Anne-Francoise Lamblin

Bharat Thyagarajan

Getiria Onsongo

Jesse Erdmann

John Chilton

Kenny Beckman

Kevin Silverstein

Matthew Bower

null null

Ying Zhang

PubMed

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POSTER PRESENTATION Open Access
CLIA-certified next-generation sequencing
analysis in the cloud
Ying Zhang1*, Jesse Erdmann1, John Chilton1, Getiria Onsongo1, Matthew Bower2,3, Kenny Beckman4,
Bharat Thyagarajan5, Kevin Silverstein1, Anne-Francoise Lamblin1, the Whole Galaxy Team at MSI1
From Beyond the Genome 2012
Boston, MA, USA. 27-29 September 2012
The development of next-generation sequencing (NGS)
technology opens new avenues for clinical researchers to
make discoveries, especially in the area of clinical diag-
nostics. However, combining NGS and clinical data pre-
sents two challenges: first, the accessibility to clinicians
of sufficient computing power needed for the analysis of
high volume of NGS data; and second, the stringent
requirements of accuracy and patient information data
governance in a clinical setting.
Cloud computing is a natural fit for addressing the
computing power requirements, while Clinical Labora-
tory Improvement Amendments (CLIA) certification
provides a baseline standard for meeting the demands on
researchers in working with clinical data. Combining a
cloud-computing environment with CLIA certification
presents its own challenges due to the level of control
users have over the cloud environment and CLIA’s stabi-
lity requirements. We have bridged this gap by creating a
locked virtual machine with a pre-defined and validated
set of workflows. This virtual machine is created using
our Galaxy VM launcher tool to instantiate a Galaxy
[http://www.usegalaxy.org] environment at Amazon with
specific versions of the tools used in the workflow. The
VM launcher tool can reliably recreate the same virtual
machine on several cloud environments. Once a baseline
virtual machine is created, the tool can launch any num-
ber of clones to analyze samples in parallel. We describe
herein a pilot project as an example of a working clinical
analysis pipeline. In order to validate the clinical diagno-
sis of diseases with a genetic cause using NGS data,
patient samples were collected by Dr Bharat Thyagarajan
and staff at the Molecular Diagnostics Laboratory,
University of Minnesota medical center-Fairview. The
patient samples were analyzed using customized hybrid-
capture bait libraries to boost read coverage in low-
coverage regions, followed by targeted enrichment
sequencing at the BioMedical Genomics Center. The
NGS data is imported to a tested Galaxy single nucleo-
tide polymorphism (SNP) detection workflow in a locked
Galaxy virtual machine on Amazon’s Elastic Compute
Cloud (EC2). This project illustrates our ability to carry
out CLIA-certified NGS analysis in the cloud, and will
provide valuable guidance in any future implementation
of NGS analysis involving clinical diagnosis.
Author details
1Research Informatics Support System, Minnesota Supercomputing Institute,
University of Minnesota, Minneapolis, MN 55455, USA. 2Division of Genetics
and Metabolism, University of Minnesota, Minneapolis, MN 55455, USA.
3Molecular Diagnostics Laboratory, University of Minnesota Medical Center-
Fairview, University of Minnesota, Minneapolis, MN 55455, USA. 4BioMedical
Genomics Center, University of Minnesota, Minneapolis, MN 55455, USA.
5Department of Laboratory Medicine and Pathology, University of Minnesota,
Minneapolis, MN 55455, USA.
Published: 1 October 2012
doi:10.1186/1753-6561-6-S6-P54
Cite this article as: Zhang et al.: CLIA-certified next-generation
sequencing analysis in the cloud. BMC Proceedings 2012 6(Suppl 6):P54.
1Research Informatics Support System, Minnesota Supercomputing Institute,
University of Minnesota, Minneapolis, MN 55455, USA
Full list of author information is available at the end of the article
Zhang et al. BMC Proceedings 2012, 6(Suppl 6):P54
http://www.biomedcentral.com/1753-6561/6/S6/P54
© 2012 Zhang et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited.


CLIA-certified next-generation sequencing analysis in the cloud

http://dx.doi.org/10.1186/1753-6561-6-S6-P54

CLIA-certified next-generation sequencing analysis in the cloud

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