Evaluation of a New Aptamer-Based Array for Soluble Suppressor of Tumorgenicity (ST2) and N-terminal Pro-B-Type Natriuretic Peptide (NTproBNP) in Heart Failure Patients

BACKGROUND

Recent advances in multi-marker platforms offer faster data generation, but the fidelity of these methods compared to the ELISA is not established. We tested the correlation and predictive performance of SOMAscan vs. ELISA methods for NTproBNP and ST2.

METHODS

Patients ≥ 18 years with heart failure and ejection fraction < 50% were enrolled. We tested the correlation between SOMA and ELISA for each biomarker and their association with outcomes.

RESULTS

There was good correlation of SOMA vs. ELISA for ST2 (ρ = 0.71) and excellent correlation for NTproBNP (ρ = 0.94). The two versions of both markers were not significantly different regarding survival association. The two ST2 assays and NTproBNP assays were similarly associated with all-cause mortality and cardiovascular mortality. These associations remained statistically significant when adjusted for MAGGIC risk score (all p < 0.05).

CONCLUSION

SOMAscan quantifications of ST2 and NTproBNP correlate to ELISA versions and carry similar prognosis.

Genome-Wide Association Study of Beta-Blocker Survival Benefit in Black and White Patients with Heart Failure with Reduced Ejection Fraction

In patients with heart failure with reduced ejection fraction (HFrEF), individual responses to beta-blockers vary. Candidate gene pharmacogenetic studies yielded significant but inconsistent results, and they may have missed important associations. Our objective was to use an unbiased genome-wide association study (GWAS) to identify loci influencing beta-blocker survival benefit in HFrEF patients. Genetic variant × beta-blocker exposure interactions were tested in Cox proportional hazards models for all-cause mortality stratified by self-identified race. The models were adjusted for clinical risk factors and propensity scores. A prospective HFrEF registry (469 black and 459 white patients) was used for discovery, and linkage disequilibrium (LD) clumped variants with a beta-blocker interaction of p < 5 × 10-5, were tested for Bonferroni-corrected validation in a multicenter HFrEF clinical trial (288 black and 579 white patients). A total of 229 and 18 variants in black and white HFrEF patients, respectively, had interactions with beta-blocker exposure at p < 5 × 10-5 upon discovery. After LD-clumping, 100 variants and 4 variants in the black and white patients, respectively, remained for validation but none reached statistical significance. In conclusion, genetic variants of potential interest were identified in a discovery-based GWAS of beta-blocker survival benefit in HFrEF patients, but none were validated in an independent dataset. Larger cohorts or alternative approaches, such as polygenic scores, are needed.

The interactions between host genome and gut microbiome increase the risk of psychiatric disorders: Mendelian randomization and biological annotation

BACKGROUND

The correlation between human gut microbiota and psychiatric diseases has long been recognized. Based on the heritability of the microbiome, genome-wide association studies on human genome and gut microbiome (mbGWAS) have revealed important host-microbiome interactions. However, establishing causal relationships between specific gut microbiome features and psychological conditions remains challenging due to insufficient sample sizes of previous studies of mbGWAS.

METHODS

Cross-cohort meta-analysis (via METAL) and multi-trait analysis (via MTAG) were used to enhance the statistical power of mbGWAS for identifying genetic variants and genes. Using two large mbGWAS studies (7,738 and 5,959 participants respectively) and12 disease-specific studies from the Psychiatric Genomics Consortium (PGC), we performed bidirectional two-sample mendelian randomization (MR) analyses between microbial features and psychiatric diseases (up to 500,199 individuals). Additionally, we conducted downstream gene- and gene-set-based analyses to investigate the shared biology linking gut microbiota and psychiatric diseases.

RESULTS

METAL and MTAG conducted in mbGWAS could boost power for gene prioritization and MR analysis. Increases in the number of lead SNPs and mapped genes were witnessed in 13/15 species and 5/10 genera after using METAL, and MTAG analysis gained an increase in sample size equivalent to expanding the original samples from 7% to 63%. Following METAL use, we identified a positive association between Bacteroides faecis and ADHD (OR, 1.09; 95 %CI, 1.02-1.16; P = 0.008). Bacteroides eggerthii and Bacteroides thetaiotaomicron were observed to be positively associated with PTSD (OR, 1.11; 95 %CI, 1.03-1.20; P = 0.007; OR, 1.11; 95 %CI, 1.01-1.23; P = 0.03). These findings remained stable across statistical models and sensitivity analyses. No genetic liabilities to psychiatric diseases may alter the abundance of gut microorganisms.Using biological annotation, we identified that those genes contributing to microbiomes (e.g., GRIN2A and RBFOX1) are expressed and enriched in human brain tissues.

CONCLUSIONS

Our statistical genetics strategy helps to enhance the power of mbGWAS, and our genetic findings offer new insights into biological pleiotropy and causal relationship between microbiota and psychiatric diseases.

MAP3K19 regulatory variation in populations with African ancestry may increase COVID-19 severity

To identify ancestry-linked genetic risk variants associated with COVID-19 hospitalization, we performed an integrative analysis of two genome-wide association studies and resolved four single nucleotide polymorphisms more frequent in COVID-19-hospitalized patients with non-European ancestry. Among them, the COVID-19 risk SNP rs16831827 shows the largest difference in minor allele frequency (MAF) between populations with African and European ancestry and also shows higher MAF in hospitalized COVID-19 patients among cohorts of mixed ancestry (odds ratio [OR] = 1.20, 95% CI: 1.10-1.30) and entirely African ancestry (OR = 1.30, 95% CI: 1.02-1.67). rs16831827 is an expression quantitative trait locus of MAP3K19. MAP3K19 expression is induced during ciliogenesis and most abundant in ciliated tissues including lungs. Single-cell RNA sequencing analyses revealed that MAP3K19 is highly expressed in multiple ciliated cell types. As rs16831827∗T is associated with reduced MAP3K19 expression, it may increase the risk of severe COVID-19 by reducing MAP3K19 expression.

Common Variants on FGD5 Increase Hazard of Mortality or Rehospitalization in Patients With Heart Failure From the ASCEND-HF Trial

BACKGROUND

Heart failure remains a global health burden, and patients hospitalized are particularly at risk, but genetic associates for subsequent death or rehospitalization are still lacking.

METHODS

The genetic substudy of the ASCEND-HF trial (Acute Study of Clinical Effectiveness of Nesiritide in Decompensated Heart Failure) was used to perform genome-wide association study and transethnic meta-analysis. The overall trial included the patients of self-reported European ancestry (n=2173) and African ancestry (n=507). The end point was death or heart failure rehospitalization within 180 days. Cox models adjusted for 11 a priori predictors of rehospitalization and 5 genetic principal components were used to test the association between single-nucleotide polymorphisms and outcome. Summary statistics from the 2 populations were combined via meta-analysis with the significance threshold considered P<5×10-8.

RESULTS

Common variants (rs2342882 and rs35850039 in complete linkage disequilibrium) located in FGD5 were significantly associated with the primary outcome in both ancestry groups (European Americans: hazard ratio [HR], 1.38; P=2.42×10-6; African ancestry: HR, 1.51; P=4.43×10-3; HR in meta-analysis, 1.41; P=4.25×10-8). FGD5 encodes a regulator of VEGF (vascular endothelial growth factor)-mediated angiogenesis, and in silico investigation revealed several previous genome-wide association study hits in this gene, among which rs748431 was associated with our outcome (HR, 1.20; meta P<0.01). Sensitivity analysis proved FGD5 common variants survival association did not appear to operate via coronary artery disease or nesiritide treatment (P>0.05); and the signal was still significant when changing the censoring time from 180 to 30 days (HR, 1.39; P=1.59×10-5).

