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"Jacobson, Sean"
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Power and Sample Size Calculations for Genetic Association Studies in the Presence of Genetic Model Misspecification
2019
Introduction: When analyzing data from large-scale genetic association studies, such as targeted or genome-wide resequencing studies, it is common to assume a single genetic model, such as dominant or additive, for all tests of association between a given genetic variant and the phenotype. However, for many variants, the chosen model will result in poor model fit and may lack statistical power due to model misspecification. Objective: We develop power and sample size calculations for tests of gene and gene × environment interaction, allowing for misspecification of the true mode of genetic susceptibility. Methods: The power calculations are based on a likelihood ratio test framework and are implemented in an open-source R package (“genpwr”). Results: We use these methods to develop an analysis plan for a resequencing study in idiopathic pulmonary fibrosis and show that using a 2-degree of freedom test can increase power to detect recessive genetic effects while maintaining power to detect dominant and additive effects. Conclusions: Understanding the impact of model misspecification can aid in study design and developing analysis plans that maximize power to detect a range of true underlying genetic effects. In particular, these calculations help identify when a multiple degree of freedom test or other robust test of association may be advantageous.
Journal Article
Multiple biomarkers predict disease severity, progression and mortality in COPD
by
Miller, Bruce E.
,
Tal-Singer, Ruth
,
Bowler, Russell P.
in
Advanced glycosylation end products
,
Aged
,
Aged, 80 and over
2017
Background
Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease characterized by multiple subtypes and variable disease progression. Blood biomarkers have been variably associated with subtype, severity, and disease progression. Just as combined clinical variables are more highly predictive of outcomes than individual clinical variables, we hypothesized that multiple biomarkers may be more informative than individual biomarkers to predict subtypes, disease severity, disease progression, and mortality.
Methods
Fibrinogen, C-Reactive Protein (CRP), surfactant protein D (SP-D), soluble Receptor for Advanced Glycation Endproducts (sRAGE), and Club Cell Secretory Protein (CC16) were measured in the plasma of 1465 subjects from the COPDGene cohort and 2746 subjects from the ECLIPSE cohort. Regression analysis was performed to determine whether these biomarkers, individually or in combination, were predictive of subtypes, disease severity, disease progression, or mortality, after adjustment for clinical covariates.
Results
In COPDGene, the best combinations of biomarkers were: CC16, sRAGE, fibrinogen, CRP, and SP-D for airflow limitation (
p
< 10
−4
), SP-D, CRP, sRAGE and fibrinogen for emphysema (
p
< 10
−3
), CC16, fibrinogen, and sRAGE for decline in FEV
1
(
p
< 0.05) and progression of emphysema (
p
< 10
−3
), and all five biomarkers together for mortality (
p
< 0.05). All associations except mortality were validated in ECLIPSE. The combination of SP-D, CRP, and fibrinogen was the best model for mortality in ECLIPSE (
p
< 0.05), and this combination was also significant in COPDGene.
Conclusion
This comprehensive analysis of two large cohorts revealed that combinations of biomarkers improve predictive value compared with clinical variables and individual biomarkers for relevant cross-sectional and longitudinal COPD outcomes.
Journal Article
Basic Science and Pathogenesis
by
Betensky, Rebecca A
,
Wisniewski, Thomas
,
Jacobson, Sean R
in
Aged
,
Aged, 80 and over
,
Alzheimer Disease - blood
2025
Neutrophils play a role in Alzheimer's disease (AD) pathology and AD-related dementias (AD/ADRD), and prior research has shown that the neutrophil to lymphocyte ratio (NLR), a marker of neutrophil-mediated inflammation, is associated with the risk of future dementia. To date, studies looking at this relationship have used small cohorts. We address whether this is generalizable to larger populations using electronic health records (EHR) data from all six sites of NYU Langone Hospitals METHOD: Our study window ranged from 2011-2023. NLR values were obtained from laboratory test results. For each patient, the first NLR obtained was used; the associated date was taken to be the time origin. The outcome was AD/ADRD incidence, defined using ICD-codes over the same study window at least 6 months post-baseline. Cause-specific Cox regression was used to determine the independent association of log-transformed NLR values with the risk of future AD/ADRD adjusting for demographic and clinical confounders and with death as a censoring event. To account for confounding effects of covariates, the Cox model was weighted by the predicted probabilities of all adjusting covariates on binarized NLR (\"high\" if >median, \"low\" if
Journal Article
Structural and functional characterization of endothelial microparticles released by cigarette smoke
2016
Circulating endothelial microparticles (EMPs) are emerging as biomarkers of chronic obstructive pulmonary disease (COPD) in individuals exposed to cigarette smoke (CS), but their mechanism of release and function remain unknown. We assessed biochemical and functional characteristics of EMPs and circulating microparticles (cMPs) released by CS. CS exposure was sufficient to increase microparticle levels in plasma of humans and mice and in supernatants of primary human lung microvascular endothelial cells. CS-released EMPs contained predominantly exosomes that were significantly enriched in let-7d, miR-191; miR-126; and miR125a, microRNAs that reciprocally decreased intracellular in CS-exposed endothelium. CS-released EMPs and cMPs were ceramide-rich and required the ceramide-synthesis enzyme acid sphingomyelinase (aSMase) for their release, an enzyme which was found to exhibit significantly higher activity in plasma of COPD patients or of CS-exposed mice. The
ex vivo
or
in vivo
engulfment of EMPs or cMPs by peripheral blood monocytes-derived macrophages was associated with significant inhibition of efferocytosis. Our results indicate that CS, via aSMase, releases circulating EMPs with distinct microRNA cargo and that EMPs affect the clearance of apoptotic cells by specialized macrophages. These targetable effects may be important in the pathogenesis of diseases linked to endothelial injury and inflammation in smokers.
