Machine learning models for blood pressure phenotypes combining multiple polygenic risk scores

We construct non-linear machine learning (ML) prediction models for systolic and diastolic blood pressure (SBP, DBP) using demographic and clinical variables and polygenic risk scores (PRSs). We developed a two-model ensemble, consisting of a baseline model, where prediction is based on demographic and clinical variables only, and a genetic model, where we also include PRSs. We evaluate the use of a linear versus a non-linear model at both the baseline and the genetic model levels and assess the improvement in performance when incorporating multiple PRSs. We report the ensemble model's performance as percentage variance explained (PVE) on a held-out test dataset. A non-linear baseline model improved the PVEs from 28.1% to 30.1% (SBP) and 14.3% to 17.4% (DBP) compared with a linear baseline model. Including seven PRSs in the genetic model computed based on the largest available GWAS of SBP/DBP improved the genetic model PVE from 4.8% to 5.1% (SBP) and 4.7% to 5% (DBP) compared to using a single PRS. Adding additional 14 PRSs computed based on two independent GWASs further increased the genetic model PVE to 6.3% (SBP) and 5.7% (DBP). PVE differed across self-reported race/ethnicity groups, with primarily all non-White groups benefitting from the inclusion of additional PRSs.

Whole genome sequence analysis of apparent treatment resistant hypertension status in participants from the Trans-Omics for Precision Medicine program

Introduction: Apparent treatment-resistant hypertension (aTRH) is characterized by the use of four or more antihypertensive (AHT) classes to achieve blood pressure (BP) control. In the current study, we conducted single-variant and gene-based analyses of aTRH among individuals from 12 Trans-Omics for Precision Medicine cohorts with whole-genome sequencing data. Methods: Cases were defined as individuals treated for hypertension (HTN) taking three different AHT classes, with average systolic BP ≥ 140 or diastolic BP ≥ 90 mmHg, or four or more medications regardless of BP (n = 1,705). A normotensive control group was defined as individuals with BP < 140/90 mmHg (n = 22,079), not on AHT medication. A second control group comprised individuals who were treatment responsive on one AHT medication with BP < 140/ 90 mmHg (n = 5,424). Logistic regression with kinship adjustment using the Scalable and Accurate Implementation of Generalized mixed models (SAIGE) was performed, adjusting for age, sex, and genetic ancestry. We assessed variants using SKAT-O in rare-variant analyses. Single-variant and gene-based tests were conducted in a pooled multi-ethnicity stratum, as well as self-reported ethnic/racial strata (European and African American). Results: One variant in the known HTN locus, KCNK3, was a top finding in the multi-ethnic analysis (p = 8.23E-07) for the normotensive control group [rs12476527, odds ratio (95% confidence interval) = 0.80 (0.74-0.88)]. This variant was replicated in the Vanderbilt University Medical Center's DNA repository data. Aggregate gene-based signals included the genes AGTPBP, MYL4, PDCD4, BBS9, ERG, and IER3. Discussion: Additional work validating these loci in larger, more diverse populations, is warranted to determine whether these regions influence the pathobiology of aTRH.

Adenotonsillectomy for Snoring and Mild Sleep Apnea in Children: A Randomized Clinical Trial

Importance

The utility of adenotonsillectomy in children who have habitual snoring without frequent obstructive breathing events (mild sleep-disordered breathing [SDB]) is unknown.

Objectives

To evaluate early adenotonsillectomy compared with watchful waiting and supportive care (watchful waiting) on neurodevelopmental, behavioral, health, and polysomnographic outcomes in children with mild SDB.

Design, Setting, and Participants

Randomized clinical trial enrolling 459 children aged 3 to 12.9 years with snoring and an obstructive apnea-hypopnea index (AHI) less than 3 enrolled at 7 US academic sleep centers from June 29, 2016, to February 1, 2021, and followed up for 12 months.

Intervention

Participants were randomized 1:1 to either early adenotonsillectomy (n = 231) or watchful waiting (n = 228).

Main Outcomes and Measures

The 2 primary outcomes were changes from baseline to 12 months for caregiver-reported Behavior Rating Inventory of Executive Function (BRIEF) Global Executive Composite (GEC) T score, a measure of executive function; and a computerized test of attention, the Go/No-go (GNG) test d-prime signal detection score, reflecting the probability of response to target vs nontarget stimuli. Twenty-two secondary outcomes included 12-month changes in neurodevelopmental, behavioral, quality of life, sleep, and health outcomes.

