Exome sequencing and analysis of 454,787 UK Biobank participants

Clonal hematopoiesis of indeterminate potential and the risk of autoimmune diseases

BACKGROUND

Clonal hematopoiesis of indeterminate potential (CHIP), characterized by the age-related expansion of blood cells carrying preleukemic mutations, is associated with immune aging. This study aimed to investigate the association between CHIP and established autoimmune diseases.

METHODS

We analyzed baseline data from 456,692 UK Biobank participants with available whole-exome sequences. The primary outcome was 19 autoimmune disorders. Associations among any CHIP (variant allele fraction ≥2%), large CHIP clones (variant allele fraction ≥10%), and gene-specific CHIP subtypes with the incidence of autoimmune diseases were assessed using Cox regression. Mediation analysis was performed to explore the role of inflammation in the link between CHIP and autoimmune diseases.

RESULTS

We identified 17,433 any CHIP and 11,970 large CHIP at baseline. Participants with any and large CHIP were associated with 44% and 43% higher risk for Crohn's disease, 25% and 33% higher risk for psoriasis, 13% and 14% higher risk for rheumatoid arthritis, and 35% and 55% higher risk for vasculitis, respectively. Participants with CHIP status were associated with increased levels of inflammatory markers, including white blood cell, platelets, neutrophils, and neutrophil-to-lymphocyte ratio, with overall mediation ratios of 16.3% for Crohn's disease, 7.1% for psoriasis, 23.2% for rheumatoid arthritis, and 7.2% for vasculitis.

CONCLUSIONS

CHIP was associated with an increased risk for incident multiple autoimmune diseases, including Crohn's disease, psoriasis, vasculitis, and rheumatoid arthritis, potentially mediated by elevated inflammatory levels. Future research is needed to clarify the mechanisms underlying these associations and to explore potential interventions to reduce the associated risk.

Quantifying and improving rheumatoid arthritis algorithm performance in biobank settings

OBJECTIVE

To quantify and improve the performance of standard rheumatoid arthritis (RA) algorithms in a biobank setting.

METHODS

This retrospective cohort study within the Mayo Clinic (MC) Biobank and MC Tapestry Study identified RA cases by presence of at least two RA codes OR positive anti-cyclic citrullinated peptide antibodies (CCP) plus disease-modifying anti-rheumatic drug (DMARD) prescription as of 7/18/2022. Rheumatology physicians manually verified all RA cases using RA criteria and/or rheumatology physician diagnosis plus DMARD use. All other biobank participants served as non-RA controls. We defined seropositivity as rheumatoid factor and/or anti-CCP positivity. We assessed rules-based and Electronic Medical Records and Genomics (eMERGE) RA algorithms using positive predictive value (PPV). Finally, we developed a novel RA algorithm using a LASSO-based machine learning approach with five-fold cross validation.

RESULTS

We identified 1,316 confirmed RA cases (968 MC Biobank, 348 Tapestry, 70 % seropositive) and 82,123 non-RA controls (mean age 65, 61 % female). The PPV of 3 RA codes was 43 %, codes plus DMARD was 54 %, and codes plus DMARD plus seropositivity was 85 %. The PPV of eMERGE was 77 %. Available in the MC Biobank, self-reported RA (PPV 10 %) only minimally improved algorithm performance (PPV from 83 % to 85 %), whereas family history of RA (PPV 3 %) worsened performance. At 90 % PPV, the novel RA algorithm incorporating key variables such as anti-CCP and DMARD use increased sensitivity by 4-11 % compared to eMERGE.

CONCLUSION

Rules-based and eMERGE RA algorithms had worse performance in biobank than administrative settings. Our novel RA algorithm outperformed these standard algorithms.

