Procrustes is a machine-learning approach that removes cross-platform batch effects from clinical RNA sequencing data.

With the increased use of gene expression profiling for personalized oncology, optimized RNA sequencing (RNA-seq) protocols and algorithms are necessary to provide comparable expression measurements between exome capture (EC)-based and poly-A RNA-seq. Here, we developed and optimized an EC-based protocol for processing formalin-fixed, paraffin-embedded samples and a machine-learning algorithm, Procrustes, to overcome batch effects across RNA-seq data obtained using different sample preparation protocols like EC-based or poly-A RNA-seq protocols. Applying Procrustes to samples processed using EC and poly-A RNA-seq protocols showed the expression of 61% of genes (N = 20,062) to correlate across both protocols (concordance correlation coefficient > 0.8, versus 26% before transformation by Procrustes), including 84% of cancer-specific and cancer microenvironment-related genes (versus 36% before applying Procrustes; N = 1,438). Benchmarking analyses also showed Procrustes to outperform other batch correction methods. Finally, we showed that Procrustes can project RNA-seq data for a single sample to a larger cohort of RNA-seq data. Future application of Procrustes will enable direct gene expression analysis for single tumor samples to support gene expression-based treatment decisions.

The intersection of nonsuicidal self-injury and suicide-related behavior: Patterns of elevated risk and implications for college mental health.

OBJECTIVE: To analyze the overlap of nonsuicidal self-injury (NSSI) and suicide-related behaviors (SRB) among college students with regard to demographics, mental health, and coping styles. PARTICIPANTS: Respondents were 572 undergraduate students at a southwestern public university. METHODS: Data were collected in 2015. Respondents completed a demographic survey and assessments of NSSI, SRB, internalizing symptoms (ie, anxiety, stress, and depression), aggression, and negative coping strategies. The survey was administered via a Web-based procedure. RESULTS: Women reported more frequent cutting behaviors than men. Endorsement of NSSI was also associated with an increased likelihood of lifetime SRB. A subgroup of students endorsing both NSSI and SRB demonstrated poorer mental health, more negative coping, and self-reported female sex. CONCLUSIONS: College healthcare providers may benefit from competency-based training in techniques for the combination treatment of NSSI and SRB, as well as culturally based models of suicide.