ucsc immunobrowser hyunsung john kim 10/16/2013. ucsc immunobrowser analyze status of adaptive...
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UCSC Immunobrowser
Hyunsung John Kim10/16/2013
UCSC Immunobrowser
• Analyze status of Adaptive Immune System• Tracks T-cells based on sequence signature in
the T-Cell Receptor Beta• Targeted Next Generation Sequencing
generates billions of data points• Can we provide Repertoire-level analysis while
preserving Receptor-level detail• Search the literature for clues on T-cell function
Adaptive Immune System
• Specific– Receptors to bind exclusively to a pathogen
• Diverse– Receptors can be designed to almost any pathogen
• Memory– Predesigned receptors are reused for subsequent
infections• Self/non-self recognition– T-Cells/B-Cells do not attack healthy self cells
Specific and Diverse Receptors
• Each receptor has a unique genome sequence
Memory
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What do B-cells and T-cells do?
http://www.unm.edu/~mpachman/Blood/t_cell_killing_cancer_cell.jpg
http://www.hu.liu.se/ike/forskning/cellbiologi/rosen-anders/rosen/1.264183/Bcell200.jpg
B-cell Helper T cell (TH) Cytotoxic T-cell (TC)
• Mature in Bone Marrow• Binds directly to antigen• Secretes soluble
antibodies• Antibodies aggregate
antigens, mark them for phagocytosis or lysis via the complement system
• Mature in Thymus• CD4+• Binds to peptide-MHC
class II molecules present only on Antigen Presenting Cells (APCs)
• Activates B-cells• Regulates Immune
response
• Mature in Thymus• CD8+• Binds to peptide-MHC
class I molecules present on most nucleated cells
• Destroys infected cells
Sciencephoto.com
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Complementarity Determining Regions (CDR) determine binding specificity
Tertiary:
Secondary:
Primary:
Specific and Diverse Receptors
CDRs
Random Receptor Sequence generated through VDJ Recombination
• ~1015-1020 Distinct TCR sequences
• Diversity generated through:– Combinatorial
Joining (left)– Random
Nucleotide addition
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Clonal Expansion Shapes the Repertoire
http://163.16.28.248/bio/activelearner/43/ch43c3.html
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What is an Immune Repertoire?
• Set of all BCR and TCR sequences in an individual– 1011 B-cells and T-cells
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Immunosequencing Workflow
Data Analysis
Sequence Recombined Regions with HTS
Amplify Recombined Regions
Enrich cells for B/T lymphocytes
Blood Draw
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Assay
Modified from Warran, et al 2009
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High throughput sequencers
454 Titanium• Long reads
– ~600bp reads• Medium throughput
– 106 reads• Preferred for B-cells
Illumina HiSeq• Short reads
– 2x100bp Paired-end reads• High throughput
– 3 x 109 reads• Preferred for T-cells
Junctional Analysis
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VJ gene segment usage
Wang et al, 2010
Boyd et al, 2009
Robins et al, 2009
Weinstein et al, 2009
UCSC Immunobrowser
• Takes in annotated sequence data• Generates Repertoire-level visuals• Persistent filters view subsets of a repertoire• Track clonal expansions over multiple samples– Identify aberrant clonal expansions (Blood cancers)– Track clonal expansions (Immune response)
• Search literature• RESTful urls makes sharing easy• (Dev) http://laozi.soe.ucsc.edu:8000
The Future
• Motif Finding• Group vs group comparisons• The personal sequencer– Regular TCR/IG sequencing• Integration with Medbook-like service
– Detect reoccurence of disease or relapse of autoimmune disease
– Know if you’ve got the flu or a cold
Fin.
• Thanks to:– Max Haeussler– Ngan Nguyen– You, for your time
• Questions?