Transcript The Immunology Database and Analysis Portal

FCM Data Management and Analysis in ImmPort
Richard H. Scheuermann, Ph.D.
Department of Pathology and Division of Biomedical Informatics
U.T. Southwestern Medical Center, Dallas, TX
Outline
• The Immunology Database and Analysis Portal –
ImmPort
• Data management challenges
– Support for large projects using diverse experiment
methodologies
– Extensive clinical data
• Automated FCM data analysis challenges
– Cross-sample comparison
• Linkage of automated FCM analysis results with
knowledge about cell types
– Use of the Cell Ontology
ImmPort Purpose and History
•
NIH/NIAID/DAIT would like to:
– maximize the return on the public investment in basic, translational and clinical
research
– allow investigators to more effectively extract meaningful information from the vast
amounts of data generated from advanced research technologies
– => data sharing policy
•
Bioinformatics Integration Support Contract (BISC) to support data sharing for all
DAIT-funded programs - basic, translational and clinical research
•
Immunology Database and Analysis Portal (ImmPort) - www.ImmPort.org
– Archive and manage basic and clinical research data
– Integrate these research data with extensive biological knowledge
– Support analysis of these integrated data
Home page
www.immport.org
Challenge 1
• Support for many large projects that use a
variety of different experiment
methodologies, including FCM
Browse Data/ ImmPort Research Data/ ImmPort Supported Programs
ImmPort Research Data | My Work Bench
Immune Function and Biodefense in Children, Elderly, and Immunocompromised Populations Program
Population Genetics Analysis Program: Immunity to Vaccines/Infections Program
HLA Region Genetics in Immune-Mediated Diseases Program
Immune Modeling Centers
Other Consortium Projects
Browse Data/ ImmPort Research Data/ ImmPort Supported Programs
ImmPort Research Data | My Work Bench
Immune Function and Biodefense in Children, Elderly, and Immunocompromised Populations Program
Grants/Contracts/Projects:
Project Title
An Improved Influenza A Vaccine for Rapid
Protection of the Elderly
Institution
The Wistar Institute
Principle
Investigator
Hildegund C. J. Ertl,
M.D.
Objective
To conduct pre-clinical studies needed to develop a vaccine
for the elderly that would provide protection in the event of a
bioterror attack with influenza A virus.
To determine the effects of chronic immunosuppressive
therapies on adaptive, innate and specific immunity
To propose a comprehensive analysis of the immunologic
Kinetic analysis of immunologic repletion and Children´s Hospital of
Sullivan, Kathleen,
response to killed trivalent influenza vaccine in different
influenza vaccine responsiveness
Philadelphia
Ph.D.
immunocompromised populations in order to understand
how to improve vaccine responses
To define comprehensively and in molecular and cellular
Immune Function and Biodefense in Children,
detail differences in recognition and response to microbeElderly, and Immunocompromised Populations:
Wilson, Christopher, derived danger signals between adults, neonates and infants,
University of Washington
TLRs in Innate Immunity and the Induction of
M.D.
and how these, in turn, contribute to differences in innate
Adaptive Immunity in the Neonate and Infant
immunity and the induction of antigen-specific (adaptive)
immunity
Oklahoma Medical
To understand why many patients with systemic lupus
Responses to Influenza Vaccination in Systemic
Thompson, Linda,
Research Foundation
erythematosus (SLE) fail to make adequate responses to
Lupus
Ph.D.
(OMRF)
immunization with the influenza vaccine.
To characterize immune markers and mechanisms in the
Immune function and Biodefense in Children, Oregon Health and Science Nikolich-Zugich,
elderly that determine their vulnerability to infectious and
Elderly and Immunocompromised Populations University
Janko, M.D., Ph.D.
bioterrorism agents in categories A-C.
To determine whether the different trimesters of pregnancy,
characterized by unique hormonal environments, are
Immune Response to Virus Infection During
Mt. Sinai School of
associated with (a) identifiable, discrete changes in maternal
Moran, Thomas, Ph.D.
Pregnancy
Medicine
systemic immunity and/or (b) recognizable alterations in
susceptibility to select bio-defense pathogens and/or (c)
differential responses to influenza vaccination
To identify the specific immune defects that make
Rochester Biodefense
University of Rochester
Sanz, Ignacio, M.D.
immunocomprised populations specially susceptible at
bioterrorists attack.
