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SLIDE 0
The Problem
Next generation sequencing panel brought online for leukemia and
myelodysplastic syndrome, needed interpretive and data
management software
Interpretation efficiency
Patient safety
Turnaround time
SLIDE 1
Project Goals
SLIDE 2
Local (Galileo)
Web Interface
Galileo Services
IonReporter
Research
Applications
Internal
Clients
SLIDE 3
SQL/Relational
ACID Compliant
Column-level encryption
Well-known deployment
NoSQL/Document
Dynamic schema
Improved read/write speeds
Easy scaling and redundancy
SLIDE 4
VarBase - Kepler
COSMIC
ClinVar
OMIM
dbSNP
Web Interface
Galileo Services
IonReporter
Research
Applications
Internal
Clients
SLIDE 5
SLIDE 6
VarBase - Kepler
Laboratory personnel
Trainee (Resident/Fellow)
Attending
Web Interface
Galileo Services
IonReporter
Research
Applications
Internal
Clients
SLIDE 7
Variants in JSON
{
"chromosome": "chr7",
"position": 148506396,
"type": "snv",
"refAllele": "A",
"altAllele": "C",
"totalReads": 1998,
"forwardReads": 1038,
"forwardRefReads": 524,
"forwardAltReads": 514,
"reverseReads": 960,
"reverseRefReads": 500,
"reverseAltReads": 460,
"refReads": 1024,
"altReads": 974,
"vaf": 48.749,
"variantRegion": "intronic",
"variantEffect": "",
"snvEffect": "A>C",
"gene": "EZH2"
SLIDE 8
SLIDE 9
System Statistics
Cloud-Based Elasticsearch Cluster
60 million variant annotations
10 million oncology annotations
S L I D E 10
Conclusions
Hybrid data store can efficiently and securely store complex data
types
Cloud-based variant annotation can be integrated into multiple
services and provides auditable interpretation information
Technology agnostic web service interfaces provide easily accessible
data interchange
S L I D E 11
Acknowledgements
Henry Rinder, MD
Alexa Siddon, MD
Richard Torres, MD
Christopher Tormey, MD
Thomas Durant, MD
Laboratory Informatics
Rodion Rathbone, MD
Nathan Price
S L I D E 12