Transabdominal motor evoked potential neuromonitoring of lumbosacral spine surgery.

BACKGROUND CONTEXT: Transcranial Motor Evoked Potentials (TcMEPs) can improve intraoperative detection of femoral plexus and nerve root injury during lumbosacral spine surgery. However, even under ideal conditions, TcMEPs are not completely free of false-positive alerts due to the immobilizing effect of general anesthetics, especially in the proximal musculature. The application of transcutaneous stimulation to activate ventral nerve roots directly at the level of the conus medularis (bypassing the brain and spinal cord) has emerged as a method to potentially monitor the motor component of the femoral plexus and lumbosacral nerves free from the blunting effects of general anesthesia. PURPOSE: To evaluate the reliability and efficacy of transabdominal motor evoked potentials (TaMEPs) compared to TcMEPs during lumbosacral spine procedures. DESIGN: We present the findings of a single-center 12-month retrospective experience of all lumbosacral spine surgeries utilizing multimodality intraoperative neuromonitoring (IONM) consisting of TcMEPs, TaMEPs, somatosensory evoked potentials (SSEPs), electromyography (EMG), and electroencephalography. PATIENT SAMPLE: Two hundred and twenty patients having one, or a combination of lumbosacral spine procedures, including anterior lumbar interbody fusion (ALIF), lateral lumbar interbody fusion (LLIF), posterior spinal fusion (PSF), and/or transforaminal lumbar interbody fusion (TLIF). OUTCOME MEASURES: Intraoperative neuromonitoring data was correlated to immediate post-operative neurologic examinations and chart review. METHODS: Baseline reliability, false positive rate, true positive rate, false negative rate, area under the curve at baseline and at alerts, and detection of pre-operative deficits of TcMEPs and TaMEPs were compared and analyzed for statistical significance. The relationship between transcutaneous stimulation voltage level and patient BMI was also examined. RESULTS: TaMEPs were significantly more reliable than TcMEPs in all muscles except abductor hallucis. Of the 27 false positive alerts, 24 were TcMEPs alone, and 3 were TaMEPs alone. Of the 19 true positives, none were detected by TcMEPs alone, 3 were detected by TaMEPs alone (TcMEPs were not present), and the remaining 16 true positives involved TaMEPs and TcMEPs. TaMEPs had a significantly larger area under the curve (AUC) at baseline than TcMEPs in all muscles except abductor hallucis. The percent decrease in TcMEP and TaMEP AUC during LLIF alerts was not significantly different. Both TcMEPs and TaMEPs reflected three pre-existing motor deficits. Patient BMI and TaMEP stimulation intensity were found to be moderately positively correlated. CONCLUSIONS: These findings demonstrate the high reliability and predictability of TaMEPs and the potential added value when TaMEPs are incorporated into multimodality IONM during lumbosacral spine surgery.

Managing genomic variant calling workflows with Swift/T.

Bioinformatics research is frequently performed using complex workflows with multiple steps, fans, merges, and conditionals. This complexity makes management of the workflow difficult on a computer cluster, especially when running in parallel on large batches of data: hundreds or thousands of samples at a time. Scientific workflow management systems could help with that. Many are now being proposed, but is there yet the "best" workflow management system for bioinformatics? Such a system would need to satisfy numerous, sometimes conflicting requirements: from ease of use, to seamless deployment at peta- and exa-scale, and portability to the cloud. We evaluated Swift/T as a candidate for such role by implementing a primary genomic variant calling workflow in the Swift/T language, focusing on workflow management, performance and scalability issues that arise from production-grade big data genomic analyses. In the process we introduced novel features into the language, which are now part of its open repository. Additionally, we formalized a set of design criteria for quality, robust, maintainable workflows that must function at-scale in a production setting, such as a large genomic sequencing facility or a major hospital system. The use of Swift/T conveys two key advantages. (1) It operates transparently in multiple cluster scheduling environments (PBS Torque, SLURM, Cray aprun environment, etc.), thus a single workflow is trivially portable across numerous clusters. (2) The leaf functions of Swift/T permit developers to easily swap executables in and out of the workflow, which makes it easy to maintain and to request resources optimal for each stage of the pipeline. While Swift/T's data-level parallelism eliminates the need to code parallel analysis of multiple samples, it does make debugging more difficult, as is common for implicitly parallel code. Nonetheless, the language gives users a powerful and portable way to scale up analyses in many computing architectures. The code for our implementation of a variant calling workflow using Swift/T can be found on GitHub at https://github.com/ncsa/Swift-T-Variant-Calling, with full documentation provided at http://swift-t-variant-calling.readthedocs.io/en/latest/.

Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models.

An obstacle to validating and benchmarking methods for genome analysis is that there are few reference datasets available for which the "ground truth" about the mutational landscape of the sample genome is known and fully validated. Additionally, the free and public availability of real human genome datasets is incompatible with the preservation of donor privacy. In order to better analyze and understand genomic data, we need test datasets that model all variants, reflecting known biology as well as sequencing artifacts. Read simulators can fulfill this requirement, but are often criticized for limited resemblance to true data and overall inflexibility. We present NEAT (NExt-generation sequencing Analysis Toolkit), a set of tools that not only includes an easy-to-use read simulator, but also scripts to facilitate variant comparison and tool evaluation. NEAT has a wide variety of tunable parameters which can be set manually on the default model or parameterized using real datasets. The software is freely available at github.com/zstephens/neat-genreads.