Multidimensional sleep health and diabetic retinopathy: Systematic review and meta-analysis.

Diabetic retinopathy (DR) is one of the most prevalent microvascular diabetic complications. Poor sleep health and obstructive sleep apnea (OSA) are risk factors for diabetes and poor glycemic control. Recent studies have suggested associations between poor sleep health/OSA and DR. Furthermore, there have been suggestions of melatonin dysregulation in the context of DR. We conducted a systematic review and meta-analysis exploring the associations between multidimensional sleep health (duration, satisfaction, efficiency, timing/regularity and alertness), OSA and melatonin with DR. Forty-two studies were included. Long, but not short sleep, was significantly associated with DR, OR 1.41 (95%CI 1.21, 1.64). Poor sleep satisfaction was also significantly associated with DR, OR 2.04 (1.41, 2.94). Sleep efficiency and alertness were not associated with DR, while the evidence on timing/regularity was scant. Having OSA was significantly associated with having DR, OR 1.34 (1.07, 1.69). Further, those with DR had significantly lower melatonin/melatonin metabolite levels than those without DR, standardized mean difference -0.94 (-1.44, -0.44). We explored whether treating OSA with continuous positive airway pressure (CPAP) led to improvement in DR (five studies). The results were mixed among studies, but potential benefits were observed in some. This review highlights the association between poor multidimensional sleep health and DR.

Community Mobility and Depressive Symptoms During the COVID-19 Pandemic in the United States.

Importance: Marked elevation in levels of depressive symptoms compared with historical norms have been described during the COVID-19 pandemic, and understanding the extent to which these are associated with diminished in-person social interaction could inform public health planning for future pandemics or other disasters. Objective: To describe the association between living in a US county with diminished mobility during the COVID-19 pandemic and self-reported depressive symptoms, while accounting for potential local and state-level confounding factors. Design, Setting, and Participants: This survey study used 18 waves of a nonprobability internet survey conducted in the United States between May 2020 and April 2022. Participants included respondents who were 18 years and older and lived in 1 of the 50 US states or Washington DC. Main Outcome and Measure: Depressive symptoms measured by the Patient Health Questionnaire-9 (PHQ-9); county-level community mobility estimates from mobile apps; COVID-19 policies at the US state level from the Oxford stringency index. Results: The 192 271 survey respondents had a mean (SD) of age 43.1 (16.5) years, and 768 (0.4%) were American Indian or Alaska Native individuals, 11 448 (6.0%) were Asian individuals, 20 277 (10.5%) were Black individuals, 15 036 (7.8%) were Hispanic individuals, 1975 (1.0%) were Pacific Islander individuals, 138 702 (72.1%) were White individuals, and 4065 (2.1%) were individuals of another race. Additionally, 126 381 respondents (65.7%) identified as female and 65 890 (34.3%) as male. Mean (SD) depression severity by PHQ-9 was 7.2 (6.8). In a mixed-effects linear regression model, the mean county-level proportion of individuals not leaving home was associated with a greater level of depression symptoms (ß, 2.58; 95% CI, 1.57-3.58) after adjustment for individual sociodemographic features. Results were similar after the inclusion in regression models of local COVID-19 activity, weather, and county-level economic features, and persisted after widespread availability of COVID-19 vaccination. They were attenuated by the inclusion of state-level pandemic restrictions. Two restrictions, mandatory mask-wearing in public (ß, 0.23; 95% CI, 0.15-0.30) and policies cancelling public events (ß, 0.37; 95% CI, 0.22-0.51), demonstrated modest independent associations with depressive symptom severity. Conclusions and Relevance: In this study, depressive symptoms were greater in locales and times with diminished community mobility. Strategies to understand the potential public health consequences of pandemic responses are needed.

Media use and vaccine resistance.

Public health requires collective action-the public best addresses health crises when individuals engage in prosocial behaviors. Failure to do so can have dire societal and economic consequences. This was made clear by the disjointed, politicized response to COVID-19 in the United States. Perhaps no aspect of the pandemic exemplified this challenge more than the sizeable percentage of individuals who delayed or refused vaccination. While scholars, practitioners, and the government devised a range of communication strategies to persuade people to get vaccinated, much less attention has been paid to where the unvaccinated could be reached. We address this question using multiple waves of a large national survey as well as various secondary data sets. We find that the vaccine resistant seems to predictably obtain information from conservative media outlets (e.g. Fox News) while the vaccinated congregate around more liberal outlets (e.g. MSNBC). We also find consistent evidence that vaccine-resistant individuals often obtain COVID-19 information from various social media, most notably Facebook, rather than traditional media sources. Importantly, such individuals tend to exhibit low institutional trust. While our results do not suggest a failure of sites such as Facebook's institutional COVID-19 efforts, as the counterfactual of no efforts is unknown, they do highlight an opportunity to reach those who are less likely to take vital actions in the service of public health.