This proposal will explore the hypothesis that altered innate
Innate Immune Responsiveness in the Elderly
immune responsiveness in the elderly and the
Yale School of Medicine Fikrig, Erol, M.D.
and the Immunosuppressed
immunosuppressed contributes to vaccine unresponsiveness
or disease susceptibility.
Protective Immunity in Transplant Recipients
Emory Transplant Center
Larsen, Christian, Ph.D.
Number of
Subjects
Mechanistic Assays
600
ELISA, ELISPOT, Flow
Cytometry
90
ELISA, ELISPOT,
Microarry, RT - PCR
54
ELISPOT, Sequencing,
Flow Cytometry
17 adults, 17
neonates
RT-PCR, ELISA, Flow
Cytometry, Microarray
60
ELISPOT, ELISA,
multiplex RT-PCR
130
Flow Cytometry, ELISA,
RT-PCR, Gene expression,
75
Flow Cytometry, multiplex
ELISA, RT-PCR
280
Flow Cytometry
1160
SNP genotyping, Flow
Cytometry, ELISA
Challenge 2
• Extensive clinical data for correlative
analysis
AUTOMATED FCM ANALYSIS
Challenge 3
• Identification of same cell populations in
multiple samples
Challenge 4
• Linkage of automated results with
knowledge about known cell types
17 B Cell Populations in Blood
A
PB
GSM
GNSM
UM3-4
CD38
B220
CD27
UM1-2
N1-3
DNM
IgD
CD24
IgG
Population characteristics
Populationa
N1
N2
N3
Colorb
Gray
Magenta
Purple
CD27c
-
IgDc
+
+
+
IgGc
-
CD38c
+
+
CD24c
int
+
+
B220c
+
+
low
Proportiond
48.94%
4.69%
4.41%
Putative cell typea
naïve (CD38+)[Bm2?]
naïve (CD38-)
naïve (CD38+B220low)
UM1
UM2
UM3
UM4
Darkred
Salmon
Darkblue
Green
+
+
+
+
+
+
int
int
-
+
+
-
+
+
+
+
+
+
low
low
1.55%
0.94%
6.16%
11.50%
unswitched memory (CD38+)
unswitched memory (CD38-)[Bm1?]
IgDlow unswitched memory (CD38+)
IgDlow unswitched memory (CD38-)
GSM1
GSM2
GSM3
Grayishgreen
Yellow
Blue
+
+
+
+
-
+
+
+
+
+
-
+
+
+
+
low
low
0.36%
4.05%
4.40%
switching memory (IgD+IgG+CD38+)
switched memory (CD38+)[early Bm5?]
switched memory (CD38-)[late Bm5?]
GNSM1
GNSM2
GNSM3
GNSM4
Cyan
Darkgreen
Teal
Orange
+
+
+
+
-
-
+
+
-
+
+
+
-
low
low
+
low
4.84%
3.84%
1.30%
0.51%
IgD-IgG- memory
IgD-IgG- memory
IgD-IgG- memory
IgD-IgG- memory
DNSM1
DNSM2
Pink
Darkgray
-
-
+
-
-
-
+
+
0.85%
0.91%
double negative memory (IgG+)
double negative memory (IgG-)
PB
Red
high
-
-
high
-
low
0.75%
plasmablasts
Summary Statistics
B cell component of the Cell Ontology
http://www.obofoundry.org/
FCM Data Challenges
• Data management challenges
– Support for large projects using diverse experiment
methodologies
– Extensive clinical data for correlative analysis
• Automated FCM data analysis challenges
– Cross-sample comparison
• Linkage of automated FCM analysis results with
knowledge about cell types
– Use of the Cell Ontology
Acknowledgments
UT Southwestern
Yu (Max) Qian
David Dougall
Megan Kong
Jamie Lee
Jennifer Cai
Jie Huang
Nishanth Marthandan
Diane Xiang
Young Bun Kim
Paula Guidry
Eva Sadat
Northrop Grumman
John Campbell
Carl Dahlke
Yue Liu
Liz Thompson
Jeff Wiser
Mike Attasi
Ignacio Sanz (Rochester)
Chungwen Wei (Rochester)
Tim Mosmann (Rochester)
Adam Seegmiller (UTSW)
Nitin Karandikar (UTSW)
Christine Martens (Emory)
Chris Ding (UTA)
Immune Tolerance Network
Dave Parrish
Keith Boyce
Tom Casale
Jeff Bluestone
Alex Diehl (Jackson Labs)
Terry Meehan (Jackson Labs)
Martin Zand (Rochester)
Supported by NIH N01AI40076 and N01AI40041