CONCLUSIONS

In this multiethnic genome-wide association study of ASCEND-HF, single-nucleotide polymorphisms in FGD5 were associated with increased risk of death or rehospitalization. Additional investigation is required to examine biological mechanisms and whether FGD5 could be a therapeutic target.

REGISTRATION

URL: https://www.

CLINICALTRIALS

gov; Unique identifier: NCT00475852.

Shifting as an executive function separate from updating and inhibition in old age: Behavioral and genetic evidence

This study aimed to examine the organization of executive functions (EFs), specifically working memory updating, prepotent response inhibition, and mental-set shifting in old age, with a particular focus on determining whether the shifting function was behaviorally and genetically separated from the other functions. A total of 248 healthy older Chinese individuals participated, and multiple measures of executive functions were collected. Additionally, measures of fluid intelligence were included to explore the varying relationships between the three executive functions and this higher-order cognitive ability. Furthermore, genetic data were gathered and analyzed to investigate the associations between EFs and six candidate single-nucleotide polymorphisms (SNPs) mapped to dopaminergic, serotonergic, or glutamatergic genes. The results indicated that both the three-factor model and the two-factor model, which combined updating and inhibition, demonstrated a good fit. Furthermore, shifting was found to be behaviorally separated from the other two functions, and the correlation between shifting and fluid intelligence was smaller compared to the correlations between updating and inhibition with fluid intelligence. Moreover, the DRD2 SNPs showed significant associations with shifting, rather than with updating and inhibition. These findings provide evidence that shifting is distinct and separate from updating and inhibition, highlighting the diversity of EFs among older adults.

Examining sociodemographic correlates of opioid use, misuse, and use disorders in the All of Us Research Program

BACKGROUND

The All of Us Research Program enrolls diverse US participants which provide a unique opportunity to better understand the problem of opioid use. This study aims to estimate the prevalence of opioid use and its association with sociodemographic characteristics from survey data and electronic health record (EHR).

METHODS

A total of 214,206 participants were included in this study who competed survey modules and shared EHR data. Adjusted logistic regressions were used to explore the associations between sociodemographic characteristics and opioid use.

RESULTS

The lifetime prevalence of street opioids was 4%, and the nonmedical use of prescription opioids was 9%. Men had higher odds of lifetime opioid use (aOR: 1.4 to 3.1) but reduced odds of current nonmedical use of prescription opioids (aOR: 0.6). Participants from other racial and ethnic groups were at reduced odds of lifetime use (aOR: 0.2 to 0.9) but increased odds of current use (aOR: 1.9 to 9.9) compared with non-Hispanic White participants. Foreign-born participants were at reduced risks of opioid use and diagnosed with opioid use disorders (OUD) compared with US-born participants (aOR: 0.36 to 0.67). Men, Younger, White, and US-born participants are more likely to have OUD.

CONCLUSIONS

All of Us research data can be used as an indicator of national trends for monitoring the prevalence of receiving prescription opioids, diagnosis of OUD, and non-medical use of opioids in the US. The program employs a longitudinal design for routinely collecting health-related data including EHR data, that will contribute to the literature by providing important clinical information related to opioids over time. Additionally, this data will enhance the estimates of the prevalence of OUD among diverse populations, including groups that are underrepresented in the national survey data.

Cross-phenotype relationship between opioid use disorder and suicide attempts: new evidence from polygenic association and Mendelian randomization analyses

Clinical epidemiological studies have found high co-occurrence between suicide attempts (SA) and opioid use disorder (OUD). However, the patterns of correlation and causation between them are still not clear due to psychiatric confounding. To investigate their cross-phenotype relationship, we utilized raw phenotypes and genotypes from >150,000 UK Biobank samples, and genome-wide association summary statistics from >600,000 individuals with European ancestry. Pairwise association and a potential bidirectional relationship between OUD and SA were evaluated with and without controlling for major psychiatric disease status (e.g., schizophrenia, major depressive disorder, and alcohol use disorder). Multiple statistical and genetics tools were used to perform epidemiological association, genetic correlation, polygenic risk score prediction, and Mendelian randomizations (MR) analyses. Strong associations between OUD and SA were observed at both the phenotypic level (overall samples [OR = 2.94, P = 1.59 ×10-14]; non-psychiatric subgroup [OR = 2.15, P = 1.07 ×10-3]) and the genetic level (genetic correlation rg = 0.38 and 0.5 with or without conditioning on psychiatric traits, respectively). Consistently, increasing polygenic susceptibility to SA is associated with increasing risk of OUD (OR = 1.08, false discovery rate [FDR] =1.71 ×10-3), and similarly, increasing polygenic susceptibility to OUD is associated with increasing risk of SA (OR = 1.09, FDR = 1.73 ×10-6). However, these polygenic associations were much attenuated after controlling for comorbid psychiatric diseases. A combination of MR analyses suggested a possible causal association from genetic liability for SA to OUD risk (2-sample univariable MR: OR = 1.14, P = 0.001; multivariable MR: OR = 1.08, P = 0.001). This study provided new genetic evidence to explain the observed OUD-SA comorbidity. Future prevention strategies for each phenotype needs to take into consideration of screening for the other one.

The genetic determinants of recurrent somatic mutations in 43,693 blood genomes

Nononcogenic somatic mutations are thought to be uncommon and inconsequential. To test this, we analyzed 43,693 National Heart, Lung and Blood Institute Trans-Omics for Precision Medicine blood whole genomes from 37 cohorts and identified 7131 non-missense somatic mutations that are recurrently mutated in at least 50 individuals. These recurrent non-missense somatic mutations (RNMSMs) are not clearly explained by other clonal phenomena such as clonal hematopoiesis. RNMSM prevalence increased with age, with an average 50-year-old having 27 RNMSMs. Inherited germline variation associated with RNMSM acquisition. These variants were found in genes involved in adaptive immune function, proinflammatory cytokine production, and lymphoid lineage commitment. In addition, the presence of eight specific RNMSMs associated with blood cell traits at effect sizes comparable to Mendelian genetic mutations. Overall, we found that somatic mutations in blood are an unexpectedly common phenomenon with ancestry-specific determinants and human health consequences.

GBC: a parallel toolkit based on highly addressable byte-encoding blocks for extremely large-scale genotypes of species

Whole -genome sequencing projects of millions of subjects contain enormous genotypes, entailing a huge memory burden and time for computation. Here, we present GBC, a toolkit for rapidly compressing large-scale genotypes into highly addressable byte-encoding blocks under an optimized parallel framework. We demonstrate that GBC is up to 1000 times faster than state-of-the-art methods to access and manage compressed large-scale genotypes while maintaining a competitive compression ratio. We also showed that conventional analysis would be substantially sped up if built on GBC to access genotypes of a large population. GBC's data structure and algorithms are valuable for accelerating large-scale genomic research.

Self-rated health as a predictor of hospitalizations in patients with bipolar disorder or major depressive disorder: A prospective cohort study of the UK Biobank

BACKGROUND

To determine the association between self-rated health (SRH) and subsequent all-cause hospitalizations in patients with bipolar disorder (BD) or major depression (MDD).

METHODS

We conducted a prospective cohort study on people with BD or MDD in the UK from 2006 to 2010 using UK Biobank touchscreen questionnaire data and linked administrative health databases. The association between SRH and 2-year all-cause hospitalizations was assessed using proportional hazard regression after adjustment for sociodemographics, lifestyle behaviors, previous hospitalization use, the Elixhauser comorbidity index, and environmental factors.

