ImmPort Data Release 27 Studies

July 2018

Study Program:

HIPC Signature Project

Title:

Correlation between human innate and adaptive immune responses to T-cell independent or dependent meningococcal vaccines.

Accession:

SDY1260

DOI:

10.21430/M3F47KSLLP

Subjects:

Study PI, contact:

Bali Pulendran, Emory Hope Clinic

Study Description:

Study objective: Thirty healthy adults (18-45 years of age) with no history of prior meningococcal vaccination and no contraindications to immunization will be vaccinated using either the meningococcal conjugate vaccine (MCV) or the meningococcal non-conjugate polysaccharide vaccine (MPSV). The study will be conducted as a randomized double blinded trial. Vaccine administration will be performed by an unblinded vaccine administrator, who will not be involved in subsequent assessments. Blood samples will be collected on Days D0 (at enrollment) and D3, D7, D14, D30 and D180 post vaccination to study innate and adaptive immunity markers. Even though meningococcal vaccination is considered safe, volunteers are asked to report any local or systemic AEs for 30 days post vaccination and any SAEs for 180 days post vaccination.

Publication(s):

Molecular signatures of antibody responses derived from a systems biology study of five human vaccines. Nature Immunology2014 Feb; 15(2): 195–204. 10.1038/ni.2789. Epub 2013 Dec 15.[PubMed]

Resources:

none

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Array	90
ELISA	711

Clinical Assessments in ImmPort:

none

Notes:

New Study

Study Program:

HIPC Signature Project

Title:

Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans

Accession:

SDY1264

DOI:

10.21430/M3XTBR8F18

Subjects:

Study PI, contact:

Bali Pulendran, Emory Hope Clinic

Study Description:

A major challenge in vaccinology is to prospectively determine vaccine efficacy. Here we have used a systems biology approach to identify early gene signatures that predicted immune responses in humans vaccinated with yellow fever vaccine YF-17D. Vaccination induced genes that regulate virus innate sensing and type I interferon production. Computational analyses identified a gene signature, including complement protein C1qB and eukaryotic translation initiation factor 2 alpha kinase 4, an orchestrator of the integrated stress response that correlated with and predicted YF-17D CD8+ T cell responses with up to 90% accuracy in an independent, blinded trial. A distinct signature, including B cell growth factor TNFRS17, predicted the neutralizing antibody response with up to 100% accuracy. These data highlight the utility of systems biology approaches in predicting vaccine efficacy.

Publication(s):

Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans. Nature Immunology 2009 Jan;10(1):116-125. doi: 10.1038/ni.1688. Epub 2008 Nov 23. [PubMed]

Resources:

none

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Array	87
Virus Neutralization	25

Clinical Assessments in ImmPort:

none

Notes:

New Study

Study Program:

HIPC Signature Project

Title:

Time series of global gene expression after trivalent influenza vaccination in humans

Accession:

SDY1276

DOI:

10.21430/M3J92GN8I3

Subjects:

226

Study PI, contact:

John Belmont, Baylor College of Medicine

Study Description:

The relationship between gene expression patterns and humoral immune response to vaccination was analyzed in order to understand the interindividual variability among immune response to vaccination

Publication(s):

Early patterns of gene expression correlate with the humoral immune response to influenza vaccination in humans. Journal of Infectious Disease 2011 Apr 1;203(7):921-9. doi: 10.1093/infdis/jiq156. Epub 2011 Feb 28. [PubMed]
Integrative genomic analysis of the human immune response to influenza vaccination. eLife 2013 Jul 16;2:e00299. doi: 10.7554/eLife.00299. [PubMed]

Resources:

Time series of global gene expression after trivalent influenza vaccination in humans (male cohort) [GSE48018]
Time series of global gene expression after trivalent influenza vaccination in humans (female cohort)[GSE480238]
Time series of global gene expression after trivalent influenza vaccination in humans [GSE48024]

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Hemagglutination Inhibition	2034
Neutralizing Antibody Titer Assay	2034
Array	848

Clinical Assessments in ImmPort:

none

Notes:

New Study

Study Program:

HIPC Signatures Project

Title:

Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses.

Accession:

SDY1289

DOI:

10.21430/M37CO9E6FQ

Subjects:

Study PI, contact:

Rafick-Pierre Sekaly, Department of Microbiology and Immunology, McGill University

Study Description:

Correlates of immune-mediated protection to most viral and cancer vaccines are still unknown. This impedes the development of novel vaccines to incurable diseases such as HIV and cancer. In this study, we have used functional genomics and polychromatic flow cytometry to define the signature of the immune response to the yellow fever (YF) vaccine 17D (YF17D) in a cohort of 40 volunteers followed for up to 1 yr after vaccination. We show that immunization with YF17D leads to an integrated immune response that includes several effector arms of innate immunity, including complement, the inflammasome, and interferons, as well as adaptive immunity as shown by an early T cell response followed by a brisk and variable B cell response. Development of these responses is preceded, as demonstrated in three independent vaccination trials and in a novel in vitro system of primary immune responses (modular immune in vitro construct [MIMIC] system), by the coordinated up-regulation of transcripts for specific transcription factors, including STAT1, IRF7, and ETS2, which are upstream of the different effector arms of the immune response. These results clearly show that the immune response to a strong vaccine is preceded by coordinated induction of master transcription factors that lead to the development of a broad, polyfunctional, and persistent immune response that integrates all effector cells of the immune system. peripheral blood samples from human newborns

Publication(s):

Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses. The Journal of Experimental Medicine 2008 Dec 22;205(13):3119-31. doi: 10.1084/jem.20082292. Epub 2008 Dec 1. [PubMed]

Resources:

NCBI GEO [GSE13699]
Publication [3119.full.pdf]

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Neutralizing Antibody Titer Assay	160
Array	142

Clinical Assessments in ImmPort:

none

Notes:

New Study

Study Program:

HIPC Signatures Project

Title:

Expression of genes associated with immunoproteasome processing of major histocompatibility complex peptides is indicative of protection with adjuvanted RTS,S malaria vaccine.

Accession:

SDY1293

DOI:

10.21430/M3ETOL8TGS

Subjects:

Study PI, contact:

Christian Ockenhouse, Malaria Research Initiative

Study Description:

Background. Patterns of expressed genes in the peripheral blood mononuclear cells of persons who were receiving RTS,S/AS01 or RTS,S/AS02 malaria vaccine and were undergoing experimental challenge with mosquito-borne falciparum malaria were examined to identify markers associated with protection.

