Publications by authors named "Carey Vincent"

Advancements in sequencing technologies and the development of new data collection methods produce large volumes of biological data. The Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) provides a cloud-based platform for democratizing access to large-scale genomics data and analysis tools. However, utilizing the full capabilities of AnVIL can be challenging for researchers without extensive bioinformatics expertise, especially for executing complex workflows.

View Article and Find Full Text PDF

Background: There have been multiple reports of the anti-IL-4Rα agent, dupilumab, being associated with the onset and/or progression of cutaneous T-cell lymphoma (CTCL).

Objective: We sought to evaluate safety signals associated with dupilumab, with a focus on CTCL, and to evaluate the possible underlying mechanism or mechanisms for the potential association.

Methods: First, we used the Food and Drug Administration's pharmacovigilance database, FAERS (FDA Adverse Event Reporting System), to evaluate whether dupilumab was associated with CTCL, including both positive outcome controls (conjunctivitis, eosinophilia, and arthralgia) and exposure controls (other medications with similar indications, including JAK inhibitors and the anti-IL-13 agent, tralokinumab) to evaluate confounding bias.

View Article and Find Full Text PDF

Chronic obstructive pulmonary disease (COPD) is a complex disease influenced by well-established environmental exposures (most notably, cigarette smoking) and incompletely defined genetic factors. The chromosome 4q region harbors multiple genetic risk loci for COPD, including signals near HHIP, FAM13A, GSTCD, TET2, and BTC. Leveraging RNA-Seq data from lung tissue in COPD cases and controls, we estimated the co-expression network for genes in the 4q region bounded by HHIP and BTC (~70MB), through partial correlations informed by protein-protein interactions.

View Article and Find Full Text PDF

Background: The COVID-19 pandemic disrupted the daily life and routines of Americans across the United States (U.S.), including those of our active-duty service members (ADSMs).

View Article and Find Full Text PDF
Article Synopsis
  • The study explores how the coronary artery calcium score (CACS) and the pulmonary artery to aorta diameter ratio (PA:A ratio) can predict cardiovascular events and COPD exacerbations in various COPD subtypes.
  • Results show that higher CACS is linked to an increased risk of cardiovascular events, while a higher PA:A ratio is associated with more frequent COPD exacerbations.
  • Participants with non-emphysema-predominant COPD displayed a stronger correlation between these measurements and adverse clinical outcomes compared to those with emphysema-predominant COPD.
View Article and Find Full Text PDF
Article Synopsis
  • The study investigates the link between COPD exacerbations and the risk of cardiovascular disease (CVD), using data from the long-term COPDGene study, which followed patients for up to 15 years.
  • It found that patients who frequently experience COPD exacerbations have a higher risk of developing CVD, regardless of their CVD status at the start of the study.
  • The results suggest that frequent exacerbators may require closer monitoring and management to address potential cardiovascular risks.
View Article and Find Full Text PDF

Background: Asthmatic symptoms often start during early childhood. Impulse oscillometry (IOS) is feasible in preschool children who may be unable to reliably perform spirometry measurements.

Objective: We sought to evaluate the use of IOS in a multicenter, multiethnic high-risk asthma cohort titled the Vitamin D Antenatal Asthma Reduction Trial.

View Article and Find Full Text PDF

The early life microbiome plays an important role in developmental and long-term health outcomes. However, it is unknown whether adverse pregnancy complications affect the offspring's gut microbiome postnatally and in early years. In a longitudinal cohort with a five-year follow-up of mother-child pairs affected by preeclampsia (PE) or spontaneous preterm birth (sPTB), we evaluated offspring gut alpha and beta diversity as well as taxa abundances considering factors like breastfeeding and mode of delivery.

View Article and Find Full Text PDF

This article provides an overview of the findings obtained from the Vitamin D Antenatal Asthma Reduction Trial (VDAART) spanning a period of 15 years. The review covers various aspects, including the trial's rationale, study design, and initial intent-to-treat analyses, as well as an explanation of why those analyses did not achieve statistical significance. Additionally, the article delves into the post hoc results obtained from stratified intent-to-treat analyses based on maternal vitamin D baseline levels and genotype-stratified analyses.

View Article and Find Full Text PDF

The literature of human and other host-associated microbiome studies is expanding rapidly, but systematic comparisons among published results of host-associated microbiome signatures of differential abundance remain difficult. We present BugSigDB, a community-editable database of manually curated microbial signatures from published differential abundance studies accompanied by information on study geography, health outcomes, host body site and experimental, epidemiological and statistical methods using controlled vocabulary. The initial release of the database contains >2,500 manually curated signatures from >600 published studies on three host species, enabling high-throughput analysis of signature similarity, taxon enrichment, co-occurrence and coexclusion and consensus signatures.

View Article and Find Full Text PDF

Background: The majority of high-throughput single-cell molecular profiling methods quantify RNA expression; however, recent multimodal profiling methods add simultaneous measurement of genomic, proteomic, epigenetic, and/or spatial information on the same cells. The development of new statistical and computational methods in Bioconductor for such data will be facilitated by easy availability of landmark datasets using standard data classes.

Results: We collected, processed, and packaged publicly available landmark datasets from important single-cell multimodal protocols, including CITE-Seq, ECCITE-Seq, SCoPE2, scNMT, 10X Multiome, seqFISH, and G&T.

