Propensity score matching for estimating a marginal hazard ratio.

Propensity score matching is commonly used to draw causal inference from observational survival data. However, its asymptotic properties have yet to be established, and variance estimation is still open to debate. We derive the statistical properties of the propensity score matching estimator of the marginal causal hazard ratio based on matching with replacement and a fixed number of matches. We also propose a double-resampling technique for variance estimation that takes into account the uncertainty due to propensity score estimation prior to matching.

bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens.

Summary: CRISPR-Cas9 and shRNA high-throughput sequencing screens have abundant applications for basic and translational research. Methods and tools for the analysis of these screens must properly account for sequencing error, resolve ambiguous mappings among similar sequences in the barcode library in a statistically principled manner, and be computationally efficient. Herein we present bcSeq, an open source R package that implements a fast and parallelized algorithm for mapping high-throughput sequencing reads to a barcode library while tolerating sequencing error. The algorithm uses a Trie data structure for speed and resolves ambiguous mappings by using a statistical sequencing error model based on Phred scores for each read. Availability and implementation: The package source code and an accompanying tutorial are available at http://bioconductor.org/packages/bcSeq/. Supplementary information: Supplementary data are available at Bioinformatics online.

Association Between Left Atrial Appendage Occlusion and Readmission for Thromboembolism Among Patients With Atrial Fibrillation Undergoing Concomitant Cardiac Surgery.

Importance: The left atrial appendage is a key site of thrombus formation in atrial fibrillation (AF) and can be occluded or removed at the time of cardiac surgery. There is limited evidence regarding the effectiveness of surgical left atrial appendage occlusion (S-LAAO) for reducing the risk of thromboembolism. Objective: To evaluate the association of S-LAAO vs no receipt of S-LAAO with the risk of thromboembolism among older patients undergoing cardiac surgery. Design, Setting, and Participants: Retrospective cohort study of a nationally representative Medicare-linked cohort from the Society of Thoracic Surgeons Adult Cardiac Surgery Database (2011-2012). Patients aged 65 years and older with AF undergoing cardiac surgery (coronary artery bypass grafting [CABG], mitral valve surgery with or without CABG, or aortic valve surgery with or without CABG) with and without concomitant S-LAAO were followed up until December 31, 2014. Exposures: S-LAAO vs no S-LAAO. Main Outcomes and Measures: The primary outcome was readmission for thromboembolism (stroke, transient ischemic attack, or systemic embolism) at up to 3 years of follow-up, as defined by Medicare claims data. Secondary end points included hemorrhagic stroke, all-cause mortality, and a composite end point (thromboembolism, hemorrhagic stroke, or all-cause mortality). Results: Among 10 524 patients undergoing surgery (median age, 76 years; 39% female; median CHA2DS2-VASc score, 4), 3892 (37%) underwent S-LAAO. Overall, at a mean follow-up of 2.6 years, thromboembolism occurred in 5.4%, hemorrhagic stroke in 0.9%, all-cause mortality in 21.5%, and the composite end point in 25.7%. S-LAAO, compared with no S-LAAO, was associated with lower unadjusted rates of thromboembolism (4.2% vs 6.2%), all-cause mortality (17.3% vs 23.9%), and the composite end point (20.5% vs 28.7%) but no significant difference in rates of hemorrhagic stroke (0.9% vs 0.9%). After inverse probability-weighted adjustment, S-LAAO was associated with a significantly lower rate of thromboembolism (subdistribution hazard ratio [HR], 0.67; 95% CI, 0.56-0.81; P < .001), all-cause mortality (HR, 0.88; 95% CI, 0.79-0.97; P = .001), and the composite end point (HR, 0.83; 95% CI, 0.76-0.91; P < .001) but not hemorrhagic stroke (subdistribution HR, 0.84; 95% CI, 0.53-1.32; P = .44). S-LAAO, compared with no S-LAAO, was associated with a lower risk of thromboembolism among patients discharged without anticoagulation (unadjusted rate, 4.2% vs 6.0%; adjusted subdistribution HR, 0.26; 95% CI, 0.17-0.40; P < .001), but not among patients discharged with anticoagulation (unadjusted rate, 4.1% vs 6.3%; adjusted subdistribution HR, 0.88; 95% CI, 0.56-1.39; P = .59). Conclusions and Relevance: Among older patients with AF undergoing concomitant cardiac surgery, S-LAAO, compared with no S-LAAO, was associated with a lower risk of readmission for thromboembolism over 3 years. These findings support the use of S-LAAO, but randomized trials are necessary to provide definitive evidence.

On the establishment of equivalence acceptance criterion in analytical similarity assessment.