Publication(s):

Expression of genes associated with immunoproteasome processing of major histocompatibility complex peptides is indicative of protection with adjuvanted RTS,S malaria vaccine. The Journal of Infectious Disease 2010 Feb 15;201(4):580-9. doi: 10.1086/650310. [PubMed]

Resources:

NCBI GEO [GSE18323]
Publication [650310]

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Array	254

Clinical Assessments in ImmPort:

none

Notes:

New Study

Study Program:

AMP RA/SLE

Title:

Identification of Three Rheumatoid Arthritis Disease Subtypes By Machine Learning Integration of Synovial Histologic Features and RNA Sequencing Data

Accession:

SDY1299

DOI:

10.21430/M3ODYABDL2

Subjects:

Study PI, contact:

Laura Donlin, Hospital for Special Surgery
Dana Orange, Hospital for Special Surgery

Study Description:

Gene expression analysis of RA and OA synovial tissue revealed 3 distinct synovial subtypes. These labels were used to generate a histologic scoring algorithm in which the histologic scores were found to be associated with parameters of systemic inflammation, including the erythrocyte sedimentation rate, CRP levels, and autoantibody levels. Comparison of gene expression patterns to clinical features revealed a potentially clinically important distinction: mechanisms of pain may differ in patients with different synovial subtypes.

Publication(s):

Identification of Three Rheumatoid Arthritis Disease Subtypes by Machine Learning Integration of Synovial Histologic Features and RNA Sequencing Data. Arthritis & Rheumetology 2018 May;70(5):690-701. doi: 10.1002/art.40428. Epub 2018 Apr 2. [PubMed]

Resources:

Hospital for Special Surgery hss
Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) AMP RA/SLE

Assays in ImmPort:

Assay Type	Number of Exp. Samples
RNA Sequencing	45
Assay	45

Clinical Assessments in ImmPort:

Arthritis Evaluations

Notes:

New Study

Study Program:

Slim Fourati

Title:

Transcriptional profiling of HBV-naive subjects before vaccination against Hepatitis A/B viruses, Diphtheria/Tetanus toxoids and Cholera.

Accession:

SDY1328

DOI:

10.21430/M3ID8ZC1AT

Subjects:

174

Study PI, contact:

Rafick-Pierre Sekaly, Case Western Reserve University,
Slim Fourati, Case Western Reserve University

Study Description:

Mechanisms of poor responses to vaccines remain unknown. Hepatitis B virus-naive elderly subjects received three vaccines, including a vaccine against hepatitis B virus (HBV). Pre-vaccination high dimensional analyses of blood using transcriptional profiling and flow cytometry revealed that subjects having increased memory B cell frequencies and higher expression of genes downstream of B cell receptor signaling responded more strongly to the HBV vaccine whereas subjects having higher expression of inflammatory related genes and greater numbers of activated innate immune cells showed a weaker response to this vaccine. The heme-induced response was associated with the poor response to the hepatitis B vaccine. Transcriptional profiling and flow cytometry results were validated in a distinct set of elderly subjects with accuracy greater than 60%. Our study is the first that identifies baseline predictors of responses to vaccines in a population of subjects known to be highly susceptible to infections.

Publication(s):

Pre-vaccination inflammation and B-cell signalling predict age-related hyporesponse to hepatitis B vaccination.Nature 2016 Jan 8;7:10369. doi: 10.1038/ncomms10369. [PubMed]

Resources:

ClinicalTrials.gov NCT01119703
Gene Expression Omnibus GSE65834

Assays in ImmPort:

Assay Type	Number of Exp. Samples
DNA Microarray	164

Clinical Assessments in ImmPort:

none

Notes:

New Study

Study Program:	Berkeley Protective Immunity Following Dengue Virus Natural Infections and Vaccination
Title:	Sequence-based HLA-A, B, C, DP, DQ, and DR typing
Accession:	SDY1337
DOI:	10.21430/M3M9Y78QLF
Subjects:	339
Study PI, contact:	Daniela Weiskopf, La Jolla Institute for Allergy and Immunology Alessandro Sette, La Jolla Institute for Allergy and Immunology
Study Description:	DNA sequence-based typing at the HLA-A, -B, -C, -DPB1, -DQA1, -DQB1, and -DRB1 loci
Publication(s):	Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 339 adults from Managua, NicaraguaHuman Immunology 2018 Jan;79(1):1-2. doi: 10.1016/j.humimm.2017.11.002. Epub 2017 Nov 7. [PubMed]
Resources:	none
Assays in ImmPort:	none
Clinical Assessments in ImmPort:	none
Notes:	New Study

Study Program:

HIPC Stanford Program

Title:

VZV vaccination in the elderly

Accession:

SDY111

DOI:

10.21430/M3ODYABDL2

Subjects:

Study PI, contact:

Jorg Goronzy, Stanford University School of Medecine

Study Description:

Healthy adults (50+ years old) with history of varicella but no history of zoster are vaccinated with Zostavax. Blood and serum are taken prior to vaccination and at several points after. A systems biology approach will be used to identify age-related decreases in immune function and potential predictors and correlates of protection.

Publication(s):

B-cell repertoire responses to varicella-zoster vaccination in human identical twins.Proc Natl Acad Sci USA 2015 Jan 13;112(2):500-5. doi: 10.1073/pnas.1415875112. Epub 2014 Dec 22. [PubMed]

Resources:

ClinicalTrials.gov [NCT01911065]

Assays in ImmPort:

Assay Type	Number of Exp. Samples
ELISA	20
ELISPOT	80
Luminex xMAP	20
HLA Typing	10
DNA Microarray	20
Luminex xMAP	40
Luminex xMAP	108

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

March of Dimes Human Microbiome

Title:

Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women.

Accession:

SDY1164

DOI:

10.21430/M37W3869AH

Subjects:

136

Study PI, contact:

David Relman, March of Dimes Prematurity Research Center at Stanford University School of Medicine

Study Description:

Recent studies about association between maternal vaginal microbiota and risks for preterm birth (PTB) conflicted along similar lines: Caucasian and Asian women cohorts showed associations between PTB and low Lactobacillus vaginal communities (BV-like) while no significant association with PTB was detected in cohorts of African-American women. This study compares two new larger cohorts of women at low and high risk for PTB, addressing two challenges: (i) low power resulting from the combination of small study populations (30–91 pregnant women), the many taxa measured by metabarcoding, and the absence of initial hypotheses more specific than some difference between preterm and term gestations; and (ii) insufficient understanding of population-specific factors that might modulate the PTB–microbiota association.