RESULTS

A total of 29,966 participants were identified, experiencing 10,279 hospitalization events. Among the cohort, the average age was 55.88 (SD 8.01) years, 64.02 % were female, and 3029 (10.11 %), 15,972 (53.30 %), 8313 (27.74 %), and 2652 (8.85 %) reported excellent, good, fair, and poor SRH, respectively. Among patients reporting poor SRH, 54.19 % had a hospitalization event within 2 years compared with 22.65 % for those having excellent SRH. In the adjusted analysis, patients with good, fair, and poor SRH had 1.31 (95 % CI 1.21-1.42), 1.82 (95 % CI 1.68-1.98), and 2.45 (95 % CI 2.22, 2.70) higher hazards of hospitalization, respectively, than those with excellent SRH.

LIMITATIONS

Selection bias can exist as our cohort cannot fully represent all the BD and MDD cases in the UK. Moreover, the causality is questionable.

CONCLUSION

SRH was independently associated with subsequent all-cause hospitalizations in patients with BD or MDD. This large study underscores the need for proactive SRH screening in this population, which might inform resource allocation in clinical care and enhance high-risk population detection.

Genome-wide screening of sex-biased genetic variants potentially associated with COVID-19 hospitalization

Sex-biased difference in coronavirus disease 2019 (COVID-19) hospitalization has been observed as that male patients tend to be more likely to be hospitalized than female patients. However, due to the insufficient sample size and existed studies that more prioritized to sex-stratified COVID-19 genome-wide association study (GWAS), the searching for sex-biased genetic variants showing differential association signals between sexes with COVID-19 hospitalization was severely hindered. We hypothesized genetic variants would show potentially sex-biased genetic effects on COVID-19 hospitalization if they display significant differential association effect sizes between male and female COVID-19 patients. By integrating two COVID-19 GWASs, including hospitalized COVID-19 patients vs. general population separated into males (case = 1,917 and control = 221,174) and females (case = 1,343 and control = 262,886), we differentiated the association effect sizes of each common single nucleotide polymorphism (SNP) within the two GWASs. Twelve SNPs were suggested to show differential COVID-19 associations between sexes. Further investigation of genes (n = 58) close to these 12 SNPs resulted in the identification of 34 genes demonstrating sex-biased differential expression in at least one GTEx tissue. Finally, 5 SNPs are mapped to 8 genes, including rs1134004 (GADD45G), rs140657166 (TRIM29 and PVRL1), rs148143613 (KNDC1 and STK32C), rs2443615 (PGAP2 and TRIM21), and rs2924725 (CSMD1). The 8 genes display significantly differential gene expression in blood samples derived from COVID-19 patients compared to healthy controls. These genes are potential genetic factors contributing to sex differences in COVID-19 hospitalization and warranted for further functional studies.

Patterns of Convergence and Divergence Between Bipolar Disorder Type I and Type II: Evidence From Integrative Genomic Analyses

Aim: Genome-wide association studies (GWAS) analyses have revealed genetic evidence of bipolar disorder (BD), but little is known about the genetic structure of BD subtypes. We aimed to investigate the genetic overlap and distinction of bipolar type I (BD I) & type II (BD II) by conducting integrative post-GWAS analyses.

Methods: We utilized single nucleotide polymorphism (SNP)–level approaches to uncover correlated and distinct genetic loci. Transcriptome-wide association analyses (TWAS) were then approached to pinpoint functional genes expressed in specific brain tissues and blood. Next, we performed cross-phenotype analysis, including exploring the potential causal associations between two BD subtypes and lithium responses and comparing the difference in genetic structures among four different psychiatric traits.

Results: SNP-level evidence revealed three genomic loci, SLC25A17, ZNF184, and RPL10AP3, shared by BD I and II, and one locus (MAD1L1) and significant gene sets involved in calcium channel activity, neural and synapsed signals that distinguished two subtypes. TWAS data implicated different genes affecting BD I and II through expression in specific brain regions (nucleus accumbens for BD I). Cross-phenotype analyses indicated that BD I and II share continuous genetic structures with schizophrenia and major depressive disorder, which help fill the gaps left by the dichotomy of mental disorders.

Conclusion: These combined evidences illustrate genetic convergence and divergence between BD I and II and provide an underlying biological and trans-diagnostic insight into major psychiatric disorders.

Detecting and distinguishing indicators of risk for suicide using clinical records

Health systems are essential for suicide risk detection. Most efforts target people with mental health (MH) diagnoses, but this only represents half of the people who die by suicide. This study seeks to discover and validate health indicators of suicide death among those with, and without, MH diagnoses. This case-control study used statistical modeling with health record data on diagnoses, procedures, and encounters. The study included 3,195 individuals who died by suicide from 2000 to 2015 and 249,092 randomly selected matched controls, who were age 18+ and affiliated with nine Mental Health Research Network affiliated health systems. Of the 202 indicators studied, 170 (84%) were associated with suicide in the discovery cohort, with 148 (86%) of those in the validation cohort. Malignant cancer diagnoses were risk factors for suicide in those without MH diagnoses, and multiple individual psychiatric-related indicators were unique to the MH subgroup. Protective effects across MH-stratified models included diagnoses of benign neoplasms, respiratory infections, and utilization of reproductive services. MH-stratified latent class models validated five subgroups with distinct patterns of indicators in both those with and without MH. The highest risk groups were characterized via high utilization with multiple healthcare concerns in both groups. The lowest risk groups were characterized as predominantly young, female, and high utilizers of preventive services. Healthcare data include many indicators of suicide risk for those with and without MH diagnoses, which may be used to support the identification and understanding of risk as well as targeting of prevention in health systems.

[Clinical characteristics of patients with obstructive sleep apnea hypopnea syndrome combined with alveolar hypoventilation]

Objective: To evaluate the clinical characteristics of patients with obstructive sleep apnea hypopnea syndrome (OSAHS) combined with alveolar hypoventilation. Methods: This retrospective study included patients who were diagnosed as OSAHS by polysomnography (PSG) and underwent daytime awake transcutaneous carbon dioxide (PtcCO₂) monitoring from November 2019 to February 2021 at the Sleep Center of the Second Affiliated Hospital of Soochow University. A total of 177 patients were enrolled in the analysis, including 167 males and 10 females, aged (40±8) years old. Patients with daytime awake PtcCO₂>45 mmHg (1 mmHg=0.133 kPa) were diagnosed as daytime alveolar hypoventilation, with which participants were divided into the daytime alveolar hypoventilation group and non-daytime alveolar hypoventilation group. Body mass index (BMI) cut-off value predicting daytime alveolar hypoventilation was calculated and the patients were divided into the high BMI group and low BMI group. The continuous nocturnal PtcCO₂ data was available for a subset of 128 patients, and the patients were divided into two groups according the daytime alveolar hypoventilation or not. Across-group differences were compared, respectively. Results: Compared with the non-daytime alveolar hypoventilation group (n=125), the BMI [27.57 (26.55, 30.33) vs 26.60 (25.06, 28.09) kg/m²], Epworth sleepiness score(ESS) score [9.50 (6.25, 12.00) vs 7.00 (4.00, 10.75)], higher oxygen desaturation index (ODI) [38.00 (15.23, 64.93) vs 26.80 (11.30, 44.30) events/h] and percentage of total time with oxygen saturation level<90% (TS90%) [11.24% (1.88%, 32.44%) vs 4.35% (0.72%, 9.87%)] of the daytime alveolar hypoventilation group(n=52) were significantly higher (P<0.05), and lowest arterial oxygen saturation (LSaO₂) [74.50% (60.25%, 82.00%) vs 79.00% (73.00%, 84.50%)], mean arterial oxygen saturation (MSaO₂) [94.00% (91.00%, 95.00%) vs 95.00% (94.00%, 96.00%)] were significantly lower (P<0.05). The BMI cut-off value for predicting daytime alveolar hypoventilation was 27.04 kg/m². Of the 177 enrolled patients, 90 were in the high BMI group and 87 were in low group. Compared with the low BMI group, the proportion of daytime sleepiness, the ESS score, the prevalence of hypertension, AHI and daytime awake PtcCO₂ in the high BMI group were significantly higher (P<0.05). Among the subset of 128 patients with nocturnal PtcCO₂ data available, the BMI, daytime PtcCO₂ level, the nocturnal CO₂ level and the prevalence of sleep related alveolar hypoventilation in the daytime alveolar hypoventilation group (n=40) were significantly higher than those in the non-daytime alveolar hypoventilation group (n=88) (P<0.05). Conclusions: The OSAHS patients with alveolar hypoventilation have higher BMI and more severe nocturnal hypoxia. OSAHS patients with BMI>27.04 kg/m² are more likely to develop sleep related alveolar hypoventilation disorder.

