Download Immune Epitope Database assays

Immune Epitope Database assays
Standard immune epitope definition
Classical (textbook) definition:
An epitope, also known as antigenic determinant, is
the part of an antigen that is recognized by the
immune system, specifically by antibodies, B cells, or
T cells; a molecular region on the surface of an
antigen capable of eliciting an immune response.
 We want to store information about all aspects of
epitopes in the IEDB
Populating the IEDB
Literature curation
Epitope discovery
contract submission
IEDB
www.iedb.org
Structure
Epitope
Source
Immunization
Context
Assay
Name
Chemical Type
Sequence
Domain / Region
Species
Strain
Antigen
Antigen Accession
Antigen Positions
Immunized Species
Immunogen Type
Administration
Antigen Type
Assay Type
Response Measured
MHC Allele
74A
Peptide/Protein
CLTEYILWV
Defined Epitope
Vaccinia virus Ankara
Ankara (MVA)
putative 21.7k protein
2772819
79-87
Homo sapiens
Source Species
Scarification
Epitope
ELISPOT
Cytokine Release-IFN-g
HLA-A*0201
Process for categorization and curation of
epitope references
Wang et al, BMC Bioinformatics, 2007
Literature Curation Status
Journal articles
Main Classes
Infectious
Disease
Allergy
Autoimmunity
Transplant
Total
Total
Relevant
Outstanding
%
Processed
8,651
395
98.9
768
38
98.3
3,889
2,858
47.5
605
582
3.8
13,913
3,873
80.4
 On track to be complete by end of this year
epitope
source
(material
entity)
organism
protein
protein
complex
High level database
structure
has part
peptide
epitope
structure
(material
entity)
discontinuous
protein
residues
is about
reference
(document)
journal
article
author
submission
carbohydrate
has participant
immune
recognition
assay
(process)
B cell response
T cell response
MHC binding
preceded by
immunization
(process)
Natural
Infection
Administered
Immunization
Vita et al, NAR, 2009
High level assay types
T
APC
MHC Binding MHC Ligand
Elution
T
B
APC
T Cell Response
B Cell Response
T cell assay example: IFN-g ELISA
T
APC
ell Response
• ELISA
=def: an assay where an enzyme linked antibody is used to detect
a plate bound material in a liquid (the evaluant) utilizing a
B
chemiluminescent
reaction. The detected signal is proxy for the
concentration of an analyte in the evaluant.
(this is actually not general enough; some ELISA formats are not
detecting an analyte but e.g. cross-blocking)
• ELISA IFN-gamma assay
=def: ELISA and analyte is IFN-gamma
Response
• BT Cell
cell epitope
ELISA IFN-g assay
=def: IFN-gamma ELISA and measurement datum is about some
‘epitope specific IFN-gamma release by T cells’
• epitope specific IFN-gamma release by T cells
=def: 'interferon-gamma production (GO_0032609)' and ('process
is result of' some 'MHC:epitope complex binding to TCR')
 Even the simplest assay we have requires implicitly that multiple
controls are analyzed, and the results compared, which looks a lot
like a study design.
No peptide
With peptide
T
T
APC
APC
With IFNg antibody
Without IFNg antibody
QTT 1 – epitope specific GO processes
GO:process
GO ID
rdfs:label (Label should be:
"epitope specific @A by T cells")
interleukin-2 production
GO_0032623 epitope specific interleukin-2
production by T cells
GO_0042098 epitope specific T cell proliferation
Definition
A process of interleukin-2 production by T cells
resulting from the recognition of a T cell epitope.
T cell proliferation
A process of T cell proliferation resulting from
the recognition of a T cell epitope.
T cell mediated cytotoxicity GO_0001913 epitope specific T cell mediated
A process of T cell mediated cytotoxicity
cytotoxicity
resulting from the recognition of a T cell epitope.
tolerance induction
GO_0002507 epitope specific tolerance induction by A process of tolerance induction by T cells
T cells
resulting from the recognition of a T cell epitope.
