CABG operation, left ventricular hypertrophy, or previous CABG.

Aged↗
PubMed2005

Is obesity a risk factor for mortality in coronary artery bypass surgery?

BACKGROUND: The published articles examining obesity and CABG surgery contain conflicting results about the role of body mass index (BMI) as a risk factor for in-hospital mortality. METHODS AND RESULTS: We studied 16 218 patients who underwent isolated CABG in the Providence Health System Cardiovascular Study Group database from 1997 to 2003. The effect of BMI on in-hospital mortality was assessed by logistic regression, with BMI group (underweight, normal, overweight, and 3 subgroups of obesity) as a categorical variable or transformations, including fractional polynomials, of BMI as a continuous variable. BMI was not a statistically significant risk factor for mortality in any of these assessments. However, using cumulative sum techniques, we found that the lowest risk-adjusted CABG in-hospital mortality was in the high-normal and that overweight BMI subgroup patients with lower or higher BMI had slightly increased mortality. CONCLUSIONS: Body size is not a significant risk factor for CABG mortality, but the lowest mortality is found in the high-normal and overweight subgroups compared with obese and underweight.

Aged↗
PubMed2005

Validation and refinement of mortality risk models for heart valve surgery.

BACKGROUND: The Northern New England Cardiovascular Disease Study Group (NNE) recently published risk models for hospital mortality after heart valve surgery. The Providence Health System Cardiovascular Study Group (PHS) has been collecting similar heart valve data for 8 years, providing an ideal opportunity to both validate the NNE risk models and attempt to produce an improved model, by using some different modeling techniques. METHODS: From 1997 to 2004, 3,324 patients aged 30 to 95 years underwent aortic valve replacement (AVR), and 1,596 underwent mitral valve replacement or repair (MVRR) at one of nine PHS medical centers. We used area under the receiver operating characteristic curve (c-index) to measure model discrimination, and Hosmer-Lemeshow statistic (H-L) to measure calibration. We modified the NNE models by ungrouping continuous variables, seeking optimal transformations of continuous variables, and imputing missing values by multiple regression. RESULTS: The prevalence and the lethality of risk factors were similar in PHS and NNE patients. The NNE models fit PHS patients well: c-index (95% confidence interval) = 0.75 (0.70 to 0.80) for AVR and 0.81 (0.76 to 0.86) for MVRR; H-L = 3.95 (p = 0.861) for AVR and 7.10 (p = 0.526) for MVRR. A single PHS model performed slightly better for both positions: c-index = 0.79 (0.75 to 0.83) for AVR and 0.84 (0.80 to 0.88) for MVRR; H-L = 2.75 (p = 0.949) for AVR and 12.21 (p = 0.142) for MVRR. CONCLUSIONS: The NNE models for aortic and mitral valve surgery were successfully validated using PHS patients. Using some different statistical approaches to modeling, we produced a new, unified model for both positions.

Adult↗
PubMed2005

Additive vs. logistic risk models for cardiac surgery mortality.

OBJECTIVE: Logistic regression is most often used to produce a cardiac operative risk model. But the logistic equation requires a computer to solve. Thus, simple additive models have been derived from logistic models by adding the odds ratios or modified coefficients. However, this simplification has no statistical justification, and the additive scores do not equal the original logistic probabilities. METHODS: The EuroSCORE risk model is a very successful and widely used cardiac surgery risk model and it comes in both an additive and a full logistic version. We applied the EuroSCORE model to the 28,337 cardiac surgeries in the Providence Health System Cardiovascular Study Group database. The discrimination of the models was assessed by the c index. The comparison of the mortality predictions of the logistic and the additive model are mostly descriptive and graphical. RESULTS: Theoretical considerations would predict that the additive model greatly underestimates the risk for the higher risk patients, and clinical data confirm this fact. For the 23,463 (83%) cases with complete data, the predicted mortality was 8.3% by the logistic model and 5.4% by the additive model. The discrimination (c index) of the additive (0.794) and logistic (0.791) models was equally good. A modified additive score is proposed (the mean of the logistic predicted mortality for each original additive score) which could be provided as a look-up table along with the scoring sheet. CONCLUSIONS: The additive EuroSCORE gives excellent discrimination, as good as the logistic risk model, but it greatly underestimates the risk of high-risk patients, compared to the logistic. The logistic equation should be used to predicate the mortality when possible. If this is not feasible, a modified additive score could be employed at the bedside. But the logistic should always be used for comparison of providers and for research publications.

Cardiac Surgical Procedures↗
PubMed2002

Statistical analysis of heart valve outcomes.

Statistics is a rapidly growing field utilizing thousands of data analysis functions, though a relatively few are used in the majority of cardiac surgical studies. Dr. Wechsler recently published a list of the statistical terms which are important for cardiothoracic surgeons to be familiar with. These can be grouped into 3 categories: General concepts; Summary and test statistics; and Special techniques. The last category includes three techniques which are widely used to describe the long-term results of heart valve series: Hazard functions, Kaplan-Meier event-free curves, and "Actual" event-free curves. Some conclusions from a review of these techniques are: (1) an event with a non-constant hazard should not be described using "Linearized" rates (the Weibull distribution adds a parameter to accommodate changing hazard); (2) for non-fatal events, "Actual" analysis provides the true event probability, which the Kaplan-Meier overestimates. These methods are used in the analysis of published heart valve series to conclude that: (1) the wide scatter in complications rates with the same valve models implicates factors other than the valve; (2) the earliest porcine series had low mean ages and low durability compared with later series.

Heart Valve Diseases↗