CLINICAL GENOMIC RESEARCH MANAGEMENT
Creators: name: BHATTACHARYYA, AMITAVA
Publisher: name: Universit� degli Studi di Milano
Year: 2013

description: Technological advancement in Genomics has propelled research in a new era,
where methods of conducting experiments have completely been renovated.
Riding the wave of Information Technology, equipped with statistical tools,
Genomics provide a revolutionized perspective unthought-of in the past. With the
completion of the Human Genome project, we have a common reference for
analysis at the level of the complete genome. High throughput technologies for
gene expression, genotyping and sequencing are propelling present research.
Attempts are now being made for the incorporation of these methods in the health
care in a structured format. Clinicians cherish the use of genomics for the
assessment disease predisposition and realizing personalized medical care for a
better health care. As genome sequencing is becoming swifter and its cost
reducing, the public genomic data has increased many folds. Data from other high
throughput technologies and annotations further increase the storage
requirements. Laboratory management software, LIMS, is now becoming the
limiting factor as automation and integration increases. Thus genomics now faces
the challenge of management of this enormous data catering to varied needs, not
limited only for the research laboratories, but extends also to health care
institutions and individual clinicians. Further, there is a growing need for the
analysis and visualization of the generated data to be integrated into the same
platform for a continuous research experience and systematic supervision. Data
security is of prime concern, especially in health care concerning human subjects.
The interest of the clinicians adds another management requirement, a delivery
system for the concerned subject.
Hypertension is a complex disorder with world-wide prevalence. HYPERGENES
project was centered on the objective of integrating biological data and processes
with Hypertension as the disease model. The HYPERGENES project focuses on
the definition of a comprehensive genetic epidemiological model of complex traits
like Essential Hypertension (EH) and intermediate phenotypes of hypertension
such as Target Organ Damage (TOD). During the HYPERGENES project, the
above mentioned challenges were comprehended and evaluated, leading to the
present work as an endeavor to provide a generalized integrated solution towards
the management of genomic and clinical data for clinical genomic research.
This PhD thesis represents the description of AD2BioDB, biological data
management platform and SeqPipe, dynamic pipeline management software, in
the path of meeting the challenges posed in the area of clinical genomics.
AD2BioDB provides the platform where data generated using different technologies
can be managed and analyzed with reporting and visualization modules for
improved understanding of the results among all research collaborators. AD2BioDB
is the management software environment in which the in-silico data can be shared
and analyzed. The analysis software is connected within AD2BioDB through the
plug-in system. SeqPipe software provides opportunity to dynamically create
pipeline workflows for the multi-step analysis of data. The interactive graphical user
interface provides the opportunity for coding free pipeline creation and analysis.
This tool is especially useful in the dynamic NGS analysis, where multiple tools
i
with different versions are in use. SeqPipe can be used as independent software or
as a plug-in analysis tool within an application like AD2BioDB.
The key features of AD2BioDB can be summarized as:
? Clinical genomics data management
? Project management
? Data security
? Dynamic creation of graphical representation.
? Distributed workflow analysis
? Reporting and alert features.
? Dynamic integration of high throughput technologies
We developed AD2BioDB as a prototype in our laboratory for providing support to
the increasing genomic data and complexity of analysis. The software aims at
providing a continuous research experience with a versatile platform that supports
data management, analysis and public knowledge integration. Through the
integration of SeqPipe into AD2BioDB, the management system becomes robust in
providing a distributed analysis environment.