Definition editor
PERSON:Randi Vita,
Jason Greenbaum, Bjoern
Peters
PERSON:Randi
Vita,
Jason Greenbaum, Bjoern
PERSON:Randi Vita,
Jason Greenbaum, Bjoern
PERSON:Randi Vita,
Jason Greenbaum, Bjoern
•Excel spreadsheet that autoconverts to OWL via MappingMaster tool
• 51 of these
• Working with Martin (creater of MM) to fix bugs
• Imported GO processes into OBI
• Maintained in OBI, but should be IO
Assay techniques
• Created general
assays in OBI
3H-thymidine proliferation assay
51 chromium release assay
assay
BrdU incorporation assay
cytokine bioassay
cytometric bead array
ELISA
ELISPOT
flow cytometry assay
in vivo assay
intracellular staining assay
MHC tetramer/multimer staining
radio immuno assay (RIA)
reporter gene assay
RNA/DNA detection assay
surface plasmon resonance response assay
x-ray crystallography
QTT 2 – T cell epitope assays
IEDB IEDB label
Assay
ID
OBI ID of epitope OBI ID of
specific biological technique
process
198
cell proliferation assay (any/other)
OBI_1110182
49
cytokine release-IL-2 assay (ELISPOT)
OBI_1110056
48
cytokine release-IFNg assay (ELISPOT)
OBI_1110185
67
cytotoxicity assay (51 chromium release) OBI_1110204
73
cytokine release-IFNg assay (ELISA)
OBI_1110185
rdfs:label (could be: 'assay
type label' of 'is about label'
OBI_0000070 assay of epitope specific T cell
proliferation by T cells
OBI_0600031 ELISPOT assay of epitope
specific interleukin-2 production
OBI_0600031 ELISPOT assay of epitope
specific interferon-gamma
OBI_9999994 chromium release assay of
epitope specific killing by T cells
OBI_0000661 ELISA of epitope specific
interferon-gamma production by T
Definition
Measuring epitope specific T cell
proliferation by T cells using an assay
Measuring epitope specific interleukin-2
production by T cells using an ELISPOT
Measuring epitope specific interferongamma production by T cells using an
Measuring epitope specific killing by T cells
using a chromium release assay
Measuring epitope specific interferongamma production by T cells using an
• Excel spreadsheet that autoconverts to OWL via MappingMaster tool
• 51 of these
• Working with Martin (creater of MM) to fix bugs
• Maintained in OBI, but should be IO
Complex ‘assays’: Assessing impact of epitope
specific intervention on clinical findings
• Two groups of NOD mice that are model for diabetes; administer insulin
epitope to one group; compare histology of pancreas after two weeks to assess
disease course
 For us still one ‘assay’ as we get a single datum out for the efficacy of that
epitope intervention
 For others this is clearly a study design
Other complex assays:
• reduction of symptoms after treatment as a result of epitope specific T cells
• exacerbation of symptoms after treatment as a result of epitope specific T cells
• reduction of the presence of infectious agent as a result of epitope specific T
cells
• reduction of the presence of tumor tissue as a result of epitope specific T cells
• survival as a result of epitope specific T cells
Past Approach (Vancouver 2010)
• Use study design instead of assay for the complex cases.
• Problem1: Is it clear that IFN-g assay is really an assay if it has
internal controls?
• Problem2: A T cell epitope ELISA IFN-g assay could also be run
outside of an investigation, but study design is reserved for
that.
• Problem3: There are plenty of ‘assays’ right now e.g.
microarray experiments, the Edingburgh handedness assay
etc. that are just as complex as the above.
 We could not identify criteria that delineate ‘assay’ and ‘study
design execution’ based on complexity
Proposal
• Make ‘experiment’ an alternative term for ‘assay’
• Allow for complex assays. This would be done by specifying
more precisely what the output of an assay is about, like we
have done for ‘epitope specific IFN-g production by T cells’.
• For the intervention type ‘assays’, we would use a ‘clinical
assessment assay’ and make a subtype ‘clinical assessment of
epitope specific intervention efficacy’, where the datum
is_about effect of epitope specific intervention
• The distinction between study design execution and assay is
minimally that the former is only in an investigation
How to guarantee interoperability
study design vs. assay
• Chris and Jie’s use case requires tagging study designs that use
certain assays (among others)
• Proposal: Use QTT to create defined classes for e.g.
‘microarray study design’
=def: study design and
is_realized_in only (has_part some microarray assay)
• Define assays for all specific methodologies (e.g. FACS) and all
specific types of information determined (e.g. proliferation
assay)
• Define study designs for how comparisons between groups of
patients are made (e.g. double blinded; case-control; )