DR39 DataRelease
Release Date: 06/04/2021
| SDY1352: INDIGO HLA and KIR part 1 | ||||||||||||||||
| Status: | New | |||||||||||||||
| Description: | High resolution HLA and KIR typing in five CNS-related diseases. | |||||||||||||||
| Program/Contract: |
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| DOI: | 10.21430/M38ED12JYE | |||||||||||||||
| Subjects: | 8708 | |||||||||||||||
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| Publications: | None | |||||||||||||||
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| Clinical Assessments: | None | |||||||||||||||
| SDY1613: Paired Heavy and Light Chain Immunoglobulin Reconstruction in Single-Cell RNA-Seq Data | |||||||
| Status: | New | ||||||
| Description: | We generated scRNA-Seq data for 20 human plasmablasts induced by seasonal flu vaccination.To reconstruct the paired heavy and light chain antibody genes, we developed several different in silico filtering strategies to enrich immunoglobulin transcripts, and then applied de novo assembly. This method successfully reconstructed productive IgH and IgL chains in 100% of cells analyzed. The accuracy of clonotype-assignment of individual cells was 94.5-98%, as validated by comparing BCR sequences reconstructed from NGS to those obtained by conventional single-B cell cloning methodology. This makes it possible to link the transcriptional programming of individual B cell clones at critical developmental stages with the eventual fate of the clonal lineage in vivo. | ||||||
| Program/Contract: |
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| DOI: | 10.21430/M351ZMQT4J | ||||||
| Subjects: | 3 | ||||||
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| Clinical Assessments: | None | ||||||
| SDY1689: Safety groups 1A & 1B: Safety, Immunogenicity, and Protective Efficacy of Radiation Attenuated Plasmodium falciparum NF54 | ||||||||||
| Status: | New | |||||||||
| Description: | A Phase 1 randomized, double blind, placebo-controlled trial to assess the safety, immunogenicity and tolerability of cryopreserved radiation attenuated Pf NF54 sporozoites (PfSPZ Vaccine) via direct venous inoculation (DVI) at increasing doses and assess the vaccine efficacy (VE) against naturally occurring infection in the main phase arms and controlled human malaria infection (CHMI) with PfSPZ Challenge (live Pf NF54 sporozoites) in the pilot phase arms of healthy African adults. After establishing safety of PfSPZ Vaccine in a pilot group (n=10), safety and efficacy was assessed by CHMI in 30 subjects who subjects received either 3 doses of PfSPZ Vaccine after pretreatment with artesunate amodiaquine (n=15) or without pretreatment (n=15). Results of CHMI was compared to 15 infectivity controls. Following the pilot studies, a randomized, double-blinded, placebo-controlled trial of safety and VE was conducted in 120 Malian adults with PfSPZ Vaccine (n=60) or normal saline (NS) placebo (n=60). VE was assessed by detection of Pf by thick blood smear (TBS) every 2 weeks or in response to symptomatic illness for 24 weeks after the last dose of vaccine or NS. | |||||||||
| Program/Contract: |
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| DOI: | 10.21430/M3TNVQXR7I | |||||||||
| Subjects: | 10 | |||||||||
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| Assays: | None | |||||||||
| Clinical Assessments: | None | |||||||||
| SDY1690: Vaccine Safety and Placebo Groups Arm 1C & 1D with CHMI: Safety, Immunogenicity, and Protective Efficacy of Radiation Attenuated Plasmodium falciparum NF54 | ||||||||||
| Status: | New | |||||||||
| Description: | A Phase 1 randomized, double blind, placebo-controlled trial to assess the safety, immunogenicity and tolerability of cryopreserved radiation attenuated Pf NF54 sporozoites (PfSPZ Vaccine) via direct venous inoculation (DVI) at increasing doses and assess the vaccine efficacy (VE) against naturally occurring infection in the main phase arms and controlled human malaria infection (CHMI) with PfSPZ Challenge (live Pf NF54 sporozoites) in the pilot phase arms of healthy African adults. After establishing safety of PfSPZ Vaccine in a pilot group (n=10), safety and efficacy was assessed by CHMI in 30 subjects who subjects received either 3 doses of PfSPZ Vaccine after pretreatment with artesunate amodiaquine (n=15) or without pretreatment (n=15). Results of CHMI was compared to 15 infectivity controls. Following the pilot studies, a randomized, double-blinded, placebo-controlled trial of safety and VE was conducted in 120 Malian adults with PfSPZ Vaccine (n=60) or normal saline (NS) placebo (n=60). VE was assessed by detection of Pf by thick blood smear (TBS) every 2 weeks or in response to symptomatic illness for 24 weeks after the last dose of vaccine or NS. | |||||||||