Results

Of the 458 participants in the analyzed sample (231 adenotonsillectomy and 237 watchful waiting; mean age, 6.1 years; 230 female [50%]; 123 Black/African American [26.9%]; 75 Hispanic [16.3%]; median AHI, 0.5 [IQR, 0.2-1.1]), 394 children (86%) completed 12-month follow-up visits. There were no statistically significant differences in change from baseline between the 2 groups in executive function (BRIEF GEC T-scores: -3.1 for adenotonsillectomy vs -1.9 for watchful waiting; difference, -0.96 [95% CI, -2.66 to 0.74]) or attention (GNG d-prime scores: 0.2 for adenotonsillectomy vs 0.1 for watchful waiting; difference, 0.05 [95% CI, -0.18 to 0.27]) at 12 months. Behavioral problems, sleepiness, symptoms, and quality of life each improved more with adenotonsillectomy than with watchful waiting. Adenotonsillectomy was associated with a greater 12-month decline in systolic and diastolic blood pressure percentile levels (difference in changes, -9.02 [97% CI, -15.49 to -2.54] and -6.52 [97% CI, -11.59 to -1.45], respectively) and less progression of the AHI to greater than 3 events/h (1.3% of children in the adenotonsillectomy group compared with 13.2% in the watchful waiting group; difference, -11.2% [97% CI, -17.5% to -4.9%]). Six children (2.7%) experienced a serious adverse event associated with adenotonsillectomy.

Conclusions

In children with mild SDB, adenotonsillectomy, compared with watchful waiting, did not significantly improve executive function or attention at 12 months. However, children with adenotonsillectomy had improved secondary outcomes, including behavior, symptoms, and quality of life and decreased blood pressure, at 12-month follow-up.

Trial Registration

ClinicalTrials.gov Identifier: NCT02562040.

Multilevel Risk Factors for Sleep-Disordered Breathing-Related Symptom Burden in an Urban Pediatric Community-Based Sample

BACKGROUND

Pediatric sleep-disordered breathing (SDB) disproportionately affects children with low socioeconomic status (SES). The multilevel risk factors that drive these associations are not well understood.

RESEARCH QUESTION

What are the associations between SDB risk factors, including individual health conditions (obesity, asthma, and allergies), household SES (maternal education), indoor exposures (environmental tobacco smoke [ETS] and pests), and neighborhood characteristics (neighborhood disadvantage), and pediatric SDB symptoms?

STUDY DESIGN AND METHODS

Cross-sectional analyses were performed on 303 children (aged 6-12 years) enrolled in the Environmental Assessment of Sleep Youth study from 2018 to 2022. Exposures were determined by caregiver reports, assays of measured settled dust from the child's bedroom, and neighborhood-level Census data (deriving the Childhood Opportunity Index to characterize neighborhood disadvantage). The primary outcome was the SDB-related symptom burden assessed by the OSA-18 questionnaire total score. Using linear regression models, we calculated associations between exposures and SDB-related symptom burden, adjusting for sociodemographic factors, then health conditions, indoor environment, and neighborhood factors.

RESULTS

The sample included 303 children (39% Hispanic, Latino, Latina, or Spanish origin; 30% Black or African American; 22% White; and 11% other). Increasing OSA-18 total scores were associated with low household SES after adjustment for demographic factors, and with asthma, allergies, ETS, pests (mouse, cockroach, and rodents), and an indoor environmental index (sum of the presence of pests and ETS; 0-2) after adjusting for sociodemographic factors. Even after further adjusting for asthma, allergies, and neighborhood disadvantage, ETS and pest exposure were associated with OSA-18 (ETS: β = 12.80; 95% CI, 7.07-18.53, also adjusted for pest; pest exposure: β = 3.69; 95% CI, 0.44-6.94, also adjusted for ETS).

INTERPRETATION

In addition to associations with ETS, a novel association was observed for indoor pest exposure and SDB symptom burden. Strategies to reduce household exposure to ETS and indoor allergens should be tested as approaches for reducing sleep health disparities.

Recommendations for clinical management of excessive daytime sleepiness in obstructive sleep apnoea - A Delphi consensus study

STUDY OBJECTIVE

Excessive daytime sleepiness is common with obstructive sleep apnoea and can persist despite efforts to optimise primary airway therapy. The literature lacks recommendations regarding differential diagnosis and management of excessive daytime sleepiness in obstructive sleep apnoea. This study sought to develop expert consensus statements to bridge the gap between existing literature/guidelines and clinical practice.

METHODS

A panel of 10 international experts was convened to undertake a modified Delphi process. Statements were developed based on available evidence identified through a scoping literature review, and expert opinion. Consensus was achieved through 3 rounds of iterative, blinded survey voting and revision to statements until a predetermined level of agreement was met (≥80 % voting "strongly agree" or "agree with reservation").

RESULTS

Consensus was achieved for 32 final statements. The panel agreed excessive daytime sleepiness is a patient-reported symptom. The importance of subjective/objective evaluation of excessive daytime sleepiness in the initial evaluation and serial management of obstructive sleep apnoea was recognised. The differential diagnosis of residual excessive daytime sleepiness in obstructive sleep apnoea was discussed. Optimizing airway therapy (eg, troubleshooting issues affecting effectiveness) was addressed. The panel recognised occurrence of residual excessive daytime sleepiness in obstructive sleep apnoea despite optimal airway therapy and the need to evaluate patients for underlying causes.

CONCLUSIONS

Excessive daytime sleepiness in patients with obstructive sleep apnoea is a public health issue requiring increased awareness, recognition, and attention. Implementation of these statements may improve patient care, long-term management, and clinical outcomes in patients with obstructive sleep apnoea.