Publication(s):

Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women.Proc Natl Acad Sci USA 2017 Sep 12;114(37):9966-9971. doi: 10.1073/pnas.1705899114. Epub 2017 Aug 28. [PubMed]

Resources:

March of Dimes Prematurity Research Center at Stanford University Stanford
SRA – Raw sequencing data [SRP115697]
Stanford Digital Repository - Sequence table and R scripts for analysis workflow [yb681vm1809]

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Sequencing	2367

Clinical Assessments in ImmPort:

Pregnancy History

Notes:

Study updated

Study Program:

March of Dimes Human Microbiome

Title:

Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA

Accession:

SDY1175

DOI:

10.21430/M33PSZ2FHV

Subjects:

Study PI, contact:

Stephen Quake, March of Dimes Prematurity Research Center at Stanford University School of Medicine

Study Description:

Sequence data from cell free DNA found in 1351 blood samples collected from 188 patient was analyzed and assembled. 3761 of the 7190 larger contiguous regions generated were novel, with little or no homology to existing sequencing data. Presence of coding sequences in the contigs was confirmed in independent experiments and by direct PCR. The organisms identified represent entirely novel taxa, showing a substantially broader diversity in the human microbiome than previously appreciated.

Publication(s):

Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA. Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):9623-9628. doi: 10.1073/pnas.1707009114. Epub 2017 Aug 22. [PubMed]

Resources:

March of Dimes Prematurity Research Center at Stanford UniversityStanford
SRA – Lung transplant sequencing data [PRJNA263522]
SRA – Bone marrow transplant sequencing data [PRJNA385009]
SRA – Heart transplant sequencing data [PRJNA222186]

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Sequencing	58

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

March Of Dimes

Title:

Early pregnancy vaginal microbiome trends and preterm birth

Accession:

SDY1206

DOI:

10.21430/M3H1U3KJMZ

Subjects:

Study PI, contact:

Methodius Tuuli, Washington University in St. Louis School of Medicine
Molly Stout, Washington University in St. Louis School of Medecine

Study Description:

Previous studies have shown that vaginal microbiota of asymptomatic, nonpregnant, reproductive age women cluster into 5 distinct “community-state types”, which differ both by dominant Lactobacillus species as well as overall community composition. A much greater proportion of African-American and Hispanic women harbored a non-Lactobacillus-dominant community, suggesting that in some women a non-Lactobacillus-based vaginal community may be a normal variant. A recent study examined vaginal microbial composition and the risk for preterm birth but had very few African-American subjects and few preterm births. This study characterizes vaginal microbial community characteristics over time in a large predominantly African-American cohort of pregnant women and test whether particular community characteristics are associated with the risk for subsequent preterm birth.

Publication(s):

Early pregnancy vaginal microbiome trends and preterm birth. Am J Obstet Gynecol 2017 Sep;217(3):356.e1-356.e18. doi: 10.1016/j.ajog.2017.05.030. Epub 2017 May 23. [PubMed]

Resources:

SRA [PRJNA294119]

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Sequencing	149

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Systems Biology Approach to Study Influenza Vaccine 2011-12 in Healthy Children (see companion studies SDY364, SDY368, SDY387)

Accession:

SDY144

DOI:

10.21430/M3ANETOJEC

Subjects:

Study PI, contact:

Octavio Ramilo, Nationwide Children's Hospital

Study Description:

The treatment of pediatric immune system dysfunctions depends upon the basic understanding of its molecular and cellular components, as well as the inherent relationships between these components. Specifically, such knowledge requires an appreciation of B-Iymphocytes, T lymphocytes, natural killer cells and dendritic cells. Research investigating these cells and their functions necessitates the availability and acquisition of peripheral blood samples from healthy children to form control data groups against which various experimental conditions can be measured. Volunteers will be asked to donate blood samples to be used to further study the circulating dendritic cell subpopulations and establish their normal ranges. Blood samples will also be used to isolate antigen specific T lymphocytes, serve as a monocyte source and establish gene signatures.

Publication(s):

Differences in antibody responses between trivalent inactivated influenza vaccine and live attenuated influenza vaccine correlate with the kinetics and magnitude of interferon signaling in children. J Infect Dis. 2014 Jul 15;210(2):224-33. doi: 10.1093/infdis/jiu079. Epub 2014 Feb 4. [PubMed]

Resources:

Gene Expression Omnibus (GEO) [GSE52005]
EMBL-EBI [E-GEOD-52005]

Assays in ImmPort:

Assay Type	Number of Exp. Samples
HAI	32
Public Repository	64
Virus Neutralization	96
Flow Cytometry	52
Flow Cytometry	62
Flow Cytometry	124
Flow Cytometry	124
Flow Cytometry	124

Clinical Assessments in ImmPort:

Medical History, Vital Signs, Vaccination History

Notes:

Study updated

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Systems scale interactive exploration reveals quantitative and qualitative differences in response to 2009-2010 Fluzone influenza vaccine and pneumococcal vaccine

Accession:

SDY180

DOI:

10.21430/M3I44H8R17

Subjects:

Study PI, contact:

A. Karolina, Palucka, Baylor Reasearch Institute

Study Description:

Systems immunology approaches were employed to investigate innate and adaptive immune responses to influenza and pneumococcal vaccines. These two non-live vaccines show different magnitudes of transcriptional responses at different time points af- ter vaccination. Software solutions were developed to explore correlates of vaccine efficacy measured as antibody titers at day 28. These enabled a further dissection of transcriptional responses. Thus, the innate response, measured within hours in the peripheral blood, was dominated by an interferon transcriptional signature after influenza vaccination and by an inflammation signature after pneumo- coccal vaccination. Day 7 plasmablast responses induced by both vaccines was more pronounced after pneumococcal vaccination. Together, these results suggest that comparing global immune responses elicited by different vaccines will be critical to our understanding of the immune mechanisms underpinning successful vaccination.

Publication(s):

Systems scale interactive exploration reveals quantitative and qualitative differences in response to influenza and pneumococcal vaccines.Immunity 2013 Apr 18;38(4):831-44. doi: 10.1016/j.immuni.2012.12.008. [PubMed]

Resources:

Gene Expression Omnibus (GEO) [GSE30101]

Assays in ImmPort:

Assay Type	Number of Exp. Samples
DNA microarray	161
Hemagglutination Inhibition	24
Flow Cytometry	22081
Luminex xMAP	182
DNA Microarray	542
Virus Neutralization	89
Hemagglutination Inhibition	42
Luminex xMAP	47
Nanostring	18

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

HIPC Stanford Project

Title:

MEASURING THE EFFECT OF AGE ON INFLUENZA VACCINE RESPONSES

Accession:

SDY183

DOI:

10.21430/M37TU3LVTU

Subjects:

Study PI, contact:

PJ Utz, Stanford University, Stanford, CA

Study Description:

To comprehensively compare the humoral immune response of young (20-31 years old) to older human subjects (60 to >90 years old) following vaccination with seasonal flu vaccine. We generated a peptide microarray featuring tiled peptides with sequences derived from the hemagglutinin proteins of multiple influenza strains. We probed the microarrays with pre- and post-vaccination serum from each age group. Serum antibody reactivity to the microarray peptides was quantified using fluorescently labeled anti-human secondary antibodies and a fluorescent microarray scanner.