Journal Article
The value of blood cytokines and chemokines in assessing COPD
2017
Background
Blood biomarkers are increasingly used to stratify high risk chronic obstructive pulmonary disease (COPD) patients; however, there are fewer studies that have investigated multiple biomarkers and replicated in multiple large well-characterized cohorts of susceptible current and former smokers.
Methods
We used two MSD multiplex panels to measure 9 cytokines and chemokines in 2123 subjects from COPDGene and 1117 subjects from SPIROMICS. These biomarkers included: interleukin (IL)-2, IL-6, IL-8, IL-10, tumor necrosis factor (TNF)-α, interferon (IFN)-γ, eotaxin/CCL-11, eotaxin-3/CCL-26, and thymus and activation-regulated chemokine (TARC)/CCL-17. Regression models adjusted for clinical covariates were used to determine which biomarkers were associated with the following COPD phenotypes: airflow obstruction (forced expiratory flow at 1 s (FEV
1
%) and FEV
1
/forced vital capacity (FEV
1
/FVC), chronic bronchitis, COPD exacerbations, and emphysema. Biomarker-genotype associations were assessed by genome-wide association of single nucleotide polymorphisms (SNPs).
Results
Eotaxin and IL-6 were strongly associated with airflow obstruction and accounted for 3–5% of the measurement variance on top of clinical variables. IL-6 was associated with progressive airflow obstruction over 5 years and both IL-6 and IL-8 were associated with progressive emphysema over 5 years. None of the biomarkers were consistently associated with chronic bronchitis or COPD exacerbations. We identified one novel SNP (rs9302690 SNP) that was associated with CCL17 plasma measurements.
Conclusion
When assessing smoking related pulmonary disease, biomarkers of inflammation such as IL-2, IL-6, IL-8, and eotaxin may add additional modest predictive value on top of clinical variables alone.
Trial registration
COPDGene (ClinicalTrials.gov Identifier:
NCT02445183
).
Subpopulations and Intermediate Outcomes Measures in COPD Study (SPIROMICS) (
ClinicalTrials.gov
Identifier:
NCT 01969344
).
Journal Article
The neutrophil to lymphocyte ratio associates with markers of Alzheimer’s disease pathology in cognitively unimpaired elderly people
by
Zetterberg, Henrik
,
Osorio, Ricardo S.
,
Pomara, Nunzio
in
Aging
,
Alzheimer's disease
,
Amyloid
2024
Background
An elevated neutrophil–lymphocyte ratio (NLR) in blood has been associated with Alzheimer’s disease (AD). However, an elevated NLR has also been implicated in many other conditions that are risk factors for AD, prompting investigation into whether the NLR is directly linked with AD pathology or a result of underlying comorbidities. Herein, we explored the relationship between the NLR and AD biomarkers in the cerebrospinal fluid (CSF) of cognitively unimpaired (CU) subjects. Adjusting for sociodemographics, APOE4, and common comorbidities, we investigated these associations in two cohorts: the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and the M.J. de Leon CSF repository at NYU. Specifically, we examined associations between the NLR and cross-sectional measures of amyloid-β42 (Aβ42), total tau (t-tau), and phosphorylated tau
181
(p-tau), as well as the trajectories of these CSF measures obtained longitudinally.
Results
A total of 111 ADNI and 190 NYU participants classified as CU with available NLR, CSF, and covariate data were included. Compared to NYU, ADNI participants were older (73.79 vs. 61.53,
p
< 0.001), had a higher proportion of males (49.5% vs. 36.8%,
p
= 0.042), higher BMIs (27.94 vs. 25.79,
p
< 0.001), higher prevalence of hypertensive history (47.7% vs. 16.3%,
p
< 0.001), and a greater percentage of Aβ-positivity (34.2% vs. 20.0%,
p
= 0.009). In the ADNI cohort, we found cross-sectional associations between the NLR and CSF Aβ42 (β = -12.193,
p
= 0.021), but not t-tau or p-tau. In the NYU cohort, we found cross-sectional associations between the NLR and CSF t-tau (β = 26.812,
p
= 0.019) and p-tau (β = 3.441,
p
= 0.015), but not Aβ42. In the NYU cohort alone, subjects classified as Aβ + (
n
= 38) displayed a stronger association between the NLR and t-tau (β = 100.476,
p
= 0.037) compared to Aβ- subjects or the non-stratified cohort. In both cohorts, the same associations observed in the cross-sectional analyses were observed after incorporating longitudinal CSF data.
