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IBM Haifa Research Lab
SPA
a Platform for
Hereditary Disease Management
and Pedigree Analytics
Rizzoli FOAK
Alex Melament, [email protected]
July 2010
IBM Haifa Research Lab: Let’s Build a Smarter Planet
IOR - Rizzoli Orthopaedic Institute
• IOR- is the main Italian institute of orthopedics
and has a status of a 'Scientific research hospital’
- About 150,000 patients examined every year
- Over 18,000 orthopedic operations every year
- Nine laboratories at the institute employing a staff
of 250 including doctors, biologists and technicians.
• Medical Genetic Unit specializes in Rare Skeletal Hereditary diseases
such as:
- Multiple Osteochondromas (MO)
-
• Osteochondroma is a cartilage capped bony projection arising on
the external surface of bone containing a marrow cavity that is
continuous with that of the underlying bone
Osteogenesis Imperfecta (OI)
• It is frequently caused by defect in the gene that produces type
1 collagen, an important building block of bone. There are
many different defects that can affect this gene.
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IBM Haifa Research Lab: Let’s Build a Smarter Planet
Project Goals
• Understanding the relationships between hereditary
diseases and their genetic background
-
Analysis of inherited diseases and their associated
phenotypes is of great importance to gain knowledge of
underlying genetic interactions
Discovering and defining a correlation between Phenotype
and Genotype data will enable
• Fit adequate treatment protocol
• Ensure appropriate clinical follow-up
• Improve patient’s quality of life
• Build Healthcare Platform that will enable efficient
treatment and productive research in Hereditary
Diseases
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IBM Haifa Research Lab: Let’s Build a Smarter Planet
IT for understanding of Hereditary Diseases
• Collects and Integrates medical images, clinical and genomic data of
each patient and his family
- Leverages standards such as DICOM and HL7
- Maintains content and context aware associations to support clinical and
research usage
• Enables secure cross Hospital data and knowledge sharing
- Leverages Industry’s Best Practices, Standards and IHE Profiles
- Enables cross Hospital Patient ID correlation through PIX&PDQ interfaces
• Enables data insights discovery
- Supports federated queries
- Provides on demand pedigree visualization
- Provides a platform for data analytics & knowledge extraction
• Enables to host third party analytics
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IBM Haifa Research Lab: Let’s Build a Smarter Planet
Pedigree Analysis
• The pedigree documents biological
relationships in families and the
presence of diseases.
- Pedigree includes number, gender and
closeness of affected relatives, their ages at
disease onset, and associated health
conditions
• Pedigree is needed to
- Assess disease risk
-
• BRCARPO risk model can indicate a
chance of having BRCA1 or BRCA2
mutations
Investigate correlation between Phenotype
and Genotype data
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IBM Haifa Research Lab: Let’s Build a Smarter Planet
Solution Architecture
Hospitals (PACS, Clinical and Genetic Labs)
EHR,
Knowledge
Systems
DICOM
HL7 v3, v2.x
Physicians and
Researchers
WS
WS
Pedigree Analytics
Cross River/Rimon
(Phenotype,Genotype)
WAS 7, DB2 Data Warehouse
WAS 7, IBM CM
Data Federation
+
WAS 7, DB2 Data Warehouse
WAS 7
Excel
BO
Cube Services
&
IBM BI
Infrastructure
CMO
Cognos
Healthcare BUS (WAS7/WPS 6.1, HL7 v2&3, WS, IHE profiles)
PIX/PDQ
Server
WAS 7
Partners (Disease risk assessment models, Pedigree clustering, classification and visualization tools)
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IBM Haifa Research Lab: Let’s Build a Smarter Planet
Pedigree Visualization
• Dynamic pedigree visualization
• Presentation of all available
information for the persons in the
pedigree
- Clinical, genomic data and medical
images
• Standard pedigree representation
- HL7 v3 Family History
- Enables standard based pedigree
interoperability
• Enables disease risk assessment
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IBM Haifa Research Lab: Let’s Build a Smarter Planet
On Demand Analytics Platform – Currently Available Algorithms
• Decision Trees – Explanation of one dimension by others; Clustering
- Random ID3
- C4.5 (entropy based)
• Bayesian Networks – Data Cleansing
- Naive Bayes
- Chu-Liu Trees
• K-Means – Clustering
- Hamming distance for category dimensions only
- Continuous dimensions only
- Discretization of Continuous dimensions by Entropy and application of
•
Hamming distance on all the dimensions.
Statistical Analysis
- Chi-Square – Association between two category dimensions
- Spearman – Association between two category dimensions
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IBM Haifa Research Lab: Let’s Build a Smarter Planet
CMO – SOA based Medical Imaging Repository
Image
Processing
• Supports DICOM, WADO, HL7,
XDS-I, PIX and PDQ
• Provides secure cross-enterprise
Imaging
Archive
Image
Consumers
sharing
• Complies with regulations for
storing and managing data
• Enables extensibility and reuse of
existing legacy assets through an
open and flexible architecture
• Leverages IBM's market-proven
middleware to ensure scalability,
high availability and disaster
recovery
Data Sources
(CT, MRI, US…, PACS)
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Fine-Grained
Authorization
Data
Analytics
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IBM Haifa Research Lab: Let’s Build a Smarter Planet
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