| Program/Contract: |
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| DOI: | 10.21430/M3TSUAJ9MA | |||||||||
| Subjects: | 45 | |||||||||
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| Assays: | None | |||||||||
| Clinical Assessments: | None | |||||||||
| SDY1691: Vaccine Efficay and Placebo Cohorts with Malaria Natural History Groups 2 & 3: Safety, Immunogenicity, and Protective Efficacy of Radiation Attenuated Plasmodium falciparum NF54 | ||||||||||
| Status: | New | |||||||||
| Description: | A Phase 1 randomized, double blind, placebo-controlled trial to assess the safety, immunogenicity and tolerability of cryopreserved radiation attenuated Pf NF54 sporozoites (PfSPZ Vaccine) via direct venous inoculation (DVI) at increasing doses and assess the vaccine efficacy (VE) against naturally occurring infection in the main phase arms and controlled human malaria infection (CHMI) with PfSPZ Challenge (live Pf NF54 sporozoites) in the pilot phase arms of healthy African adults. After establishing safety of PfSPZ Vaccine in a pilot group (n=10), safety and efficacy was assessed by CHMI in 30 subjects who subjects received either 3 doses of PfSPZ Vaccine after pretreatment with artesunate amodiaquine (n=15) or without pretreatment (n=15). Results of CHMI was compared to 15 infectivity controls. Following the pilot studies, a randomized, double-blinded, placebo-controlled trial of safety and VE was conducted in 120 Malian adults with PfSPZ Vaccine (n=60) or normal saline (NS) placebo (n=60). VE was assessed by detection of Pf by thick blood smear (TBS) every 2 weeks or in response to symptomatic illness for 24 weeks after the last dose of vaccine or NS. | |||||||||
| Program/Contract: |
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| DOI: | 10.21430/M3CI9DVM22 | |||||||||
| Subjects: | 120 | |||||||||
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| Clinical Assessments: | None | |||||||||
| SDY1700: Safety, Tolerability, and Immunogenicity of Plasmodium falciparum Sporozoite Vaccine Administered by Direct Venous Inoculation to Infants and Young Children | |||||||
| Status: | New | ||||||
| Description: | KSPZV1 is a single center study conducted in 2 parts. Part 1 is an age de-escalating, dose-escalating, randomized, double-blind, placebo-controlled trial enrolling malaria-exposed Kenyan children ages 5 months to 9 years at the time of first vaccination. One or two doses of the radiation-attenuated sporozoite-based PfSPZ Vaccine (8 per group) or normal saline placebo (4 per group) were administered by DVI at up to 5 different dosing levels using a staggered, dose-escalating design. Dosages include: 1.35 x10^5, 2.7 x10^5 (lowest two doses only in the two younger age groups), 4.5 x10^5, 9.0 x10^5, and 1.8 x10^6 PfSPZ in 13 cohorts of 12 participants each (3 dose cohorts among 5?9-year-olds, 5 among 1?5-year-olds, and 5 among 5?12-month-olds). Part 2 is a randomized, placebo controlled, double blind study in 5-12 month olds comparing the 3 highest does of PfSPZ Vaccine that are tolerated in part 1 (4.5 x10^5, 9.0 x10^5, and 1.8 x10^6 PfSPZ) with a normal saline placebo (randomized 1:1:1:1) to evaluate the safety , tolerability, immunogenicity and vaccine efficacy. | ||||||
| Program/Contract: |
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| DOI: | 10.21430/M3LMDEGZ3W | ||||||
| Subjects: | 165 | ||||||
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| Assays: | None | ||||||
| Clinical Assessments: | None | ||||||
| SDY1711: Safety, Tolerability, and Immunogenicity of Plasmodium falciparum Sporozoite Vaccine Administered by Direct Venous Inoculation to Infants and Young Children | |||||||
| Status: | New | ||||||
| Description: | KSPZV1 is a single center study conducted in 2 parts. Part 1 is an age de-escalating, dose-escalating, randomized, double-blind, placebo-controlled trial enrolling malaria-exposed Kenyan children ages 5 months to 9 years at the time of first vaccination. One or two doses of the radiation-attenuated sporozoite-based PfSPZ Vaccine (8 per group) or normal saline placebo (4 per group) were administered by DVI at up to 5 different dosing levels using a staggered, dose-escalating design. Dosages include: 1.35 x10^5, 2.7 x10^5 (lowest two doses only in the two younger age groups), 4.5 x10^5, 9.0 x10^5, and 1.8 x10^6 PfSPZ in 13 cohorts of 12 participants each (3 dose cohorts among 5?9-year-olds, 5 among 1?5-year-olds, and 5 among 5?12-month-olds). Part 2 is a randomized, placebo controlled, double blind study in malaria exposed infants ages 5-12 months, comparing the 3 highest does of PfSPZ Vaccine that are tolerated in part 1 (4.5 x10^5, 9.0 x10^5, and 1.8 x10^6 PfSPZ) with a normal saline placebo (randomized 1:1:1:1) to evaluate the safety , tolerability, immunogenicity and vaccine efficacy. | ||||||
