Automated Workflow for Somatic and Germline Next Generation Sequencing Analysis in Routine Clinical Cancer Diagnostics.

Thanks to personalized medicine trends and collaborations between industry, clinical research groups and regulatory agencies, next generation sequencing (NGS) is turning into a common practice faster than one could have originally expected. When considering clinical applications of NGS in oncology, a rapid workflow for DNA extraction from formalin-fixed paraffin-embedded (FFPE) tissue samples, as well as producing high quality library preparation, can be real challenges. Here we consider these targets and how applying effective automation technology to NGS workflows may help improve yield, timing and quality-control. We firstly evaluated DNA recovery from archived FFPE blocks from three different manual extraction methods and two automated extraction workstations. The workflow was then implemented to somatic (lung/colon panel) and germline (BRCA1/2) library preparation for NGS analysis exploiting two automated workstations. All commercial kits gave good results in terms of DNA yield and quality. On the other hand, the automated workstation workflow has been proven to be a valid automatic extraction system to obtain high quality DNA suitable for NGS analysis (lung/colon Ampli-seq panel). Moreover, it can be efficiently integrated with an open liquid handling platform to provide high-quality libraries from germline DNA with more reproducibility and high coverage for targeted sequences in less time (BRCA1/2). The introduction of automation in routine workflow leads to an improvement of NGS standardization and increased scale up of sample preparations, reducing labor and timing, with optimization of reagents and management.

A novel electromagnetic tracking system for surgery navigation.

OBJECTIVE: This paper proposes the development of a novel electromagnetic tracking system for navigation surgery. Main objective is to provide a system able to operate in a wide tracking volume to make easier and efficient the surgical procedures by assuring high measurement accuracy. METHODS: A new field generator consisting in five transmitting coils excited with Frequency Division Multiplexing technique has been developed. Attention is devoted to designing and arrangement of the coils to assure high sensitivity, system scalability and a homogeneous magnetic field inside working volume. A suitable technique based on Look-Up-Table is applied for sensor position calculation and an anthropomorphic robot is used for table calibration. RESULTS: Experimental tests highlight a good repeatability of the measurement data and a negligible noise influence for the proposed system. The obtained tracking volume is wider with respect to the commercial tracking device used in surgical applications and seem promising. CONCLUSION: The main characteristic of the developed system consists of: scalable and modular configuration of Field Generator, high measured sensitivity due to the increased number of transmitting coils with respect to the classical configuration and large tracking volume. The development of the proposed magnetic tracking systems with high accuracy and wide working volume allows to promote broader utilization of advantaged techniques in surgery procedures for both improving the effectiveness and decreasing the invasiveness of medical interventions.