Anaerobic pathogens associated with OSA may contribute to pathophysiology via amino-acid depletion

BACKGROUND

The human microbiome is linked to multiple metabolic disorders such as obesity and diabetes. Obstructive sleep apnoea (OSA) is a common sleep disorder with several metabolic risk factors. We investigated the associations between the gut microbiome composition and function, and measures of OSA severity in participants from a prospective community-based cohort study: the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).

METHODS

Bacterial-Wide Association Analysis (BWAS) of gut microbiome measured via metagenomics with OSA measures was performed adjusting for clinical, lifestyle and co-morbidities. This was followed by functional analysis of the OSA-enriched bacteria. We utilized additional metabolomic and transcriptomic associations to suggest possible mechanisms explaining the microbiome effects on OSA.

FINDINGS

Several uncommon anaerobic human pathogens were associated with OSA severity. These belong to the Lachnospira, Actinomyces, Kingella and Eubacterium genera. Functional analysis revealed enrichment in 49 processes including many anaerobic-related ones. Severe OSA was associated with the depletion of the amino acids glycine and glutamine in the blood, yet neither diet nor gene expression revealed any changes in the production or consumption of these amino acids.

INTERPRETATION

We show anaerobic bacterial communities to be a novel component of OSA pathophysiology. These are established in the oxygen-poor environments characteristic of OSA. We hypothesize that these bacteria deplete certain amino acids required for normal human homeostasis and muscle tone, contributing to OSA phenotypes. Future work should test this hypothesis as well as consider diagnostics via anaerobic bacteria detection and possible interventions via antibiotics and amino-acid supplementation.

FUNDING

Described in methods.

Redefining Comorbid Insomnia and Sleep Apnea: The Association of Sleep Breathing Impairment and Insomnia with Incident Diabetes

Rationale: Obstructive sleep apnea (OSA) is a prevalent sleep disorder that is frequently comorbid with insomnia and often accompanied by metabolic diseases such as type 2 diabetes. Although the apnea-hypopnea index (AHI) is currently the diagnostic criterion for gauging the severity of OSA, the AHI has not consistently predicted incident diabetes. Objectives: To test whether a combined insomnia-OSA (COMISA) phenotype based on comorbid insomnia and sleep breathing impairment index (COMISA-SBII) predicts incident diabetes and to compare the association with an AHI definition of COMISA (COMISA-AHI) in the MrOS (Osteoporotic Fractures in Men) study. Methods: The study samples came from participants in the MrOS sleep study without diabetes at their baseline examination. The SBII was derived as the product of the duration of each respiratory event (apnea and hypopnea) and the accompanying desaturation area from baseline unattended polysomnography. A subgroup of individuals classified as having comorbid insomnia (difficulties falling asleep, waking up in the middle of the night and/or early morning awakenings >15 times per month, and daytime impairments) and sleep breathing impairment (greater than 50th percentile of SBII) were identified at baseline. The primary outcome was incident diabetes during the follow-up visits. Cox proportional models were built to assess the adjusted hazard ratios of COMISA-AHI and COMISA-SBII. Prediction model performances of incident diabetes were compared across different models. Results: A total of 2,365 men (mean age, 76 yr) without diabetes at baseline were included. During a median follow-up of 10.0 years, diabetes developed in 181. After adjusting for demographic characteristics, comorbidities, and behavioral risk factors, participants with COMISA-SBII had a higher risk of incident diabetes (hazard ratio, 1.82; 95% confidence interval, 1.15-2.89) than those without sleep disorders (those with an SBII ⩽13.17 and no insomnia). The result remained significant in the risk competing model. Compared with COMISA-AHI, the addition of COMISA-SBII to a crude model with established risk factors significantly improved the predictive value of incident diabetes. Conclusions: COMISA-SBII, but not COMISA-AHI, predicted incident diabetes after accounting for multiple covariates in a cohort of older men. A comorbid insomnia phenotype based on SBII plus insomnia symptoms may be an important clinical subtype.

Hypoxic burden to guide CPAP treatment allocation in patients with obstructive sleep apnoea: a post hoc study of the ISAACC trial

BACKGROUND

Hypoxic burden (HB) has emerged as a strong predictor of cardiovascular risk in obstructive sleep apnoea (OSA). We aimed to assess the potential of HB to predict the cardiovascular benefit of treating OSA with continuous positive airway pressure (CPAP).

METHODS

This was a post hoc analysis of the ISAACC trial (ClinicalTrials.gov: NCT01335087) including non-sleepy patients with acute coronary syndrome (ACS) diagnosed with OSA (apnoea-hypopnoea index ≥15 events·h-1) by respiratory polygraphy. Patients were randomised to CPAP or usual care and followed for a minimum of 1 year. HB was calculated as the total area under all automatically identified desaturations divided by total sleep time. Patients were categorised as having high or low baseline HB according to the median value (73.1%min·h-1). Multivariable Cox regression models were used to assess whether the effect of CPAP on the incidence of cardiovascular outcomes was dependent on the baseline HB level.

