title: Implementation of Cloud based next generation sequencing data analysis in a clinical laboratory.
abstract: BACKGROUND
  The introduction of next generation sequencing (NGS) has revolutionized molecular diagnostics, though several challenges remain limiting the widespread adoption of NGS testing into clinical practice. One such difficulty includes the development of a robust bioinformatics pipeline that can handle the volume of data generated by high-throughput sequencing in a cost-effective manner. Analysis of sequencing data typically requires a substantial level of computing power that is often cost-prohibitive to most clinical diagnostics laboratories.
  
  
  RESULTS
  To address this challenge, our institution has developed a Galaxy-based data analysis pipeline which relies on a web-based, cloud-computing infrastructure to process NGS data and identify genetic variants. It provides additional flexibility, needed to control storage costs, resulting in a pipeline that is cost-effective on a per-sample basis. It does not require the usage of EBS disk to run a sample.
  
  
  CONCLUSIONS
  We demonstrate the validation and feasibility of implementing this bioinformatics pipeline in a molecular diagnostics laboratory. Four samples were analyzed in duplicate pairs and showed 100% concordance in mutations identified. This pipeline is currently being used in the clinic and all identified pathogenic variants confirmed using Sanger sequencing further validating the software.
authors.forename: Getiria
authors.initials: G
authors.lastname: Onsongo
authors.forename: Jesse
authors.initials: J
authors.lastname: Erdmann
authors.forename: Michael D
authors.initials: MD
authors.lastname: Spears
authors.forename: John
authors.initials: J
authors.lastname: Chilton
authors.forename: Kenneth B
authors.initials: KB
authors.lastname: Beckman
authors.forename: Adam
authors.initials: A
authors.lastname: Hauge
authors.forename: Sophia
authors.initials: S
authors.lastname: Yohe
authors.forename: Matthew
authors.initials: M
authors.lastname: Schomaker
authors.forename: Matthew
authors.initials: M
authors.lastname: Bower
authors.affiliation: Research Informatics Support Systems, Minnesota Supercomputing Institute, University of Minnesota, Room 599 Walter Library 117 Pleasant St SE, Minneapolis, MN 55455, USA. kats@umn.edu.
authors.forename: Kevin A T
authors.initials: KA
authors.lastname: Silverstein
authors.forename: Bharat
authors.initials: B
authors.lastname: Thyagarajan
mesh_terms: D019411:Clinical Laboratory Techniques / Q000191:economics; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics / Q000379:methods*; D006801:Humans; D020407:Internet / Q000191:economics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000191:economics / Q000379:methods*; D013223:Statistics as Topic