Publication(s):

Characterization of influenza vaccine immunogenicity using influenza antigen microarrays. PLoS One. 2013 May 29;8(5):e64555. doi: 10.1371/journal.pone.0064555. Print 2013. [PubMed]
Apoptosis and other immune biomarkers predict influenza vaccine responsiveness. Mol Syst Biol 2013 Apr 16;9:659. doi: 10.1038/msb.2013.15. [PubMed]

Resources:

Gene Expression Omnibus (GEO) [GSE43446]
Immune Epitope Database (IEDB) [1027229]

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Protein microarray	152

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Systems Biology Approach to Analysis of 2011-12 TIV Fluzone Influenza Vaccine Response in Healthy Individuals (see companion studies SDY74, SDY301)

Accession:

SDY296

DOI:

10.21430/M300RMFHZQ

Subjects:

Study PI, contact:

A. Karolina Palucka, Baylor Research Institute

Study Description:

This project will contribute to the overall vision and goals of this U19 by analyzing the immune response to Flu vaccination in healthy individuals. The knowledge generated in this Project will be transferred to Projects 3-5 where immune effects of vaccination will be studied in patients with underlying immune system alterations.

Publication(s):

none

Resources:

none

Assays in ImmPort:

Assay Type	Number of Exp. Samples
HAI	74
Virus Neutralization	74
Flow Cytometry	325
Flow Cytometry	325
Flow Cytometry	325
Flow Cytometry	219
Public Repository	42
Public Repository	36

Clinical Assessments in ImmPort:

Vaccination History

Notes:

Study updated

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Systems Biology Analysis of the response to Licensed Hepatitis B Vaccine (HEPLISAV) in Whole Blood (see companion studies SDY816 and SDY690)

Accession:

SDY299

DOI:

10.21430/M34QI37OT9

Subjects:

Study PI, contact:

Robert Coffman, Dynavax Technologies Corporation

Study Description:

This project will contribute to the overall vision and goals of this U19 by analyzing the role of adjuvants in the humoral response to hep B vaccination in healthy individuals.

Publication(s):

none

Resources:

None

Assays in ImmPort:

Assay Type	Number of Exp. Samples
DNA microarray	225
Nanostring	75

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Healthy Human DC and monocyte subsets transcriptional regulations in response to Fluzone 2010-2011 and pneumococcal vaccinations

Accession:

SDY300

DOI:

10.21430/M3FJJ9G9ZZ

Subjects:

Study PI, contact:

A. Karolina Palucka, Baylor Research Institute

Study Description:

The described experiments in this study were designed to deconvolute the molecular signature observed in the whole blood of healthy subsets at early time points following the administration of Fluzone 2010-2011 vaccines. RNA-seq data generated from sorted purified cell populations, including mDC and monocyte subsets will permit us to reveal distinct roles that DC and monocyte subsets play in eliciting immune responses to vaccines against flu in healthy adults using system biology approaches.

Publication(s):

none

Resources:

none

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Sequencing	90

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Systems Biology Approach to Analysis of 2012-13 TIV Fluzone Influenza Vaccine Response in Healthy Individuals (see companion studies SDY74, SDY296)

Accession:

SDY301

DOI:

Subjects:

Study PI, contact:

A. Karolina Palucka, Baylor Research Institute

Study Description:

Publication(s):

None

Resources:

none

Assays in ImmPort:

Assay Type	Number of Exp. Samples
FCM	642
HAI	213
Virus Neutralization	240
Public Repository	38

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

HIPC Stanford Project

Title:

T cell responses to H1N1v and a longitudinal study of seasonal influenza vaccination (TIV) - 2010 (See companion studies SDY315 2012 / SDY312 2009 / SDY314 2008 / SDY112 2011)

Accession:

SDY311

DOI:

0.21430/M3T0BGMGGC

Subjects:

Study PI, contact:

Mark Davis PhD, Stanford-LPCH Vaccine Program

Study Description:

Systems biology approach to examine effects of seasonal flu vaccination in adults of different ages on gene expression, cytokine stimulation and serum cytokines with parameters such as immune senescence to uncover new markers and mechanisms behind failure of immune function in many older people.

Publication(s):

none

Resources:

ClinicalTrials.gov [NCT01827462]

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Hemagglutination Inhibition	140
DNA microarray	73
CyTOF	79
Luminex xMAP	426
Flow Cytometry	464

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

HIPC Stanford Project

Title:

T cell responses to H1N1v and a longitudinal study of seasonal influenza vaccination (TIV) - 2009 (See companion studies SDY315 2012 / SDY314 2008 / SDY311 2010 / SDY112 2011)

Accession:

SDY312

DOI:

10.21430/M3G230OYOM

Subjects:

Study PI, contact:

Mark Davis PhD, Stanford University, Stanford, CA

Study Description:

Publication(s):

Defective Signaling in the JAK-STAT Pathway Tracks with Chronic Inflammation and Cardiovascular Risk in Aging Humans. Cell Syst. 2016 Oct 26;3(4):374-384.e4. doi: 10.1016/j.cels.2016.09.009. Epub 2016 Oct 13. [PubMed]

Resources:

ClinicalTrials.gov [NCT01827462]

Assays in ImmPort:

Assay Type	Number of Exp. Samples
DNA microarray	73
HAI	158
Flow Cytometry	531
Luminex xMAP	484
Flow Cytometry	624

Clinical Assessments in ImmPort:

ClinicalTrials.gov [NCT01827462]

Notes:

Study updated

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Systems Biology Approach to Study Influenza Vaccine 2012-13 in Healthy Children

Accession:

SDY364

DOI:

10.21430/M3U11KLQFF

Subjects:

Study PI, contact:

Mark M. Davis, Stanford University School of Medicine, Stanford, CA

Study Description:

Publication(s):

None

Resources:

None

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Flow Cytometry	348
Hemagglutination Inhibition	92
Virus Neutralization	138
DNA microarray	79

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Systems Biology Approach to Study Influenza Vaccine 2013-14 in Healthy Children

Accession:

SDY368

DOI:

10.21430/M3VUYLMJSR

Subjects:

Study PI, contact:

OCTAVIO RAMILO, NATIONWIDE CHILDREN'S HOSPITAL

Study Description:

Publication(s):

None

Resources:

None

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Hemagglutination Inhibition	132
Virus Neutralization	132
DNA microarray	87
Flow Cytometry	352

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Systems Biology Approach to Study Influenza Vaccine in Children with Autoimmunity (Juvenile Dermatomyositis JDM) 2011/2012 Cohort

Accession:

SDY369

DOI:

10.21430/M38SIW861C

Subjects:

Study PI, contact:

Virginia Pascual, Baylor Institute for Immunology Research

Study Description:

This Project will study vaccine responses in healthy and sick children. It will address the following questions: 1) which are the best biomarkers of protective immune response to influenza vaccine in healthy children; 2) how unique autoimmune backgrounds set the stage for responsiveness/unresponsiveness to vaccines; 3) whether vaccination contributes to increase the breadth of autoimmunity in a disease-specific manner. Ultimately, we expect that these studies will shed light on basic aspects of humoral immune responses to vaccines and will permit us to discover biomarkers of response that can be applied to healthy children and to the general population.