RESULTS

The population (362 patients assigned to CPAP and 365 patients assigned to usual care) was middle-aged (mean age 59.7 years), overweight/obese and mostly male (84.5%). A significant interaction was found between the treatment arm and the HB categories. In the high HB group, CPAP treatment was associated with a significant reduction in the incidence of cardiovascular events (HR 0.57, 95% CI 0.34-0.96). In the low HB group, CPAP-treated patients exhibited a trend toward a higher risk of cardiovascular outcomes than those receiving usual care (HR 1.33, 95% CI 0.79-2.25). The differential effect of the treatment depending on the baseline HB level followed a dose-response relationship.

CONCLUSION

In non-sleepy ACS patients with OSA, high HB levels were associated with a long-term protective effect of CPAP on cardiovascular prognosis.

Association Between Slow-Wave Sleep Loss and Incident Dementia

Importance

Slow-wave sleep (SWS) supports the aging brain in many ways, including facilitating the glymphatic clearance of proteins that aggregate in Alzheimer disease. However, the role of SWS in the development of dementia remains equivocal.

Objective

To determine whether SWS loss with aging is associated with the risk of incident dementia and examine whether Alzheimer disease genetic risk or hippocampal volumes suggestive of early neurodegeneration were associated with SWS loss.

Design, Setting, and Participants

This prospective cohort study included participants in the Framingham Heart Study who completed 2 overnight polysomnography (PSG) studies in the time periods 1995 to 1998 and 2001 to 2003. Additional criteria for individuals in this study sample were an age of 60 years or older and no dementia at the time of the second overnight PSG. Data analysis was performed from January 2020 to August 2023.

Exposure

Changes in SWS percentage measured across repeated overnight sleep studies over a mean of 5.2 years apart (range, 4.8-7.1 years).

Main Outcome

Risk of incident all-cause dementia adjudicated over 17 years of follow-up from the second PSG.

Results

From the 868 Framingham Heart Study participants who returned for a second PSG, this cohort included 346 participants with a mean age of 69 years (range, 60-87 years); 179 (52%) were female. Aging was associated with SWS loss across repeated overnight sleep studies (mean [SD] change, -0.6 [1.5%] per year; P < .001). Over the next 17 years of follow-up, there were 52 cases of incident dementia. In Cox regression models adjusted for age, sex, cohort, positivity for at least 1 APOE ε4 allele, smoking status, sleeping medication use, antidepressant use, and anxiolytic use, each percentage decrease in SWS per year was associated with a 27% increase in the risk of dementia (hazard ratio, 1.27; 95% CI, 1.06-1.54; P = .01). SWS loss with aging was accelerated in the presence of Alzheimer disease genetic risk (ie, APOE ε4 allele) but not hippocampal volumes measured proximal to the first PSG.

Conclusions and Relevance

This cohort study found that slow-wave sleep percentage declined with aging and Alzheimer disease genetic risk, with greater reductions associated with the risk of incident dementia. These findings suggest that SWS loss may be a modifiable dementia risk factor.

Characterization of sleep apnea among a sample of adults from Samoa

Sleep apnea is a public health concern around the world, but little research has been dedicated to examining this issue in low- and middle-income countries, including Samoa. Using data collected through the Soifua Manuia ("Good Health") study, which aimed to investigate the impact of the body mass index (BMI)-associated genetic variant rs373863828 in CREB3 Regulatory Factor ( CREBRF ) on metabolic traits in Samoan adults, we examined the sample prevalence and characteristics of sleep apnea using data collected with a validated home sleep apnea device (WatchPAT, Itamar). A total of 330 participants (sampled to overrepresent the obesity-risk allele of interest) had sleep data available. Participants (53.3% female) had a mean (SD) age of 52.0 (9.9) years and BMI of 35.5 (7.5) kg/m 2 and 36.3% of the sample had type 2 diabetes. Based on the 3% and 4% apnea hypopnea indices (AHI) and the 4% oxygen desaturation index (ODI), descriptive analyses revealed that many participants had potentially actionable sleep apnea defined as >5 events/hr (87.9%, 68.5%, and 71.2%, respectively) or clinically actionable sleep apnea defined as ≥15 events/hr (54.9%, 31.5%, and 34.5%, respectively). Sleep apnea was more severe in men; for example, clinically actionable sleep apnea (≥15) based on the AHI 3% definition was observed in 61.7% of men and 48.9% of women. Correction for non-representational sampling related to the CREBRF obesity-risk allele resulted in only slightly lower estimates. Across the AHI 3%, AHI 4%, and ODI 4%, multiple linear regression revealed associations between a greater number of events/hr and higher age, male sex, higher body mass index, higher abdominal-hip circumference ratio, and geographic region of residence. Our study identified a much higher frequency of sleep apnea in Samoa compared with published data from other studies, but similar predictors. Continued research addressing generalizability of these findings, as well as a specific focus on diagnosis and affordable and equitable access to treatment, is needed to alleviate the burden of sleep apnea in Samoa and around the world.