DLRAPom: a hybrid pipeline of Optimized XGBoost-guided integrative multiomics analysis for identifying targetable disease-related lncRNA-miRNA-mRNA regulatory axes

The lack of a reliable and easy-to-operate screening pipeline for disease-related noncoding RNA regulatory axis is a problem that needs to be solved urgently. To address this, we designed a hybrid pipeline, disease-related lncRNA-miRNA-mRNA regulatory axis prediction from multiomics (DLRAPom), to identify risk biomarkers and disease-related lncRNA-miRNA-mRNA regulatory axes by adding a novel machine learning model on the basis of conventional analysis and combining experimental validation. The pipeline consists of four parts, including selecting hub biomarkers by conventional bioinformatics analysis, discovering the most essential protein-coding biomarkers by a novel machine learning model, extracting the key lncRNA-miRNA-mRNA axis and validating experimentally. Our study is the first one to propose a new pipeline predicting the interactions between lncRNA and miRNA and mRNA by combining WGCNA and XGBoost. Compared with the methods reported previously, we developed an Optimized XGBoost model to reduce the degree of overfitting in multiomics data, thereby improving the generalization ability of the overall model for the integrated analysis of multiomics data. With applications to gestational diabetes mellitus (GDM), we predicted nine risk protein-coding biomarkers and some potential lncRNA-miRNA-mRNA regulatory axes, which all correlated with GDM. In those regulatory axes, the MALAT1/hsa-miR-144-3p/IRS1 axis was predicted to be the key axis and was identified as being associated with GDM for the first time. In short, as a flexible pipeline, DLRAPom can contribute to molecular pathogenesis research of diseases, effectively predicting potential disease-related noncoding RNA regulatory networks and providing promising candidates for functional research on disease pathogenesis.

Genetic determinants of telomere length from 109,122 ancestrally diverse whole-genome sequences in TOPMed

Genetic studies on telomere length are important for understanding age-related diseases. Prior GWAS for leukocyte TL have been limited to European and Asian populations. Here, we report the first sequencing-based association study for TL across ancestrally-diverse individuals (European, African, Asian and Hispanic/Latino) from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program. We used whole genome sequencing (WGS) of whole blood for variant genotype calling and the bioinformatic estimation of telomere length in n=109,122 individuals. We identified 59 sentinel variants (p-value <5×10-9) in 36 loci associated with telomere length, including 20 newly associated loci (13 were replicated in external datasets). There was little evidence of effect size heterogeneity across populations. Fine-mapping at OBFC1 indicated the independent signals colocalized with cell-type specific eQTLs for OBFC1 (STN1). Using a multi-variant gene-based approach, we identified two genes newly implicated in telomere length, DCLRE1B (SNM1B) and PARN. In PheWAS, we demonstrated our TL polygenic trait scores (PTS) were associated with increased risk of cancer-related phenotypes.

Integrative omics of schizophrenia: from genetic determinants to clinical classification and risk prediction

Schizophrenia (SCZ) is a debilitating neuropsychiatric disorder with high heritability and complex inheritance. In the past decade, successful identification of numerous susceptibility loci has provided useful insights into the molecular etiology of SCZ. However, applications of these findings to clinical classification and diagnosis, risk prediction, or intervention for SCZ have been limited, and elucidating the underlying genomic and molecular mechanisms of SCZ is still challenging. More recently, multiple Omics technologies - genomics, transcriptomics, epigenomics, proteomics, metabolomics, connectomics, and gut microbiomics - have all been applied to examine different aspects of SCZ pathogenesis. Integration of multi-Omics data has thus emerged as an approach to provide a more comprehensive view of biological complexity, which is vital to enable translation into assessments and interventions of clinical benefit to individuals with SCZ. In this review, we provide a broad survey of the single-omics studies of SCZ, summarize the advantages and challenges of different Omics technologies, and then focus on studies in which multiple omics data are integrated to unravel the complex pathophysiology of SCZ. We believe that integration of multi-Omics technologies would provide a roadmap to create a more comprehensive picture of interactions involved in the complex pathogenesis of SCZ, constitute a rich resource for elucidating the potential molecular mechanisms of the illness, and eventually improve clinical assessments and interventions of SCZ to address clinical translational questions from bench to bedside.

The genomics of heart failure: design and rationale of the HERMES consortium

Aims

The HERMES (HEart failure Molecular Epidemiology for Therapeutic targetS) consortium aims to identify the genomic and molecular basis of heart failure.

Methods and results

The consortium currently includes 51 studies from 11 countries, including 68 157 heart failure cases and 949 888 controls, with data on heart failure events and prognosis. All studies collected biological samples and performed genome‐wide genotyping of common genetic variants. The enrolment of subjects into participating studies ranged from 1948 to the present day, and the median follow‐up following heart failure diagnosis ranged from 2 to 116 months. Forty‐nine of 51 individual studies enrolled participants of both sexes; in these studies, participants with heart failure were predominantly male (34–90%). The mean age at diagnosis or ascertainment across all studies ranged from 54 to 84 years. Based on the aggregate sample, we estimated 80% power to genetic variant associations with risk of heart failure with an odds ratio of ≥1.10 for common variants (allele frequency ≥ 0.05) and ≥1.20 for low‐frequency variants (allele frequency 0.01–0.05) at P < 5 × 10⁻⁸ under an additive genetic model.

Conclusions

HERMES is a global collaboration aiming to (i) identify the genetic determinants of heart failure; (ii) generate insights into the causal pathways leading to heart failure and enable genetic approaches to target prioritization; and (iii) develop genomic tools for disease stratification and risk prediction.

Plasma Proteomic Profile Predicts Survival in Heart Failure With Reduced Ejection Fraction

BACKGROUND

It remains unclear whether the plasma proteome adds value to established predictors in heart failure (HF) with reduced ejection fraction (HFrEF). We sought to derive and validate a plasma proteomic risk score (PRS) for survival in patients with HFrEF (HFrEF-PRS).

METHODS

Patients meeting Framingham criteria for HF with EF<50% were enrolled (N=1017) and plasma underwent SOMAscan profiling (4453 targets). Patients were randomly divided 2:1 into derivation and validation cohorts. The HFrEF-PRS was derived using Cox regression of all-cause mortality adjusted for clinical score and NT-proBNP (N-terminal pro-B-type natriuretic peptide), then was tested in the validation cohort. Risk stratification improvement was evaluated by C statistic, integrated discrimination index, continuous net reclassification index, and median improvement in risk score for 1-year and 3-year mortality.

