Critical reasoning on the co-expression module QTL in the dorsolateral prefrontal cortex.

Expression quantitative trait locus (eQTL) analysis is a popular method of gaining insight into the function of regulatory variation. While cis-eQTL resources have been instrumental in linking genome-wide association study variants to gene function, complex trait heritability may be additionally mediated by other forms of gene regulation. Toward this end, novel eQTL methods leverage gene co-expression (module-QTL) to investigate joint regulation of gene modules by single genetic variants. Here we broadly define a "module-QTL" as the association of a genetic variant with a summary measure of gene co-expression. This approach aims to reduce the multiple testing burden of a trans-eQTL search through the consolidation of gene-based testing and provide biological context to eQTLs shared between genes. In this article we provide an in-depth examination of the co-expression module eQTL (module-QTL) through literature review, theoretical investigation, and real-data application of the module-QTL to three large prefrontal cortex genotype-RNA sequencing datasets. We find module-QTLs in our study that are disease associated and reproducible are not additionally informative beyond cis- or trans-eQTLs for module genes. Through comparison to prior studies, we highlight promises and limitations of the module-QTL across study designs and provide recommendations for further investigation of the module-QTL framework.

Genetically Regulated Gene Expression in the Brain Associated With Chronic Pain: Relationships With Clinical Traits and Potential for Drug Repurposing.

BACKGROUND: Chronic pain is a common, poorly understood condition. Genetic studies including genome-wide association studies have identified many relevant variants, which have yet to be translated into full understanding of chronic pain. Transcriptome-wide association studies using transcriptomic imputation methods such as S-PrediXcan can help bridge this genotype-phenotype gap. METHODS: We carried out transcriptomic imputation using S-PrediXcan to identify genetically regulated gene expression associated with multisite chronic pain in 13 brain tissues and whole blood. Then, we imputed genetically regulated gene expression for over 31,000 Mount Sinai BioMe participants and performed a phenome-wide association study to investigate clinical relationships in chronic pain-associated gene expression changes. RESULTS: We identified 95 experiment-wide significant gene-tissue associations (p < 7.97 × 10-7), including 36 unique genes and an additional 134 gene-tissue associations reaching within-tissue significance, including 53 additional unique genes. Of the 89 unique genes in total, 59 were novel for multisite chronic pain and 18 are established drug targets. Chronic pain genetically regulated gene expression for 10 unique genes was significantly associated with cardiac dysrhythmia, metabolic syndrome, disc disorders/dorsopathies, joint/ligament sprain, anemias, and neurologic disorder phecodes. Phenome-wide association study analyses adjusting for mean pain score showed that associations were not driven by mean pain score. CONCLUSIONS: We carried out the largest transcriptomic imputation study of any chronic pain trait to date. Results highlight potential causal genes in chronic pain development and tissue and direction of effect. Several gene results were also drug targets. Phenome-wide association study results showed significant associations for phecodes including cardiac dysrhythmia and metabolic syndrome, thereby indicating potential shared mechanisms.

Mapping anorexia nervosa genes to clinical phenotypes.

BACKGROUND: Anorexia nervosa (AN) is a psychiatric disorder with complex etiology, with a significant portion of disease risk imparted by genetics. Traditional genome-wide association studies (GWAS) produce principal evidence for the association of genetic variants with disease. Transcriptomic imputation (TI) allows for the translation of those variants into regulatory mechanisms, which can then be used to assess the functional outcome of genetically regulated gene expression (GReX) in a broader setting through the use of phenome-wide association studies (pheWASs) in large and diverse clinical biobank populations with electronic health record phenotypes. METHODS: Here, we applied TI using S-PrediXcan to translate the most recent PGC-ED AN GWAS findings into AN-GReX. For significant genes, we imputed AN-GReX in the Mount Sinai BioMe™ Biobank and performed pheWASs on over 2000 outcomes to test the clinical consequences of aberrant expression of these genes. We performed a secondary analysis to assess the impact of body mass index (BMI) and sex on AN-GReX clinical associations. RESULTS: Our S-PrediXcan analysis identified 53 genes associated with AN, including what is, to our knowledge, the first-genetic association of AN with the major histocompatibility complex. AN-GReX was associated with autoimmune, metabolic, and gastrointestinal diagnoses in our biobank cohort, as well as measures of cholesterol, medications, substance use, and pain. Additionally, our analyses showed moderation of AN-GReX associations with measures of cholesterol and substance use by BMI, and moderation of AN-GReX associations with celiac disease by sex. CONCLUSIONS: Our BMI-stratified results provide potential avenues of functional mechanism for AN-genes to investigate further.

Evaluation of imputation performance of multiple reference panels in a Pakistani population.

Genotype imputation is crucial for GWAS, but reference panels and existing benchmarking studies prioritize European individuals. Consequently, it is unclear which publicly available reference panel should be used for Pakistani individuals, and whether ancestry composition or sample size of the panel matters more for imputation accuracy. Our study compared different reference panels to impute genotype data in 1814 Pakistani individuals, finding the best performance balancing accuracy and coverage with meta-imputation with TOPMed and the expanded 1000 Genomes (ex1KG) reference. Imputation accuracy of ex1KG outperformed TOPMed despite its 30-fold smaller sample size, supporting efforts to create future panels with diverse populations.

Predicted gene expression in ancestrally diverse populations leads to discovery of susceptibility loci for lifestyle and cardiometabolic traits.

