Introduction to Bioinformatics Core Facilitya bioinformatics analysis move to BICF –Technical...
Transcript of Introduction to Bioinformatics Core Facilitya bioinformatics analysis move to BICF –Technical...
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Outline
1. Goals
2. Structure
3. Services
4. Flagship Projects
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BICF Goals
• To build a core facility open to the research community at UTSW with recognizable impact on the scope and quality of clinical and basic cancer research.
• Major Funding Source: CPRIT Core Grant and Cancer Center
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BICF Structure
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BICF Recruits New Hires • Brandi Cantarel, Ph.D., Computational Biologist III, started on
11/1/2015 • He Zhang, Ph.D., Computational Biologists III, started on 1/22/2016 • Xiu Luo, Ph.D., Data Scientist I, in process.
Open Positions • Computational Biologist – OPEN, high activity • Computational Biologist – OPEN, high activity • Data Scientist – OPEN SOON • Scientific Programmer – OPEN SOON
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BICF Services
1. Curated Databases 2. Software Pipelines 3. Educational Programs 4. Helpdesk Consults
5. Fellows Program 6. Program Development 7. Collaborations 8. Flagship Projects
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BICF Services
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Public / Curated Databases • Research data are increasingly available in the public domain
Gene Expression Omnibus (GEO) The Cancer Genomics Atlas (TCGA) Cancer Cell Line Encyclopedia (CCLE) Literature…
• Utilizing these data are challenging
Scattered around in different places and frequently updated Organized in different formats and used different terminology Required specialized expertise to process
• BICF provides centralized infrastructure for public and curated databases and intuitive-to-use tools to access these resources.
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BICF Services
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Next-generation Sequencing Analysis Pipelines
Next Step: Incorporate the pipeline into BioHPC cloud system and set up educational programs for all researchers on campus.
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Custom Software Probemapper – EntrezToProbe engine for handling mappings between probes and genes in microarray data.
MBCB – R package that provides model-based background correction incorporating negative control beads in Illumina BeadArray data.
Pipeclip – Pipeline for identifying cross-linking sites in PAR-CLIP, HITS-CLIP, and iCLIP data.
SbacHTS – R package for detecting and correcting spatial background noise in RNAi screening experimental results.
BAYSIC – Variant Integration Tools, which uses Bayesian posterior probabilities to determine highly confident variants predicted from a combination of variant calling tools.
Term2Gene - Online tool for identifying list of genes associated with specific diseases/biological pathways using PubMed's query term definitions.
Lung Cancer Explorer – Online tool that lets you explore and analyze gene expression data from dozens of lung cancer datasets.
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BICF Services
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BICF Educational Programs
• Monthly Lectures – part of BioHPC training.
• Nano Courses – 2 day courses with lectures and hands-on exercises.
Check BioHPC Training Calendar.
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BICF Upcoming Courses
• 03/23: Introduction to Statistical Testing: Going beyond the T-test to pick the right test for your data analysis.
• 04/27: Sequence Homology and Alignments: Understanding how does BLAST/FASTA work in order to optimize your sequence similarity searches.
• 05/25: Next Generation Sequence Technologies: From Sanger to MinIONs, choosing the sequencing technology for your experiments.
• 06/22: Introduction to Sequence Variation: SNV, INDELS and SVs, predicting human variation in healthy vs. disease populations.
Organizer: Dr. Brandi Cantarel <[email protected]>
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BICF Upcoming Courses
• 07/27: Introduction to ClipSeq Analysis: ClipSeq as a
method for detecting of genome-wide protein-RNA interaction maps.
• 09/28: RNAseq Analysis: Gene expression profiling to determine molecular functional differences in cells and tissues.
• 11/16: Introduction to Microbiome ‘Omics Technologies: What is a microbiome and how can it be studied?
Organizer: Dr. Brandi Cantarel <[email protected]>
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BICF Services
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BICF Help Desk • Open to all UTSW research community.