RESULTS

Participants' mean age was 68 years, 48% identified as Black, 35% were female, and 296 deaths occurred. In derivation (n=681), 128 proteins associated with mortality, 8 comprising the optimized HFrEF-PRS. In validation (n=336) the HFrEF-PRS associated with mortality (hazard ratio, 2.27 [95% CI, 1.84-2.82], P=6.3×10^-14), Kaplan-Meier curves differed significantly between HFrEF-PRS quartiles (P=2.2×10^-6), and it remained significant after adjustment for clinical score and NT-proBNP (hazard ratio, 1.37 [95% CI, 1.05-1.79], P=0.021). The HFrEF-PRS improved metrics of risk stratification (C statistic change, 0.009, P=0.612; integrated discrimination index, 0.041, P=0.010; net reclassification index=0.391, P=0.078; median improvement in risk score=0.039, P=0.016) and associated with cardiovascular death and HF phenotypes (eg, 6-minute walk distance, EF change). Most HFrEF-PRS proteins had little known connection to HFrEF.

CONCLUSIONS

A plasma multiprotein score improved risk stratification in patients with HFrEF and identified novel candidates.

Mapping the 17q12-21.1 Locus for Variants Associated with Early-Onset Asthma in African Americans

Rationale: The 17q12-21.1 locus is one of the most highly replicated genetic associations with asthma. Individuals of African descent have lower linkage disequilibrium in this region, which could facilitate identifying causal variants.Objectives: To identify functional variants at 17q12-21.1 associated with early-onset asthma among African American individuals.Methods: We evaluated African American participants from SAPPHIRE (Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity) (n = 1,940), SAGE II (Study of African Americans, Asthma, Genes and Environment) (n = 885), and GCPD-A (Study of the Genetic Causes of Complex Pediatric Disorders-Asthma) (n = 2,805). Associations with asthma onset at ages under 5 years were meta-analyzed across cohorts. The lead signal was reevaluated considering haplotypes informed by genetic ancestry (i.e., African vs. European). Both an expression-quantitative trait locus analysis and a phenome-wide association study were performed on the lead variant.Measurements and Main Results: The meta-analyzed results from SAPPHIRE, SAGE II, and the GCPD-A identified rs11078928 as the top association for early-onset asthma. A haplotype analysis suggested that the asthma association partitioned most closely with the rs11078928 genotype. Genetic ancestry did not appear to influence the effect of this variant. In the expression-quantitative trait locus analysis, rs11078928 was related to alternative splicing of GSDMB (gasdermin-B) transcripts. The phenome-wide association study of rs11078928 suggested that this variant was predominantly associated with asthma and asthma-associated symptoms.Conclusions: A splice-acceptor polymorphism appears to be a causal variant for asthma at the 17q12-21.1 locus. This variant appears to have the same magnitude of effect in individuals of African and European descent.

Asthma and its relationship to mitochondrial copy number: Results from the Asthma Translational Genomics Collaborative (ATGC) of the Trans-Omics for Precision Medicine (TOPMed) program

Background

Mitochondria support critical cellular functions, such as energy production through oxidative phosphorylation, regulation of reactive oxygen species, apoptosis, and calcium homeostasis.

Objective

Given the heightened level of cellular activity in patients with asthma, we sought to determine whether mitochondrial DNA (mtDNA) copy number measured in peripheral blood differed between individuals with and without asthma.

Methods

Whole genome sequence data was generated as part of the Trans-Omics for Precision Medicine (TOPMed) Program on participants from the Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-ethnicity (SAPPHIRE) and the Study of African Americans, Asthma, Genes, & Environment II (SAGE II). We restricted our analysis to individuals who self-identified as African American (3,651 asthma cases and 1,344 controls). Mitochondrial copy number was estimated using the sequencing read depth ratio for the mitochondrial and nuclear genomes. Respiratory complex expression was assessed using RNA-sequencing.

Results

Average mitochondrial copy number was significantly higher among individuals with asthma when compared with controls (SAPPHIRE: 218.60 vs. 200.47, P<0.001; SAGE II: 235.99 vs. 223.07, P<0.001). Asthma status was significantly associated with mitochondrial copy number after accounting for potential explanatory variables, such as participant age, sex, leukocyte counts, and mitochondrial haplogroup. Despite the consistent relationship between asthma status and mitochondrial copy number, the latter was not associated with time-to-exacerbation or patient-reported asthma control. Mitochondrial respiratory complex gene expression was disproportionately lower in individuals with asthma when compared with individuals without asthma and other protein-encoding genes.

Conclusions

We observed a robust association between asthma and higher mitochondrial copy number. Asthma having an effect on mitochondria function was also supported by lower respiratory complex gene expression in this group.

Inherited causes of clonal haematopoiesis in 97,691 whole genomes

Age is the dominant risk factor for most chronic human diseases; yet the mechanisms by which aging confers this risk are largely unknown.¹ Recently, the age-related acquisition of somatic mutations in regenerating hematopoietic stem cell populations leading to clonal expansion was associated with both hematologic cancer ^2–4 and coronary heart disease⁵, a phenomenon termed ‘Clonal Hematopoiesis of Indeterminate Potential’ (CHIP).⁶ Simultaneous germline and somatic whole genome sequence analysis now provides the opportunity to identify root causes of CHIP. Here, we analyze high-coverage whole genome sequences from 97,691 participants of diverse ancestries in the NHLBI TOPMed program and identify 4,229 individuals with CHIP. We identify associations with blood cell, lipid, and inflammatory traits specific to different CHIP genes. Association of a genome-wide set of germline genetic variants identified three genetic loci associated with CHIP status, including one locus at TET2 that was African ancestry specific. In silico-informed in vitro evaluation of the TET2 germline locus identified a causal variant that disrupts a TET2 distal enhancer resulting in increased hematopoietic stem cell self-renewal. Overall, we observe that germline genetic variation shapes hematopoietic stem cell function leading to CHIP through mechanisms that are both specific to clonal hematopoiesis and shared mechanisms leading to somatic mutations across tissues.

Polygenic Score for β-Blocker Survival Benefit in European Ancestry Patients With Reduced Ejection Fraction Heart Failure

BACKGROUND

β-Blockers (BBs) are mainstay therapy for heart failure with reduced ejection fraction. However, individual patient responses to BB vary, which may be partially due to genetic variation. The goal of this study was to derive and validate the first polygenic response predictor (PRP) for BB survival benefit in heart failure with reduced ejection fraction patients.

METHODS

Derivation and validation analyses were performed in n=1436 total HF patients of European descent and with ejection fraction <50%. The PRP was derived in a random subset of the Henry Ford Heart Failure Pharmacogenomic Registry (n=248) and then validated in a meta-analysis of the remaining patients from Henry Ford Heart Failure Pharmacogenomic Registry (n=247), the TIME-CHF (Trial of Intensified Versus Standard Medical Therapy in Elderly Patients With Congestive Heart Failure; n=431), and HF-ACTION trial (Heart Failure: a Controlled Trial Investigating Outcomes of Exercise Training; n=510). The PRP was constructed from a genome-wide analysis of BB×genotype interaction predicting time to all-cause mortality, adjusted for Meta-Analysis Global Group in Chronic Heart Failure score, genotype, level of BB exposure, and BB propensity score.

RESULTS

Five-fold cross-validation summaries out to 1000 single-nucleotide polymorphisms identified optimal prediction with a 44 single-nucleotide polymorphism score and cutoff at the 30th percentile. In validation testing (n=1188), greater BB exposure was associated with reduced all-cause mortality in patients with low PRP score (n=251; hazard ratio, 0.19 [95% CI, 0.04-0.51]; P=0.0075) but not high PRP score (n=937; hazard ratio, 0.84 [95% CI, 0.53-1.3]; P=0.448)-a difference that was statistically significant (P interaction, 0.0235). Results were consistent regardless of atrial fibrillation, ejection fraction (≤40% versus 41%-50%), or when examining cardiovascular death.

