Publications by authors named "Tamar Sofer"

109 Publications

Whole-genome association analyses of sleep-disordered breathing phenotypes in the NHLBI TOPMed program.

Genome Med 2021 Aug 26;13(1):136. Epub 2021 Aug 26.

Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, 10461, USA.

Background: Sleep-disordered breathing is a common disorder associated with significant morbidity. The genetic architecture of sleep-disordered breathing remains poorly understood. Through the NHLBI Trans-Omics for Precision Medicine (TOPMed) program, we performed the first whole-genome sequence analysis of sleep-disordered breathing.

Methods: The study sample was comprised of 7988 individuals of diverse ancestry. Common-variant and pathway analyses included an additional 13,257 individuals. We examined five complementary traits describing different aspects of sleep-disordered breathing: the apnea-hypopnea index, average oxyhemoglobin desaturation per event, average and minimum oxyhemoglobin saturation across the sleep episode, and the percentage of sleep with oxyhemoglobin saturation < 90%. We adjusted for age, sex, BMI, study, and family structure using MMSKAT and EMMAX mixed linear model approaches. Additional bioinformatics analyses were performed with MetaXcan, GIGSEA, and ReMap.

Results: We identified a multi-ethnic set-based rare-variant association (p = 3.48 × 10) on chromosome X with ARMCX3. Additional rare-variant associations include ARMCX3-AS1, MRPS33, and C16orf90. Novel common-variant loci were identified in the NRG1 and SLC45A2 regions, and previously associated loci in the IL18RAP and ATP2B4 regions were associated with novel phenotypes. Transcription factor binding site enrichment identified associations with genes implicated with respiratory and craniofacial traits. Additional analyses identified significantly associated pathways.

Conclusions: We have identified the first gene-based rare-variant associations with objectively measured sleep-disordered breathing traits. Our results increase the understanding of the genetic architecture of sleep-disordered breathing and highlight associations in genes that modulate lung development, inflammation, respiratory rhythmogenesis, and HIF1A-mediated hypoxic response.
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http://dx.doi.org/10.1186/s13073-021-00917-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8394596PMC
August 2021

BinomiRare: A robust test for association of a rare genetic variant with a binary outcome for mixed models and any case-control proportion.

HGG Adv 2021 Jul 12;2(3). Epub 2021 Jun 12.

Framingham Heart Study, Framingham, MA, USA.

Whole-genome sequencing (WGS) and whole-exome sequencing studies have become increasingly available and are being used to identify rare genetic variants associated with health and disease outcomes. Investigators routinely use mixed models to account for genetic relatedness or other clustering variables (e.g., family or household) when testing genetic associations. However, no existing tests of the association of a rare variant with a binary outcome in the presence of correlated data control the type 1 error where there are (1) few individuals harboring the rare allele, (2) a small proportion of cases relative to controls, and (3) covariates to adjust for. Here, we address all three issues in developing a framework for testing rare variant association with a binary trait in individuals harboring at least one risk allele. In this framework, we estimate outcome probabilities under the null hypothesis and then use them, within the individuals with at least one risk allele, to test variant associations. We extend the BinomiRare test, which was previously proposed for independent observations, and develop the Conway-Maxwell-Poisson (CMP) test and study their properties in simulations. We show that the BinomiRare test always controls the type 1 error, while the CMP test sometimes does not. We then use the BinomiRare test to test the association of rare genetic variants in target genes with small-vessel disease (SVD) stroke, short sleep, and venous thromboembolism (VTE), in whole-genome sequence data from the Trans-Omics for Precision Medicine (TOPMed) program.
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http://dx.doi.org/10.1016/j.xhgg.2021.100040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8321319PMC
July 2021

Perceived Home Sleep Environment: Associations of Household-level Factors and In-bed Behaviors with Actigraphy-based Sleep Duration and Continuity in the Jackson Heart Sleep Study.

Sleep 2021 Jul 20. Epub 2021 Jul 20.

Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston MA USA.

Study Objectives: In an older African-American sample (n=231) we tested associations of the household environment and in-bed behaviors with sleep duration, efficiency, and wakefulness after sleep onset (WASO).

Methods: Older adult participants completed a household-level sleep environment questionnaire, a sleep questionnaire, and underwent 7-day wrist actigraphy for objective measures of sleep. Perceived household environment (self-reported) was evaluated using questions regarding safety, physical comfort, temperature, noise, and light disturbances. In-bed behaviors included: watching television, listening to radio/music, use of computer/tablet/phone, playing video games, reading books, and eating. To estimate the combined effect of the components in each domain (perceived household environment and in-bed behaviors), we calculated and standardized a weighted score per sleep outcome (e.g., duration, efficiency, WASO), with a higher score indicating worse conditions. The weights were derived from the coefficients of each component estimated from linear regression models predicting each sleep outcome while adjusting for covariates.

Results: A standard deviation increase in an adverse household environment score was associated with lower self-reported sleep duration (β=-13.9 minutes, 95% confidence interval: -21.6, -1.7) and actigraphy-based sleep efficiency (β=-0.7%, -1.4, 0.0). A standard deviation increase in the in-bed behaviors score was associated with lower actigraphy-based sleep duration (β=-9.7 minutes, -18.0, -1.3), sleep efficiency (β=-1.2%, -0.9, -0.6), and higher WASO (5.3 minutes, 2.1, 8.6).

Conclusion: Intervening on the sleep environment, including healthy sleep practices, may improve sleep duration and continuity among African-Americans.
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http://dx.doi.org/10.1093/sleep/zsab163DOI Listing
July 2021

Mendelian randomization analysis of arsenic metabolism and pulmonary function within the Hispanic Community Health Study/Study of Latinos.

