DR24 DataRelease
Release Date: 07/11/2017
| SDY673: Characterization of maternal serum gene expression and microbiome | |||||||||
| Status: | New | ||||||||
| 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. | ||||||||
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| DOI: | 10.21430/M3OARGGSY0 | ||||||||
| Subjects: | 50 | ||||||||
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| Clinical Assessments: | None | ||||||||
| SDY776: Causal Relationship of Maternal Height on Birth Size and Gestational Age at Birth | ||||||||||
| Status: | New | |||||||||
| Description: | Mendelian randomization analysis was conducted to assess the relationship between maternal height, gestational age and fetal growth measures. This study looked at 3 cohorts of Mother-Child pairs from Danemark (dbGAP study dbGAP https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000103.v1.p1), Norway (Norwegian Mother and Child Cohort: https://www.fhi.no/en/studies/moba/) and Finland (previous study http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1001365#pgen.1001365-Sacher1) The findings suggest that the observed association between maternal height and fetal growth measurements is mainly determined by the genetics of the baby. They also provide weak evidence that the association between maternal height and gestational age is causal. | |||||||||
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| DOI: | 10.21430/M3AM8G2I2Q | |||||||||
| Subjects: | 0 | |||||||||
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| Assays: | None | |||||||||
| Clinical Assessments: | None | |||||||||
| SDY888: Human Immune Signature of Dengue virus infection- Gene Expression of CD4 subsets | |||||||
| Status: | New | ||||||
| Description: | The human Immune Signature of Dengue virus infection was studied in two endemic areas. T cell responses were compared in infected patients and uninfected individuals also from Dengue endemic areas. | ||||||
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| DOI: | 10.21430/M3C4L4WD2Z | ||||||
| Subjects: | 79 | ||||||
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| Clinical Assessments: | None | ||||||
| SDY997: AMP Lupus Network Project: Molecular Characterization of Lupus Nephritis and Correlation with Response to Therapy | ||||||||||
| Status: | New | |||||||||
| Description: | Phase I will be devoted to the study of at least 45 subjects with lupus nephritis and 25 controls with the intent of achieving the following goals: (i) to assess feasibility of obtaining a sufficient yield of high quality data based on current and refined AMP SOPs, (ii) to assess recruitment rates and the number of sites necessary to effectively recruit for Phase II, (iii) to ensure that the technologies developed in Phase 0 are working well, especially with regard to transport and scaling up to handle specimens from multiple sites; (iv) to demonstrate that the selected technologies can be used for the purpose of reliably differentiating lupus nephritis kidneys from kidney tissue without lupus nephritis, (v) where necessary, to further refine the technologies before embarking on a large-scale project; and most importantly (vi) to provide critical data upon which to make rational decisions about key elements of the Phase II study design (e.g., eligibility criteria, estimates of variation for power calculations, and site-specific capability regarding patient recruitment, specimen handling, etc.). | |||||||||
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| DOI: | 10.21430/M35FLWNXH1 | |||||||||
| Subjects: | 105 | |||||||||
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| Publications: | None | |||||||||
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| SDY998: AMP Rheumatoid Arthritis Arthroplasty Phase 1 | ||||||||||||||||||||||||||||
| Status: | New | |||||||||||||||||||||||||||
| Description: | The primary goal for RA arthroplasty P1 studies are: To establish if molecular signatures and pathways identified using core AMP technologies differ between OA and RA in 20 RA surgical samples and 10 OA arthroplasty samples. | |||||||||||||||||||||||||||
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| DOI: | 10.21430/M3KXJHSP4T | |||||||||||||||||||||||||||
| Subjects: | 40 | |||||||||||||||||||||||||||
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| Publications: | None | |||||||||||||||||||||||||||
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| SDY999: AMP Rheumatoid Arthritis Synovial Phase 1 | |||||||||||||||||||||||||
| Status: | New | ||||||||||||||||||||||||
| Description: | The primary goal for RA synovial P1 studies are: To establish feasibility of obtaining ultrasound-guided synovial biopsies in the United States (U.S.) by comparing to frozen synovial biopsies obtained in the United Kingdom (U.K.) | ||||||||||||||||||||||||
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| DOI: | 10.21430/M3XRJHRPBC | ||||||||||||||||||||||||
| Subjects: | 22 | ||||||||||||||||||||||||
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| Publications: | None | ||||||||||||||||||||||||
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| SDY1109: CD4 Nicaragua Epitope ID | |||||||
| Status: | New | ||||||
| Description: | We performed DENV-specific epitope screening studies in the general population of Managua. Peptides with the capacity to bind HLA DR molecules most common in the Nicaraguan population have been predicted and screened in an HLA matched fashion in blood donors from the Nicaraguan Red Cross previously exposed to dengue virus. | ||||||
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| DOI: | 10.21430/M3VF5F8ANE | ||||||
| Subjects: | 128 | ||||||
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| Publications: | None | ||||||
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| Clinical Assessments: | None | ||||||
| SDY1173: Genetic Associations with Gestational Duration and Spontaneous Preterm Birth | ||||||||||
| Status: | New | |||||||||
| Description: | A genome wide association study was performed in a discovery set of samples obtained from 43,568 women of European ancestry using gestational duration as a continuous trait and term or preterm (<37 weeks) birth as a dichotomous outcome. Samples from three Nordic data sets (involving a total of 8643 women) were used to test for replication of genomic loci that had significant genome wide association (P<5.0?10?8) or an association with suggestive significance (P<1.0?10?6) in the discovery set. Four loci were associated significantly with gestational duration, and three showed association with preterm birth with genome wide significance. An analysis of mother?infant dyads suggested that these variants act at the level of the maternal genome. Data is shared at http://www.genestation.org/analysis/gwas/Zhang_2017/discovery | |||||||||