| Program/Contract: |
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| DOI: | 10.21430/M3EJ9N4NC2 | ||||||
| Subjects: | 336 | ||||||
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| Assays: | None | ||||||
| Clinical Assessments: | None | ||||||
| SDY1715: A Retrospective Multicenter study to Determine Up to 5 Year Clinical Outcomes in Subjects Previously Randomized in the CTOT-11 Study (CTOT-23) | |||||||
| Status: | New | ||||||
| Description: | This study is a multicenter, non-randomized, retrospective, chart review study to collect long term (3 to 5 years post-transplant +/- 8 months) clinical outcome data on subjects previously enrolled in the CTOT-11 study. The CTOT-11 study randomized 163 subjects from September 2011 to September 2014. Eleven subjects withdrew consent, were lost to follow up, or died over the study period, and will not be included in the CTOT-23 study. This study will include up to 152 subjects. This study will be completed no later than December 2017. Each center will complete a retrospective chart review for the selected clinical variables identified in the Schedule of Events (Appendix 1), and enter the data in the Statistical and Clinical Coordinating Center (SACCC) electronic data capture system. | ||||||
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| DOI: | 10.21430/M3YRXTC32Z | ||||||
| Subjects: | 140 | ||||||
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| Assays: | None | ||||||
| Clinical Assessments: | None | ||||||
| SDY1734: Controlled malaria infection in Europeans and Africans | |||||||||
| Status: | New | ||||||||
| Description: | LACHMI-001 is a human trial to study immunity against Plasmodium falciparum in a controlled infection setting. | ||||||||
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| DOI: | 10.21430/M3UL8417LG | ||||||||
| Subjects: | 25 | ||||||||
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| Clinical Assessments: | None | ||||||||
| SDY1768: Evolutionary transcriptomics implicates HAND2 | ||||||||||
| Status: | New | |||||||||
| Description: | The developmental origins and evolutionary histories of cell types, tissues, and organs contribute to the ways in which their dysfunction produces disease. In mammals, the nature, development and evolution of maternal-fetal interactions likely influence diseases of pregnancy. Here we show genes that evolved expression at the maternal-fetal interface in Eutherian mammals play essential roles in the evolution of pregnancy and are associated with immunological disorders and preterm birth. Among these genes is HAND2, a transcription factor that suppresses estrogen signaling, a Eutherian innovation allowing blastocyst implantation. We found dynamic HAND2 expression in the decidua throughout the menstrual cycle and pregnancy, gradually decreasing to a low at term. HAND2 regulates a distinct set of genes in endometrial stromal fibroblasts including IL15, a cytokine also exhibiting dynamic expression throughout the menstrual cycle and gestation, promoting migration of natural killer cells and extravillous cytotrophoblasts. We demonstrate that HAND2 promoter loops to an enhancer containing SNPs implicated in birth weight and gestation length regulation. Collectively, these data connect HAND2 expression at the maternal-fetal interface with evolution of implantation and gestational regulation, and preterm birth. | |||||||||
| Program/Contract: |
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| DOI: | 10.21430/M3TSWJOVTM | |||||||||
| Subjects: | 1 | |||||||||
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| Clinical Assessments: | None | |||||||||
| SDY1769: Maternal and Infant Immune Repertoire Sequencing in PPROM study | |||||||
| Status: | New | ||||||