For the assessment of biosimilarity of biosimilar products, the United States (US) Food and Drug Administration (FDA) proposed a stepwise approach for providing the totality-of-the-evidence of similarity between a proposed biosimilar product and a US-licensed (reference) product. The stepwise approach starts with the assessment of critical quality attributes (CQAs) that are relevant to clinical outcomes in structural and functional characterization in the manufacturing process of the proposed biosimilar product. FDA suggests that these critical quality relevant attributes be identified and classified into three tiers depending on their criticality or risk ranking. To assist the sponsors, FDA also suggests some statistical approaches for the assessment of analytical similarity for CQAs from different tiers, namely equivalence test for Tier 1, quality range approach for Tier 2, and descriptive raw data and graphical comparison for Tier 3. Analytical similarity assessment for CQAs in Tier 1 is performed based on the equivalence acceptance criterion (EAC), which depends upon the estimate of variability of the reference product. The FDA's recommended approach often underestimates the variability of the reference product because it does not take the worst possible lots into consideration. In this article, we examine the statistical properties of the FDA's recommended approach and proposed alternative methods in establishing an alternative approach under the scenario where multiple samples drew from each lot.

Use of left atrial appendage occlusion among older cardiac surgery patients with preoperative atrial fibrillation: a national cohort study.

PURPOSE: Patients with atrial fibrillation (AF) undergoing cardiac surgery are at substantially increased risk for stroke. Increasing evidence has suggested that surgical left atrial appendage occlusion (S-LAAO) may have the potential to substantially mitigate this stroke risk; however, S-LAAO is performed in a minority of patients with AF undergoing cardiac surgery. We sought to identify factors associated with usage of S-LAAO. METHODS: In a nationally-representative, contemporary cohort (07/2011-06/2012) of older patients undergoing cardiac surgery with preoperative AF (n = 11,404) from the Medicare-linked Society of Thoracic Surgeons Adult Cardiac Surgery Database, we evaluated patient and hospital characteristics associated with S-LAAO use by employing logistic and linear regression models. RESULTS: In this cohort (average age, 76 years; 39% female), 4177 (37%) underwent S-LAAO. Neither S-LAAO nor discharge anticoagulation was used in 25% ("unprotected" patients). The overall propensity for S-LAAO decreased significantly with increasing CHA2DS2-VASc (congestive heart failure; hypertension; age 75 years or older; diabetes mellitus; stroke, transient ischemic attack, or thromboembolism; vascular disease; age 65 to 74 years; sex category (female)) score (ptrend < 0.001). There was substantial variability in S-LAAO use across geographic regions, and S-LAAO was more commonly performed at academic and higher-volume valve surgery centers. CONCLUSIONS: Substantial variability in use of S-LAAO exists. In many instances, the procedure is being deferred in the patients that may be poised to benefit the most (i.e., those with increased CHA2DS2-VASc score-defined stroke risk).

Asparaginase-induced hepatotoxicity: rapid development of cholestasis and hepatic steatosis.

BACKGROUND: L-Asparaginase is a bacterial enzyme used in the treatment of acute lymphoblastic leukemia. In the ongoing U.S. Drug-Induced Liver Injury Network (DILIN) prospective study, standard and pegylated asparaginase were the most frequent cause of liver injury with jaundice among anti-cancer agents (8 of 40: 20%). The unique features of this hepatotoxicity are described. METHODS: Eight cases from 5 DILIN centers were reviewed for clinical course, laboratory values, imaging, and histopathology. RESULTS: Seven females, aged 29-59 years, and one 8-year-old boy, all with leukemia, developed jaundice within 9-21 days (median 15 days) of starting asparaginase or pegaspargase, during the first (n = 6) or second (n = 2) cycle. Prominent symptoms were jaundice (n = 8), fatigue (6), abdominal pain (6) but rarely pruritus (1). Initial median ALT level was 284 U/L (range 83-1076), Alk P 159 U/L (64-452), and bilirubin 4.4 mg/dL (3.7-8.4). Bilirubin levels rose thereafter in all patients to median peak of 17.5 mg/dL (11.7-25.7), INR rose to 1.1-1.7 and serum albumin fell to 1.5-2.6 g/dL. Hepatic imaging revealed fatty liver in all patients. Liver biopsy showed steatosis but minimal hepatocyte necrosis. One patient restarted on pegaspargase re-developed less severe injury. CONCLUSION: Asparaginase is a common cause of antineoplastic-induced liver injury with jaundice, typically with short latency, marked steatosis, and prolonged jaundice, which can lead to delays in antileukemic therapy. The cause of injury is likely direct inhibition of hepatic protein synthesis caused by asparagine depletion.