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| DOI: | 10.21430/M3F345ZL81 | |||||||||
| Subjects: | 0 | |||||||||
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| Assays: | None | |||||||||
| Clinical Assessments: | None | |||||||||
| SDY1175: Human microbiome characterization through massive shotgun sequencing of circulating cell-free DNA. | |||||||
| Status: | New | ||||||
| Description: | Cell-free DNA-derived microbiomes of 1,351 samples from 188 patients in four longitudinally sampled cohorts were analyzed. The majority of assembled sequences from cfDNA are derived from previously unidentified organisms, for instance numerous novel anelloviruses in immunocompromised patients, which represent a doubling of identified members in that viral family. Over two thirds of the sequences are bacterial, and the majority are most similar to proteobacteria; however, many large contigs can only be classified at the phylum or superkingdom level. Numerous novel phages were also found throughout the population. Multiple independent analyses confirm the existence of these novel sequences. | ||||||
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| DOI: | 10.21430/M33PSZ2FHV | ||||||
| Subjects: | 16 | ||||||
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| Clinical Assessments: | None | ||||||
| SDY1176: Extensive homeostatic T cell phenotypic variation within the Collaborative Cross | |||||||
| Status: | New | ||||||
| Description: | The Collaborative Cross (CC) is a panel of reproducible recombinant inbred mouse strains with high levels of standing genetic variation, thereby affording unprecedented opportunity to perform experiments in a small animal model containing controlled genetic diversity while allowing for genetic replicates. Here, we advance the utility of this unique mouse resource for immunology research, as it allows for both examination and genetic dissection of mechanisms behind adaptive immune states in mice with distinct and defined genetic makeups. This approach is founded on quantitative trait locus mapping: identifying genetically variant genome regions associated with phenotypic variance in traits-of-interest. Furthermore, the CC can be utilized for mouse model development; distinct strains have unique immunophenotypes and immune properties, making them suitable for research on particular diseases and infections. Here, we describe variation in cellular immune phenotypes across F1 crosses of CC strains, and reveal novel quantitative trait loci responsible for several immune phenotypes. | ||||||
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| DOI: | 10.21430/M3RKBKOYKS | ||||||
| Subjects: | 476 | ||||||
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| Publications: | None | ||||||
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| Clinical Assessments: | None | ||||||
| SDY1182: 35th Multicenter Airway Research Collaboration (MARC-35) | |||||||
| Status: | New | ||||||
| Description: | For enrolled infants hospitalized for bronchiolitis, structured interviews of the parents/guardians were performed by site investigators and clinical details were collected via emergency department and hospital inpatient chart reviews. Site teams collected both NS and NPA samples from infants within 24 hours of hospitalization. The composition of NS and NPA microbiota were characterized by sequencing the bacterial 16S rRNA gene V4 region on the Illumina MiSeq platform. Results indicated that there was considerable overlap between NS and NPA microbiota. Additionally, microbiota from both specimen types were associated with bronchiolitis severity. | ||||||
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| DOI: | 10.21430/M30E3B8H7H | ||||||
| Subjects: | 0 | ||||||
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| Assays: | None | ||||||
| Clinical Assessments: | None | ||||||
| SDY67: Bioinformatics Approach to 2010-2011 TIV Influenza A/H1N1 Vaccine Immune Profiling | |||||||||||||||||||||||||
| Status: | Updated | ||||||||||||||||||||||||
| 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 | ||||||||||||||||||||||||
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| DOI: | 10.21430/M3OYWCJHO1 | ||||||||||||||||||||||||
| Subjects: | 159 | ||||||||||||||||||||||||
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| Clinical Assessments: | None | ||||||||||||||||||||||||
| SDY144: Systems Biology Approach to Study Influenza Vaccine 2011-12 in Healthy Children (see companion studies SDY364, SDY368, SDY387) | |||||||||||
| Status: | Updated | ||||||||||
| 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. The assay results from SDY144's EXP13603, EXP11769, and EXP13604 are the same as for this study. The difference is how the floe cytometry results were analyzed in this study versus SDY144. |
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| DOI: | 10.21430/M3ANETOJEC | ||||||||||
| Subjects: | 17 | ||||||||||
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| SDY465: Exploring the human maternal microbiome and its contribution to preterm birth | |||||||
| Status: | Updated | ||||||
| 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 | ||||||
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| DOI: | 10.21430/M3D491LGDT | ||||||
| Subjects: | 47 | ||||||
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| SDY522: 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 (see companion studies SDY144, SDY360) | |||||||||||
| Status: | Updated | ||||||||||
| 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. | ||||||||||
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| DOI: | 10.21430/M3XZMA3XL4 | ||||||||||
| Subjects: | 20 | ||||||||||
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| SDY788: Immune Profiles to Predict Response to Desensitization Therapy in Highly HLA-Sensitized Kidney Transplant Candidates | |||||||||
| Status: | Updated | ||||||||
| Description: | Single-cell mass cytometry by time-of-flight (CyTOF) phenotyping, gene arrays, and phosphoepitope flow cytometry were performed in 20 highly sensitized kidney transplant candidates undergoing desensitization therapy. | ||||||||
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| DOI: | 10.21430/M3R0UUBC6K | ||||||||
| Subjects: | 22 | ||||||||
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| Clinical Assessments: | None | ||||||||