CONCLUSIONS

Among patients of European ancestry with heart failure with reduced ejection fraction, a PRP distinguished patients who derived substantial survival benefit from BB exposure from a larger group that did not. Additional work is needed to prospectively test clinical utility and to develop PRPs for other population groups and other medications.

Suppression tumorigenicity 2 (ST2) turbidimetric immunoassay compared to enzyme-linked immunosorbent assay in predicting survival in heart failure patients with reduced ejection fraction

BACKGROUND

Suppressor of tumorigenicity 2 (ST2) is a powerful marker of prognosis and treatment response in heart failure (HF), however, it is an enzyme-linked immunosorbent assay (ELISA) which may be cumbersome and costly. A turbidimetric immunoassay (TIA) that can run on common chemistry analyzers could overcome this. We studied a novel TIA for ST2, comparing it to commercial ST2 (ELISA).

METHODS

Patients age ≥ 18 years meeting Framingham definition for HF were enrolled in a prospective registry (Oct 2007 - March 2015) at Henry Ford Hospital and donated blood samples. Participants with reduced ejection fraction (<50%) and available plasma samples were included and valid ST2 measurements were obtained on the same sample using both TIA and ELISA (N = 721). The primary endpoint was all cause death. Correlation between the methods was quantified. The association with survival was tested using unadjusted and adjusted (for MAGGIC score and NTproBNP) Cox models and comparing the Area Under the Curve (AUC).

RESULTS

The inter-assay Spearman correlation coefficient was 0.77. Nonparametric regression showed no significant proportional difference (slope = 0.97) and a very small systematic difference (3.2 ng/mL). In univariate analyses, both TIA and ELISA ST2 were significant associates of survival with similar effect sizes (HR 4.46 and 3.50, respectively, both p < 0.001). In models adjusted for MAGGIC score, both ST2 remained significant in Cox models and incrementally improved AUC vs. MAGGIC alone (MAGGIC AUC = 0.757; TIA + MAGGIC AUC = 0.786, p = 0.025; ELISA + MAGGIC AUC = 0.793, p = 0.033). In models with both MAGGIC and NTproBNP included, both ST2 still remained significant but did not improve AUC.

CONCLUSIONS

A novel TIA method for ST2 quantification correlates highly with ELISA and offers similarly powerful risk-stratification.

Lung Function in African American Children with Asthma Is Associated with Novel Regulatory Variants of the KIT Ligand KITLG/SCF and Gene-By-Air-Pollution Interaction

Baseline lung function, quantified as forced expiratory volume in the first second of exhalation (FEV1), is a standard diagnostic criterion used by clinicians to identify and classify lung diseases. Using whole-genome sequencing data from the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine project, we identified a novel genetic association with FEV1 on chromosome 12 in 867 African American children with asthma (P = 1.26 × 10-8, β = 0.302). Conditional analysis within 1 Mb of the tag signal (rs73429450) yielded one major and two other weaker independent signals within this peak. We explored statistical and functional evidence for all variants in linkage disequilibrium with the three independent signals and yielded nine variants as the most likely candidates responsible for the association with FEV1 Hi-C data and expression QTL analysis demonstrated that these variants physically interacted with KITLG (KIT ligand, also known as SCF), and their minor alleles were associated with increased expression of the KITLG gene in nasal epithelial cells. Gene-by-air-pollution interaction analysis found that the candidate variant rs58475486 interacted with past-year ambient sulfur dioxide exposure (P = 0.003, β = 0.32). This study identified a novel protective genetic association with FEV1, possibly mediated through KITLG, in African American children with asthma. This is the first study that has identified a genetic association between lung function and KITLG, which has established a role in orchestrating allergic inflammation in asthma.

Whole Genome Sequencing Identifies CRISPLD2 as a Lung Function Gene in Children With Asthma

BACKGROUND

Asthma is a common respiratory disorder with a highly heterogeneous nature that remains poorly understood. The objective was to use whole genome sequencing (WGS) data to identify regions of common genetic variation contributing to lung function in individuals with a diagnosis of asthma.

METHODS

WGS data were generated for 1,053 individuals from trios and extended pedigrees participating in the family-based Genetic Epidemiology of Asthma in Costa Rica study. Asthma affection status was defined through a physician's diagnosis of asthma, and most participants with asthma also had airway hyperresponsiveness (AHR) to methacholine. Family-based association tests for single variants were performed to assess the associations with lung function phenotypes.

RESULTS

A genome-wide significant association was identified between baseline FEV1/FVC ratio and a single-nucleotide polymorphism in the top hit cysteine-rich secretory protein LCCL domain-containing 2 (CRISPLD2) (rs12051168; P = 3.6 × 10-8 in the unadjusted model) that retained suggestive significance in the covariate-adjusted model (P = 5.6 × 10-6). Rs12051168 was also nominally associated with other related phenotypes: baseline FEV1 (P = 3.3 × 10-3), postbronchodilator (PB) FEV1 (7.3 × 10-3), and PB FEV1/FVC ratio (P = 2.7 × 10-3). The identified baseline FEV1/FVC ratio and rs12051168 association was meta-analyzed and replicated in three independent cohorts in which most participants with asthma also had confirmed AHR (combined weighted z-score P = .015) but not in cohorts without information about AHR.

CONCLUSIONS

These findings suggest that using specific asthma characteristics, such as AHR, can help identify more genetically homogeneous asthma subgroups with genotype-phenotype associations that may not be observed in all children with asthma. CRISPLD2 also may be important for baseline lung function in individuals with asthma who also may have AHR.

Association of Regulatory Genetic Variants for Protein Kinase Cα with Mortality and Drug Efficacy in Patients with Heart Failure

PURPOSE

Protein kinase C alpha (gene: PRKCA) is a key regulator of cardiac contractility. Two genetic variants have recently been discovered to regulate PRKCA expression in failing human heart tissue (rs9909004 [T → C] and rs9303504 [C → G]). The association of those variants with clinical outcomes in patients with heart failure (HF), and their interaction with HF drug efficacy, is unknown.

METHODS

Patients with HF in a prospective registry starting in 2007 were genotyped by whole genome array (n = 951). The primary outcome was all-cause mortality. Cox proportional hazards models adjusted for established clinical risk factors and genomic ancestry tested the independent association of rs9909004 or rs9303504 and the variant interactions with cornerstone HF pharmacotherapies (beta-blockers or angiotensin-converting enzyme inhibitors/angiotensin receptor blockers) in additive genetic models.

RESULTS

The minor allele of rs9909004, but not of rs9303504, was independently associated with a decreased risk for all-cause mortality: adjusted HR = 0.81 (95% CI = 0.67-0.98), p = 0.032. The variants did not significantly interact with mortality benefit associated with cornerstone HF pharmacotherapies (p > 0.1 for all).

CONCLUSIONS

A recently discovered cardiac-specific regulatory variant for PRKCA (rs9909004) was independently associated with a decreased risk for all-cause mortality in patients with HF. The variant did not interact with mortality benefit associated with cornerstone HF pharmacotherapies.