Prevalence and Correlates of Long COVID Symptoms Among US Adults.

Importance: Persistence of COVID-19 symptoms beyond 2 months, or long COVID, is increasingly recognized as a common sequela of acute infection. Objectives: To estimate the prevalence of and sociodemographic factors associated with long COVID and to identify whether the predominant variant at the time of infection and prior vaccination status are associated with differential risk. Design, Setting, and Participants: This cross-sectional study comprised 8 waves of a nonprobability internet survey conducted between February 5, 2021, and July 6, 2022, among individuals aged 18 years or older, inclusive of all 50 states and the District of Columbia. Main Outcomes and Measures: Long COVID, defined as reporting continued COVID-19 symptoms beyond 2 months after the initial month of symptoms, among individuals with self-reported positive results of a polymerase chain reaction test or antigen test. Results: The 16 091 survey respondents reporting test-confirmed COVID-19 illness at least 2 months prior had a mean age of 40.5 (15.2) years; 10 075 (62.6%) were women, and 6016 (37.4%) were men; 817 (5.1%) were Asian, 1826 (11.3%) were Black, 1546 (9.6%) were Hispanic, and 11 425 (71.0%) were White. From this cohort, 2359 individuals (14.7%) reported continued COVID-19 symptoms more than 2 months after acute illness. Reweighted to reflect national sociodemographic distributions, these individuals represented 13.9% of those who had tested positive for COVID-19, or 1.7% of US adults. In logistic regression models, older age per decade above 40 years (adjusted odds ratio [OR], 1.15; 95% CI, 1.12-1.19) and female gender (adjusted OR, 1.91; 95% CI, 1.73-2.13) were associated with greater risk of persistence of long COVID; individuals with a graduate education vs high school or less (adjusted OR, 0.67; 95% CI, 0.56-0.79) and urban vs rural residence (adjusted OR, 0.74; 95% CI, 0.64-0.86) were less likely to report persistence of long COVID. Compared with ancestral COVID-19, infection during periods when the Epsilon variant (OR, 0.81; 95% CI, 0.69-0.95) or the Omicron variant (OR, 0.77; 95% CI, 0.64-0.92) predominated in the US was associated with diminished likelihood of long COVID. Completion of the primary vaccine series prior to acute illness was associated with diminished risk for long COVID (OR, 0.72; 95% CI, 0.60-0.86). Conclusions and Relevance: This study suggests that long COVID is prevalent and associated with female gender and older age, while risk may be diminished by completion of primary vaccination series prior to infection.

Prevalence of Firearm Ownership Among Individuals With Major Depressive Symptoms.

Importance: Both major depression and firearm ownership are associated with an increased risk for death by suicide in the United States, but the extent of overlap among these major risk factors is not well characterized. Objective: To assess the prevalence of current and planned firearm ownership among individuals with depression. Design, Setting, and Participants: Cross-sectional survey study using data pooled from 2 waves of a 50-state nonprobability internet survey conducted between May and July 7, 2021. Internet survey respondents were 18 years of age or older and were sampled from all 50 US states and the District of Columbia. Main Outcomes and Measures: Self-reported firearm ownership; depressive symptoms as measured by the 9-item Patient Health Questionnaire. Results: Of 24 770 survey respondents (64.6% women and 35.4% men; 5.0% Asian, 10.8% Black, 7.5% Hispanic, and 74.0% White; mean [SD] age 45.8 [17.5]), 6929 (28.0%) reported moderate or greater depressive symptoms; this group had mean (SD) age of 38.18 (15.19) years, 4587 were female (66.2%), and 406 were Asian (5.9%), 725 were Black (10.5%), 652 were Hispanic (6.8%), and 4902 were White (70.7%). Of those with depression, 31.3% reported firearm ownership (n = 2167), of whom 35.9% (n = 777) reported purchasing a firearm within the past year. In regression models, the presence of moderate or greater depressive symptoms was not significantly associated with firearm ownership (adjusted odds ratio [OR], 1.07; 95% CI, 0.98-1.17) but was associated with greater likelihood of a first-time firearm purchase during the COVID-19 pandemic (adjusted OR, 1.77; 95% CI, 1.56-2.02) and greater likelihood of considering a future firearm purchase (adjusted OR, 1.53; 95% CI, 1.23-1.90). Conclusions and Relevance: In this study, current and planned firearm ownership was common among individuals with major depressive symptoms, suggesting a public health opportunity to address this conjunction of suicide risk factors.