Whole-exome sequencing identifies 5 novel genes associated with carpal tunnel syndrome

Carpal tunnel syndrome (CTS), a common peripheral nerve entrapment disorder, has a high estimated heritability index. Although previous genome-wide association studies have assessed common genetic components of CTS, the risk contributed by coding variants is still not well understood. Here, we performed the largest exome-wide analyses using UK Biobank data from 350 770 participants to find coding variants associated with CTS. We then explored the relative contribution of both rare mutations and polygenic risk score (PRS) to CTS risk in survival analyses. Finally, we investigated the functional pathways of the CTS-related coding genes identified above. Aside from conforming 6 known CTS genes, 5 novel genes were identified (SPSB1, SYNC, ITGB5, MUC13 and LOXL4). The associations of most genes we identified with incident CTS were striking in survival analyses. Additionally, we provided evidence that combining rare coding alleles and polygenic risk score can improve the genetic prediction of CTS. Functional enrichment analyses revealed potential roles of the identified coding variants in CTS pathogenesis, where they contributed to extracellular matrix organization. Our results evaluated the contribution to CTS etiology from quantities of coding variants accessible to exome sequencing data.

Polygenic Risk Scores in Dilated Cardiomyopathy: Towards the Future

PURPOSE OF REVIEW

Genome-wide association studies (GWASs) have recently shown that common genetic variations significantly affect the risk of developing dilated cardiomyopathy (DCM). This has enabled the development of polygenic scores (PGSs), which aim to aggregate the impact of multiple common genetic variants across the genome to provide an overall genetic risk score for disease manifestation and disease severity. In this review, we discuss the latest findings pertaining to GWASs and PGSs for DCM and various ways in which PGSs could improve the management of patients with DCM or risk of developing DCM.

RECENT FINDINGS

In 2024 the two largest GWAS meta-analyses for DCM were published. Notably, both studies produced PGSs that were able to discriminate healthy subjects from DCM patients which brings promise for potential clinical application of the scores. Large-scale GWAS have identified common genetic variants associated with DCM, leading to the development of PGS, which show strong associations with disease risk and hold potential for clinical applications. However, before clinical implementation, further research is needed to explore their utility in real-world settings and across diverse populations.

Protein-truncating variants in UQCRC1 are associated with Parkinson's disease: evidence from half-million people

Recent studies have suggested a potential but inconsistent link between UQCRC1 and Parkinson's disease (PD). For the first time, we systematically investigated the association between non-synonymous variants in UQCRC1 and PD risk using data from the UK Biobank with half-million participants, which provide evidence supporting the role of UQCRC1 Protein-truncating variants (PTVs) in PD (P = 1.20 × 10-6, OR = 6.59) and highlight the importance of large-scale population studies in identifying rare genetic risk factors.

Clonal Hematopoiesis of Indeterminate Potential Is Associated With Incident Abdominal Aortic Aneurysm

BACKGROUND

Clonal hematopoiesis of indeterminate potential (CHIP) is an emerging risk factor for cardiovascular diseases. Genetic IL (interleukin)-6 signaling deficiency reduced cardiovascular disease risk in CHIP carriers. However, the association between CHIP and incident abdominal aortic aneurysm (AAA) and whether IL-6 signaling inhibition attenuates AAA risk among individuals with CHIP remained unclear.

METHODS

Participants without prevalent AAA from the UK Biobank were included. The associations of any CHIP (variant allele fraction, ≥2%), large CHIP (variant allele fraction, ≥10%), and gene-specific CHIP subtypes with incident AAA were investigated. The protection role of IL6R p.Asp358Ala, a genetic proxy for IL-6 deficiency, was tested after stratification by CHIP status. Furthermore, the interaction and joint effects of CHIP and genetic susceptibility on AAA risk were tested.

RESULTS

This study included 425 211 participants. Any CHIP and large CHIP was identified in 13 768 (3.2%) and 8576 (2.0%) participants, respectively. CHIP was associated with an increased risk of incident AAA (hazard ratio [HR], 1.21 [95% CI, 1.01-1.44]; P=0.034), with large CHIP clones exhibiting greater effect size (HR, 1.35 [95% CI, 1.10-1.66]; P=0.0045). Driver gene-specific analyses revealed that ASXL1-mediated CHIP exerted the strongest effect size on AAA risk (HR, 2.10 [95% CI, 1.54-2.88]; P<0.001). The presence of 2 IL6R p.Asp358Ala alleles attenuated the risk of AAA in large CHIP carriers (HR, 0.48 [95% CI, 0.23-0.99]; P=0.046). In the joint analysis, participants with CHIP and high genetic risk had a higher risk of developing AAA than those without CHIP and with low genetic risk (HR, 2.15 [95% CI, 1.63-2.85]; P<0.001).

