bioinformatics consulting operation at the dana-farber cancer institute
TRANSCRIPT
Collaborative Consulting Operation at Center for Cancer Computational Biology
Yaoyu E Wang, Ph.DAssociate Director
Center for Cancer Computational BiologyDana-Farber Cancer Institute
Overview
Bioinformatics in current genomic research paradigm
Bioinformatics analysis through collaborative research consulting
Project examples
?
Genomic Research Paradigm
Introduction to the CCCB
CCCB Service Offering
IT Infrastructure
- Application hosting- Data management- Custom software
development- Comprehensive
collaboration portals
CCCB Service Offering
Next-Gen Sequencing
- Sample prep and QC- Customized sequencing
experiments- Integrated standard
informatics
IT Infrastructure
CCCB Service Offering
Analytical Consulting
- Bioinformatics / statistical data analysis
- Experimental design- Project based fee for service
collaborative consulting
Next-Gen Sequencing
IT Infrastructure
CCCB Service Offering
Analytical Consulting
- Bioinformatics / statistical data analysis
- Experimental design- Project based fee for service
collaborative consulting
Next-Gen Sequencing
IT Infrastructure
CCCB Service Offering
Analytical Consulting
Next-Gen Sequencing
IT Infrastructure
Collaborative Consulting Cycle
Analytical Consulting
How a bioinformatics consulting session often started…
“I just spend $$$$$$$ to run a bunch of MS spec, and I have no clue what is in there. My BOSS is !#!@$%^&*@, and he is going to KILL ME!!!”
Client’s Start-Up
- Client realizes the presenting priority and need for a consultant
Cham, phdcomics
Engagement and Agreement
- Client and consultant meet to discuss presenting problem- Identify information needed to analyze presenting
problem- Organize and analyze presenting problem- Form an initial agreement about how to work together
Preliminary Discovery
- Analyze project priorities - Literature and method review- Information quality control- Identify limitation of project scope- Develop plans for evaluation and deliverables
Action Planning and Alignment
- Formalize project plans (Statement of Work)- Allocate physical and human resources- Devise a budget justification- Communicate with client to agree upon the budget
Implementation Evaluation
Project Termination (End Project)- Final project presentation- Agree on data deliverables- Agreement on acknowledgement/authorship for
publication- Billing
“Why isn’t it statistically significant ?”
Summary
Collaborative research consulting is a fee for service operation
Stepwise short and focused project objectives
Fast turn-around time (~2-3 weeks) Reiteration the same process for long
term collaboration
Case 1 HIV Brain Sequence Database
CASE 2: Predict Cyclin D1 functions from mass spectrum data of cancer cell lines
Jirawatnotai et al, Nature, 2011
a. MS data from cancer cell linesb. Functional Enrichment analysisc. Protein-Protein Interaction analysis
c
Sequencing Platform
De Novo Assembly Analysis
Refence Guided Assembly
Annotation
Assemble reads into contigs by:• Velvet• Trinity• transABySS
MiSeq
5’ 3’
ExRNA without selection
5’ 3’
RNA-Seq library for directional Sequencing
RNA library prep
Align to reference genome sequence:• TopHat2• BWA
Refine alignment with local realignment
t1 t2 t3 t4
Cou
nt
Transcript quantification by htseq
t1 t2 t3 t4
Cou
nt
Transcript quantification
Compare and characterize transcripts to public domain databases:• CoRAL• miRBase• NONCODE• RNAdb• Rfam
Compare library prep methods/DNase treatment
ScriptSeq NEB
SMARTer
Sequence Analysis Pipeline
Comparison
CASE 4: Lung Genomic Research Consortium Portal