Publication(s):

None

Resources:

None

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Flow Cytometry	100
DNA microarray	12
Hemagglutination Inhibition	27
Virus Neutralization	27

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Systems Biology Approach to Study Influenza Vaccine in Children with Autoimmunity (Juvenile Dermatomyositis JDM) 2011/2012 Cohort

Accession:

SDY372

DOI:

10.21430/M3NOD39G06

Subjects:

Study PI, contact:

Virginia Pascual, Baylor Institute for Immunology Research

Study Description:

Publication(s):

None

Resources:

None

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Flow Cytometry	266
DNA microarray	71
Hemagglutination Inhibition	153
Virus Neutralization	153

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Systems Biology Approach to Study Influenza Vaccine in Children with Autoimmunity (Juvenile Dermatomyositis JDM) 2011/2012 Cohort

Accession:

SDY376

DOI:

10.21430/M37IMDD0RO

Subjects:

Study PI, contact:

Virginia Pascual, Baylor Institute for Immunology Research

Study Description:

Publication(s):

None

Resources:

None

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Flow Cytometry	196
DNA microarray	47
Hemagglutination Inhibition	66
Virus Neutralization	66

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Systems Biology Approach to Study Influenza Vaccine 2010-11 in Healthy Children

Accession:

SDY387

DOI:

10.21430/M34N2JOQQM

Subjects:

Study PI, contact:

Octavio Ramilo, Nationwide Children's Hospital

Study Description:

Publication(s):

Induction of ICOS+CXCR3+CXCR5+ TH cells correlates with antibody responses to influenza vaccination. Sci Transl Med. 2013 Mar 13;5(176):176ra32. doi: 10.1126/scitranslmed.3005191. [PubMed]

Resources:

None

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Flow Cytometry	195
Hemagglutination Inhibition	40
Virus Neutralization	120
DNA microarray	80

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

March of Dimes

Title:

Exploring the human maternal microbiome and its contribution to preterm birth

Accession:

SDY465

DOI:

10.21430/M3D491LGDT

Subjects:

Study PI, contact:

David Relman, March of Dimes Prematurity Research Center at Stanford University School of Medicine

Study Description:

Preterm births occur in 12 percent of pregnancies. Preterm infants are at risk for long term health problems such as impaired hearing and vision, cerebral palsy and developmental delays. This study will characterize the human maternal microbiome and host response profiles associated with term and preterm births and identify features of each that are predicitive of preterm labor and delivery.

Publication(s):

Temporal and spatial variation of the human microbiota during pregnancy. Proc Natl Acad Sci USA 2015 Sep 1;112(35):11060-5. doi: 10.1073/pnas.1502875112. Epub 2015 Aug 17. [PubMed]

Resources:

March of Dimes Prematurity Research Center at Stanford University Stanford
Stanford University R Markdown PNASRR

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Sequencing	4122

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Differences in Antibody Responses Between Trivalent Inactivated Influenza Vaccine and Live Attenuated Influenza Vaccine (2011-12) Correlate With the Kinetics and Magnitude of Interferon Signaling in Children

Accession:

SDY522

DOI:

10.21430/M3XZMA3XL4

Subjects:

Study PI, contact:

Octavio Ramilo, Nationwide Children's Hospital

Study Description:

Publication(s):

Differences in antibody responses between trivalent inactivated influenza vaccine and live attenuated influenza vaccine correlate with the kinetics and magnitude of interferon signaling in children. J Infect Dis 2014 Jul 15;210(2):224-33. doi: 10.1093/infdis/jiu079. Epub 2014 Feb 4. [PubMed]

Resources:

None

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Flow Cytometry	72
Hemagglutination Inhibition	36
Virus Neutralization	36
DNA microarray	72

Clinical Assessments in ImmPort:

Medical History, Vital Signs, Vaccination History

Notes:

Study updated

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Transcriptional specialization of human dendritic cell subsets in response to microbial vaccines

Accession:

SDY597

DOI:

10.21430/M3AC1WMBDO

Subjects:

Study PI, contact:

Romain Banchereau, Baylor Institute for Immunology Research

Study Description:

The mechanisms by which microbial vaccines interact with human APCs remain elusive.

Publication(s):

Transcriptional specialization of human dendritic cell subsets in response to microbial vaccines. Nat Commun 2014 Oct 22;5:5283. doi: 10.1038/ncomms6283. [PubMed]

Resources:

DC Modules [cdmodules]

Assays in ImmPort:

Assay Type	Number of Exp. Samples
DNA Microarray	413

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:

Population Genetics Analysis Program: Smallpox Vaccine Immunogenetics

Title:

Mayo Clinic Smallpox Vaccine Immunogenetics Replication Study

Accession:

SDY614

DOI:

10.21430/M3EEL6ILMK

Subjects:

1061

Study PI, contact:

Gregory Poland, Mayo Clinic

Study Description:

Smallpox Vaccine Immunogenetics

Publication(s):

Genome-wide association study of antibody response to smallpox vaccine. Vaccine 2012 Jun 13;30(28):4182-9. doi: 10.1016/j.vaccine.2012.04.055. Epub 2012 Apr 25. [PubMed]
A large population-based association study between HLA and KIR genotypes and measles vaccine antibody responses. PLoS One. 2017 Feb 3;12(2):e0171261. doi: 10.1371/journal.pone.0171261. eCollection 2017. [PubMed]

Resources:

none

Assays in ImmPort:

Assay Type	Number of Exp. Samples
ELISA	6197
ELISA	6201
ELISA	6282
ELISA	6282
ELISA	6226
ELISA	6274
ELISA	6282
ELISPOT	6330
ELISPOT	5958
Virus Neutralization	2136

Clinical Assessments in ImmPort:

None

Notes:

Study updated

Study Program:

SP2 Wistar.Defining defects in anti-viral immunity in the aged

Title:

Humoral responses to Influenza vaccination in aged populations - Year 2 2012

Accession:

SDY622

DOI:

10.21430/M34F1R11OM

Subjects:

Study PI, contact:

E. John Wherry, University of Pennsylvania
Hildegund Ertl, The Wistar Institute

Study Description:

The purpose of this study was to measure the B cell responses to the Trivalent Inactivated influenza Vaccine(TIV) in young and aged subjects, and measure their different B cell subsets.