CONCLUSIONS

CHIP is associated with an increased risk of AAA. Genetic IL-6 signaling deficiency attenuates the risk of AAA in large CHIP carriers. CHIP may serve as an attractive target for the prevention and treatment of AAA.

Expanding scope of genetic studies in the era of biobanks

Biobanks have become pivotal in genetic research, particularly through genome-wide association studies (GWAS), driving transformative insights into the genetic basis of complex diseases and traits through the integration of genetic data with phenotypic, environmental, family history, and behavioral information. This review explores the distinct design and utility of different biobanks, highlighting their unique contributions to genetic research. We further discuss the utility and methodological advances in combining data from disease-specific study or consortia with that of biobanks, especially focusing on summary statistics based meta-analysis. Subsequently we review the spectrum of additional advantages offered by biobanks in genetic studies in representing population differences, calibration of polygenic scores, assessment of pleiotropy and improving post-GWAS in silico analyses. Advances in sequencing technologies, particularly whole-exome and whole-genome sequencing, have further enabled the discovery of rare variants at biobank scale. Among recent developments, the integration of large-scale multi-omics data especially proteomics and metabolomics, within biobanks provides deeper insights into disease mechanisms and regulatory pathways. Despite challenges like ascertainment strategies and phenotypic misclassification, biobanks continue to evolve, driving methodological innovation and enabling precision medicine. We highlight the contributions of biobanks to genetic research, their growing integration with multi-omics, and finally discuss their future potential for advancing healthcare and therapeutic development.

Rare predicted loss-of-function and damaging missense variants in CFHR5 associate with protection from age-related macular degeneration

Age-related macular degeneration (AMD) is a leading cause of blindness among older adults worldwide, but treatment options are limited. Genetics studies have implicated the CFH locus, containing CFH and five CFHR genes, CFHR1-5, in AMD. While CFH has been robustly linked with AMD risk, potential additional roles for the CFHR genes remain unclear, obscured by strong linkage disequilibrium across the locus. Investigating rare coding variants can help to identify causal genes in such regions. We used whole-exome sequencing data from 406,952 UK Biobank participants to examine AMD associations with genes at the CFH locus. For each gene, we used burden testing to examine associations of rare (minor-allele frequency [MAF] < 1%) predicted loss-of-function (pLoF) and predicted damaging missense variants with AMD. We considered "broadly defined AMD" (ICD-10 35.3; ncases = 10,700) and "strictly defined AMD" (dry or wet AMD; ncases = 346). Adjusting for CFH-region variants known to independently associate with AMD, we find that CFHR5 rare variant burden significantly associates with a decreased risk of broadly defined AMD (odds ratio [OR] = 0.75, p = 7 × 10-4), with this association primarily driven by pLoF variants. Furthermore, the association of CFHR5 rare variants with AMD protection is estimated to be stronger for individuals with the CFH rs1061170 AMD risk allele (p.Tyr402His [p.Y402H]; interaction p = 0.04). Corresponding analyses of strict AMD were underpowered. However, we observe that thinning of the photoreceptor layer outer segment strongly predicts strict AMD and find that CFHR5 rare variant burden is significantly associated with increased thickness of this retinal layer (+0.34 SD, p = 4 × 10-4, n = 45,365). These findings suggest CFHR5 inhibition as a potential therapeutic approach for AMD.

Whole exome sequencing identified six novel genes for depressive symptoms

Previous genome-wide association studies of depression have primarily focused on common variants, limiting our comprehensive understanding of the genetic architecture. In contrast, whole-exome sequencing can capture rare coding variants, helping to explore the phenotypic consequences of altering protein-coding genes. Here, we conducted a large-scale exome-wide association study on 296,199 participants from the UK Biobank, assessing their depressive symptom scores through the Patient Health Questionnaire-4. We identified 22 genes associated with depressive symptoms, including 6 newly discovered genes (TRIM27, UBD, SVOP, ADGRB2, IRF2BPL, and ANKRD12). Both ontology enrichment analysis and plasma proteomics association analysis consistently revealed that the identified genes were associated with immune responses. Furthermore, we identified associations between these genes and brain regions related to depression, such as anterior cingulate cortex and orbitofrontal cortex. Additionally, phenome-wide association analysis demonstrated that TRIM27 and UBD were associated with neuropsychiatric, cognitive, biochemistry, and inflammatory traits. Our findings offer new insights into the potential mechanisms and genetic architecture of depressive symptoms.

