Content

Advancements in next generation sequencing (NGS)

technology have allowed researchers and clinicians to

generate genome-wide datasets. However, current

information systems, which predate the arrival of NGS

technology, lack adequate methods for NGS analysis and

remain isolated from the systems which generate the

data. In order to add meaningful annotations to clinical

NGS data, we developed a system that allows us to

request and dynamically format sequencing data for a

variety of software applications.

Design

Overall Program Design

Results

Easily consumable web services support NGS interpretation in clinical

and research scenarios, without adversely impacting system

performance

Third party applications can be easily integrated through web service interfaces

Minimal knowledge of data model is required

Server based authorization allows patient- and field-based data restriction

Results easily returned to data management system

Conclusion

The ability to generate genome-wide sequences and analyze the

data in a clinically meaningful way are two distinct entities, which

have been discordant in their points of evolution. With NGS

technology evolving at a rapid pace, the technology used to

interpret it struggles to keep up. To increase efficiency and provide

increased data access, applications that easily and securely allow

access to third-party research applications, such as web services,

are important for furthering our understanding of sequencing data.

Integration of Third Party Genetic Analysis Software into a ClinicalNext Generation Sequencing Data Platform

THOMAS JS DURANT MD, WADE L. SCHULZ MD, PhDYALE SCHOOL OF MEDICINE, DEPARTMENT OF LABORATORY MEDICINE, NEW HAVEN CT, 06520

Authenticate user to web service

Web service call to VarBase

Deserialize returned data model

Parse VCF data with Python script

Analyze output with SciClone

Send result to VarBase web serviceV

CF

Dat

a Pa

rser

VarBase Architecture Integration Workflow

Data Parsing Data Analysis

Technology Data management system (VarBase-Galileo) hosted on

Windows Server 2012 (Microsoft, Redmond, WA; USA)

RESTful web service interface

Research software packages run on Linux-based virtual machines (CentOS)

Web service responses consumed and parsed using Python 2.7

Visualized in R (version 3.1.2) using the SciClone R package