View Article and Find Full Text PDF

Problem: Promotion of a healthy pregnancy is dependent on a coordinated immune response that minimizes inflammation at the maternal-fetal interface. Few studies investigated the effect of fetal sex on proinflammatory biomarkers during pregnancy and whether maternal race could impact this association. We aimed to examine whether fetal sex could, independently of maternal race/ethnicity and the condition of pregnancy (normal vs.

View Article and Find Full Text PDF

Background: Findings from observational studies suggest that dietary patterns may offer protective benefits against cognitive decline, but data from clinical trials are limited. The Mediterranean-DASH Intervention for Neurodegenerative Delay, known as the MIND diet, is a hybrid of the Mediterranean diet and the DASH (Dietary Approaches to Stop Hypertension) diet, with modifications to include foods that have been putatively associated with a decreased risk of dementia.

Methods: We performed a two-site, randomized, controlled trial involving older adults without cognitive impairment but with a family history of dementia, a body-mass index (the weight in kilograms divided by the square of the height in meters) greater than 25, and a suboptimal diet, as determined by means of a 14-item questionnaire, to test the cognitive effects of the MIND diet with mild caloric restriction as compared with a control diet with mild caloric restriction.

View Article and Find Full Text PDF

Associations of omega-3 fatty acids (-3) with allergic diseases are inconsistent, perhaps in part due to genetic variation. We sought to identify and validate genetic variants that modify associations of -3 with childhood asthma or atopy in participants in the Vitamin D Antenatal Asthma Reduction Trial (VDAART) and the Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC). Dietary -3 was derived from food frequency questionnaires and plasma -3 was measured via untargeted mass spectrometry in early childhood and children aged 6 years old.

View Article and Find Full Text PDF

Summary: The RaggedExperiment R / Bioconductor package provides lossless representation of disparate genomic ranges across multiple specimens or cells, in conjunction with efficient and flexible calculations of rectangular-shaped summaries for downstream analysis. Applications include statistical analysis of somatic mutations, copy number, methylation, and open chromatin data. RaggedExperiment is compatible with multimodal data analysis as a component of MultiAssayExperiment data objects, and simplifies data representation and transformation for software developers and analysts.

View Article and Find Full Text PDF

Background: Excessive weight is associated with the development of childhood asthma. However, trends among preterm and term offspring may differ.

Objective: To assess whether the association of longitudinal weight for age (WFA) and odds of asthma/recurrent wheeze in early life differs between children born preterm and those born at term.

View Article and Find Full Text PDF

Background: Prior studies suggest that vitamin D may modify the effects of environmental exposures; however, none have investigated gestational vitamin D and cumulative tobacco smoke exposure (TSE) throughout pregnancy and early life.

Objectives: This study investigated the effects of early life TSE on child lung function and the modulatory effects of gestational vitamin D on this association.

Methods: The VDAART (Vitamin D Antenatal Asthma Reduction Trial) recruited nonsmoking pregnant women and followed the mother-child pairs to age 6 years.

View Article and Find Full Text PDF

Background: The infant fecal microbiome is known to impact subsequent asthma risk, but the environmental exposures impacting this association, the role of the maternal microbiome, and how the microbiome impacts different childhood asthma phenotypes are unknown.

Methods: Our objective was to identify associations between features of the prenatal and early-life fecal microbiomes and child asthma phenotypes. We analyzed fecal 16 s rRNA microbiome profiling and fecal metabolomic profiling from stool samples collected from mothers during the third trimester of pregnancy (n = 120) and offspring at ages 3-6 months (n = 265), 1 (n = 436) and 3 years (n = 506) in a total of 657 mother-child pairs participating in the Vitamin D Antenatal Asthma Reduction Trial.

View Article and Find Full Text PDF
Article Synopsis
  • Scientists have a lot of data about gene activity saved in public places, but most of it isn’t used to help understand new experiments.
  • A new method helps researchers compare new gene data to this existing information without needing super fancy computers.
  • The tool, called GenomicSuperSignature, makes it easy for scientists to see how new data relates to old data and understand it better, even if their computer isn’t super powerful.
View Article and Find Full Text PDF

The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) was developed to address a widespread community need for a unified computing environment for genomics data storage, management, and analysis. In this perspective, we present AnVIL, describe its ecosystem and interoperability with other platforms, and highlight how this platform and associated initiatives contribute to improved genomic data sharing efforts.

View Article and Find Full Text PDF

Multiple studies have demonstrated an increased risk of chronic obstructive pulmonary disease (COPD) in heterozygous carriers of the AAT (alpha-1 antitrypsin) Z allele. However, it is not known if MZ subjects with COPD are phenotypically different from noncarriers (MM genotype) with COPD. To assess if MZ subjects with COPD have different clinical features compared with MM subjects with COPD.

View Article and Find Full Text PDF

Objective: To evaluate the properties of the cognitive battery used in the The is a randomized control trial to determine the relative effectiveness of the MIND diet in slowing cognitive decline and reducing brain atrophy in older adults at risk for Alzheimer's dementia.

Methods: The MIND cognitive function battery was administered at baseline to 604 participants of an average age of 70 years, who agreed to participate in the diet intervention study, and was designed to measure change over time. The battery included 12 cognitive tests, measuring the 4 cognitive domains of executive function, perceptual speed, episodic memory, and semantic memory.

View Article and Find Full Text PDF

There is emerging evidence linking fruit and vegetable consumption and cognitive function. However, studies focusing on the nutrients underlying this relationship are lacking. We aim to examine the association between plasma nutrients and cognition in a population at risk for cognitive decline with a suboptimal diet.

View Article and Find Full Text PDF