Cardiomyopathy-Associated Gene Variants in Atrial Fibrillation

Importance

Patients with atrial fibrillation (AF), a common morbid arrhythmia, are more likely to carry rare genetic variants associated with inherited cardiomyopathies. Prior studies on rare pathogenic variants in AF relied on small, hospital referral populations, and knowledge on clinical outcomes remains limited.

Objective

To evaluate the prevalence and prognostic implications of cardiomyopathy-associated pathogenic or likely pathogenic (CMP-PLP) genetic variants in patients with AF.

Design, Setting, and Participants

In 2 prospective cohort studies, the prevalence of CMP-PLP variants was assessed in the population of patients with AF and early-onset AF. The association between carrying a CMP-PLP variant and the risk of incident cardiomyopathy or heart failure (CMP/HF) after AF diagnosis was evaluated. Finally, the joint contributions of CMP-PLP variants, clinical risk, and polygenic risk were assessed. Included in this study were 2 large longitudinal cohort studies, the UK Biobank (UKB) (data 2006-2023) and the All of Us Research Program (AllofUs) (2018-2022). The UKB and AllofUs cohorts, respectively, contained 393 768 and 193 232 unrelated genotyped participants.

Exposures

CMP-PLP variants.

Main Outcomes and Measures

Prevalence of CMP-PLP variants and risk of incident CMP/HF after AF diagnosis.

Results

In the UKB cohort, 32 281 participants (8%) had AF (mean [SD] age, 62 [6] years; 20 459 male [63.4%]). In the AllofUs cohort, 11 901 participants (6%) had AF (mean [SD] age, 67 [12] years; 6576 male [55.3%]). Compared with the biobank populations, CMP-PLP variants were twice as prevalent in patients with AF (UKB, 2.04%; 95% CI, 1.89%-2.20%; AllofUs, 2.52%; 95% CI, 2.25%-2.82%) and 5 times as prevalent in AF with onset before age 45 years (UKB, 4.99%; 95% CI, 3.07%-7.91%; AllofUs, 4.66%; 3.40%-6.32%). Cumulative incidence of CMP/HF was high in patients with AF (18%) compared with patients without AF (3%). Still, among patients with AF without prior CMP/HF (UKB, 20 226; AllofUs, 8330), carrying a CMP-PLP variant was associated with 1.6-fold risk of incident CMP/HF (meta-analysis, 95% CI, 1.32-1.90). Finally, CMP-PLP variants, a polygenic score, and clinical risk factors were independent estimators of CMP/HF.

Conclusions and Relevance

Results of this cohort study suggest that the prevalence of CMP-PLP variants was substantial in patients with early-onset AF. Patients with AF carrying a CMP-PLP variant had an associated increased risk of future CMP/HF, independent of clinical and polygenic risk. These results indicate that genetic testing in patients with AF may identify individuals at higher risk for developing CMP/HF.

Immunomodulatory function of cannabinoid receptor 2 and its agonist osteogenic growth peptide in health and cancer: a study in mice and humans

Colon carcinoma is among the most prevalent malignant tumors, with inflammation being the primary risk factor. Cannabinoid receptor 2 (CB2/CNR2) has complex immunomodulatory functions. Therefore, we investigated the role of osteogenic growth peptide (OGP), an endogenous selective CB2 agonist, in colon carcinogenesis and immune modulation in transgenic mice (ApcMin/+).We injected 8-week-old (progression phase) or five-week-old (initiation phase) ApcMin/+ mice with OGP or vehicle weekly for 8 weeks or 4 weeks, respectively. During the progression phase, OGP-treated mice displayed significantly fewer tumors in the large intestine and smaller tumors in the small intestine. During the initiation phase, OGP significantly attenuated adenomagenesis in both the small and large intestine, decreased IL-6 and IL-4 levels, increased splenic anti-tumor CD8+ T cells, and diminished populations of tumor-promoting myeloid-derived suppressor cells. Further, we used exomic analyses of UKBiobank patients to determine the relationship between CNR2 polymorphisms and tumor-associated myeloid cells in humans. We found that the common CNR2-Q63R polymorphism is associated with monocyte count. Our results suggest that CB2 activation via OGP attenuates tumorigenesis and adenoma growth by modulating immune cells, corroborated by a significant association between CNR2 polymorphisms and monocytopoiesis in humans.