Sci Rep 2021 Jun 29;11(1):13470. Epub 2021 Jun 29.

School of Public Health, University of Illinois at Chicago, 1603 W. Taylor Street, MC923, Chicago, IL, 60612, USA.

Arsenic exposure has been linked to poor pulmonary function, and inefficient arsenic metabolizers may be at increased risk. Dietary rice has recently been identified as a possible substantial route of exposure to arsenic, and it remains unknown whether it can provide a sufficient level of exposure to affect pulmonary function in inefficient metabolizers. Within 12,609 participants of HCHS/SOL, asthma diagnoses and spirometry-based measures of pulmonary function were assessed, and rice consumption was inferred from grain intake via a food frequency questionnaire. After stratifying by smoking history, the relationship between arsenic metabolism efficiency [percentages of inorganic arsenic (%iAs), monomethylarsenate (%MMA), and dimethylarsinate (%DMA) species in urine] and the measures of pulmonary function were estimated in a two-sample Mendelian randomization approach (genotype information from an Illumina HumanOmni2.5-8v1-1 array), focusing on participants with high inferred rice consumption. Among never-smoking high inferred consumers of rice (n = 1395), inefficient metabolism was associated with past asthma diagnosis and forced vital capacity below the lower limit of normal (LLN) (OR 1.40, p = 0.0212 and OR 1.42, p = 0.0072, respectively, for each percentage-point increase in %iAs; OR 1.26, p = 0.0240 and OR 1.24, p = 0.0193 for %MMA; OR 0.87, p = 0.0209 and OR 0.87, p = 0.0123 for the marker of efficient metabolism, %DMA). Among ever-smoking high inferred consumers of rice (n = 1127), inefficient metabolism was associated with peak expiratory flow below LLN (OR 1.54, p = 0.0108/percentage-point increase in %iAs, OR 1.37, p = 0.0097 for %MMA, and OR 0.83, p = 0.0093 for %DMA). Less efficient arsenic metabolism was associated with indicators of pulmonary dysfunction among those with high inferred rice consumption, suggesting that reductions in dietary arsenic could improve respiratory health.
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http://dx.doi.org/10.1038/s41598-021-92911-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8242019PMC
June 2021

Genome-wide association study of body fat distribution traits in Hispanics/Latinos from the HCHS/SOL.

Hum Mol Genet 2021 Jun 24. Epub 2021 Jun 24.

Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, 91101, USA.

Central obesity is a leading health concern with a great burden carried by ethnic minority populations, especially Hispanics/Latinos. Genetic factors contribute to the obesity burden overall and to inter-population differences. We aimed to identify loci associated with central adiposity measured as waist-to-hip ratio (WHR), waist circumference (WC), and hip circumference (HIP) adjusted for body mass index (adjBMI), using the Hispanic Community Health Study/Study of Latinos (HCHS/SOL); determine if differences in associations differ by background group within HCHS/SOL; and determine whether previously reported associations generalize to HCHS/SOL. Our analyses included 7472 women and 5200 men of mainland (Mexican, Central and South American) and Caribbean (Puerto Rican, Cuban, and Dominican) background residing in the US. We performed genome-wide association analyses stratified and combined across sexes using linear mixed-model regression. We identified 16 variants for WHRadjBMI, 22 for WCadjBMI, and 28 for HIPadjBMI that reached suggestive significance (P < 1x10-6). Many loci exhibited differences in strength of associations by ethnic background and sex. We brought a total of 66 variants forward for validation in cohorts (N = 34 161) with participants of Hispanic/Latino, African and European descent. We confirmed 4 novel loci (P < 0.05 and consistent direction of effect, and P < 5x10-8 after meta-analysis), including 2 for WHRadjBMI (rs13301996, rs79478137); 1 for WCadjBMI (rs3168072); and 1 for HIPadjBMI (rs28692724). Also, we generalized previously reported associations to HCHS/SOL, (8 for WHRadjBMI; 10 for WCadjBMI; 12 for HIPadjBMI). Our study highlights the importance of large-scale genomic studies in ancestrally diverse Hispanic/Latino populations for identifying and characterizing central obesity-susceptibility that may be ancestry-specific.
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http://dx.doi.org/10.1093/hmg/ddab166DOI Listing
June 2021

A composite sleep and pulmonary phenotype predicting hypertension.

EBioMedicine 2021 Jun 15;68:103433. Epub 2021 Jun 15.

Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 221 Longwood Ave, Boston MA 02115, room 225C, USA. Electronic address:

Background: Multiple aspects of sleep and Sleep Disordered Breathing (SDB) have been linked to hypertension. However, the standard measure of SDB, the Apnoea Hypopnea Index (AHI), has not identified patients likely to experience large improvements in blood pressure with SDB treatment.

Methods: To use machine learning to select sleep and pulmonary measures associated with hypertension development when considered jointly, we applied feature screening followed by Elastic Net penalized regression in association with incident hypertension using a wide array of polysomnography measures, and lung function, derived for the Sleep Heart Health Study (SHHS).

Findings: At baseline, n=860 SHHS individuals with complete data were age 61 years, on average. Of these, 291 developed hypertension ~5 years later. A combination of pulmonary function and 18 sleep phenotypes predicted incident hypertension (OR=1.43, 95% confidence interval [1.14, 1.80] per 1 standard deviation (SD) of the phenotype), while the apnoea-hypopnea index (AHI) had low evidence of association with incident hypertension (OR =1.13, 95% confidence interval [0.97, 1.33] per 1 SD). In a generalization analysis in 923 individuals from the Multi-Ethnic Study of Atherosclerosis, aged 65 on average with 615 individuals with hypertension, the new phenotype was cross-sectionally associated with hypertension (OR=1.26, 95% CI [1.10, 1.45]).