One mechanism by which genetic factors influence complex traits and diseases is altering gene expression. Direct measurement of gene expression in relevant tissues is rarely tenable; however, genetically regulated gene expression (GReX) can be estimated using prediction models derived from large multi-omic datasets. These approaches have led to the discovery of many gene-trait associations, but whether models derived from predominantly European ancestry (EA) reference panels can map novel associations in ancestrally diverse populations remains unclear. We applied PrediXcan to impute GReX in 51,520 ancestrally diverse Population Architecture using Genomics and Epidemiology (PAGE) participants (35% African American, 45% Hispanic/Latino, 10% Asian, and 7% Hawaiian) across 25 key cardiometabolic traits and relevant tissues to identify 102 novel associations. We then compared associations in PAGE to those in a random subset of 50,000 White British participants from UK Biobank (UKBB50k) for height and body mass index (BMI). We identified 517 associations across 47 tissues in PAGE but not UKBB50k, demonstrating the importance of diverse samples in identifying trait-associated GReX. We observed that variants used in PrediXcan models were either more or less differentiated across continental-level populations than matched-control variants depending on the specific population reflecting sampling bias. Additionally, variants from identified genes specific to either PAGE or UKBB50k analyses were more ancestrally differentiated than those in genes detected in both analyses, underlining the value of population-specific discoveries. This suggests that while EA-derived transcriptome imputation models can identify new associations in non-EA populations, models derived from closely matched reference panels may yield further insights. Our findings call for more diversity in reference datasets of tissue-specific gene expression.

Comparison of confound adjustment methods in the construction of gene co-expression networks.

Adjustment for confounding sources of expression variation is an important preprocessing step in large gene expression studies, but the effect of confound adjustment on co-expression network analysis has not been well-characterized. Here, we demonstrate that the choice of confound adjustment method can have a considerable effect on the architecture of the resulting co-expression network. We compare standard and alternative confound adjustment methods and provide recommendations for their use in the construction of gene co-expression networks from bulk tissue RNA-seq datasets.

Corrigendum: Evaluation of Wearable Technology in Dementia: A Systematic Review and Meta-Analysis.

[This corrects the article DOI: 10.3389/fmed.2020.501104.].

Evaluation of Wearable Technology in Dementia: A Systematic Review and Meta-Analysis.

Background: The objective of this analysis was to systematically review studies employing wearable technology in patients with dementia by quantifying differences in digitally captured physiological endpoints. Methods: This systematic review and meta-analysis was based on web searches of Cochrane Database, PsycInfo, Pubmed, Embase, and IEEE between October 25-31st, 2017. Observational studies providing physiological data measured by wearable technology on participants with dementia with a mean age ≥50. Data were extracted according to PRISMA guidelines and methodological quality assessed independently using Downs and Black criteria. Standardized mean differences between cases and controls were estimated using random-effects models. Results: Forty-eight studies from 18,456 screened abstracts (Dementia: n = 2,516, Control: n = 1,224) met inclusion criteria for the systematic review. Nineteen of these studies were included in one or multiple meta-analyses (Dementia: n = 617, Control: n = 406). Participants with dementia demonstrated lower levels of daily activity (standardized mean difference (SMD), -1.60; 95% CI, -2.66 to -0.55), decreased sleep efficiency (SMD, -0.52; 95% CI, -0.89 to -0.16), and greater intradaily circadian variability (SMD, 0.46; 95% CI, 0.27 to 0.65) than controls, among other measures. Statistical between-study heterogeneity was observed, possibly due to variation in testing duration, device type or patient setting. Conclusions and Relevance: Digitally captured data using wearable devices revealed that adults with dementia were less active, demonstrated increased fragmentation of their sleep-wake cycle and a loss of typical diurnal variation in circadian rhythm as compared to controls.

Evaluation of the use of the Scale for the Assessment and Rating of Ataxia (SARA) in healthy volunteers and patients with schizophrenia.

OBJECTIVE: The Scale for the Assessment and Rating of Ataxia (SARA) is a semi-quantitative assessment used to evaluate ataxia. The goal of these studies was to assess and evaluate the utility of this instrument in a Healthy Volunteer (HV) group and subjects with Schizophrenia (SCZ). METHODS: Two studies were completed to collect SARA data, in a HV group and in a stable SCZ group. 177 HVs (18-65 years) and 16 SCZs (18-58 years) provided written consent and were assessed using the SARA. Of 177 HV subjects, 88 had 2 SARA assessments (within 2 days of initial visit) while all 16 SCZ had 3 SARA assessments (within 14 days of initial visit). RESULTS: For the HV group, the mean score ±â€¯Std for the SARA on visit-1 was 0.39 ±â€¯0.72, and 0.34 ±â€¯0.64 for visit-2. The Pearson correlation coefficient between visit-1 and visit-2 was 0.7486 and an ICC of 0.743. For the SCZ group, the mean score for the SARA was 0.63 ±â€¯0.65 on visit-1, 0.84 ±â€¯1.19 on visit-2, and 0.84 ±â€¯0.94 on visit-3. The Pearson correlation coefficient between visit-1 and visit-2 was 0.6545, between visit-1 and visit-3 was 0.6635 and between visit-2 and visit-3 was 0.7613 and an ICC of 0.650. There was no significant difference in baseline SARA scores between the HV and SCZ group p = .063. A statistically significant positive association between age and total SARA scores was observed in HV (r = 0.345) and SCZ (r = 0.676). CONCLUSIONS: A strong association was observed in both the HV and SCZ groups in the reassessment of signs of ataxia using the SARA scale. Both groups demonstrated minimal signs of ataxia, with no statistically significant difference between the two groups in their visit-1 scores.