Exploring the association between systemic lupus erythematosus and osteonecrosis by Mendelian randomization analysis

Patients with systemic lupus erythematosus (SLE) have been shown to have a high risk of osteonecrosis, but the potential causal relationship between genetic susceptibility and risk of osteonecrosis is unclear. In this study, we used Mendelian randomization to investigate the effects of SLE, gout and rheumatoid arthritis on osteonecrosis, and performed post-GWAS localization and functional analyses of GWAS studies related to osteonecrosis, with the aim of obtaining a more in-depth understanding of the mechanisms of osteonecrosis. In this study, a total of 45 single nucleotide polymorphisms (SNPS) data associated with SLE from publicly available genome-wide association study (GIS) datasets were selected for magnetic resonance estimation using inverse-variance weighting, MR-Eagle method and weighted median method. The Cochrane Q-test, MR-Egger interception, MR-multidirectional residual and outlier methods, entrance/exit analysis and funnel plot were applied for sensitivity analysis. Two-sample Mendelian randomization analysis of the 19 SNPs obtained from screening showed no significant causal effect of SLE and osteonecrosis, and IVW and MR-Egger heterogeneity analyses showed no significant heterogeneity between the instrumental variables (P > 0.05). Multi-phenotype MR analysis showed no significant causal effect between gout and rheumatoid arthritis and osteonecrosis (p > 0.05). The available evidence does not support a significant causal effect of gout and rheumatoid arthritis on osteonecrosis, and the causal effect of SLE on the increased risk of osteonecrosis is only supported by the IVW method, which is of insufficient evidence validity, but suggests a better theoretical basis for the study of heritability related to SLE.

LRRK2 rare-variant per-domain genetic burden in Parkinson's Disease: association confined to the kinase domain

LRRK2 variants are key genetic risk factors for Parkinson's Disease (PD). We conducted a per-domain rare coding variant burden analysis, including 8,888 PD cases and 69,412 controls. In meta-analysis, the Kinase domain was strongly associated with PD (Exonic: PFDR = 1.61 × 10-22, Non-synonymous: PFDR = 1.54 × 10-23, CADD > 20: PFDR = 3.09 × 10-24). Excluding the p.G2019S variant nullified this effect. Nominal associations were found in the ANK and Roc-COR domains, with potentially protective variants, p.R793M and p.Q1353K.

Genetic determinants of proteomic aging

Changes in the proteome and its dysregulation have long been known to be a hallmark of aging. We derived a proteomic aging trait using data on 1459 plasma proteins from 44,435 UK Biobank individuals measured using an antibody-based assay. This metric is strongly associated with four age-related disease outcomes, even after adjusting for chronological age. Survival analysis showed that one-year older proteomic age, relative to chronological age, increases all-cause mortality hazard by 13 percent. We performed a genome-wide association analysis of proteomic age acceleration (proteomic aging trait minus chronological age) to identify its biological determinants. Proteomic age acceleration showed modest genetic correlations with four epigenetic clocks (Rg = 0.17 to 0.19) and telomere length (Rg = -0.2). Once we removed associations that were explained by a single pQTL, we were left with three signals mapping to BRCA1, POLR2A and TET2 with apparent widespread effects on plasma proteomic aging. Genetic variation at these three loci has been shown to affect other omics-related aging measures. Mendelian randomisation analyses showed causal effects of higher BMI and type 2 diabetes on faster proteomic age acceleration. This supports the idea that obesity and other features of metabolic syndrome have an adverse effect on the processes of human aging.