Interpretation: A unique combination of sleep and pulmonary function measures better predicts hypertension compared to the AHI. The composite measure included indices capturing apnoea and hypopnea event durations, with shorter event lengths associated with increased risk of hypertension.

Funding: This research was supported by National Heart, Lung, and Blood Institute (NHLBI) contracts HHSN268201500003I, N01-HC-95159, N01-HC-95160, N01-HC-95161, N01-HC-95162, N01-HC-95163, N01-HC-95164, N01-HC-95165, N01-HC-95166, N01-HC-95167, N01-HC-95168, and N01-HC-95169 and by National Center for Advancing Translational Sciences grants UL1-TR- 000040, UL1-TR-001079, and UL1-TR-001420. The MESA Sleep ancillary study was supported by NHLBI grant HL-56984. Pulmonary phenotyping in MESA was funded by NHLBI grants R01-HL077612 and R01-HL093081. This work was supported by NHLBI grant R35HL135818 to Susan Redline.
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http://dx.doi.org/10.1016/j.ebiom.2021.103433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8217680PMC
June 2021

Variant-specific inflation factors for assessing population stratification at the phenotypic variance level.

Nat Commun 2021 06 9;12(1):3506. Epub 2021 Jun 9.

Department of Biostatistics, University of Washington, Seattle, WA, USA.

In modern Whole Genome Sequencing (WGS) epidemiological studies, participant-level data from multiple studies are often pooled and results are obtained from a single analysis. We consider the impact of differential phenotype variances by study, which we term 'variance stratification'. Unaccounted for, variance stratification can lead to both decreased statistical power, and increased false positives rates, depending on how allele frequencies, sample sizes, and phenotypic variances vary across the studies that are pooled. We develop a procedure to compute variant-specific inflation factors, and show how it can be used for diagnosis of genetic association analyses on pooled individual level data from multiple studies. We describe a WGS-appropriate analysis approach, implemented in freely-available software, which allows study-specific variances and thereby improves performance in practice. We illustrate the variance stratification problem, its solutions, and the proposed diagnostic procedure, in simulations and in data from the Trans-Omics for Precision Medicine Whole Genome Sequencing Program (TOPMed), used in association tests for hemoglobin concentrations and BMI.
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http://dx.doi.org/10.1038/s41467-021-23655-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8190158PMC
June 2021

The trans-ancestral genomic architecture of glycemic traits.

Nat Genet 2021 06 31;53(6):840-860. Epub 2021 May 31.

Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.

Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; P < 5 × 10), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution.
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http://dx.doi.org/10.1038/s41588-021-00852-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7610958PMC
June 2021

Benchmarking association analyses of continuous exposures with RNA-seq in observational studies.

Brief Bioinform 2021 May 20. Epub 2021 May 20.

Harbor-UCLA Medical Center at the Lundquist Institute, USA.

Large datasets of hundreds to thousands of individuals measuring RNA-seq in observational studies are becoming available. Many popular software packages for analysis of RNA-seq data were constructed to study differences in expression signatures in an experimental design with well-defined conditions (exposures). In contrast, observational studies may have varying levels of confounding transcript-exposure associations; further, exposure measures may vary from discrete (exposed, yes/no) to continuous (levels of exposure), with non-normal distributions of exposure. We compare popular software for gene expression-DESeq2, edgeR and limma-as well as linear regression-based analyses for studying the association of continuous exposures with RNA-seq. We developed a computation pipeline that includes transformation, filtering and generation of empirical null distribution of association P-values, and we apply the pipeline to compute empirical P-values with multiple testing correction. We employ a resampling approach that allows for assessment of false positive detection across methods, power comparison and the computation of quantile empirical P-values. The results suggest that linear regression methods are substantially faster with better control of false detections than other methods, even with the resampling method to compute empirical P-values. We provide the proposed pipeline with fast algorithms in an R package Olivia, and implemented it to study the associations of measures of sleep disordered breathing with RNA-seq in peripheral blood mononuclear cells in participants from the Multi-Ethnic Study of Atherosclerosis.
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http://dx.doi.org/10.1093/bib/bbab194DOI Listing
May 2021

Longer sleep improves cardiovascular outcomes: time to make sleep a priority.

Eur Heart J 2021 Sep;42(34):3358-3360

Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1093/eurheartj/ehab248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8423457PMC
September 2021

Cutting the fat: advances and challenges in sleep apnoea genetics.

Eur Respir J 2021 05 6;57(5). Epub 2021 May 6.

Division of Sleep and Circadian Disorders, Dept of Medicine, Brigham and Women's Hospital, Boston, MA, USA.

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http://dx.doi.org/10.1183/13993003.04644-2020DOI Listing
May 2021

Genome-wide association study of neck circumference identifies sex-specific loci independent of generalized adiposity.

Int J Obes (Lond) 2021 07 27;45(7):1532-1541. Epub 2021 Apr 27.

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

Background/objectives: Neck circumference, an index of upper airway fat, has been suggested to be an important measure of body-fat distribution with unique associations with health outcomes such as obstructive sleep apnea and metabolic disease. This study aims to study the genetic bases of neck circumference.

Methods: We conducted a multi-ethnic genome-wide association study of neck circumference, adjusted and unadjusted for BMI, in up to 15,090 European Ancestry (EA) and African American (AA) individuals. Because sexually dimorphic associations have been observed for anthropometric traits, we conducted both sex-combined and sex-specific analysis.