Publication(s):

A shortened interval between vaccinations with the trivalent inactivated influenza vaccine increases responsiveness in the aged. Aging (Albany NY) 2015 Dec;7(12):1077-85. [PubMed]
BTLA expression declines on B cells of the aged and is associated with low responsiveness to the trivalent influenza vaccine. Oncotarget. 2015 Aug 14;6(23):19445-55. [PubMed]
Circulating CXCR5+PD-1+ response predicts influenza vaccine antibody responses in young adults but not elderly adults. J Immunol. 2014 Oct 1;193(7):3528-37. doi: 10.4049/jimmunol.1302503. Epub 2014 Aug 29. [PubMed]
Vaccine-induced boosting of influenza virus-specific CD4 T cells in younger and aged humans. PLoS One 2013 Oct 14;8(10):e77164. doi: 10.1371/journal.pone.0077164. eCollection 2013. [PubMed]
B cell responses to the 2011/12 - influenza vaccine in the agedAging (Albany NY) 2013 Mar;5(3):209-26. [PubMed]

Resources:

H. Ertl's Laboratory Wistar

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Flow Cytometry	186
ELISA	1134
Virus Neutralization	378
Flow Cytometry	944
DNA Microarray	132

Clinical Assessments in ImmPort:

None

Notes:

Study updated

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Systems Biology Approach to Study Influenza Vaccine in Children with Autoimmunity

Accession:

SDY645

DOI:

10.21430/M35HMSDTHH

Subjects:

Study PI, contact:

Virginia Pascual, Baylor Institute for Immunology Research

Study Description:

Publication(s):

None

Resources:

None

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Flow Cytmoetry	160
DNA Microarray	39
Hemagglutination Inhibition	464
Virus Neutralization	464
Array	234

Clinical Assessments in ImmPort:

None

Notes:

Study updated

Study Program:

SP2 Wistar.Defining defects in anti-viral immunity in the aged

Title:

Humoral responses to Influenza vaccination in aged populations - Year 3 2013

Accession:

SDY648

DOI:

10.21430/M3E3VOEDY2

Subjects:

Study PI, contact:

Hildegund Ertl, The Wistar Institute
E. John Wherry, University of Pennsylvania

Study Description:

The purpose of this study was to measure the B celland T cell responses to the Trivalent Inactivated influenza Vaccine(TIV) in young and aged subjects, and measure their different B cell subsets.

Publication(s):

A shortened interval between vaccinations with the trivalent inactivated influenza vaccine increases responsiveness in the aged. Aging (Albany NY). 2015 Dec;7(12):1077-85. [PubMed]
BTLA expression declines on B cells of the aged and is associated with low responsiveness to the trivalent influenza vaccine. Oncotarget. 2015 Aug 14;6(23):19445-55. [PubMed]
Circulating CXCR5+PD-1+ response predicts influenza vaccine antibody responses in young adults but not elderly adults. J Immunol. 2014 Oct 1;193(7):3528-37. doi: 10.4049/jimmunol.1302503. Epub 2014 Aug 29. [PubMed]
Vaccine-induced boosting of influenza virus-specific CD4 T cells in younger and aged humans. PLoS One 2013 Oct 14;8(10):e77164. doi: 10.1371/journal.pone.0077164. eCollection 2013. [PubMed]
B cell responses to the 2011/12 - influenza vaccine in the agedAging (Albany NY) 2013 Mar;5(3):209-26. [PubMed]

Resources:

H. Ertl's Laboratory [H. Ertl's Laboratory]

Assays in ImmPort:

Assay Type	Number of Exp. Samples
ELISA	1134
Virus Neutralization	378
Flow Cytometry	125
Flow Cytometry	124
Flow Cytometry	629
Flow Cytometry	126
Flow Cytometry	126
DNA microarray	124

Clinical Assessments in ImmPort:

none

Notes:

Study updated

Study Program:	HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans
Title:	The immune signature of palmoplantar pustulosis
Accession:	SDY667
DOI:	10.21430/M34NBAVDGJ
Subjects:	50
Study PI, contact:	Gerlinde Obermoser, Baylor Institute for Immunology research
Study Description:	This study will compare adult patients with CPP(chronic plaque type psoriasis ), who are currently not undergoing topical, systemic or biologic treatment and matched healthy controls. Baseline demographics and psoriasis history will be recorded. All PPP patients will be comprehensively phenotyped and psoriasis severity assessed including the body surface area (BSA) involved, Psoriasis Area and Severity Index (PASI), Physicians Global assessment (PGA) and Dermatology Life Quality Index (DLQI).
Publication(s):	None
Resources:	None
Assays in ImmPort:	none
Clinical Assessments in ImmPort:	none
Notes:	Study updated

Study Program:	Mayo HIPC Bioinformatics Approach to Influenza A/H1N1 Vaccine Immune Profiling
Title:	Bioinformatics Approach to 2010-2011 TIV Influenza A/H1N1 Vaccine Immune Profiling
Accession:	SDY67
DOI:	10.21430/M3OYWCJHO1
Subjects:	159
Study PI, contact:	Gregory Poland M.D., Mayo Clinic
Study Description:	Aim 1: Characterize Immune Profiles Over Time, Aim 2: Correlate Immune Profiles with Vaccine Immunogenicity,Aim 3: Replication of Immune Profiles and Verification of Models
Publication(s):	System-Wide Associations between DNA-Methylation, Gene Expression, and Humoral Immune Response to Influenza Vaccination. PLoS One. 2016 Mar 31;11(3):e0152034. doi: 10.1371/journal.pone.0152034. eCollection 2016. [PubMed] Gene signatures related to HAI response following influenza A/H1N1 vaccine in older individuals. Heliyon. 2016 May 6;2(5):e00098. doi: 10.1016/j.heliyon.2016.e00098. eCollection 2016 May. [PubMed] The impact of immunosenescence on humoral immune response variation after influenza A/H1N1 vaccination in older subjects. PLoS One 2015 Mar 27;10(3):e0122282. doi: 10.1371/journal.pone.0122282. eCollection 2015. [PubMed]
Resources:	NIH Reporter 5U01AI089859-05 [8695082]
Assays in ImmPort:	none
Clinical Assessments in ImmPort:	none
Notes:	Study updated with new data

Study Program:

MOLECULAR PROFILING AND IMMUNOMODULATORY INTERVENTIONS (CTOT-03, CTOT-04)

Title:

Correlation of Donor Proinflammatory mRNA Profiles with Early Outcomes of Thoracic and Abdominal Transplantation)

Accession:

SDY670

DOI:

10.21430/M3GLG1R2NY

Subjects:

311

Study PI, contact:

Abraham Shaked, University of Pennsylvania Medical Center

Study Description:

Inflammation and injuries to transplanted organs during the immediate post-operative period may be linked to early organ dysfunction and higher rates of transplant rejection in the recipient. Currently, mRNA expression of proinflammatory genes in donor tissues is thought to be a risk factor for early organ transplant dysfunction, increased expression of the recipients cell-mediated immunity genes, and organ rejection. The purpose of this study is to test the association between proinflammatory mRNA expression in donor samples and subsequent development of early organ dysfunction in kidney, lung, and liver transplant recipients. This study will also test the effects of proinflammatory mediators expressed in the transplanted organ pre- and post-reperfusion on organ rejection and genes expressed in cell mediated immune responses. This will be achieved by identifying the proinflammatory immune responses and their mechanisms.