Hypertension increases PPV for polycystic kidney disease in PKD1 and PKD2 variant carriers

Autosomal dominant polycystic kidney disease (ADPKD) is the leading genetic form of KD. Although rare causal variants in the PKD1 and PKD2 genes have been identified, their penetrance and the disease progression and outcome are known to vary, and treatment efficacy in these carriers lags compared to patients with other forms of chronic KD (CKD). To develop a population screening strategy with high sensitivity to individuals likely to develop disease, we characterize the presentation and progression of ADPKD in variant carriers, identified in a multi-center all-comers cohort, as well as the UK Biobank. We show that the positive predictive value of hypertension for future diagnosis of KD is extremely high: 74% and 66% for PKD1 and PKD2, respectively. It is also highly preemptive, with hypertension occurring an average of 11 years before a KD diagnosis. Using pre-disease time point measurements of kidney function prior to their ADPKD diagnosis, we find that PKD1 and PKD2 variant carriers show significantly decreased kidney function (EGFR) an average of 5 years before their clinical diagnosis. Unlike other CKD patients, 54% of variant carriers with hypertension meet the diagnostic threshold for CKD years prior to their disease diagnosis, and their EGFRs are statistically indistinguishable from variant carriers who have already been diagnosed. These findings suggest that a population screening strategy using a combination of targeted sequencing and routine monitoring could identify cases of ADPKD with high sensitivity and support initiating treatment years prior to the current standard of care.

Evidence to shared genetic correlation of ischemic stroke and intracerebral hemorrhage and cardiovascular related traits

BACKGROUND

Previous studies have demonstrated the genetic basis of stroke and also revealed their genetic correlation with some cardiovascular related diseases or traits at the entire genome, which, however, would not give the answer which regions may mainly account for the genetic overlap. This study aims to identify specific genetic loci that contribute to the shared genetic basis between ischemic stroke subtypes and common cardiovascular traits.

METHODS

We used Local Analysis of [co]Variant Annotation (LAVA), a recent developed local genetic correlation method, to perform a system local genetic correlation analysis on GWAS summary data of two major subtypes of stroke, including any ischemic stroke (AIS) and intracerebral hemorrhage (ICH), and ten common cardiovascular related diseases or traits (CRTs). We further used colocalization analysis to explore potential shared causal genes in loci with significant local genetic correlation. In addition, we also performed Transcriptome-wide association (TWAS) analysis and fine-mapping for each phenotype to functionally annotate significant loci.

RESULTS

LAVA analysis identified a total of 3 significant local genetic correlations (Bonferroni-adjusted P <  0.05) across 3 chromosomes between AIS and systolic blood pressure (SBP), AIS and hypertension (HT), and ICH and body mass index (BMI), among which locus 7.24 explicated to harbor a shared causal variant for AIS and SBP. TWIST1 in locus 7.24 was defined to be nominally associated with SBP, but not for AIS. Fine-mapping analysis also only identified TWIST1 a credible causal gene for BMI.

CONCLUSIONS

Our study revealed the local genetic correlations between two stroke subtypes and ten common CRTs. Gene-level analyses indicated that biological explanations underlying these identified local genetic correlations may existed elsewhere beyond a common pattern of genetic-gene expression regulation.

Rare genetic variants involved in increased risk of paroxysmal atrial fibrillation in a Japanese population

Atrial fibrillation (AF) is the most prevalent arrhythmia in the world and can cause serious complications such as stroke or heart failure. Paroxysmal atrial fibrillation (PAF), a subtype of AF, accounts for approximately 25% of AF cases and is estimated to affect approximately 30 million people worldwide. Despite extensive genetic research on AF, the genetic factors involved in PAF in East Asian (EAS) populations remain unidentified. The aim of our study was to identify genetic factors associated with PAF in the Japanese population, contributing to our understanding of the genetic architecture of AF in Japanese populations. We conducted whole-exome sequencing on a cohort of 1176 PAF individuals and 1172 non-PAF control subjects in a Japanese population. We processed the sequencing data in accordance with the best practices outlined in the Genome Analysis Toolkit (GATK) and conducted gene-based association tests under three variant grouping strategies (masks) using the burden test, SKAT, and SKAT-O. We then performed a meta-analysis of the resulting P-values, which revealed that four genes-ZNF785, SMPD3, GFRA4, and LGALS1-were significantly associated with PAF, representing novel findings. These findings provide new insights into PAF pathogenesis and suggest potential biomarkers for early detection.