Results: We identified rs227724 near the Noggin (NOG) gene as a possible quantitative locus for neck circumference in men (N = 8831, P = 1.74 × 10) but not in women (P = 0.08). The association was replicated in men (N = 1554, P = 0.045) in an independent dataset. This locus was previously reported to be associated with human height and with self-reported snoring. We also identified rs13087058 on chromosome 3 as a suggestive locus in sex-combined analysis (N = 15090, P = 2.94 × 10; replication P =0.049). This locus was also associated with electrocardiogram-assessed PR interval and is a cis-expression quantitative locus for the PDZ Domain-containing ring finger 2 (PDZRN3) gene. Both NOG and PDZRN3 interact with members of transforming growth factor-beta superfamily signaling proteins.

Conclusions: Our study suggests that neck circumference may have unique genetic basis independent of BMI.
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http://dx.doi.org/10.1038/s41366-021-00817-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8236408PMC
July 2021

Multi-ancestry genome-wide gene-sleep interactions identify novel loci for blood pressure.

Mol Psychiatry 2021 Apr 15. Epub 2021 Apr 15.

Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.

Long and short sleep duration are associated with elevated blood pressure (BP), possibly through effects on molecular pathways that influence neuroendocrine and vascular systems. To gain new insights into the genetic basis of sleep-related BP variation, we performed genome-wide gene by short or long sleep duration interaction analyses on four BP traits (systolic BP, diastolic BP, mean arterial pressure, and pulse pressure) across five ancestry groups in two stages using 2 degree of freedom (df) joint test followed by 1df test of interaction effects. Primary multi-ancestry analysis in 62,969 individuals in stage 1 identified three novel gene by sleep interactions that were replicated in an additional 59,296 individuals in stage 2 (stage 1 + 2 P < 5 × 10), including rs7955964 (FIGNL2/ANKRD33) that increases BP among long sleepers, and rs73493041 (SNORA26/C9orf170) and rs10406644 (KCTD15/LSM14A) that increase BP among short sleepers (P < 5 × 10). Secondary ancestry-specific analysis identified another novel gene by long sleep interaction at rs111887471 (TRPC3/KIAA1109) in individuals of African ancestry (P = 2 × 10). Combined stage 1 and 2 analyses additionally identified significant gene by long sleep interactions at 10 loci including MKLN1 and RGL3/ELAVL3 previously associated with BP, and significant gene by short sleep interactions at 10 loci including C2orf43 previously associated with BP (P < 10). 2df test also identified novel loci for BP after modeling sleep that has known functions in sleep-wake regulation, nervous and cardiometabolic systems. This study indicates that sleep and primary mechanisms regulating BP may interact to elevate BP level, suggesting novel insights into sleep-related BP regulation.
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http://dx.doi.org/10.1038/s41380-021-01087-0DOI Listing
April 2021

Machine and Deep Learning in Molecular and Genetic Aspects of Sleep Research.

Neurotherapeutics 2021 01 7;18(1):228-243. Epub 2021 Apr 7.

Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.

Epidemiological sleep research strives to identify the interactions and causal mechanisms by which sleep affects human health, and to design intervention strategies for improving sleep throughout the lifespan. These goals can be advanced by further focusing on the environmental and genetic etiology of sleep disorders, and by development of risk stratification algorithms, to identify people who are at risk or are affected by, sleep disorders. These studies rely on comprehensive sleep-related data which often contains complex multi-dimensional physiological and molecular measurements across multiple timepoints. Thus, sleep research is well-suited for the application of computational approaches that can handle high-dimensional data. Here, we survey recent advances in machine and deep learning together with the availability of large human cohort studies with sleep data that can jointly drive the next breakthroughs in the sleep-research field. We describe sleep-related data types and datasets, and present some of the tasks in the field that can be targets for algorithmic approaches, as well as the challenges and opportunities in pursuing them.
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http://dx.doi.org/10.1007/s13311-021-01014-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8116376PMC
January 2021

The Sleep Apnea-Specific Pulse-Rate Response Predicts Cardiovascular Morbidity and Mortality.

Am J Respir Crit Care Med 2021 06;203(12):1546-1555

Division of Sleep and Circadian Disorders, Brigham and Women's Hospital and Harvard Medical School, Harvard University, Boston, Massachusetts.

Randomized controlled trials have been unable to detect a cardiovascular benefit of continuous positive airway pressure in unselected patients with obstructive sleep apnea (OSA). We hypothesize that deleterious cardiovascular outcomes are concentrated in a subgroup of patients with a heightened pulse-rate response to apneas and hypopneas (ΔHR). We measured the ΔHR in the MESA (Multi-Ethnic Study of Atherosclerosis) ( = 1,395) and the SHHS (Sleep Heart Health Study) ( = 4,575). MESA data were used to determine the functional form of the association between the ΔHR and subclinical cardiovascular biomarkers, whereas primary analyses tested the association of the ΔHR with nonfatal or fatal cardiovascular disease (CVD) and all-cause mortality in longitudinal data from the SHHS. In the MESA, U-shaped relationships were observed between subclinical CVD biomarkers (coronary artery calcium, NT-proBNP [N-terminal prohormone BNP], and Framingham risk score) and the ΔHR; notably, a high ΔHR (upper quartile) was associated with elevated biomarker scores compared with a midrange ΔHR (25th-75th centiles). In the SHHS, individuals with a high ΔHR compared with a midrange ΔHR were at increased risk of nonfatal or fatal CVD and all-cause mortality (nonfatal adjusted hazard ratio [95% confidence interval (CI)], 1.60 [1.28-2.00]; fatal adjusted hazard ratio [95% CI], 1.68 [1.22-2.30]; all-cause adjusted hazard ratio [95% CI], 1.29 [1.07-1.55]). The risk associated with a high ΔHR was particularly high in those with a substantial hypoxic burden (nonfatal, 1.93 [1.36-2.73]; fatal, 3.50 [2.15-5.71]; all-cause, 1.84 [1.40-2.40]) and was exclusively observed in nonsleepy individuals. Individuals with OSA who demonstrate an elevated ΔHR are at increased risk of cardiovascular morbidity and mortality. This study identifies a prognostic biomarker for OSA that appears useful for risk stratification and patient selection for future clinical trials.
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http://dx.doi.org/10.1164/rccm.202010-3900OCDOI Listing
June 2021

Non-REM Apnea and Hypopnea Duration Varies across Population Groups and Physiologic Traits.