Primary yolk sac tumour of the prostate mimicking small round blue cell tumour

Prostatic yolk sac tumour is a germ cell tumour with a wide range of age of occurrence, unusual anatomic locations, diverse morphologic patterns, and aggressive biologic behavior, posing challenges both to diagnosis and clinical management. We report a rare case of primary yolk sac tumour of the prostate with extensive local and liver metastasis, the latter of which exhibited sheets of small blue cells expressing CD99 and focal sall4 on biopsy. Positivity for CD99 and gata3 in the initial biopsy raised the differential diagnosis of Ewing sarcoma and poorly differentiated carcinoma. The primary tumour demonstrated an admixture of solid and glandular growth patterns and occasional Schiller-Duval bodies. A panel of immunohistochemical stains showing positivity for AE1/3, sall4, cdx2, and focal alpha-fetoprotein, and negativity for oct-4, facilitated the diagnosis. A thorough review of the literature and our current report indicate that a large tumour load, incomplete tumour resection, limited response to preoperative neoadjuvant chemotherapy, and late stage of the disease are predictive factors for a poor clinical outcome.

P6336Plasma proteomic profile predicts survival in heart failure with reduced ejection fraction

Background

Whether the plasma proteome can predict the course of heart failure (HF) and has incremental value to established predictors is uncertain.

Methods

Patients meeting Framingham HF criteria with history of reduced ejection fraction (n=1017) were prospectively enrolled in a registry and donated fasting blood samples. Plasma underwent analysis on the SOMAscan proteomic discovery platform, quantifying 4789 proteins using standard assay and quality controls. Patients were randomly divided into derivation (n=681) and validation (n=336) cohorts. We derived a proteomic risk score (PRS) in the derivation cohort using Lasso-penalized Cox regression and then tested it in the validation cohort. Both models were adjusted for an establish HF clinical risk score (MAGGIC) and NTproBNP. We assessed risk stratification improvement in the validation cohort by comparing models with and without PRS using the model C statistic, continuous net reclassification index (NRI), integrated discrimination index (IDI), and the median improvement in risk score (MIRS).

Results

Overall 47.5% of patients were African American, 35.2% were female, mean ejection fraction was 34.8%, and average age was 67.9 years. After median follow-up of 3.6 years, there were 296 deaths (194 in derivation and 102 in validation). Optimized modeling defined a 32 protein PRS (hazard ratio [HR] 2.33, p<2.00E-16) which was also statistically significant when tested in the validation cohort (PRS HR=1.19, p=4.87E-02) and showed some improvement in risk stratification (Table).

Methods Variables Estimate 95% CI P Validation Testing MAGGIC 1.06 1.027, 1.092 2.84E-04 NTproBNP 1.84 1.430, 2.359 1.88E-06 PRS 1.19 1.001, 1.408 4.87E-02 Risk Stratification Assessment C-statistic improvement 0.012 −0.076, 0.101 8.30E-01 IDI 0.034 0.007, 0.095 <2.00E-16 Continuous-NRI 0.286 −0.062, 0.475 9.00E-02 Median Improvement in Risk Score 0.015 0.001, 0.078 2.00E-02

Conclusion

A plasma multi-protein predictive score can improve risk stratification in HF patients on top of a validated clinical score and NTproBNP. Additional investigation is warranted to define mechanisms underlying individual proteins and explore proteomic clinical applications.

Performance of the Meta-Analysis Global Group in Chronic Heart Failure Score in Black Patients Compared With Whites

BACKGROUND

Risk stratification is critical in heart failure (HF) and the Meta-Analysis Global Group in Chronic HF (MAGGIC) score is a validated tool derived from ~40,000 patients. However, few of these patients self-identified as black, raising uncertainty regarding performance in blacks with HF.

METHODS AND RESULTS

This study analyzed a racially diverse group of 4046 patients (1646 black and 2400 white) from a single center from 2007 to 2015. Baseline characteristics were collected to tabulate MAGGIC score and test its discrimination and calibration within race groups. The primary end point was all-cause mortality. Death was detected using system records and the social security death master file. Discrimination was tested using Cox models of MAGGIC score stratified by race, and combined analysis including MAGGIC, race, and MAGGIC×race. Calibration was assessed using linear regression models and plots of observed versus predicted data. Overall, 901 (21%) patients died during 1-year follow-up. MAGGIC score discrimination was similar in both race groups in terms of C statistic (0.707±0.027 versus 0.725±0.014, for black versus white; P=0.556) and the hazard ratio (HR) per MAGGIC point was 1.12 in black patients (95% CI, 1.10-1.14) and 1.13 in white patients (95% CI, 1.12-1.14). Race was a significant correlate of survival, with better survival in black patients compared with white (HR, 0.66; 95% CI, 0.56-0.78), but the interaction of MAGGIC×race was not significant (β=-0.013; P=0.16), and adding race to the model did not improve discrimination (C statistic for MAGGIC versus MAGGIC+race, 0.721 versus 0.722; P=0.79). In calibration testing, the slope was not significantly different from 1 in either group, but the groups differed from each other, and it was closer to unity among black patients (0.94 versus 1.4; P=0.004).

CONCLUSIONS

These data support the use of the MAGGIC score to risk stratify black patients with HF.

Genetics of heart rate in heart failure patients (GenHRate)

BACKGROUND

Elevated resting heart rate (HR) is a risk factor and therapeutic target in patients with heart failure (HF) and reduced ejection fraction (HFrEF). Previous studies indicate a genetic contribution to HR in population samples but there is little data in patients with HFrEF.

METHODS

Patients who met Framingham criteria for HF and had an ejection fraction < 50% were prospectively enrolled in a genetic HF registry (2007-2015, n = 1060). All participants donated blood for DNA and underwent genome-wide genotyping with additional variants called via imputation. We performed testing of previously identified variant "hits" (43 loci) as well as a genome-wide association (GWAS) of HR, adjusted for race, using Efficient Mixed-Model Association Expedited (EMMAX).

RESULTS

The cohort was 35% female, 51% African American, and averaged 68 years of age. There was a 2 beats per minute (bpm) difference in HR by race, AA being slightly higher. Among 43 candidate variants, 4 single nucleotide polymorphisms (SNPs) in one gene (GJA1) were significantly associated with HR. In genome-wide testing, one statistically significant association peak was identified on chromosome 22q13, with strongest SNP rs535263906 (p = 3.3 × 10^-8). The peak is located within the gene Cadherin EGF LAG Seven-Pass G-Type Receptor 1 (CELSR1), encoding a cadherin super-family cell surface protein identified in GWAS of other phenotypes (e.g., stroke). The highest associated SNP was specific to the African American population.

CONCLUSIONS

These data confirm GJA1 association with HR in the setting of HFrEF and identify novel candidate genes for HR in HFrEF patients, particularly CELSR1. These associations should be tested in additional cohorts.

Analysis of Genetic Polymorphism and Genetic Distance of 19 Autosomal STR Loci in Jiangsu Han Population

OBJECTIVES

To investigate the distribution of alleles in 19 autosomal short tandem repeat （STR） loci in Jiangsu Han population.

METHODS

Goldeneye^® 20A kit was used to detect 9 025 samples. Genetic analysis was performed on typing data of 19 autosomal STR loci, and genetic distance with other 17 populations was analyzed.

RESULTS

All the 19 autosomal STR loci were consistent with the Hardy-Weinberg equilibrium （P>0.05）, with the heterozygosity 0.616 1-0.916 3, probability of match 0.012 8-0.202 6, discrimination power 0.797 4-0.987 2, probability of paternity exclusion 0.310 8-0.828 8, and polymorphic information content 0.561 7-0.913 6. The cumulative discrimination power and cumulative probability of exclusion were 0.999 999 999 999 999 998 434 1 and 0.999 999 989, respectively. The Jiangsu Han population had close genetic distances with the Han population in Tianjin, Hunan and Jilin, and significant difference with Han population in Aletai region in Xinjiang （P<0.05）.