Association of Major Depressive Symptoms With Endorsement of COVID-19 Vaccine Misinformation Among US Adults.

Importance: Misinformation about COVID-19 vaccination may contribute substantially to vaccine hesitancy and resistance. Objective: To determine if depressive symptoms are associated with greater likelihood of believing vaccine-related misinformation. Design, Setting, and Participants: This survey study analyzed responses from 2 waves of a 50-state nonprobability internet survey conducted between May and July 2021, in which depressive symptoms were measured using the Patient Health Questionnaire 9-item (PHQ-9). Survey respondents were aged 18 and older. Population-reweighted multiple logistic regression was used to examine the association between moderate or greater depressive symptoms and endorsement of at least 1 item of vaccine misinformation, adjusted for sociodemographic features. The association between depressive symptoms in May and June, and new support for misinformation in the following wave was also examined. Exposures: Depressive symptoms. Main Outcomes and Measures: The main outcome was endorsing any of 4 common vaccine-related statements of misinformation. Results: Among 15 464 survey respondents (9834 [63.6%] women and 5630 [36.4%] men; 722 Asian respondents [4.7%], 1494 Black respondents [9.7%], 1015 Hispanic respondents [6.6%], and 11 863 White respondents [76.7%]; mean [SD] age, 47.9 [17.5] years), 4164 respondents (26.9%) identified moderate or greater depressive symptoms on the PHQ-9, and 2964 respondents (19.2%) endorsed at least 1 vaccine-related statement of misinformation. Presence of depression was associated with increased likelihood of endorsing misinformation (crude odds ratio [OR], 2.33; 95% CI, 2.09-2.61; adjusted OR, 2.15; 95% CI, 1.91-2.43). Respondents endorsing at least 1 misinformation item were significantly less likely to be vaccinated (crude OR, 0.40; 95% CI, 0.36-0.45; adjusted OR, 0.45; 95% CI, 0.40-0.51) and more likely to report vaccine resistance (crude OR, 2.54; 95% CI, 2.21-2.91; adjusted OR, 2.68; 95% CI, 2.89-3.13). Among 2809 respondents who answered a subsequent survey in July, presence of depression in the first survey was associated with greater likelihood of endorsing more misinformation compared with the prior survey (crude OR, 1.98; 95% CI, 1.42-2.75; adjusted OR, 1.63; 95% CI, 1.14-2.33). Conclusions and Relevance: This survey study found that individuals with moderate or greater depressive symptoms were more likely to endorse vaccine-related misinformation, cross-sectionally and at a subsequent survey wave. While this study design cannot address causation, the association between depression and spread and impact of misinformation merits further investigation.

Association Between Social Media Use and Self-reported Symptoms of Depression in US Adults.

Importance: Some studies suggest that social media use is associated with risk for depression, particularly among children and young adults. Objective: To characterize the association between self-reported use of individual social media platforms and worsening of depressive symptoms among adults. Design, Setting, and Participants: This survey study included data from 13 waves of a nonprobability internet survey conducted approximately monthly between May 2020 and May 2021 among individuals aged 18 years and older in the US. Data were analyzed in July and August 2021. Main Outcomes and Measures: Logistic regression was applied without reweighting, with a 5 point or greater increase in 9-item Patient Health Questionnaire (PHQ-9) score as outcome and participant sociodemographic features, baseline PHQ-9, and use of each social media platform as independent variables. Results: In total, 5395 of 8045 individuals (67.1%) with a PHQ-9 score below 5 on initial survey completed a second PHQ-9. These respondents had a mean (SD) age of 55.8 (15.2) years; 3546 respondents (65.7%) identified as female; 329 respondents (6.1%) were Asian, 570 (10.6%) Black, 256 (4.7%) Hispanic, 4118 (76.3%) White, and 122 (2.3%) American Indian or Alaska Native, Pacific Islander or Native Hawaiian, or other. Among eligible respondents, 482 (8.9%) reported 5 points or greater worsening of PHQ-9 score at second survey. In fully adjusted models for increase in symptoms, the largest adjusted odds ratio (aOR) associated with social media use was observed for Snapchat (aOR, 1.53; 95% CI, 1.19-1.96), Facebook (aOR, 1.42; 95% CI, 1.10-1.81), and TikTok (aOR, 1.39; 95% CI, 1.03-1.87). Conclusions and Relevance: Among survey respondents who did not report depressive symptoms initially, social media use was associated with greater likelihood of subsequent increase in depressive symptoms after adjustment for sociodemographic features and news sources. These data cannot elucidate the nature of this association, but suggest the need for further study to understand how social media use may factor into depression among adults.