Am J Respir Crit Care Med 2021 05;203(9):1173-1182

Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts.

Symptoms and morbidities associated with obstructive sleep apnea (OSA) vary across individuals and are not predicted by the apnea-hypopnea index (AHI). Respiratory event duration is a heritable trait associated with mortality that may further characterize OSA. We evaluated how hypopnea and apnea durations in non-REM (NREM) sleep vary across demographic groups and quantified their associations with physiological traits (loop gain, arousal threshold, circulatory delay, and pharyngeal collapsibility). Data were analyzed from 1,546 participants from the Multi-Ethnic Study of Atherosclerosis with an AHI ≥5. Physiological traits were derived using a validated model fit to the polysomnographic airflow signal. Multiple linear regression models were used to evaluate associations of event duration with demographic and physiological factors. Participants had a mean age ± SD of 68.9 ± 9.2 years, mean NREM hypopnea duration of 21.73 ± 5.60, and mean NREM apnea duration of 23.87 ± 7.44 seconds. In adjusted analyses, shorter events were associated with younger age, female sex, higher body mass index ( < 0.01, all), and Black race ( < 0.05). Longer events were associated with Asian race ( < 0.01). Shorter event durations were associated with lower circulatory delay (2.53 ± 0.13 s,  < 0.01), lower arousal threshold (1.39 ± 0.15 s,  < 0.01), reduced collapsibility (-0.71 ± 0.16 s,  < 0.01), and higher loop gain (-0.27 ± 0.11 s,  < 0.05) per SD change. Adjustment for physiological traits attenuated age, sex, and obesity associations and eliminated racial differences in event duration. Average event duration varies across population groups and provides information on ventilatory features and airway collapsibility not captured by the AHI.
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http://dx.doi.org/10.1164/rccm.202005-1808OCDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8314913PMC
May 2021

APOE alleles' association with cognitive function differs across Hispanic/Latino groups and genetic ancestry in the study of Latinos-investigation of neurocognitive aging (HCHS/SOL).

Alzheimers Dement 2021 03 6;17(3):466-474. Epub 2020 Nov 6.

Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.

Introduction: Apolipoprotein E (APOE) alleles are associated with cognitive decline, mild cognitive impairment (MCI), and Alzheimer's disease in Whites, but have weaker and inconsistent effects reported in Latinos. We hypothesized that this heterogeneity is due to ancestry-specific genetic effects.

Methods: We investigated the associations of the APOE alleles with significant cognitive decline and MCI in 4183 Latinos, stratified by six Latino backgrounds, and explored whether the proportion of continental genetic ancestry (European, African, and Amerindian) modifies these associations.

Results: APOE ε4 was associated with an increased risk of significant cognitive decline (odds ratio [OR] = 1.15, P-value = 0.03), with the strongest association in Cubans (OR = 1.46, P-value = 0.007). APOE-ε2 was associated with decreased risk of MCI (OR = 0.37, P-value = 0.04) in Puerto Ricans. Amerindian genetic ancestry was found to protect from the risk conferred by APOE ε4 on significant cognitive decline.

Discussion: Results suggest that APOE alleles' effects on cognitive outcomes differ across six Latino backgrounds and are modified by continental genetic ancestry.
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http://dx.doi.org/10.1002/alz.12205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8016734PMC
March 2021

Rare variants association testing for a binary outcome when pooling individual level data from heterogeneous studies.

Authors:
Tamar Sofer Na Guo

Genet Epidemiol 2021 02 22;45(1):115-127. Epub 2020 Oct 22.

Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts, USA.

Whole genome sequencing (WGS) and whole exome sequencing studies are used to test the association of rare genetic variants with health traits. Many existing WGS efforts now aggregate data from heterogeneous groups, for example, combining sets of individuals of European and African ancestries. We here investigate the statistical implications on rare variant association testing with a binary trait when combining together heterogeneous studies, defined as studies with potentially different disease proportion and different frequency of variant carriers. We study and compare in simulations the Type 1 error control and power of the naïve score test, the saddlepoint approximation to the score test, and the BinomiRare test in a range of settings, focusing on low numbers of variant carriers. We show that Type 1 error control and power patterns depend on both the number of carriers of the rare allele and on disease prevalence in each of the studies. We develop recommendations for association analysis of rare genetic variants. (1) The Score test is preferred when the case proportion in the sample is 50%. (2) Do not down-sample controls to balance case-control ratio, because it reduces power. Rather, use a test that controls the Type 1 error. (3) Conduct stratified analysis in parallel with combined analysis. Aggregated testing may have lower power when the variant effect size differs between strata.
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http://dx.doi.org/10.1002/gepi.22359DOI Listing
February 2021

Increased RNA editing in maternal immune activation model of neurodevelopmental disease.

Nat Commun 2020 10 16;11(1):5236. Epub 2020 Oct 16.

The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.