Rest-activity rhythms across the lifespan: cross-sectional findings from the US representative National Health and Nutrition Examination Survey

STUDY OBJECTIVES

Rest-activity rhythms (RAR) may mark development, aging, and physical and mental health. Understanding how they differ between people may inform intervention and health promotion efforts. However, RAR characteristics across the lifespan have not been well-studied. Therefore, we investigated the association between RAR measures with demographic and lifestyle factors in a US nationally representative study.

METHODS

RAR metrics of interdaily stability (IS), intradaily variability (IV), relative amplitude (RA), and mean amplitude and timing of high (M10) and low (L5) activity were derived from 2011 to 2012 and 2013 to 2014 National Health and Nutrition Examination Survey (NHANES) actigraphy data. Population-weighted linear and logistic regression models were fit to examine the associations of age, gender, smoking, alcohol, season, body mass index (BMI), income-to-poverty ratio, and race/ethnicity with RAR. Significance was based on a false-discovery rate-corrected P-value of <0.05.

RESULTS

Among n = 12 526 NHANES participants (3-≥80 years), IS (higher = greater day-to-day regularity) and RA (higher = greater rhythm strength) generally decreased with age and were lower among males, whereas IV (higher = greater rhythm fragmentation) increased with age (p < 0.05). Dynamic changes in RAR trajectories were observed during childhood and adolescence. Income, BMI, smoking, and alcohol use were associated with RAR metrics, as well as season among children and teenagers (p < 0.05). RAR also differed by race/ethnicity (p < 0.05), with trajectories initially diverging in childhood and continuing into adulthood.

CONCLUSIONS

RAR differed by demographic and health-related factors, representing possible windows for public health intervention and sleep health promotion. RAR differences by race/ethnicity begin in childhood, are evident in early adolescence, and persist throughout adulthood.

A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies

Large-scale whole-genome sequencing (WGS) studies have improved our understanding of the contributions of coding and noncoding rare variants to complex human traits. Leveraging association effect sizes across multiple traits in WGS rare variant association analysis can improve statistical power over single-trait analysis, and also detect pleiotropic genes and regions. Existing multi-trait methods have limited ability to perform rare variant analysis of large-scale WGS data. We propose MultiSTAAR, a statistical framework and computationally-scalable analytical pipeline for functionally-informed multi-trait rare variant analysis in large-scale WGS studies. MultiSTAAR accounts for relatedness, population structure and correlation among phenotypes by jointly analyzing multiple traits, and further empowers rare variant association analysis by incorporating multiple functional annotations. We applied MultiSTAAR to jointly analyze three lipid traits (low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides) in 61,861 multi-ethnic samples from the Trans-Omics for Precision Medicine (TOPMed) Program. We discovered new associations with lipid traits missed by single-trait analysis, including rare variants within an enhancer of NIPSNAP3A and an intergenic region on chromosome 1.

Hypoxic Burden Based on Automatically Identified Desaturations Is Associated with Adverse Health Outcomes

Rationale: Recent studies have shown that sleep apnea-specific intermittent hypoxemia quantified by the hypoxic burden (HB) predicted cardiovascular disease (CVD)-related mortality in community-based and clinical cohorts. Calculation of HB is based on manual scoring of hypopneas and apneas, which is time-consuming and prone to interscorer variability. Objective: To validate a novel method to quantify the HB that is based on automatically scored desaturations. Methods: The sample included 5,655 middle-aged or older adults from the Sleep Heart Health Study (52.8% women; age, 63.2 ± 11.3 yr). The original HB method was based on a subject-specific search window obtained from an ensemble average of oxygen saturation signals (as measured by pulse oximetry) and synchronized with respect to the termination of scored respiratory events. In this study, however, the search window was obtained from ensemble average of oxygen saturation signals that synchronized with respect to the minimum of all automatically identified desaturations (⩾2% and other thresholds, including 3% and 4%, in sensitivity analyses). The time interval between the two maxima around the minimum saturation was defined as the search window. The oximetry-derived HB (HBOxi) was defined as the total area under all desaturation curves (restricted by the search window) divided by the total sleep time. Logistic and Cox regression models assessed the adjusted odds ratio (aOR)/hazard ratio of excessive daytime sleepiness (EDS), hypertension (HTN), and CVD mortality per 1-standard deviation increase in HBOxi after adjusting for several covariates and confounders. Results: The Spearman's rank correlation between HB (median [interquartile range], 34.4 [18.4-59.8] % min/h) and HBOxi (median [interquartile range], 34.5 [21.6-53.8] % min/h) was 0.81 (P < 0.001). Similar to HB, HBOxi was significantly associated with EDS (aOR [95% confidence interval (CI)], 1.17 [1.09-1.26] per standard deviation), HTN (aOR [95% CI], 1.13 [1.05-1.21]), and CVD mortality (adjusted hazard ratio [95% CI], 1.15 [1.01-1.30]) in fully adjusted models. Conclusions: The HBOxi was highly correlated with the HB based on manually scored apneas and hypopneas and was associated with EDS, HTN, and CVD mortality with similar effect sizes as previously reported. This method could be incorporated into wearable technology that accurately records oxygen saturation signals.