Gender-specificity of resilience in major depressive disorder.

INTRODUCTION: The major stressors associated with the COVID-19 pandemic provide an opportunity to understand the extent to which protective factors against depression may exhibit gender-specificity. METHOD: This study examined responses from multiple waves of a 50 states non-probability internet survey conducted between May 2020 and January 2021. Participants completed the PHQ-9 as a measure of depression, as well as items characterizing social supports. We used logistic regression models with population reweighting to examine association between absence of even mild depressive symptoms and sociodemographic features and social supports, with interaction terms and stratification used to investigate sex-specificity. RESULTS: Among 73,917 survey respondents, 31,199 (42.2%) reported absence of mild or greater depression-11,011/23,682 males (46.5%) and 20,188/50,235 (40.2%) females. In a regression model, features associated with greater likelihood of depression-resistance included at least weekly attendance of religious services (odds ratio [OR]: 1.10, 95% confidence interval [CI]: 1.04-1.16) and greater trust in others (OR: 1.04 for a 2-unit increase, 95% CI: 1.02-1.06), along with level of social support measured as number of social ties available who could provide care (OR: 1.05, 95% CI: 1.02-1.07), talk to them (OR: 1.10, 95% CI: 1.07-1.12), and help with employment (OR: 1.06, 95% CI: 1.04-1.08). The first two features showed significant interaction with gender (p < .0001), with markedly greater protective effects among women. CONCLUSION: Aspects of social support are associated with diminished risk of major depressive symptoms, with greater effects of religious service attendance and trust in others observed among women than men.

Persistence of symptoms up to 10 months following acute COVID-19 illness.

IMPORTANCE: COVID-19 symptoms are increasingly recognized to persist among a subset of individual following acute infection, but features associated with this persistence are not well-understood. OBJECTIVE: We aimed to identify individual features that predicted persistence of symptoms over at least 2 months at the time of survey completion.Design: Non-probability internet survey. Participants were asked to identify features of acute illness as well as persistence of symptoms at time of study completion. We used logistic regression models to examine association between sociodemographic and clinical features and persistence of symptoms at or beyond 2 months. SETTING: Ten waves of a fifty-state survey between June 13, 2020 and January 13, 2021. PARTICIPANTS: 6,211 individuals who reported symptomatic COVID-19 illness confirmed by positive test or clinician diagnosis. EXPOSURE: symptomatic COVID-19 illness. RESULTS: Among 6,211 survey respondents reporting COVID-19 illness, with a mean age of 37.8 (SD 12.2) years and 45.1% female, 73.9% white, 10.0% Black, 9.9% Hispanic, and 3.1% Asian, a total of 4946 (79.6%) had recovered within less than 2 months, while 491 (7.9%) experienced symptoms for 2 months or more. Of the full cohort, 3.4% were symptomatic for 4 months or more and 2.2% for 6 months or more. In univariate analyses, individuals with persistent symptoms on average reported greater initial severity. In logistic regression models, older age was associated with greater risk of persistence (OR 1.10, 95% CI 1.01-1.19 for each decade beyond 40); otherwise, no significant associations with persistence were identified for gender, race/ethnicity, or income. Presence of headache was significantly associated with greater likelihood of persistence (OR 1.44, 95% CI 1.11-1.86), while fever was associated with diminished likelihood of persistence (OR 0.66, 95% CI 0.53-0.83). CONCLUSION AND RELEVANCE: A subset of individuals experience persistent symptoms from 2 to more than 10 months after acute COVID-19 illness, particularly those who recall headache and absence of fever. In light of this prevalence, strategies for predicting and managing such sequelae are needed. TRIAL REGISTRATION: NA. KEY POINTS: Question: Which individuals are at greatest risk for post-acute sequelae of COVID-19?Findings: In this non-probability internet survey, among 6,211 individuals with symptomatic COVID-19 illness, 7.9% experienced persistence of symptoms lasting 2 months or longer. Older age, but not other sociodemographic features, was associated with risk for persistence, as was headache.Meaning: Identifying individuals at greater risk for symptomatic persistence may facilitate development of targeted interventions.