The etiology of major neurodevelopmental disorders such as schizophrenia and autism is unclear, with evidence supporting a combination of genetic factors and environmental insults, including viral infection during pregnancy. Here we utilized a mouse model of maternal immune activation (MIA) with the viral mimic PolyI:C infection during early gestation. We investigated the transcriptional changes in the brains of mouse fetuses following MIA during the prenatal period, and evaluated the behavioral and biochemical changes in the adult brain. The results reveal an increase in RNA editing levels and dysregulation in brain development-related gene pathways in the fetal brains of MIA mice. These MIA-induced brain editing changes are not observed in adulthood, although MIA-induced behavioral deficits are observed. Taken together, our findings suggest that MIA induces transient dysregulation of RNA editing at a critical time in brain development.
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http://dx.doi.org/10.1038/s41467-020-19048-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7567798PMC
October 2020

Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants.

Nat Commun 2020 10 14;11(1):5182. Epub 2020 Oct 14.

The Institute for Translational Genomics and Population Sciences, The Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA.

Chronic obstructive pulmonary disease (COPD), diagnosed by reduced lung function, is a leading cause of morbidity and mortality. We performed whole genome sequence (WGS) analysis of lung function and COPD in a multi-ethnic sample of 11,497 participants from population- and family-based studies, and 8499 individuals from COPD-enriched studies in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program. We identify at genome-wide significance 10 known GWAS loci and 22 distinct, previously unreported loci, including two common variant signals from stratified analysis of African Americans. Four novel common variants within the regions of PIAS1, RGN (two variants) and FTO show evidence of replication in the UK Biobank (European ancestry n ~ 320,000), while colocalization analyses leveraging multi-omic data from GTEx and TOPMed identify potential molecular mechanisms underlying four of the 22 novel loci. Our study demonstrates the value of performing WGS analyses and multi-omic follow-up in cohorts of diverse ancestry.
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http://dx.doi.org/10.1038/s41467-020-18334-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7598941PMC
October 2020

Multi-ethnic GWAS and meta-analysis of sleep quality identify MPP6 as a novel gene that functions in sleep center neurons.

Sleep 2021 03;44(3)

The Alan Edwards Centre for Research on Pain, McGill University, Montréal, QC, Canada.

Poor sleep quality can have harmful health consequences. Although many aspects of sleep are heritable, the understandings of genetic factors involved in its physiology remain limited. Here, we performed a genome-wide association study (GWAS) using the Pittsburgh Sleep Quality Index (PSQI) in a multi-ethnic discovery cohort (n = 2868) and found two novel genome-wide loci on chromosomes 2 and 7 associated with global sleep quality. A meta-analysis in 12 independent cohorts (100 000 individuals) replicated the association on chromosome 7 between NPY and MPP6. While NPY is an important sleep gene, we tested for an independent functional role of MPP6. Expression data showed an association of this locus with both NPY and MPP6 mRNA levels in brain tissues. Moreover, knockdown of an orthologue of MPP6 in Drosophila melanogaster sleep center neurons resulted in decreased sleep duration. With convergent evidence, we describe a new locus impacting human variability in sleep quality through known NPY and novel MPP6 sleep genes.
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http://dx.doi.org/10.1093/sleep/zsaa211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953222PMC
March 2021

Correction: Mesenchymal stem cells derived extracellular vesicles improve behavioral and biochemical deficits in a phencyclidine model of schizophrenia.

Transl Psychiatry 2020 Oct 6;10(1):341. Epub 2020 Oct 6.

Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41398-020-01030-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7538569PMC
October 2020

Correction: Mesenchymal stem cells derived extracellular vesicles improve behavioral and biochemical deficits in a phencyclidine model of schizophrenia.

Transl Psychiatry 2020 Sep 22;10(1):327. Epub 2020 Sep 22.

Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.

In the original Article, Dr. Angela Ruban's name was misspelled as "Aangela Ruban". This has been corrected in the PDF, HTML, and XML versions of this Article.
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http://dx.doi.org/10.1038/s41398-020-01016-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7508953PMC
September 2020

Mesenchymal stem cells derived extracellular vesicles improve behavioral and biochemical deficits in a phencyclidine model of schizophrenia.

Transl Psychiatry 2020 09 1;10(1):305. Epub 2020 Sep 1.

Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.

Schizophrenia is a debilitating psychiatric disorder with a significant number of patients not adequately responding to treatment. Phencyclidine (PCP) is used as a validated model for schizophrenia, shown to reliably induce positive, negative and cognitive-like behaviors in rodents. It was previously shown in our lab that behavioral phenotypes of PCP-treated mice can be alleviated after intracranial transplantation of mesenchymal stem cells (MSC). Here, we assessed the feasibility of intranasal delivery of MSCs-derived-extracellular vesicles (EVs) to alleviate schizophrenia-like behaviors in a PCP model of schizophrenia. As MSCs-derived EVs were already shown to concentrate at the site of lesion in the brain, we determined that in PCP induced injury the EVs migrate to the prefrontal cortex (PFC) of treated mice, a most involved area of the brain in schizophrenia. We show that intranasal delivery of MSC-EVs improve social interaction and disruption in prepulse inhibition (PPI) seen in PCP-treated mice. In addition, immunohistochemical studies demonstrate that the EVs preserve the number of parvalbumin-positive GABAergic interneurons in the PFC of treated mice. Finally, MSCs-EVs reduced glutamate levels in the CSF of PCP-treated mice, which might explain the reduction of toxicity. In conclusion, we show that MSCs-EVs improve the core schizophrenia-like behavior and biochemical markers of schizophrenia and might be used as a novel treatment for this incurable disorder.
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http://dx.doi.org/10.1038/s41398-020-00988-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7463024PMC
September 2020

Associations of Sleep-disordered Breathing and Insomnia with Incident Hypertension and Diabetes. The Hispanic Community Health Study/Study of Latinos.