Mosaic chromosomal alterations in blood across ancestries using whole-genome sequencing

Megabase-scale mosaic chromosomal alterations (mCAs) in blood are prognostic markers for a host of human diseases. Here, to gain a better understanding of mCA rates in genetically diverse populations, we analyzed whole-genome sequencing data from 67,390 individuals from the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine program. We observed higher sensitivity with whole-genome sequencing data, compared with array-based data, in uncovering mCAs at low mutant cell fractions and found that individuals of European ancestry have the highest rates of autosomal mCAs and the lowest rates of chromosome X mCAs, compared with individuals of African or Hispanic ancestry. Although further studies in diverse populations will be needed to replicate our findings, we report three loci associated with loss of chromosome X, associations between autosomal mCAs and rare variants in DCPS, ADM17, PPP1R16B and TET2 and ancestry-specific variants in ATM and MPL with mCAs in cis.

The association of upper airway anatomy with cognitive test performance: the Multi-Ethnic Study of Atherosclerosis

BACKGROUND

Numerous upper airway anatomy characteristics are risk factors for sleep apnea, which affects 26% of older Americans, and more severe sleep apnea is associated with cognitive impairment. This study explores the pathophysiology and links between upper airway anatomy, sleep, and cognition.

METHODS

Participants in the Multi-Ethnic Study of Atherosclerosis underwent an upper airway MRI, polysomnography to assess sleep measures including the apnea-hypopnea index (AHI) and completed the Cognitive Abilities Screening Instrument (CASI). Two model selection techniques selected from among 67 upper airway measures those that are most strongly associated with CASI score. The associations of selected upper airway measures with AHI, AHI with CASI score, and selected upper airway anatomy measures with CASI score, both alone and after adjustment for AHI, were assessed using linear regression.

RESULTS

Soft palate volume, maxillary divergence, and upper facial height were significantly positively associated with higher CASI score, indicating better cognition. The coefficients were small, with a 1 standard deviation (SD) increase in these variables being associated with a 0.83, 0.75, and 0.70 point higher CASI score, respectively. Additional adjustment for AHI very slightly attenuated these associations. Larger soft palate volume was significantly associated with higher AHI (15% higher AHI (95% CI 2%,28%) per SD). Higher AHI was marginally associated with higher CASI score (0.43 (95% CI 0.01,0.85) per AHI doubling).

CONCLUSIONS

Three upper airway measures were weakly but significantly associated with higher global cognitive test performance. Sleep apnea did not appear to be the mechanism through which these upper airway and cognition associations were acting. Further research on the selected upper airway measures is recommended.

Determinants of mosaic chromosomal alteration fitness

Clonal hematopoiesis (CH) is characterized by the acquisition of a somatic mutation in a hematopoietic stem cell that results in a clonal expansion. These driver mutations can be single nucleotide variants in cancer driver genes or larger structural rearrangements called mosaic chromosomal alterations (mCAs). The factors that influence the variations in mCA fitness and ultimately result in different clonal expansion rates are not well-understood. We used the Passenger-Approximated Clonal Expansion Rate (PACER) method to estimate clonal expansion rate for 6,381 individuals in the NHLBI TOPMed cohort with gain, loss, and copy-neutral loss of heterozygosity mCAs. Our estimates of mCA fitness were correlated (R 2 = 0.49) with an alternative approach that estimated fitness of mCAs in the UK Biobank using a theoretical probability distribution. Individuals with lymphoid-associated mCAs had a significantly higher white blood cell count and faster clonal expansion rate. In a cross-sectional analysis, genome-wide association study of estimates of mCA expansion rate identified TCL1A , NRIP1 , and TERT locus variants as modulators of mCA clonal expansion rate.

Light exposure during sleep is associated with irregular sleep timing: the Multi-Ethnic Study of Atherosclerosis (MESA)

Objective

Exposure to light at night (LAN) may influence sleep timing and regularity. Here, we test whether greater light exposure during sleep (LEDS) associates with greater irregularity in sleep onset timing in a large cohort of older adults.

Methods

Light exposure and activity patterns, measured via wrist-worn actigraphy (ActiWatch Spectrum), were analyzed in 1,933 participants with 6+ valid days of data in the Multi-Ethnic Study of Atherosclerosis (MESA) Exam 5 Sleep Study. Summary measures of LEDS averaged across nights were evaluated in linear and logistic regression analyses to test the association with standard deviation (SD) in sleep onset timing (continuous variable) and irregular sleep onset timing (SD≥1.36 hours, binary). Night-to-night associations between LEDS and absolute differences in nightly sleep onset timing were also evaluated with distributed lag non-linear models and mixed models.