– consultation re data access – consultation re routine data analysis – consultation re study design – consultation re grant application
• Triage of proposals for collaboration. • Triage of proposals for hourly consulting. • Help desk hours:
Daily 10:00am – 11:00am
NB5.604 [email protected]
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BICF Hourly Consulting
• Help Desk consults needing more than brief interactions can be scheduled as a fee-for-service basis. – more involved data access
– performance of simple data analysis
– more involved standard support in study design
– more involved standard support with grant application
• Review / triage toward prog dev and collab level
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BICF Services
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BICF Fellows Program • 5 - 10 slots available • Postdoctoral fellows and graduate students engaged in
a bioinformatics analysis move to BICF – Technical super-vision by trained staff – Environment with quantitative thinking – Peer-to-peer training among fellows – Integration with the Department of Bioinformatics
• Scientific responsibility and financing remains with fellow’s lab
• Use of CPRIT funds – Bridge funds for unbillable FTEs of staff working with
fellows
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BICF Services
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Program Development
• To provide bioinformatics expertise to newly forming project teams.
– Attendance of project meetings
– Dedicated contributions to study design
– Acquisition of preliminary data
– Participation in grant application
• Application through helpdesk consultation.
• Prioritization by Steering Committee.
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BICF Services
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BICF Collaborations
• Provide cancer community with -‘bioinformatics personnel on demand’.
• Application through helpdesk consultation.
• Prioritization by Steering Committee.
– Staff stays located in BICF or moves temporarily to project lab.
– FTEs paid by project lab.
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Selected publications 1. Cell, 2012 May 11, 149(4) 768-779
2. Cell. 2013 Sep 12;154(6):1269-84
3. Cell, 2013 Aug 29;154(5):1085-99
4. Nature. 2011 Dec 1;480(7375):113-7
5. Nature, 2012 Jan 26; 481:511-515
6. Nature. 2014 Aug 17. doi: 10.1038/nature13671
7. Science. 2012 Nov; 338(6109):956-959
8. Science. 2014 Sep 5;345(6201):1139-45.
9. Lancet, 2012 Mar 3;379(9818):785-7
10. Nature Biotechnology. 2014 Dec;32(12):1213-22.
11. Nature Biotechnology. 2015 Aug 10. [Epub ahead of print]
12. Science Signaling 2013 Oct 15;6(297):ra90
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BICF Services
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Flagship Projects
• Clinical Sequencing Project (Collaborate with Dr. Jim Malter, Dr. Ward Wakeland)
• Lung Cancer Project (Collaborate with Dr. David Gerber and John Minna)
• Kidney Cancer Project (Collaborate with Dr. Jim Brugarolas)
• Clinical Database Developments
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Flagship Projects
• Clinical Sequencing Project (Collaborate with Dr. Jim Malter, Dr. Ward Wakeland) – Set up the testing clinical server with local back ups
– Developed and tested the germline mutation calling pipeline
– developed and testing somatic mutation calling pipeline
– developed database and web portal for storing the raw data and results
– curating available database/resources for clinical actionable mutations
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Flagship Projects
• Lung Cancer Project (Collaborate with Dr. David Gerber and John Minna)
– Developed Lung Cancer Explorer for public data
– Team joined the IRB protocol for accessing UTSW lung cancer patient and tumor sample data
– Work with John Minna and Adi Gazdar to develop lung cancer cell line database
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Comprehensive database development Lung Cancer Explorer
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Data curation and analysis
Identification of appropriate datasets
Data curation and quality assessment
Data processing
Statistical analysis Alignment and integration
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Analysis functions for database infrastructure
Survival analysis Correlation analysis Group comparison
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Flagship Projects
• Kidney Cancer Project (Collaborate with Dr. Jim Brugarolas)
– Working with IR, Jim Brugarolas, Payal Kapur and others on clinical data curation
– Developing prototype database and web portal
– Transferred, stored and analyzed large amount of sequencing data
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Pilot Kidney Cancer Explorer Data
Kidney Cancer Program Total RNA-Seq1 Mutation
2
Patients 1402 95 101
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Goal of the clinical database
Secure Account System
User-friendly Data Input and Search
Track Account Login History
Track Clinical Data Change History
Collaborators Online Record Tool
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Thank you