Am J Respir Crit Care Med 2021 02;203(3):356-365

Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Harvard University, Boston, Massachusetts.

Sleep disorders are associated with hypertension and diabetes, which are primary risk factors for cardiovascular diseases and mortality. It is important to understand these associations in Hispanic/Latino individuals, in whom cardiovascular death is the leading cause of mortality. To investigate the prospective associations of sleep-disordered breathing (SDB) and insomnia with incident hypertension and diabetes among U.S. Hispanic/Latino people over 6 years of follow-up and to assess potential sex differences in these associations. Data from 11,623 Hispanic/Latino participants in the Hispanic Community Health Study/Study of Latinos (visit 1, 2008-2011; visit 2, 2014-2017) were analyzed using survey logistic regression models, adjusting for potential confounders. SDB (apnea-hypopnea index of 5 or more) and insomnia (Women's Health Initiative Insomnia Rating Scale of 9 or more) were measured at baseline. Incident hypertension (stage 2 or greater) and diabetes were defined according to national guidelines. In the target population, 52.6% were women, with a mean age of 41.1 ± 14.9 years at baseline. SDB was associated with 1.54 higher adjusted odds of incident hypertension (95% confidence interval [CI], 1.18-2.00) and 1.33 higher odds of incident diabetes (95% CI, 1.05-1.67) compared with no SDB. Insomnia was associated with incident hypertension (odds ratio, 1.37; 95% CI, 1.11-1.69) but not with diabetes. The association between insomnia and incident hypertension was stronger among men than among women. SDB was associated with incident hypertension and diabetes. Insomnia was associated with incident hypertension. These findings support the importance of sleep disorders as modifiable targets for disease prevention and reduction.
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http://dx.doi.org/10.1164/rccm.201912-2330OCDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7874314PMC
February 2021

Genome-wide association study of cognitive function in diverse Hispanics/Latinos: results from the Hispanic Community Health Study/Study of Latinos.

Transl Psychiatry 2020 07 22;10(1):245. Epub 2020 Jul 22.

Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.

Cognitive function such as reasoning, attention, memory, and language is strongly correlated with brain aging. Compared to non-Hispanic whites, Hispanics/Latinos have a higher risk of cognitive impairment and dementia. The genetic determinants of cognitive function have not been widely explored in this diverse and admixed population. We conducted a genome-wide association analysis of cognitive function in up to 7600 middle aged and older Hispanics/Latinos (mean = 55 years) from the Hispanic Community Health Study / Study of Latinos (HCHS/SOL). Four cognitive measures were examined: the Brief Spanish English Verbal Learning Test (B-SEVLT), the Word Fluency Test (WFT), the Digit Symbol Substitution Test (DSST), the Six-Item Screener (SIS). Four novel loci were identified: one for B-SEVLT at 4p14, two for WFT at 3p14.1 and 6p21.32, and one for DSST at 10p13. These loci implicate genes highly expressed in brain and previously connected to neurological diseases (UBE2K, FRMD4B, the HLA gene complex). By applying tissue-specific gene expression prediction models to our genotype data, additional genes highly expressed in brain showed suggestive associations with cognitive measures possibly indicating novel biological mechanisms, including IFT122 in the hippocampus for SIS, SNX31 in the basal ganglia for B-SEVLT, RPS6KB2 in the frontal cortex for WFT, and CSPG5 in the hypothalamus for DSST. These findings provide new information about the genetic determinants of cognitive function in this unique population. In addition, we derived a measure of general cognitive function based on these cognitive tests and generated genome-wide association summary results, providing a resource to the research community for comparison, replication, and meta-analysis in future genetic studies in Hispanics/Latinos.
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http://dx.doi.org/10.1038/s41398-020-00930-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7376098PMC
July 2020

Low oxygen saturation during sleep reduces CD1D and RAB20 expressions that are reversed by CPAP therapy.

EBioMedicine 2020 Jun 5;56:102803. Epub 2020 Jun 5.

Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA.

Background: Sleep Disordered Breathing (SDB) is associated with a wide range of pathophysiological changes due, in part, to hypoxemia during sleep. We sought to identify gene transcription associations with measures of SDB and hypoxemia during sleep, and study their response to treatment.

Methods: In two discovery cohorts, Framingham Offspring Study (FOS; N = 571) and the Multi-Ethnic Study of Atherosclerosis (MESA; N = 580), we studied gene expression in peripheral blood mononuclear cells in association with three measures of SDB: Apnea Hypopnea Index (AHI); average oxyhemoglobin saturation (avgO2) during sleep; and minimum oxyhemoglobin saturation (minO2) during sleep. Associated genes were used for analysis of gene expression in the blood of 15 participants with moderate or severe obstructive sleep apnea (OSA) from the Heart Biomarkers In Apnea Treatment (HeartBEAT) trial. These genes were studied pre- and post-treatment (three months) with continuous positive airway pressure (CPAP). We also performed Gene Set Enrichment Analysis (GSEA) on all traits and cohort analyses.

Findings: Twenty-two genes were associated with SDB traits in both MESA and FOS. Of these, lower expression of CD1D and RAB20 was associated with lower avgO2 in MESA and FOS. CPAP treatment increased the expression of these genes in HeartBEAT participants. Immunity and inflammation pathways were up-regulated in subjects with lower avgO2; i.e., in those with a more severe SDB phenotype (MESA), whereas immuno-inflammatory processes were down-regulated following CPAP treatment (HeartBEAT).