Results

In between-individual linear and logistic models adjusted for demographic, health, and seasonal factors, every 5-lux unit increase in LEDS was associated with an increase of 7.8 minutes in sleep onset SD (β=0.13 hours, 95%CI:0.09-0.17) and 40% greater odds (OR=1.40, 95%CI:1.24-1.60) of irregular sleep onset. In within-individual night-to-night mixed model analyses, every 5-lux unit increase in LEDS the night prior (lag0) was associated with a 2.2-minute greater deviation of sleep onset the next night (β=0.036 hours, p<0.05). Conversely, every 1-hour increase in sleep deviation (lag0) was associated with a 0.35-lux increase in future LEDS (β=0.347 lux, p<0.05).

Conclusion

LEDS was associated with greater irregularity in sleep onset in between-individual analyses and subsequent deviation in sleep timing in within-individual analyses, supporting a role for LEDS in exacerbating irregular sleep onset timing. Greater deviation in sleep onset was also associated with greater future LEDS, suggesting a bidirectional relationship. Maintaining a dark sleeping environment and preventing LEDS may promote sleep regularity and following a regular sleep schedule may limit LEDS.

Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed whole-genome sequencing study

Long non-coding RNAs (lncRNAs) are known to perform important regulatory functions in lipid metabolism. Large-scale whole-genome sequencing (WGS) studies and new statistical methods for variant set tests now provide an opportunity to assess more associations between rare variants in lncRNA genes and complex traits across the genome. In this study, we used high-coverage WGS from 66,329 participants of diverse ancestries with measurement of blood lipids and lipoproteins (LDL-C, HDL-C, TC, and TG) in the National Heart, Lung, and Blood Institute (NHLBI) Trans-Omics for Precision Medicine (TOPMed) program to investigate the role of lncRNAs in lipid variability. We aggregated rare variants for 165,375 lncRNA genes based on their genomic locations and conducted rare-variant aggregate association tests using the STAAR (variant-set test for association using annotation information) framework. We performed STAAR conditional analysis adjusting for common variants in known lipid GWAS loci and rare-coding variants in nearby protein-coding genes. Our analyses revealed 83 rare lncRNA variant sets significantly associated with blood lipid levels, all of which were located in known lipid GWAS loci (in a ±500-kb window of a Global Lipids Genetics Consortium index variant). Notably, 61 out of 83 signals (73%) were conditionally independent of common regulatory variation and rare protein-coding variation at the same loci. We replicated 34 out of 61 (56%) conditionally independent associations using the independent UK Biobank WGS data. Our results expand the genetic architecture of blood lipids to rare variants in lncRNAs.

Sleep Apnea Physiological Burdens and Cardiovascular Morbidity and Mortality

Rationale: Obstructive sleep apnea is characterized by frequent reductions in ventilation, leading to oxygen desaturations and/or arousals. Objectives: In this study, association of hypoxic burden with incident cardiovascular disease (CVD) was examined and compared with that of "ventilatory burden" and "arousal burden." Finally, we assessed the extent to which the ventilatory burden, visceral obesity, and lung function explain variations in hypoxic burden. Methods: Hypoxic, ventilatory, and arousal burdens were measured from baseline polysomnograms in the Multi-Ethnic Study of Atherosclerosis (MESA) and the Osteoporotic Fractures in Men (MrOS) studies. Ventilatory burden was defined as event-specific area under ventilation signal (mean normalized, area under the mean), and arousal burden was defined as the normalized cumulative duration of all arousals. The adjusted hazard ratios for incident CVD and mortality were calculated. Exploratory analyses quantified contributions to hypoxic burden of ventilatory burden, baseline oxygen saturation as measured by pulse oximetry, visceral obesity, and spirometry parameters. Measurements and Main Results: Hypoxic and ventilatory burdens were significantly associated with incident CVD (adjusted hazard ratio [95% confidence interval] per 1 SD increase in hypoxic burden: MESA, 1.45 [1.14, 1.84]; MrOS, 1.13 [1.02, 1.26]; ventilatory burden: MESA, 1.38 [1.11, 1.72]; MrOS, 1.12 [1.01, 1.25]), whereas arousal burden was not. Similar associations with mortality were also observed. Finally, 78% of variation in hypoxic burden was explained by ventilatory burden, whereas other factors explained only <2% of variation. Conclusions: Hypoxic and ventilatory burden predicted CVD morbidity and mortality in two population-based studies. Hypoxic burden is minimally affected by measures of adiposity and captures the risk attributable to ventilatory burden of obstructive sleep apnea rather than a tendency to desaturate.

Multivariate prediction of cognitive performance from the sleep electroencephalogram

Human cognitive performance is a key function whose biological foundations have been partially revealed by genetic and brain imaging studies. The sleep electroencephalogram (EEG) is tightly linked to structural and functional features of the central nervous system and serves as another promising biomarker. We used data from MrOS, a large cohort of older men and cross-validated regularized regression to link sleep EEG features to cognitive performance in cross-sectional analyses. In independent validation samples 2.5-10% of variance in cognitive performance can be accounted for by sleep EEG features, depending on the covariates used. Demographic characteristics account for more covariance between sleep EEG and cognition than health variables, and consequently reduce this association by a greater degree, but even with the strictest covariate sets a statistically significant association is present. Sigma power in NREM and beta power in REM sleep were associated with better cognitive performance, while theta power in REM sleep was associated with worse performance, with no substantial effect of coherence and other sleep EEG metrics. Our findings show that cognitive performance is associated with the sleep EEG (r = 0.283), with the strongest effect ascribed to spindle-frequency activity. This association becomes weaker after adjusting for demographic (r = 0.186) and health variables (r = 0.155), but its resilience to covariate inclusion suggest that it also partially reflects trait-like differences in cognitive ability.