| Description: | To identify distinct features of immunoglobulin and T-cell receptor development in Preterm labor, the study analyzed T-cell receptor beta chain (TCR-?) and immunoglobulin heavy chain (IgH) diversity, CDR3 lengths, clonal sharing, and preferential usage of variable (V), diversity (D), and joining (J) gene segments. Additionally, the rates of somatic hypermutation (SHM) in IgH were studied. Overall, the cord blood IgH repertoires had significantly (padj < 0.05) lower rates of SHM and both TCR-? and IgH repertoires had shorter CDR3s compared to maternal blood. From the comparative analysis of term vs PPROM cord blood samples, RESULTs 1) CDR3 lengths correlated with gestational age, with the shorter CDR3s in preterm neonates suggesting a `less developed? repertoire. 2) Preterm cord blood displayed preferential usage of a number of V genes and J genes. 3) the term maternal repertoires displayed significant preferential usage of TRBV7-8 compared to preterm maternal repertoires. 4) Significantly higher prevalence of convergent clones between mother/baby pairs in preterm pregnancies. Together, these results suggest the repertoire of preterm infants displays a combination of immature features yet preferential use of particular genes and convergence with maternal TCR-? clones. While the higher TCR-? diversity might reflect less clonal expansion, the higher clonal convergence between mothers and infants in PTL could represent mother and fetus both responding to a shared stimulus like an infection. These data provide a detailed analysis of the maternal-fetal immune repertoire in term and preterm patients, and contribute to a better understanding of neonate immune repertoire development and potential changes associated with preterm labor | ||||||
| Program/Contract: |
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| DOI: | 10.21430/M3GUQMUDWL | ||||||
| Subjects: | 48 | ||||||
| Study PI, contact: |
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| Publications: | None | ||||||
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| Clinical Assessments: | None | ||||||
| SDY1772: Proteomic Signatures Predict Preeclampsia in Individual Cohorts but not Across Cohorts | |||||||
| Status: | New | ||||||
| Description: | Early identification of pregnant women at risk for preeclampsia (PE) is important. The study aimed to establish generalizability of quantitative analyses of plasma proteins (using SomaLogic multiplex aptamer-based platform) in two cohorts (Stanford, Detroit). A second aim was to examine the generalizability of protein signatures predictive of gestational age (GA) in uncomplicated pregnancies in the same cohorts to contrast physiological and pathological pregnancy outcomes. Serial blood samples were collected during the first, second, and third trimesters in 18 women who developed PE and 18 women with uncomplicated pregnancies (Stanford cohort). The second cohort (Detroit), used for comparative analysis, consisted of 76 women with PE and 90 women with uncomplicated pregnancies. Multivariate analyses were applied to infer predictive and cohort-specific proteomic models, which were then tested in the alternate cohort. Gene ontology (GO) analysis was performed to identify biological processes that were over-represented among top-ranked proteins associated with PE. Results: The model derived in the Stanford cohort was highly significant (p?=?3.9E?15) and predictive (AUC = 0.96), but failed validation in the Detroit cohort (p?=?9.7E?01, AUC = 0.50). The similarly result was for the Detroit cohort. By contrast, proteomic models predicting GA were readily validated across the two cohorts, indicating that the proteomic assay performed well enough to infer a generalizable model across studied cohorts. The study highlighted the need for performing such studies in diverse and well-phenotyped patient populations that are large enough to characterize subsets of patients with shared pathophysiologies to then derive subset-specific signatures of sufficient predictive power | ||||||
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| DOI: | 10.21430/M324Y3362V | ||||||
| Subjects: | 202 | ||||||
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| Clinical Assessments: | None | ||||||
| SDY404: Immunologic and genomic signatures of influenza vaccine response - 2011 (see companion studies SDY63, SDY400, SDY520) | |||||||||||
| Status: | Updated | ||||||||||
| Description: | Project 1: Immunologic and genomic signatures of influenza vaccine response - year2 2011 | ||||||||||
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| DOI: | 10.21430/M3GWQRC8DT | ||||||||||
| Subjects: | 72 | ||||||||||
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| Clinical Assessments: | None | ||||||||||
| SDY1469: B-cell Immunity to Influenza (SLVP017) 2011 | |||||||||
| Status: | Updated | ||||||||
| 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. | ||||||||
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| DOI: | 10.21430/M3HXQPVM9E | ||||||||
| Subjects: | 22 | ||||||||
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| Clinical Assessments: | None | ||||||||