Genetic Risk Score Analysis in Early-Onset Bipolar Disorder.

OBJECTIVE: In this study, we performed a candidate genetic risk score (GRS) analysis of early-onset bipolar disorder (BD). METHODS: Treatment of Early Age Mania (TEAM) study enrollment and sample collection took place from 2003 to 2008. Mayo Clinic Bipolar Biobank samples were collected from 2009 to 2013. Genotyping and analyses for the present study took place from 2013 to 2014. The diagnosis of BD was based on Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revision criteria. Eight single-nucleotide polymorphisms (SNPs), previously reported in genome-wide association studies to be associated with BD, were chosen for GRS analysis in early-onset bipolar disease. These SNPs map to 3 genes: CACNA1C (calcium channel, voltage-dependent, L type, alpha 1C subunit), ANK3 (ankyrin-3, node of Ranvier [ankyrin G]), and ODZ4 (teneurin transmembrane protein 4 [formerly "odz, odd Oz/10-m homolog 4 {Drosophila}, ODZ4"]). The 8 candidate SNPs were genotyped in patients from the TEAM study (n = 69); adult patients with BD (n = 732), including a subset with early-onset illness (n = 192); and healthy controls (n = 776). GRS analyses were performed to compare early-onset cases with controls. In addition, associations of early-onset BD with individual SNPs and haplotypes were explored. RESULTS: GRS analysis revealed associations of the risk score with early-onset BD (P = .01). Gene-level haplotype analysis comparing TEAM patients with controls suggested association of early-onset BD with a CACNA1C haplotype (global test, P = .01). At the level of individual SNPs, comparison of TEAM cases with healthy controls provided nominally significant evidence for association of SNP rs10848632 in CACNA1C with early-onset BD (P = .017), which did not remain significant after correction for multiple comparisons. CONCLUSIONS: These preliminary analyses suggest that previously identified BD risk loci, especially CACNA1C, have a role in early-onset BD, possibly with stronger effects than for late-onset BD.

Examination of the Involvement of Cholinergic-Associated Genes in Nicotine Behaviors in European and African Americans.

INTRODUCTION: Cigarette smoking is a physiologically harmful habit. Nicotinic acetylcholine receptors (nAChRs) are bound by nicotine and upregulated in response to chronic exposure to nicotine. It is known that upregulation of these receptors is not due to a change in mRNA of these genes, however, more precise details on the process are still uncertain, with several plausible hypotheses describing how nAChRs are upregulated. We have manually curated a set of genes believed to play a role in nicotine-induced nAChR upregulation. Here, we test the hypothesis that these genes are associated with and contribute risk for nicotine dependence (ND) and the number of cigarettes smoked per day (CPD). METHODS: Studies with genotypic data on European and African Americans (EAs and AAs, respectively) were collected and a gene-based test was run to test for an association between each gene and ND and CPD. RESULTS: Although several novel genes were associated with CPD and ND at P < 0.05 in EAs and AAs, these associations did not survive correction for multiple testing. Previous associations between CHRNA3, CHRNA5, CHRNB4 and CPD in EAs were replicated. CONCLUSIONS: Our hypothesis-driven approach avoided many of the limitations inherent in pathway analyses and provided nominal evidence for association between cholinergic-related genes and nicotine behaviors. IMPLICATIONS: We evaluated the evidence for association between a manually curated set of genes and nicotine behaviors in European and African Americans. Although no genes were associated after multiple testing correction, this study has several strengths: by manually curating a set of genes we circumvented the limitations inherent in many pathway analyses and tested several genes that had not yet been examined in a human genetic study; gene-based tests are a useful way to test for association with a set of genes; and these genes were collected based on literature review and conversations with experts, highlighting the importance of scientific collaboration.

No Reliable Association between Runs of Homozygosity and Schizophrenia in a Well-Powered Replication Study.

