ReQTL: Identifying correlations between expressed SNVs and gene expression using RNA-sequencing data

This is the author accepted manuscript. The final version is available on open access from OUP via the DOI in this recordBy testing for associations between DNA genotypes and gene expression levels, expression quantitative trait locus (eQTL) analyses have been instrumental in understanding how thousands of single nucleotide variants (SNVs) may affect gene expression. As compared to DNA genotypes, RNA genetic variation represents a phenotypic trait that reflects the actual allele content of the studied system. RNA genetic variation at expressed SNV loci can be estimated using the proportion of alleles bearing the variant nucleotide (variant allele fraction, VAFRNA). VAFRNA is a continuous measure which allows for precise allele quantitation in loci where the RNA alleles do not scale with the genotype count. We describe a method to correlate VAFRNA to gene expression, and assess its ability to identify genetically regulated expression solely from RNA-sequencing (RNA-seq) datasets.We introduce ReQTL, an eQTL modification which substitutes the DNA allele count for the variant allele fraction at expressed SNV loci in the transcriptome (VAFRNA). We exemplify the method on sets of RNA-seq data from human tissues obtained though the Genotype-Tissue Expression Project (GTEx) and demonstrate that ReQTL analyses are computationally feasible and can identify a subset of expressed eQTL loci.A toolkit to perform ReQTL analyses is available at https://github.com/HorvathLab/ReQTL.Re_QTL_Supplementary_Data.zipMcCormick Genomic and Proteomic Center (MGPC), The George Washington UniversityNIH National Center for Advancing Translational Scienc

Outcomes after intra-aortic balloon pump insertion in cardiac surgery patients

Objective: To assess whether preoperative versus intraoperative insertion of an intra-aortic balloon pump is associated with lower 30-day mortality or reduced length of hospital stay among patients who had an intra-aortic balloon pump inserted for cardiac surgery. Methods: This was an observational study of patients who had an intraaortic balloon pump inserted in the preoperative or intraoperative period of cardiac surgery in our department between 2000 and 2012. We assessed the association between preoperative versus intraoperative insertion of an intra-aortic balloon pump and 30-day mortality in a multivariable logistic regression analysis, including preoperative New York Heart Association class, postoperative atrial fibrillation, reoperation, postoperative creatinine and isolated coronary bypass grafting as cofactors. We used a multivariate linear model to assess whether a preoperative versus intraoperative intra-aortic balloon pump was associated with length of postoperative hospital stay, adjusting for reoperation, isolated coronary bypass grafting, heart valve surgery, sex, age, cardiopulmonary bypass time, aortic cross-clamp time, preoperative patients' status (elective, urgency or emergency surgery) and preoperative myocardial infarction. Results: Overall, 7,540 consecutive patients underwent open heart surgery in our department, and an intra-aortic balloon pump was inserted pre- or intraoperatively in 322 (4.2%) patients. The mean age was 67 ± 10.2 years old, the 30-day mortality was 12.7%, and the median length of hospital stay was 9 days (7 - 13). Preoperative versus intraoperative intra-aortic balloon pump insertion did not affect the incidence of 30-day mortality (adjusted OR = 0.69; 95% CI, 0.15 - 3.12; p = 0.63) and length of postoperative hospital stay (β = 5.3; 95%CI, -1.6 to 12.8; p = 0.13). Conclusion: Preoperative insertion of an intra-aortic balloon pump was not associated with a lower 30- day mortality or reduced length of postoperative hospital stay compared to intraoperative insertion. © 2020 Associacao de Medicina Intensiva Brasileira - AMIB. All rights reserved