Publication(s):

Validation of a current definition of early allograft dysfunction in liver transplant recipients and analysis of risk factors. Liver Transpl. 2010 Aug;16(8):943-9. doi: 10.1002/lt.22091. [PubMed]
Gene set enrichment analysis identifies key innate immune pathways in primary graft dysfunction after lung transplantation. Am J Transplant. 2013 Jul;13(7):1898-904. doi: 10.1111/ajt.12283. Epub 2013 May 24. Epub 2014 Oct 7. [PubMed]
Peripheral Blood Gene Expression Changes Associated With Primary Graft Dysfunction After Lung Transplantation. Am J Transplant. 2017 Jul;17(7):1770-1777. doi: 10.1111/ajt.14209. Epub 2017 Feb 17. [PubMed]

Resources:

ClinicalTrials.gov [NCT00531921]
NIH Reporter [25772230]

Assays in ImmPort:

Assay Type	Number of Exp. Samples
HLA Typing	495
DNA microarray	286

Clinical Assessments in ImmPort:

Electrocardiogram, Rejection, Biopsy, Pathology

Notes:

Study updated with new data

Study Program:

March of Dimes Human Microbiome

Title:

Simultaneously Monitoring Immune Response and Microbial Infections During Pregnancy through Plasma cfRNA Sequencing

Accession:

SDY673

DOI:

10.21430/M3OARGGSY0

Subjects:

Study PI, contact:

Stephen Quake, March of Dimes Prematurity Research Center at Stanford University School of Medicine

Study Description:

Plasma cell-free RNA (cfRNA) encompasses a broad spectrum of RNA species that can be derived from both human cells and microbes. Because cfRNA is fragmented and of low concentration, it has been challenging to profile its transcriptome using standard RNA-seq methods. This study assessed several recent RNA-seq methods on cfRNA samples to analyze the dynamic changes of both the human transcriptome and the microbiome of plasma during pregnancy. cfRNA reflected a well-orchestrated immune modulation during pregnancy: an up-regulation of anti-inflammatory genes and an increased abundance of anti-microbial genes, while the plasma microbiome remained relatively stable during pregnancy. The bacteria Ureaplasma shows an increased prevalence and increased abundance at postpartum, which is likely to be associated with postpartum infection. This study demonstrated that cfRNA-seq can be used to detect a number of human pathogens, including high loads of human parvovirus B19 virus (B19V), known to be a potential cause of complications in pregnancy.

Publication(s):

Simultaneously Monitoring Immune Response and Microbial Infections During Pregnancy through Plasma cfRNA Sequencing. Clin Chem. 2017 Nov;63(11):1695-1704. doi: 10.1373/clinchem.2017.273888. Epub 2017 Sep 13. [PubMed]

Resources:

MOD_Stanford_Prematurity_Center Stanford
SRA [PRJNA400333]

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Sequencing	58
RNA Sequencing	230
Q-PCR	111

Clinical Assessments in ImmPort:

None

Notes:

Study updated with new data

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Systems Biology Study to Investigate Immune Correlates to Hepatitis B Vaccine Engerix-B comparing cellular responses and gene expression patterns between PBMCs (cell sorts) and whole blood samples collected from healthy older adults

Accession:

SDY690

DOI:

10.21430/M3F8W7VA7O

Subjects:

Study PI, contact:

Robert Coffman, Dynavax Technologies Corporation

Study Description:

This project will contribute to the overall vision and goals of this U19 by analyzing the role of adjuvants in the humoral response to hep B vaccination in healthy individuals.

Publication(s):

none

Resources:

None

Assays in ImmPort:

Assay Type	Number of Exp. Samples
DNA microarray	192

Clinical Assessments in ImmPort:

None

Notes:

Study updated with new data

Study Program:

SP2 Wistar.Defining defects in anti-viral immunity in the aged

Title:

Humoral responses to Influenza vaccination in aged populations - Year 4 2014

Accession:

SDY739

DOI:

10.21430/M3F8W7VA7O

Subjects:

Study PI, contact:

Hildegund Ertl, The Wistar Institute

Study Description:

The purpose of this study was to measure the B celland T cell responses to the Trivalent Inactivated influenza Vaccine(TIV) in young and aged subjects, and measure their different B cell subsets.

Publication(s):

Resources:

H. Ertl's Laboratory Wistar

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Flow Cytometry	378
ELISA	1134
Virus Neutralization	378
Flow Cytometry	120
DNA microarray	126

Clinical Assessments in ImmPort:

None

Notes:

Study updated with new data

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Systems Biology Approach to Analysis of 2010-11 TIV Fluzone Influenza Vaccine Response in Healthy Individuals

Accession:

SDY74

DOI:

10.21430/M3EJ72RVRG

Subjects:

Study PI, contact:

A. Karolina Palucka, Baylor Research Institute

Study Description:

This study will measure the immune response to the influenza vaccine The long-term goal is to develop improved vaccines to infectious diseases such as influenza. Blood will be collected from patients at several visits before and after vaccination. The blood will be used in a series of immunological tests to measure the strength and breadth of immune response. These assays may include T cell and B cell activation assays, microarray testing, Epimax, Epigen, and flow cytometry.

Publication(s):

Induction of ICOS+CXCR3+CXCR5+ TH cells correlates with antibody responses to influenza vaccination. Sci Transl Med 2013 Mar 13;5(176):176ra32. doi: 10.1126/scitranslmed.3005191. [PubMed]

Resources:

None

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Flow Cytometry	459
DNA microarray	60

Clinical Assessments in ImmPort:

Vital Signs

Notes:

Study updated with new data

Study Program:

Mayo HIPC Bioinformatics Approach to Influenza A/H1N1 Vaccine Immune Profiling

Title:

Investigating Alterations to the Nasal Microbiome after Vaccination with LAIV

Accession:

SDY753

DOI:

10.21430/M3ENN2D3SZ

Subjects:

Study PI, contact:

Gregory Poland, Mayo Clinic

Study Description:

The goal of this proposal is to characterize alterations to the nasal microbiome after vaccination with the 2012-2013 seasonal LAIV and to correlate these changes with LAIV-specific immune responses (A/California/7/2009 (H1N1) and A/Victoria/361/2011 (H3N2)).