It is well known that inbreeding increases the risk of recessive monogenic diseases, but it is less certain whether it contributes to the etiology of complex diseases such as schizophrenia. One way to estimate the effects of inbreeding is to examine the association between disease diagnosis and genome-wide autozygosity estimated using runs of homozygosity (ROH) in genome-wide single nucleotide polymorphism arrays. Using data for schizophrenia from the Psychiatric Genomics Consortium (n = 21,868), Keller et al. (2012) estimated that the odds of developing schizophrenia increased by approximately 17% for every additional percent of the genome that is autozygous (ß = 16.1, CI(ß) = [6.93, 25.7], Z = 3.44, p = 0.0006). Here we describe replication results from 22 independent schizophrenia case-control datasets from the Psychiatric Genomics Consortium (n = 39,830). Using the same ROH calling thresholds and procedures as Keller et al. (2012), we were unable to replicate the significant association between ROH burden and schizophrenia in the independent PGC phase II data, although the effect was in the predicted direction, and the combined (original + replication) dataset yielded an attenuated but significant relationship between Froh and schizophrenia (ß = 4.86,CI(ß) = [0.90,8.83],Z = 2.40,p = 0.02). Since Keller et al. (2012), several studies reported inconsistent association of ROH burden with complex traits, particularly in case-control data. These conflicting results might suggest that the effects of autozygosity are confounded by various factors, such as socioeconomic status, education, urbanicity, and religiosity, which may be associated with both real inbreeding and the outcome measures of interest.

Whole-genome pathway analysis on 132,497 individuals identifies novel gene-sets associated with body mass index.

Whole genome pathway analysis is a powerful tool for the exploration of the combined effects of gene-sets within biological pathways. This study applied Interval Based Enrichment Analysis (INRICH) to perform whole-genome pathway analysis of body-mass index (BMI). We used a discovery set composed of summary statistics from a meta-analysis of 123,865 subjects performed by the GIANT Consortium, and an independent sample of 8,632 subjects to assess replication of significant pathways. We examined SNPs within nominally significant pathways using linear mixed models to estimate their contribution to overall BMI heritability. Six pathways replicated as having significant enrichment for association after correcting for multiple testing, including the previously unknown relationships between BMI and the Reactome regulation of ornithine decarboxylase pathway, the KEGG lysosome pathway, and the Reactome stabilization of P53 pathway. Two non-overlapping sets of genes emerged from the six significant pathways. The clustering of shared genes based on previously identified protein-protein interactions listed in PubMed and OMIM supported the relatively independent biological effects of these two gene-sets. We estimate that the SNPs located in examined pathways explain ∼20% of the heritability for BMI that is tagged by common SNPs (3.35% of the 16.93% total).

Runs of homozygosity implicate autozygosity as a schizophrenia risk factor.

Autozygosity occurs when two chromosomal segments that are identical from a common ancestor are inherited from each parent. This occurs at high rates in the offspring of mates who are closely related (inbreeding), but also occurs at lower levels among the offspring of distantly related mates. Here, we use runs of homozygosity in genome-wide SNP data to estimate the proportion of the autosome that exists in autozygous tracts in 9,388 cases with schizophrenia and 12,456 controls. We estimate that the odds of schizophrenia increase by ~17% for every 1% increase in genome-wide autozygosity. This association is not due to one or a few regions, but results from many autozygous segments spread throughout the genome, and is consistent with a role for multiple recessive or partially recessive alleles in the etiology of schizophrenia. Such a bias towards recessivity suggests that alleles that increase the risk of schizophrenia have been selected against over evolutionary time.

Multiple testing in high-throughput sequence data: experiences from Group 8 of Genetic Analysis Workshop 17.

The use of high-throughput sequence data in genetic epidemiology allows the investigation of common and rare variants in the entire genome, thus increasing the amount of information and the potential number of statistical tests performed within one study. As a consequence, the problem of multiple testing may become even more pressing than in previous studies. As an important challenge, the exact number of statistical tests depends on the actual statistical method used. Furthermore, many statistical approaches for the analysis of sequence data require permutation. Thus it may be difficult to also use permutation to estimate correct type I error levels as in genome-wide association studies. In view of this, a separate group at Genetic Analysis Workshop 17 was formed with a focus on multiple testing. Here, we present the approaches used for the workshop. Apart from tackling the multiple testing problem, the new group focused on different issues. Some contributors developed and investigated modifications of existing collapsing methods. Others aimed at improving the identification of functional variants through a reduction and analysis of the underlying data dimensions. Two research groups investigated the overall accumulation of rare variation across the genome and its value in predicting phenotypes. Finally, other investigators left the path of traditional statistical analyses by reversing null and alternative hypotheses and by proposing a novel resampling method. We describe and discuss all these approaches.

