A cloud-based bioinformatic analytic infrastructure and Data Management Core for the Expanded Program on Immunization Consortium

Vignolo, Sofia M.; Diray‐Arce, Joann; McEnaney, Kerry; Rao, Shun; Shannon, Casey P.; Idoko, Olubukola T.; Cole, Fatoumata; Darboe, Alansana; Cessay, Fatoumatta; Ben‐Othman, Rym; Tebbutt, Scott J.; Kampmann, Beate; Levy, Ofer; Ozonoff, Al

doi:10.1017/cts.2020.546

Cited by 7 publications

(5 citation statements)

References 19 publications

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“…The Amazon Web Services (AWS) ( 52 ) ( https://aws.amazon.com ) cloud computing platform is used for encrypted, access-controlled data storage and data analysis resources. A data and analysis dashboard allows IMPACC investigators to upload and store raw and processed computable data, and features a centralized computing environment enabling investigators to perform their analyses ( 53 ). Therefore, the AWS platform provides a computing environment for developing, testing, and running scripts, and performing QC and QA on the raw data generated by the Core Labs.…”

Section: Data Management and Analysis Planmentioning

confidence: 99%

Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study

Team¹

2021

Sci. Immunol.

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The IMmunoPhenotyping Assessment in a COVID-19 Cohort (IMPACC) is a prospective longitudinal study designed to enroll 1000 hospitalized patients with COVID-19 (NCT04378777). IMPACC collects detailed clinical, laboratory and radiographic data along with longitudinal biologic sampling of blood and respiratory secretions for in depth testing. Clinical and lab data are integrated to identify immunologic, virologic, proteomic, metabolomic and genomic features of COVID-19-related susceptibility, severity and disease progression. The goals of IMPACC are to better understand the contributions of pathogen dynamics and host immune responses to the severity and course of COVID-19 and to generate hypotheses for identification of biomarkers and effective therapeutics, including optimal timing of such interventions. In this report we summarize the IMPACC study design and protocols including clinical criteria and recruitment, multi-site standardized sample collection and processing, virologic and immunologic assays, harmonization of assay protocols, high-level analyses and the data sharing plans.

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Section: Data Management and Analysis Planmentioning

confidence: 99%

Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study

Team¹

2021

Sci. Immunol.

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“…Data management and deposition. Data management for this project utilized a centralized cloud computing based management approach as previously described (54,55). Using quality control (QC) procedures for clinical, immunologic and epigenetic data, we implemented rigorous checks to ensure the reliability and accuracy of the datasets.…”

Section: Discussionmentioning

confidence: 99%

Respiratory Infection- and Asthma-prone, Low Vaccine Responder Children Demonstrate Distinct Mononuclear Cell DNA Methylation Pathways

Martino,

Schultz,

Kaur

et al. 2024

Preprint

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Background Infants with frequent viral and bacterial respiratory infections exhibit compromised immunity to routine immunisations. They are also more likely to develop chronic respiratory diseases in later childhood. This study investigated the feasibility of epigenetic profiling to reveal endotype-specific molecular pathways with potential for early identification and immuno-modulation. Peripharal immune cells from respiratory infection allergy/asthma prone (IAP) infants were retrospectively selected for genome-wide DNA methylation and single nucleotide polymorphism analysis. The IAP infants were enriched for the low vaccine responsiveness (LVR) phenotype (Fishers Exact p-value = 0.01). Results An endotype signature of 813 differentially methylated regions (DMRs) comprising 238 lead CpG associations (FDR < 0.05) emerged, implicating pathways related to asthma, mucin production, antigen presentation and inflammasome activation. Allelic variation explained only a minor portion of this signature. Stimulation of mononuclear cells with monophosphoryl lipid A (MPLA), a TLR agonist, partially reversing this signature at a subset of CpGs, suggesting the potential for epigenetic remodelling. Conclusions This proof-of-concept study establishes a foundation for precision endotyping of IAP children and highlights the potential for immune modulation strategies using adjuvants for furture investigation.

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“…Data management for this project utilized a centralized cloud computing-based management approach as previously described [ 53 , 54 ]. Using quality control (QC) procedures for clinical, immunologic and epigenetic data, we implemented rigorous checks to ensure the reliability and accuracy of the datasets.…”

Section: Methodsmentioning

confidence: 99%

Respiratory infection- and asthma-prone, low vaccine responder children demonstrate distinct mononuclear cell DNA methylation pathways

Martino,

Schultz,

Kaur

et al. 2024

Clin Epigenet

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Background Infants with frequent viral and bacterial respiratory infections exhibit compromised immunity to routine immunizations. They are also more likely to develop chronic respiratory diseases in later childhood. This study investigated the feasibility of epigenetic profiling to reveal endotype-specific molecular pathways with potential for early identification and immuno-modulation. Peripheral blood mononuclear cells from respiratory infection allergy/asthma-prone (IAP) infants and non-infection allergy/asthma prone (NIAP) were retrospectively selected for genome-wide DNA methylation and single nucleotide polymorphism analysis. The IAP infants were enriched for the low vaccine responsiveness (LVR) phenotype (Fisher's exact p-value = 0.02). Results An endotype signature of 813 differentially methylated regions (DMRs) comprising 238 lead CpG associations (FDR < 0.05) emerged, implicating pathways related to asthma, mucin production, antigen presentation and inflammasome activation. Allelic variation explained only a minor portion of this signature. Stimulation of mononuclear cells with monophosphoryl lipid A (MPL), a TLR agonist, partially reversed this signature at a subset of CpGs, suggesting the potential for epigenetic remodeling. Conclusions This proof-of-concept study establishes a foundation for precision endotyping of IAP children and highlights the potential for immune modulation strategies using adjuvants for future investigation.

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A cloud-based bioinformatic analytic infrastructure and Data Management Core for the Expanded Program on Immunization Consortium

Abstract: This version may be subject to change during the production process.

Cited by 7 publications

References 19 publications

Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study

Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study

Respiratory Infection- and Asthma-prone, Low Vaccine Responder Children Demonstrate Distinct Mononuclear Cell DNA Methylation Pathways

Respiratory infection- and asthma-prone, low vaccine responder children demonstrate distinct mononuclear cell DNA methylation pathways

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