UCSC Immunobrowser
Hyunsung John Kim
10/16/2013
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
What do B-cells and T-cells do?
http://www.hu.liu.se/ike/forskning/cellbiologi/ros
en-anders/rosen/1.264183/Bcell200.jpg
Sciencephoto.com
http://www.unm.edu/~mpachman/Blood/t_cel
l_killing_cancer_cell.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
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Complementarity Determining Regions
(CDR) determine binding specificity
Tertiary:
Secondary:
Primary:
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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
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
Blood Draw
Enrich cells for B/T lymphocytes
Amplify Recombined Regions
Sequence Recombined Regions with HTS
Data Analysis
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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
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Junctional Analysis
VJ gene segment usage
Wang et al, 2010
Robins et al, 2009
Boyd et al, 2009
Weinstein et al, 2009
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UCSC Immunobrowser
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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?