Chronotype, Unhealthy Lifestyle, and Diabetes Risk in Middle-Aged U.S. Women : A Prospective Cohort Study

BACKGROUND

Evening chronotype may promote adherence to an unhealthy lifestyle and increase type 2 diabetes risk.

OBJECTIVE

To evaluate the role of modifiable lifestyle behaviors in the association between chronotype and diabetes risk.

DESIGN

Prospective cohort study.

SETTING

Nurses' Health Study II.

PARTICIPANTS

63 676 nurses aged 45 to 62 years with no history of cancer, cardiovascular disease, or diabetes in 2009 were prospectively followed until 2017.

MEASUREMENTS

Self-reported chronotype using a validated question from the Morningness-Eveningness Questionnaire. The lifestyle behaviors that were measured were diet quality, physical activity, alcohol intake, body mass index (BMI), smoking, and sleep duration. Incident diabetes cases were self-reported and confirmed using a supplementary questionnaire.

RESULTS

Participants reporting a "definite evening" chronotype were 54% (95% CI, 49% to 59%) more likely to have an unhealthy lifestyle than participants reporting a "definite morning" chronotype. A total of 1925 diabetes cases were documented over 469 120 person-years of follow-up. Compared with the "definite morning" chronotype, the adjusted hazard ratio (HR) for diabetes was 1.21 (CI, 1.09 to 1.35) for the "intermediate" chronotype and 1.72 (CI, 1.50 to 1.98) for the "definite evening" chronotype after adjustment for sociodemographic factors, shift work, and family history of diabetes. Further adjustment for BMI, physical activity, and diet quality attenuated the association comparing the "definite evening" and "definite morning" chronotypes to 1.31 (CI, 1.13 to 1.50), 1.54 (CI, 1.34 to 1.77), and 1.59 (CI, 1.38 to 1.83), respectively. Accounting for all measured lifestyle and sociodemographic factors resulted in a reduced but still positive association (HR comparing "definite evening" vs. "definite morning" chronotype, 1.19 [CI, 1.03 to 1.37]).

LIMITATIONS

Chronotype assessment using a single question, self-reported data, and homogeneity of the study population.

CONCLUSION

Middle-aged nurses with an evening chronotype were more likely to report unhealthy lifestyle behaviors and had increased diabetes risk compared with those with a morning chronotype. Accounting for BMI, physical activity, diet, and other modifiable lifestyle factors attenuated much but not all of the increased diabetes risk.

PRIMARY FUNDING SOURCE

National Institutes of Health.

Associations of Slow-Wave Sleep With Prevalent and Incident Type 2 Diabetes in the Multi-Ethnic Study of Atherosclerosis

CONTEXT

N3 sleep (i.e., slow-wave sleep), a marker of deep restorative sleep, is implicated in hormonal and blood pressure regulation and may impact cardiometabolic health.

OBJECTIVE

We conducted cross-sectional and prospective analyses to test whether a higher proportion and longer duration of N3 sleep are associated with reduced type 2 diabetes risk.

METHODS

A subsample of participants from the Multi-Ethnic Study of Atherosclerosis completed 1-night polysomnography at Exam 5 (2010-2013) and were prospectively followed until Exam 6 (2016-2018). We used modified Poisson regression to examine the cross-sectional associations of N3 proportion and duration with prevalent diabetes and Cox proportional hazards models to estimate risk of diabetes according to N3 measures.

RESULTS

In cross-sectional analyses (n = 2026, mean age: 69 years), diabetes prevalence was 28% (n = 572). Compared with the first quartile (Q1) of the N3 proportion (<2.0%), participants in Q4 (≥15.4%) were 29% (95% CI 0.58, 0.87) less likely to have prevalent diabetes (P trend = .0016). The association attenuated after adjustment for demographics, lifestyles, and sleep-related factors (P trend = .3322). In prospective analyses of 1251 participants and 129 incident cases over 6346 person-years of follow-up, a curvilinear relationship was observed between N3 proportion and incident diabetes risk. In the fully adjusted model, the hazard ratio (95% CI) of developing diabetes vs Q1 was 0.47 (0.26, 0.87) for Q2, 0.34 (0.15, 0.77) for Q3, and 0.32 (0.10, 0.97) for Q4 (P nonlinearity = .0213). The results were similar for N3 duration.

CONCLUSION

Higher N3 proportion and longer N3 duration were prospectively associated with lower type 2 diabetes risk in a nonlinear fashion among older American adults.