biwa summit15
TRANSCRIPT
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Oracle BIWA Summit 2015
Personalized Healthcare using large genomic datasets and Oracle Exadata
René Kuipers, Principal Consultant VX Company
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Oracle BIWA Summit 2015
It’s all in the genes Personalized Healthcare using large genomic datasets and Oracle Exadata
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Oracle BIWA Summit 2015
About me
Principal Consultant Data and BI Solutions Datawarehouse Architect Business Intelligence specialist Master degree in Biochemistry – molecular biology – cancer genetics
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Oracle BIWA Summit 2015
Agenda
Basic genetics – analyses
Technology behind this What does it look like The next step: combining genomic data with patient data When both worlds meet
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Oracle BIWA Summit 2015
BASIC GENETICS Set the context
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Oracle BIWA Summit 2015
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Oracle BIWA Summit 2015
Chromosomes
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Oracle BIWA Summit 2015
Genes
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Oracle BIWA Summit 2015
DETERMINING THE GENETIC SEQUENCE
basic genetics
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Oracle BIWA Summit 2015
Genetic sequence
Blood / cancer tissue DNA isolation DNA amplification DNA Sequencing (40x - 80x)
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Oracle BIWA Summit 2015
Genetic sequence
approx. 5% of DNA is gene approx. 95% of DNA is referred to as ‘junk-DNA’ 99% of entire DNA sequence is stable Genetic variations are normal
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Oracle BIWA Summit 2015
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Oracle BIWA Summit 2015
DNA (Next Generation) Sequencing From blood-sample to DNA sequence 3 billion basepairs 2 TB per sample unique: whole genomes
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Oracle BIWA Summit 2015
Abnormal genetic variations
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Oracle BIWA Summit 2015
Searching for the unknown genetic variations normal genetic variations cancer better diagnoses require better analyses. Upfront (predictive) diagnoses require a lot of data and processing power. result: less-invasive treatment, better patient-life. What did we not know (yet)
– and can be learned from Ultimate goal: centralized DNA library for statistical purposes
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Oracle BIWA Summit 2015
THE TECHNOLOGY BEHIND THIS
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Oracle BIWA Summit 2015
DNA (Next Generation) Sequencing
3 billion basepairs 2 TB per sample Whole genomes
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Oracle BIWA Summit 2015
Handling large volumes Oracle Database
– Partitioning – Optimized data model
Oracle Exadata Database Machine – Optimized to run Oracle Database – Specific performance features
- Smart Scans - Exadata Hybrid Columnar Compression
Performance increase: 700x
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Oracle BIWA Summit 2015
Handling large volumes - database benefits
Datamodel V1 – Sample-oriented (partitioned) – Each base-position stored (compared to reference genome)
- leads to 95% no-calls – 206 samples --> 800 GB
- max 2500 samples on Exadata – Indexes are (still) needed: Index size 5x larger than sample-size
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Oracle BIWA Summit 2015
Handling large volumes - database benefits
Datamodel V2 – Sample-oriented (partitioned) – positions are stored as regions (buckets)
- 1000 positions per region – Buckets are indexed – EHCC Compression – Reduce redundant data
- Store allele 1 and 2 as 1 row when values are equal – Storage 99GB (246 samples)
- Up to 20.000 samples
– Indexes require less space than in Datamodel V1
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Oracle BIWA Summit 2015
Exadata benefits
Flash Parallel processing Smart Scans Exadata Hybrid Columnar Compression Let’s have a look…
– video’s courtesy of Frits Hoogland
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Oracle BIWA Summit 2015
Executed tests
Nr Exadata features Parallel Disk type
1 - Serial HDD2 - Serial FDD3 - 64 HDD4 - 64 FDD5 SS Serial HDD6 SS Serial FDD7 SS 64 HDD8 SS 64 FDD9 SS + EHCC 64 FDD
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Oracle BIWA Summit 2015
Executed tests
Nr Exadata features Parallel Disk type
1 - Serial HDD2 - Serial FDD3 - 64 HDD4 - 64 FDD5 SS Serial HDD6 SS Serial FDD7 SS 64 HDD8 SS 64 FDD9 SS + EHCC 64 FDD
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Oracle BIWA Summit 2015
Executed tests
Nr Exadata features Parallel Disk type
1 - Serial HDD2 - Serial FDD3 - 64 HDD4 - 64 FDD5 SS Serial HDD6 SS Serial FDD7 SS 64 HDD8 SS 64 FDD9 SS + EHCC 64 FDD
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Oracle BIWA Summit 2015
Executed tests
Nr Exadata features Parallel Disk type
1 - Serial HDD2 - Serial FDD3 - 64 HDD4 - 64 FDD5 SS Serial HDD6 SS Serial FDD7 SS 64 HDD8 SS 64 FDD9 SS + EHCC 64 FDD
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Oracle BIWA Summit 2015
Executed tests
Nr Exadata features Parallel Disk type
1 - Serial HDD2 - Serial FDD3 - 64 HDD4 - 64 FDD5 SS Serial HDD6 SS Serial FDD7 SS 64 HDD8 SS 64 FDD9 SS + EHCC 64 FDD
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Oracle BIWA Summit 2015
Query performance (times are seconds)
Nr Exadata features Parallel Disk type 11.2.0.1 11.2.0.2
1 - Serial HDD 695 153 2 - Serial FDD 403 91 3 - 64 HDD 19 18 4 - 64 FDD 16 13 5 SS Serial HDD 41 6 SS Serial FDD 37 7 SS 64 HDD 13 8 SS 64 FDD 6 9 SS + EHCC 64 FDD 1
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Oracle BIWA Summit 2015
WHAT DOES IT LOOK LIKE ?
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Oracle BIWA Summit 2015
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Oracle BIWA Summit 2015
Why is this important?
Speed – Faster results – ‘No’ is found earlier
Volume (Centralized DNA Library)
– Better statistical basis – Less-invasive treatments for patients – Personalized healthcare
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Oracle BIWA Summit 2015
Even more…
Add clinical data to genomic data. – Patient history – Drug treatment history – Demographics
Clinical Data Biobanks
Lab Systems Omic Data
Integration of Data
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Oracle BIWA Summit 2015
Oracle Translational Research Center (TRC)
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Oracle BIWA Summit 2015
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Oracle BIWA Summit 2015
Advanced visualizations
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Oracle BIWA Summit 2015
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Oracle BIWA Summit 2015
Future
• Extend Huvariome to use Hadoop for raw reads. • Big Data Discovery • Big Data SQL
• Advanced visualizations • D3 • Spotfire
• RNA expression data • Pigs / cows / chickens • Multitenancy • Cloud offering • In-memory analyses
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Oracle BIWA Summit 2015
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Oracle BIWA Summit 2015
Summary
Care is primary. – Technology is supporting.
Oracle offers platforms to provide better care – Database – Exadata – TRC
Clinical and Genomic data are complimentary. Not everything is in the genes…
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Oracle BIWA Summit 2015
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Oracle BIWA Summit 2015