CONCLUSIONS

The STR allele polymorphism data and population genetic parameters of Jiangsu Han population can provide data support for the forensic application of these STR loci in Jiangsu Han population.

Author Correction: Genome-wide association and HLA fine-mapping studies identify risk loci and genetic pathways underlying allergic rhinitis

In the version of this article initially published, in Fig. 3, the y-axis numbering did not match the log scale indicated in the axis label. The error has been corrected in the HTML and PDF version of the article.

Multiethnic meta-analysis identifies ancestry-specific and cross-ancestry loci for pulmonary function

Nearly 100 loci have been identified for pulmonary function, almost exclusively in studies of European ancestry populations. We extend previous research by meta-analyzing genome-wide association studies of 1000 Genomes imputed variants in relation to pulmonary function in a multiethnic population of 90,715 individuals of European (N = 60,552), African (N = 8429), Asian (N = 9959), and Hispanic/Latino (N = 11,775) ethnicities. We identify over 50 additional loci at genome-wide significance in ancestry-specific or multiethnic meta-analyses. Using recent fine-mapping methods incorporating functional annotation, gene expression, and differences in linkage disequilibrium between ethnicities, we further shed light on potential causal variants and genes at known and newly identified loci. Several of the novel genes encode proteins with predicted or established drug targets, including KCNK2 and CDK12. Our study highlights the utility of multiethnic and integrative genomics approaches to extend existing knowledge of the genetics of lung function and clinical relevance of implicated loci.

Genome-wide association and HLA fine-mapping studies identify risk loci and genetic pathways underlying allergic rhinitis

Allergic rhinitis is the most common clinical presentation of allergy, affecting 400 million people worldwide, with increasing incidence in westernized countries^1,2. To elucidate the genetic architecture and understand the underlying disease mechanisms, we carried out a meta-analysis of allergic rhinitis in 59,762 cases and 152,358 controls of European ancestry and identified a total of 41 risk loci for allergic rhinitis, including 20 loci not previously associated with allergic rhinitis, which were confirmed in a replication phase of 60,720 cases and 618,527 controls. Functional annotation implicated genes involved in various immune pathways, and fine mapping of the HLA region suggested amino acid variants important for antigen binding. We further performed genome-wide association study (GWAS) analyses of allergic sensitization against inhalant allergens and nonallergic rhinitis, which suggested shared genetic mechanisms across rhinitis-related traits. Future studies of the identified loci and genes might identify novel targets for treatment and prevention of allergic rhinitis.

Prenatal immune activation alters the adult neural epigenome but can be partly stabilised by a n-3 polyunsaturated fatty acid diet

An unstable epigenome is implicated in the pathophysiology of neurodevelopmental disorders such as schizophrenia and autism. This is important because the epigenome is potentially modifiable. We have previously reported that adult offspring exposed to maternal immune activation (MIA) prenatally have significant global DNA hypomethylation in the hypothalamus. However, what genes had altered methylation state, their functional effects on gene expression and whether these changes can be moderated, have not been addressed. In this study, we used next-generation sequencing (NGS) for methylome profiling in a MIA rodent model of neurodevelopmental disorders. We assessed whether differentially methylated regions (DMRs) affected the chromatin state by mapping known DNase I hypersensitivity sites (DHSs), and selected overlapping genes to confirm a functional effect of MIA on gene expression using qPCR. Finally, we tested whether methylation differences elicited by MIA could be limited by post-natal dietary (omega) n-3 polyunsaturated fatty acid (PUFA) supplementation. These experiments were conducted using hypothalamic brain tissue from 12-week-old offspring of mice injected with viral analogue PolyI:C on gestation day 9 of pregnancy or saline on gestation day 9. Half of the animals from each group were fed a diet enriched with n-3 PUFA from weaning (MIA group, n = 12 units, n = 39 mice; Control group, n = 12 units, n = 38 mice). The results confirmed our previous finding that adult offspring exposed to MIA prenatally had significant global DNA hypomethylation. Furthermore, genes linked to synaptic plasticity were over-represented among differentially methylated genes following MIA. More than 80% of MIA-induced hypomethylated sites, including those affecting chromatin state and MECP2 binding, were stabilised by the n-3 PUFA intervention. MIA resulted in increased expression of two of the 'top five' genes identified from an integrated analysis of DMRs, DHSs and MECP2 binding sites, namely Abat (t = 2.46, p < 0.02) and Gnas9 (t = 2.96, p < 0.01), although these changes were not stabilised by dietary intervention. Thus, prenatal MIA exposure impacts upon the epigenomic regulation of gene pathways linked to neurodevelopmental conditions; and many of the changes can be attenuated by a low-cost dietary intervention.

Rare variants and de novo variants in mesial temporal lobe epilepsy with hippocampal sclerosis

Objective

We investigated the role of rare genetic variants and of de novo variants in the pathogenesis of mesial temporal lobe epilepsy related to hippocampal sclerosis (MTLE-HS).

Methods

Whole-exome sequencing (WES) was performed in patients with MTLE-HS and their unaffected parents (trios). Genes or gene sets that were enriched with predicted damaging rare variants in the patients as compared to population controls were identified. Patients and their parents were compared to identify whether the variants were de novo or inherited.

Results

After quality control, WES data from 47 patients (26 female), including 23 complete trios, were available for analysis. Compared with population controls, significant enrichment of rare variants was observed in SEC24B. Integration of gene set data describing neuronal functions and psychiatric disorders showed enrichment signal on fragile X mental retardation protein (FMRP) targets. Twenty-one de novo variants were identified, with many known to cause neuropsychiatric disorders. The FMRP-targeted genes also carried more de novo variants. Inherited compound heterozygous and homozygous variants were identified.

Conclusions

The genetic architecture underlying MTHE-HS is complex. Multiple genes carrying de novo variants and rare variants among FMRP targets were identified, suggesting a pathogenic role. MTLE-HS and other neuropsychiatric disorders may have shared biology.

Race and Beta-Blocker Survival Benefit in Patients With Heart Failure: An Investigation of Self-Reported Race and Proportion of African Genetic Ancestry

Background

It remains unclear whether beta‐blockade is similarly effective in black patients with heart failure and reduced ejection fraction as in white patients, but self‐reported race is a complex social construct with both biological and environmental components. The objective of this study was to compare the reduction in mortality associated with beta‐blocker exposure in heart failure and reduced ejection fraction patients by both self‐reported race and by proportion African genetic ancestry.

Methods and Results

Insured patients with heart failure and reduced ejection fraction (n=1122) were included in a prospective registry at Henry Ford Health System. This included 575 self‐reported blacks (129 deaths, 22%) and 547 self‐reported whites (126 deaths, 23%) followed for a median 3.0 years. Beta‐blocker exposure (BBexp) was calculated from pharmacy claims, and the proportion of African genetic ancestry was determined from genome‐wide array data. Time‐dependent Cox proportional hazards regression was used to separately test the association of BBexp with all‐cause mortality by self‐reported race or by proportion of African genetic ancestry. Both sets of models were evaluated unadjusted and then adjusted for baseline risk factors and beta‐blocker propensity score. BBexp effect estimates were protective and of similar magnitude both by self‐reported race and by African genetic ancestry (adjusted hazard ratio=0.56 in blacks and adjusted hazard ratio=0.48 in whites). The tests for interactions with BBexp for both self‐reported race and for African genetic ancestry were not statistically significant in any model (P>0.1 for all).

Conclusions

Among black and white patients with heart failure and reduced ejection fraction, reduction in all‐cause mortality associated with BBexp was similar, regardless of self‐reported race or proportion African genetic ancestry.