Genetic effects of sequence-conserved enhancer-like elements on human complex traits

BACKGROUND

The vast majority of findings from human genome-wide association studies (GWAS) map to non-coding sequences, complicating their mechanistic interpretations and clinical translations. Non-coding sequences that are evolutionarily conserved and biochemically active could offer clues to the mechanisms underpinning GWAS discoveries. However, genetic effects of such sequences have not been systematically examined across a wide range of human tissues and traits, hampering progress to fully understand regulatory causes of human complex traits.

RESULTS

Here we develop a simple yet effective strategy to identify functional elements exhibiting high levels of human-mouse sequence conservation and enhancer-like biochemical activity, which scales well to 313 epigenomic datasets across 106 human tissues and cell types. Combined with 468 GWAS of European (EUR) and East Asian (EAS) ancestries, these elements show tissue-specific enrichments of heritability and causal variants for many traits, which are significantly stronger than enrichments based on enhancers without sequence conservation. These elements also help prioritize candidate genes that are functionally relevant to body mass index (BMI) and schizophrenia but were not reported in previous GWAS with large sample sizes.

CONCLUSIONS

Our findings provide a comprehensive assessment of how sequence-conserved enhancer-like elements affect complex traits in diverse tissues and demonstrate a generalizable strategy of integrating evolutionary and biochemical data to elucidate human disease genetics.

Daily Affective Dynamics in Major Depressive Disorder: The Role of Daily Stressors and Positive Events

This study examined daily affective dynamic indices among individuals with a major depressive disorder (MDD) diagnosis in the past one year at the time of the interview, focusing on affective variability and change in affect in response to daily events (affective reactivity). Data were from the main survey and daily diary project of the Midlife in the United States (MIDUS) study. Participants (N = 1,970; nMDD = 202; nnon-MDD = 1,768) completed structured clinical interviews on mental health and telephone interviews about their daily experiences spanning eight consecutive days. Multilevel models revealed that the MDD group experienced greater positive (PA) and negative affect (NA) variability than the non-MDD group. On days that at least one stressful event was reported, the MDD group experienced a greater decrease in PA and a greater increase in NA. On days that at least one positive event was reported, the MDD group experienced a greater increase in PA and a greater decrease in NA. Changes in affect to daily events, particularly the mood brightening effect, may be indicators of depression and potential targets for intervention. Limitations of the study include a community sample, reliance on self-reported measures of daily stressors and positive events, inclusion of remitted and current MDD participants, and the DSM-III-R based criteria for MDD diagnosis.

SciComm Optimizer for Policy Engagement: a randomized controlled trial of the SCOPE model on state legislators' research use in public discourse

BACKGROUND

While prior work has revealed conditions that foster policymakers' use of research evidence, few studies have rigorously investigated the effectiveness of theory-based practices. Specifically, policymakers are most apt to use research evidence when it is timely, relevant, brief, and messaged appropriately, as well as when it facilitates interactive engagement. This study sought to experimentally evaluate an enhanced research dissemination intervention, known as the SciComm Optimizer for Policy Engagement (SCOPE), implemented during the COVID-19 pandemic among US state legislators.

METHODS

State legislators assigned to health committees and their staff were randomized to receive the SCOPE intervention. This involved providing academic researchers with a pathway for translating and disseminating research relevant to current legislative priorities via fact sheets emailed directly to officials. The intervention occurred April 2020-March 2021. Research language was measured in state legislators' social media posts.

RESULTS

Legislators randomized to receive the intervention, relative to the control group, produced 24% more social media posts containing research language related to COVID-19. Secondary analyses revealed that these findings were driven by two different types of research language. Intervention officials produced 67% more COVID-related social media posts referencing technical language (e.g., statistical methods), as well as 28% more posts that referenced research-based concepts. However, they produced 31% fewer posts that referenced creating or disseminating new knowledge.

CONCLUSIONS

This study suggests that strategic, targeted science communication efforts may have the potential to change state legislators' public discourse and use of evidence. Strategic science communication efforts are particularly needed in light of the role government officials have played in communicating about the pandemic to the general public.