Publication(s):

None

Resources:

None

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Sequencing	121
ELISA	94

Clinical Assessments in ImmPort:

Vital Signs

Notes:

Study updated with new data

Study Program:

March of Dimes Human Microbiome

Title:

Inability to distinguish placental microbiome samples from contamination controls

Accession:

SDY775

DOI:

10.21430/M3PZM1ERD2

Subjects:

Study PI, contact:

Frederic Bushman, University of Pennsylvania School of Medicine
Samuel Parry, University of Pennsylvania School of Medicine

Study Description:

Placental samples from healthy deliveries were compared to an extensive set of bacterial contamination controls as well as to oral and vaginal samples from the same women. This control study was unable to distinguish bacterial species and abundance between placental and contamination control samples.

Publication(s):

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota. Microbiome 10.1186/s40168-016-0172-3 [PubMed]

Resources:

None

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Sequencing	69
Q-PCR	69

Clinical Assessments in ImmPort:

None

Notes:

Study updated with new data

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Systems Biology Analysis of the response to Licensed Hepatitis B Vaccine

Accession:

SDY816

DOI:

10.21430/M3HV9NRS67

Subjects:

Study PI, contact:

Robert Coffman, Dynavax Technologies Corporation

Study Description:

Out of 10 Donors, PBMC and 7 sort fractions were processed for 5 Donors(HEPLISAV-001,HEPLISAV-010,HEPLISAV-011,HEPLISAV-017,HEPLISAV-025) to assess for Microarray for all 9 time points. Further PBMC and 7 sort fractions were processed for 5 additional donors (HEPLISAV-002,HEPLISAV-005,HEPLISAV-019,HEPLISAV-024,HEPLISAV-026) to assess for Microarray for timepoint (days 0,1,7 and 35).

Publication(s):

None

Resources:

None

Assays in ImmPort:

Assay Type	Number of Exp. Samples
DNA Microarray	509
Q-PCR	69

Clinical Assessments in ImmPort:

None

Notes:

Study updated with new data

Study Program:

Immunogenetics of Measles Immunity - Mayo

Title:

The Immunogenetics of Measles Immunity

Accession:

SDY839

DOI:

10.21430/M3XWLPC8A2

Subjects:

2681

Study PI, contact:

Gregory Poland, Mayo Clinic

Study Description:

Specific Aim 1 (Discover) Genome-Wide Association Study [GWAS];Specific Aim 2 (Replicate) Targeted Association Studies;Specific Aim 3: (Validate) Functional Studies

Publication(s):

A large population-based association study between HLA and KIR genotypes and measles vaccine antibody responses. PLoS One. 2017 Feb 3;12(2):e0171261. doi: 10.1371/journal.pone.0171261. eCollection 2017. [PubMed]

Resources:

None

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Sequencing	54
ELISPOT	14598
Virus Neutralization	2626

Clinical Assessments in ImmPort:

None

Notes:

Study updated with new data

Study Program:

HIPC Baylor Systems Biology Approach to Study Influenza Vaccine in Healthy and Hyporesponsive Humans

Title:

Systems Biology Analysis of the response to Licensed Hepatitis B Vaccine (Engerix-B)

Accession:

SDY89

DOI:

10.21430/M3AYWX8NOT

Subjects:

Study PI, contact:

Robert Coffman, Dynavax Technologies Corporation

Study Description:

This project will contribute to the overall vision and goals of this U19 by analyzing the role of adjuvants in the humoral response to hep B vaccination in healthy individuals.

Publication(s):

None

Resources:

None

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Virus Neutralization	147
Flow Cytometry	384
DNA microarray	441

Clinical Assessments in ImmPort:

None

Notes:

Study updated with new data

Study Program:

RAVE

Title:

Rituximab for the Treatment of Wegener's Granulomatosis and Microscopic Polyangiitis (RAVE ITN021AI)

Accession:

SDY91

DOI:

10.21430/M3TK42R0QR

Subjects:

197

Study PI, contact:

Ulrich Specks, Mayo Clinic
John H. Stone, Johns Hopkins University

Study Description:

Antineutrophil cytoplasmic antibodies (ANCA)-associated vasculitis is the most common type of small blood vessel inflammation in adults. ANCA-associated vasculitis includes Wegener's granulomatosis (WG) and microscopic polyangiitis (MPA). Rituximab is a man-made antibody used to treat certain types of cancer. The purpose of this study is to determine the effectiveness of rituximab in treating patients with WG and MPA

Publication(s):

Rituximab versus cyclophosphamide for ANCA-associated vasculitis. J Am Soc Nephrol 2015 Apr;26(4):976-85. doi: 10.1681/ASN.2014010046. Epub 2014 Nov 7. [PubMed]
Design of the Rituximab in ANCA-associated Vasculitis (RAVE) Trial. The Open Arthritis Journal 2011, 4, 1-18 [PubMed]
Circulating angiopoietin-2 as a biomarker in ANCA-associated vasculitis. PLoS One. 2012;7(1):e30197. doi: 10.1371/journal.pone.0030197. Epub 2012 Jan 18. [PubMed]
Circulating markers of vascular injury and angiogenesis in antineutrophil cytoplasmic antibody-associated vasculitis. Arthritis Rheum. 2011 Dec;63(12):3988-97. doi: 10.1002/art.30615. [PubMed]
Efficacy of remission-induction regimens for ANCA-associated vasculitis. N Engl J Med 2013 Aug 1;369(5):417-27. doi: 10.1056/NEJMoa1213277. [PubMed]
Reanalysis of the Rituximab in ANCA-Associated Vasculitis trials identifies granulocyte subsets as a novel early marker of successful treatment. Arthritis Res Ther. 2015 Sep 21;17:262. doi: 10.1186/s13075-015-0778-z. [PubMed]
Pro: Should all patients with anti-neutrophil cytoplasmic antibody-associated vasculitis be primarily treated with rituximab? Nephrol Dial Transplant. 2015 Jul;30(7):1083-7. doi: 10.1093/ndt/gfv217. Epub 2015 May 21. [PubMed]

Resources:

Clinicaltrials.gov NCT00104299
The Open Arthritis Journal RAVE
ImmuneTolerance.org immunetolerance
ImmuneTolerance.org itntrialshare

Assays in ImmPort:

Assay Type	Number of Exp. Samples
Flow Cytometry	1151
ELISA	1175

Clinical Assessments in ImmPort:

Vasculitis Damage Index, Baseline Height, SF-36, Baseline Weight, Remission, BVAS/WG, Flares, Prednisone Taper

Notes:

Study updated with new data