Recent methods for polygenic analysis of genome-wide data implicate an important effect of common variants on cardiovascular disease risk.

BACKGROUND: Traditional genome-wide association studies are generally limited in their ability explain a large portion of genetic risk for most common diseases. We sought to use both traditional GWAS methods, as well as more recently developed polygenic genome-wide analysis techniques to identify subsets of single-nucleotide polymorphisms (SNPs) that may be involved in risk of cardiovascular disease, as well as estimate the heritability explained by common SNPs. METHODS: Using data from the Framingham SNP Health Association Resource (SHARe), three complimentary methods were applied to examine the genetic factors associated with the Framingham Risk Score, a widely accepted indicator of underlying cardiovascular disease risk. The first method adopted a traditional GWAS approach - independently testing each SNP for association with the Framingham Risk Score. The second two approaches involved polygenic methods with the intention of providing estimates of aggregate genetic risk and heritability. RESULTS: While no SNPs were independently associated with the Framingham Risk Score based on the results of the traditional GWAS analysis, we were able to identify cardiovascular disease-related SNPs as reported by previous studies. A predictive polygenic analysis was only able to explain approximately 1% of the genetic variance when predicting the 10-year risk of general cardiovascular disease. However, 20% to 30% of the variation in the Framingham Risk Score was explained using a recently developed method that considers the joint effect of all SNPs simultaneously. CONCLUSION: The results of this study imply that common SNPs explain a large amount of the variation in the Framingham Risk Score and suggest that future, better-powered genome-wide association studies, possibly informed by knowledge of gene-pathways, will uncover more risk variants that will help to elucidate the genetic architecture of cardiovascular disease.

Detecting autozygosity through runs of homozygosity: a comparison of three autozygosity detection algorithms.

BACKGROUND: A central aim for studying runs of homozygosity (ROHs) in genome-wide SNP data is to detect the effects of autozygosity (stretches of the two homologous chromosomes within the same individual that are identical by descent) on phenotypes. However, it is unknown which current ROH detection program, and which set of parameters within a given program, is optimal for differentiating ROHs that are truly autozygous from ROHs that are homozygous at the marker level but vary at unmeasured variants between the markers. METHOD: We simulated 120 Mb of sequence data in order to know the true state of autozygosity. We then extracted common variants from this sequence to mimic the properties of SNP platforms and performed ROH analyses using three popular ROH detection programs, PLINK, GERMLINE, and BEAGLE. We varied detection thresholds for each program (e.g., prior probabilities, lengths of ROHs) to understand their effects on detecting known autozygosity. RESULTS: Within the optimal thresholds for each program, PLINK outperformed GERMLINE and BEAGLE in detecting autozygosity from distant common ancestors. PLINK's sliding window algorithm worked best when using SNP data pruned for linkage disequilibrium (LD). CONCLUSION: Our results provide both general and specific recommendations for maximizing autozygosity detection in genome-wide SNP data, and should apply equally well to research on whole-genome autozygosity burden or to research on whether specific autozygous regions are predictive using association mapping methods.

Mutational load analysis of unrelated individuals.

Evolutionary genetic models predict that the cumulative effect of rare deleterious mutations across the genome-known as mutational load burden-increases the susceptibility to complex disease. To test the mutational load burden hypothesis, we adopted a two-tiered approach: assessing the impact of whole-exome minor allele load burden and then conducting individual-gene screening. For our primary analysis, we examined various minor allele frequency (MAF) thresholds and weighting schemes to examine the overall effect of minor allele load on affection status. We found a consistent association between minor allele load and affection status, but this effect did not markedly increase within rare and/or functional single-nucleotide polymorphisms (SNPs). Our follow-up analysis considered minor allele load in individual genes to see whether only one or a few genes were driving the overall effect. Examining our most significant result-minor allele load of nonsynonymous SNPs with MAF < 2.4%-we detected no significantly associated genes after Bonferroni correction for multiple testing. After moderately significant genes (p < 0.05) were removed, the overall effect of rare nonsynonymous allele load remained significant. Overall, we did not find clear support for mutational load burden on affection status; however, these results are ultimately dependent on and limited by the nature of the Genetic Analysis Workshop 17 simulation.