Novel EDGE encoding method enhances ability to identify genetic interactions

Assumptions are made about the genetic model of single nucleotide polymorphisms (SNPs) when choosing a traditional genetic encoding: additive, dominant, and recessive. Furthermore, SNPs across the genome are unlikely to demonstrate identical genetic models. However, running SNP-SNP interaction analyses with every combination of encodings raises the multiple testing burden. Here, we present a novel and flexible encoding for genetic interactions, the elastic data-driven genetic encoding (EDGE), in which SNPs are assigned a heterozygous value based on the genetic model they demonstrate in a dataset prior to interaction testing. We assessed the power of EDGE to detect genetic interactions using 29 combinations of simulated genetic models and found it outperformed the traditional encoding methods across 10%, 30%, and 50% minor allele frequencies (MAFs). Further, EDGE maintained a low false-positive rate, while additive and dominant encodings demonstrated inflation. We evaluated EDGE and the traditional encodings with genetic data from the Electronic Medical Records and Genomics (eMERGE) Network for five phenotypes: age-related macular degeneration (AMD), age-related cataract, glaucoma, type 2 diabetes (T2D), and resistant hypertension. A multi-encoding genome-wide association study (GWAS) for each phenotype was performed using the traditional encodings, and the top results of the multi-encoding GWAS were considered for SNP-SNP interaction using the traditional encodings and EDGE. EDGE identified a novel SNP-SNP interaction for age-related cataract that no other method identified: rs7787286 (MAF: 0.041; intergenic region of chromosome 7)–rs4695885 (MAF: 0.34; intergenic region of chromosome 4) with a Bonferroni LRT p of 0.018. A SNP-SNP interaction was found in data from the UK Biobank within 25 kb of these SNPs using the recessive encoding: rs60374751 (MAF: 0.030) and rs6843594 (MAF: 0.34) (Bonferroni LRT p: 0.026). We recommend using EDGE to flexibly detect interactions between SNPs exhibiting diverse action.

Although traditional genetic encodings are widely implemented in genetics research, including in genome-wide association studies (GWAS) and epistasis, each method makes assumptions that may not reflect the underlying etiology. Here, we introduce a novel encoding method that estimates and assigns an individualized data-driven encoding for each single nucleotide polymorphism (SNP): the elastic data-driven genetic encoding (EDGE). With simulations, we demonstrate that this novel method is more accurate and robust than traditional encoding methods in estimating heterozygous genotype values, reducing the type I error, and detecting SNP-SNP interactions. We further applied the traditional encodings and EDGE to biomedical data from the Electronic Medical Records and Genomics (eMERGE) Network for five phenotypes, and EDGE identified a novel interaction for age-related cataract not detected by traditional methods, which replicated in data from the UK Biobank. EDGE provides an alternative approach to understanding and modeling diverse SNP models and is recommended for studying complex genetics in common human phenotypes.

The geography of sentiment towards the Women's March of 2017

The Women's March of 2017 generated unprecedented levels of participation in the largest, single day, protest in history to date. The marchers protested the election of President Donald Trump and rallied in support of several civil issues such as women's rights. "Sister marches" evolved in at least 680 locations across the United States. Both positive and negative reactions to the March found their way into social media, with criticism stemming from certain, conservative, political sources and other groups. In this study, we investigate the extent to which this notable, historic event influenced sentiment on Twitter, and the degree to which responses differed by geographic area within the continental U.S. Tweets about the event rose to an impressive peak of over 12% of all geo-located tweets by mid-day of the March, Jan. 21. Messages included in tweets associated with the March tended to be positive in sentiment, on average, with a mean of 0.34 and a median of 0.07 on a scale of -4 to +4. In fact, tweets associated with the March were more positive than all other geo-located tweets during the day of the March. Exceptions to this pattern of positive sentiment occurred only in seven metropolitan areas, most of which involved very small numbers of tweets. Little evidence surfaced of extensive patterns of negative, aggressive messages towards the event in this set of tweets. Given the widespread nature of online harassment and sexist tweets, more generally, the results are notable. In sum, online reactions to the March on this social media platform suggest that this modern arm of the Women's Movement received considerable, virtual support across the country.