Interpretation: Low oxygen saturation during sleep is associated with alterations in gene expression and transcriptional programs that are partially reversed by CPAP treatment.
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http://dx.doi.org/10.1016/j.ebiom.2020.102803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7276515PMC
June 2020

Gene-educational attainment interactions in a multi-ancestry genome-wide meta-analysis identify novel blood pressure loci.

Mol Psychiatry 2021 Jun 5;26(6):2111-2125. Epub 2020 May 5.

Health Disparities Research Section, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA.

Educational attainment is widely used as a surrogate for socioeconomic status (SES). Low SES is a risk factor for hypertension and high blood pressure (BP). To identify novel BP loci, we performed multi-ancestry meta-analyses accounting for gene-educational attainment interactions using two variables, "Some College" (yes/no) and "Graduated College" (yes/no). Interactions were evaluated using both a 1 degree of freedom (DF) interaction term and a 2DF joint test of genetic and interaction effects. Analyses were performed for systolic BP, diastolic BP, mean arterial pressure, and pulse pressure. We pursued genome-wide interrogation in Stage 1 studies (N = 117 438) and follow-up on promising variants in Stage 2 studies (N = 293 787) in five ancestry groups. Through combined meta-analyses of Stages 1 and 2, we identified 84 known and 18 novel BP loci at genome-wide significance level (P < 5 × 10). Two novel loci were identified based on the 1DF test of interaction with educational attainment, while the remaining 16 loci were identified through the 2DF joint test of genetic and interaction effects. Ten novel loci were identified in individuals of African ancestry. Several novel loci show strong biological plausibility since they involve physiologic systems implicated in BP regulation. They include genes involved in the central nervous system-adrenal signaling axis (ZDHHC17, CADPS, PIK3C2G), vascular structure and function (GNB3, CDON), and renal function (HAS2 and HAS2-AS1, SLIT3). Collectively, these findings suggest a role of educational attainment or SES in further dissection of the genetic architecture of BP.
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http://dx.doi.org/10.1038/s41380-020-0719-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7641978PMC
June 2021

The Sleep Apnea-Specific Hypoxic Burden Predicts Incident Heart Failure.

Chest 2020 08 13;158(2):739-750. Epub 2020 Apr 13.

Division of Sleep and Circadian Disorders, Brigham and Women's Hospital and Harvard Medical School, Boston, MA.

Background: Heart failure (HF) is a leading cause of morbidity and mortality and although it is linked to sleep apnea, which physiological stressors most strongly associate with incident disease is unclear. We tested whether sleep apnea-specific hypoxic burden (SASHB) predicts incident HF in two independent cohort studies.

Research Question: In comparison with apnea-hypopnea index (AHI), how does sleep apnea-specific hypoxic burden predict incident HF?

Study Design And Methods: The samples were derived from two cohort studies: The Sleep Heart Health Study (SHHS), which included 4,881 middle-aged and older adults (54.4% women), age 63.6 ± 11.1 years; and the Outcomes of Sleep Disorders in Older Men (MrOS), which included 2,653 men, age 76.2 ± 5.4 years. We computed SASHB as the sleep apnea-specific area under the desaturation curve from pre-event baseline. We used Cox models for incident HF to estimate the adjusted hazard ratios (HRs) for natural log-transformed SASHB and AHI adjusting for multiple confounders.

Results: The SASHB predicted incident HF in men in both cohorts, whereas AHI did not. Men in SHHS and MrOS had adjusted HRs (per 1SD increase in SASHB) of 1.18 (95% CI, 1.02-1.37) and 1.22 (95% CI, 1.02-1.45), respectively. Associations with SASHB were observed in men with both low and high AHI levels. Associations were not significant in women.

Interpretation: In men, the hypoxic burden of sleep apnea was associated with incident HF after accounting for demographic factors, smoking, and co-morbidities. The findings Suggest that quantification of an easily measured index of sleep apnea-related hypoxias may be useful for identifying individuals at risk for heart disease, while also suggesting targets for intervention.
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http://dx.doi.org/10.1016/j.chest.2020.03.053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7417383PMC
August 2020

A sleep apnea prediction model developed for African Americans: the Jackson Heart Sleep Study.

J Clin Sleep Med 2020 07;16(7):1171-1178

Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts.

Study Objectives: African Americans have a high prevalence of severe sleep apnea that is often undiagnosed. We developed a prediction model for sleep apnea and compared the predictive values of that model to other prediction models among African Americans in the Jackson Heart Sleep Study.

Methods: Participants in the Jackson Heart Sleep Study underwent a type 3 home sleep apnea study and completed standardized measurements and questionnaires. We identified 26 candidate predictors from 17 preselected measures capturing information on demographics, anthropometry, sleep, and comorbidities. To develop the optimal prediction model, we fit logistic regression models using all possible combinations of candidate predictors. We then implemented a series of steps: comparisons of equivalent models based on the C-statistics, bootstrap to evaluate the finite sample properties of the C-statistics between models, and fivefold cross-validation to prevent overfitting.

Results: Of 719 participants, 38% had moderate or severe sleep apnea, 34% were male, and 38% reported habitual snoring. The average age and body mass index were 63.2 (standard deviation:10.7) years and 32.2 (standard deviation: 7.0) kg/m². The final prediction model included age, sex, body mass index, neck circumference, depressive symptoms, snoring, restless sleep, and witnessed apneas. The final model has an equal sensitivity and specificity of 0.72 and better predictive properties than commonly used prediction models.

Conclusions: In comparing a prediction model developed for African Americans in the Jackson Heart Sleep Study to widely used screening tools, we found a model that included measures of demographics, anthropometry, depressive symptoms, and sleep patterns and symptoms better predicted sleep apnea.
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http://dx.doi.org/10.5664/jcsm.8452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7954057PMC
July 2020
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