Conclusions
We report associations between the NLR and Aβ42 in the older ADNI cohort, and between the NLR and t-tau and p-tau in the younger NYU cohort. Associations persisted after adjusting for comorbidities, suggesting a direct link between the NLR and AD. However, changes in associations between the NLR and specific AD biomarkers may occur as part of immunosenescence.
Journal Article
Antidepressant exposure and long‐term dementia risk in a nationwide retrospective study on US veterans with midlife major depressive disorder
by
Corrigan, June K.
,
Madanes, Sharon
,
Brophy, Mary
in
Alzheimer's disease
,
antidepressants
,
dementia risk
2024
INTRODUCTION The use of antidepressants in major depressive disorder (MDD) has been reported to influence long‐term risk of Alzheimer's disease (AD) and AD‐related dementias (AD/ADRD), but studies are conflicting. METHODS We used inverse probability weighted (IPW) Cox models with time‐varying covariates in a retrospective cohort study among midlife veterans with MDD within the US Veterans Affairs healthcare system from January 1, 2000 to June 1, 2022. RESULTS A total of 35,200 patients with MDD were identified. No associations were seen regarding the effect of being exposed to any antidepressant versus no exposure on AD/ADRD risk (events = 1,056, hazard ratio = 0.94, 95% confidence interval: 0.81 to 1.09) or the exposure to specific antidepressant classes versus no exposure. A risk reduction was observed for female patients in a stratified analysis; however, the number of cases was small. DISCUSSION Our study suggests that antidepressant exposure has no effect on AD/ADRD risk. The association in female patients should be interpreted with caution and requires further attention. Highlights We studied whether antidepressant use was associated with future dementia risk. We specifically focused on patients after their first‐ever diagnosis of depression. We used IPW Cox models with time‐varying covariates and a large observation window. Our study did not identify an effect of antidepressant use on dementia risk. A risk reduction was observed in female patients, but the number of cases was small.
Journal Article
Basic Science and Pathogenesis
by
Jacobson, Sean R
,
Cejudo, Jaime Ramos
,
Figueredo, Luisa F
in
Aged
,
Alzheimer Disease - cerebrospinal fluid
,
Amyloid beta-Peptides - cerebrospinal fluid
2024
An elevated neutrophil-lymphocyte ratio (NLR) has been associated with Alzheimer's disease (AD). However, an elevated NLR has also been implicated in many other conditions that are risk factors for AD, prompting investigation into whether the NLR is directly linked with AD pathology or a result of underlying comorbidities.
We explored the relationship between the NLR and AD biomarkers in the cerebrospinal fluid (CSF) of cognitively unimpaired (CU) subjects. Adjusting for sociodemographics, APOE4, and common comorbidities, we investigated these associations in two cohorts: the Alzheimer's Disease Neuroimaging Initiative (ADNI) and NYU Center for Brain Health (CBH). Specifically, we examined associations between the NLR and cross-sectional measures of amyloid-β42 (Aβ42), total tau (t-tau), and phosphorylated tau
(p-tau
), as well as the trajectories of these CSF measures obtained longitudinally.
A total of 111 ADNI and 190 NYU participants classified as CU with available NLR, CSF, and covariate data were included. Compared to NYU, ADNI participants were older (73.79 vs. 61.53, p<0.001), had a higher proportion of males (49.5% vs. 36.8%, p = 0.042), higher BMIs (27.94 vs. 25.79, p<0.001), higher prevalence of hypertensive history (47.7% vs. 16.3%, p<0.001), and a greater percentage of Aβ-positivity (34.2% vs. 20.0%, p = 0.009) (Table 1). In the ADNI cohort, we found cross-sectional associations between the NLR and CSF Aβ42 (β = -12.193, p = 0.021), but not t-tau or p-tau
. In the NYU cohort, we found cross-sectional associations between the NLR and CSF t-tau (β = 26.812, p = 0.019) and p-tau
(β = 3.441, p<0.001), but not Aβ42. In the NYU cohort alone, subjects classified as Aβ+ (n = 38) displayed a stronger association between the NLR and t-tau (β = 100.476, p = 0.037) compared to Aβ- subjects or the non-stratified cohort (Figure 1). In both cohorts, the same associations observed in the cross-sectional analyses were observed after incoporating longitudinal CSF data (Figure 2).
We report associations between the NLR and Aβ42 in the older ADNI cohort, and between the NLR and t-tau and p-tau
in the younger NYU cohort. Associations persisted after adjusting for comorbidities, suggesting a direct link between the NLR and AD. However, changes in associations between the NLR and specific AD-biomarkers may occur as part of immunosenescence.
Journal Article
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