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Molecular markers are essential for cancer diagnosis, clinical trial enrollment, and some surgical decision making, motivating ultra-rapid, intraoperative variant detection. Sequencing-based detection is considered the gold standard approach, but typically takes hours to perform due to time-consuming DNA extraction, targeted amplification, and library preparation times. In this work, we present a proof-of-principle approach for sub-1 hour targeted variant detection using real-time DNA sequencers. By modifying existing protocols, optimizing for diagnostic time-to-result, we demonstrate confirmation of a hot-spot mutation from tumor tissue in ~52 minutes. To further reduce time, we explore rapid, targeted Loop-mediated Isothermal Amplification (LAMP) and design a bioinformatics tool—LAMPrey—to process sequenced LAMP product. LAMPrey's concatemer aware alignment algorithm is designed to maximize recovery of diagnostically relevant information leading to a more rapid detection versus standard read alignment approaches. Using LAMPrey, we demonstrate confirmation of a hot-spot mutation (250x support) from tumor tissue in less than 30 minutes. A method for detection of somatic variants is presented for the intraoperative evaluation of tumor mutations in less than 30 min, using rapid DNA extraction, in silico optimized LAMP amplification, and a LAMP product analysis tool: LAMPrey. [ABSTRACT FROM AUTHOR]

Background: Spinal dysraphism is suspected in patients with midline abnormalities, especially in those with lumbosacral cutaneous markings. A recent prospective study demonstrated that isolated cutaneous infantile hemangiomas (IH) of the lumbosacral region have one of the highest risks (relative risk of 438) of associated spinal dysraphism. Objective: The specific types of dysraphism and radiological findings associated with cutaneous IH of the lumbosacral region have not been described in detail, to the best of our knowledge. The aim of this multicenter study is to retrospectively classify types of spinal anomalies associated with the cutaneous lumbosacral IH. Materials and methods: The radiological images of 20 cases of lumbosacral infantile hemangioma associated with spinal dysraphism were reviewed. Results: Tethered cord was found in 60% of the 20 cases, spinal lipoma was present in 50% and 45% had intraspinal hemangiomas. Sinus tract was found in 40% of the children. Conclusion: A range of spinal anomalies is associated with cutaneous lumbosacral infantile hemangiomas and MRI can be used to characterize these abnormalities. [ABSTRACT FROM AUTHOR]