Exome sequencing identifies protein-coding variants associated with loneliness and social isolation

BACKGROUND

Loneliness and social isolation are serious yet underappreciated public health problems, with their genetic underpinnings remaining largely unknown. We aimed to explore the role of protein-coding variants in the manifestation of loneliness and social isolation.

METHODS

We conducted the first exome-wide association analysis on loneliness and social isolation, utilizing 336,115 participants of white-British ancestry for loneliness and 346,115 for social isolation. Sensitivity analyses were performed to validate the genetic findings. We estimated the genetic burden heritability of loneliness and social isolation and provided biological insights into them.

RESULTS

We identified six novel risk genes (ANKRD12, RIPOR2, PTEN, ARL8B, NF1, and PIMREG) associated with loneliness and two (EDARADD and GIGYF1) with social isolation through analysis of rare coding variants. Brain-wide association analysis uncovered 47 associations between identified genes and brain structure phenotypes, many of which are critical for social processing and interaction. Phenome-wide association analysis established significant links between these genes and phenotypes across five categories, mostly blood biomarkers and cognitive measures.

LIMITATIONS

The measurements of loneliness and social isolation in UK Biobank are brief for these multi-layer social factors, some relevant aspects may be missed.

CONCLUSIONS

Our study revealed 13 risk genes associated with loneliness and 6 with social isolation, with the majority being novel discoveries. These findings advance our understanding of the genetic basis of these two traits. The study provides a foundation for future studies aimed at exploring the functional mechanisms of these genes and their potential implications for public health interventions targeting loneliness and social isolation.

Evolution of genome-wide methylation profiling technologies

In this mini-review, we explore the advancements in genome-wide DNA methylation profiling, tracing the evolution from traditional methods such as methylation arrays and whole-genome bisulfite sequencing to the cutting-edge single-molecule profiling enabled by long-read sequencing (LRS) technologies. We highlight how LRS is transforming clinical and translational research, particularly by its ability to simultaneously measure genetic and epigenetic information, providing a more comprehensive understanding of complex disease mechanisms. We discuss current challenges and future directions in the field, emphasizing the need for innovative computational tools and robust, reproducible approaches to fully harness the capabilities of LRS in molecular diagnostics.

Germline Pathogenic DROSHA Variants Are Linked to Pineoblastoma and Wilms Tumor Predisposition

PURPOSE

DROSHA, DGCR8, and DICER1 regulate miRNA biogenesis and are commonly mutated in cancer. Although DGCR8 and DICER1 germline pathogenic variants (GPV) cause autosomal dominant tumor predisposition, no association between DROSHA GPVs and clinical phenotypes has been reported.

EXPERIMENTAL DESIGN

After obtaining informed consent, sequencing was performed on germline and tumor samples from all patients. The occurrence of germline DROSHA GPVs was investigated in large pediatric and adult cancer datasets. The population prevalence of DROSHA GPVs was investigated in the UK Biobank and Geisinger DiscovEHR cohorts.

RESULTS

We describe nine children from eight families with heterozygous DROSHA GPVs and a diagnosis of pineoblastoma (n = 8) or Wilms tumor (n = 1). A somatic second hit in DROSHA was detected in all eight tumors analyzed. All pineoblastoma tumors analyzed were classified as miRNA processing-altered 1 subtype. We estimate the population prevalence of germline DROSHA loss-of-function variants to be 1:3,875 to 1:4,843 but find no evidence for increased adult cancer risk.

CONCLUSIONS

This is the first report of DROSHA-related tumor predisposition. As pineoblastoma and Wilms tumor are also associated with DICER1 GPVs, our results suggest that the tissues of origin for these tumors are uniquely tolerant of general miRNA loss. The miRNA processing-altered 1 pineoblastoma subtype is associated with older age of diagnosis and better outcomes than other subtypes, suggesting DROSHA GPV status may have important clinical and prognostic significance. We suggest that genetic testing for DROSHA GPVs be considered for patients with pineoblastoma, Wilms tumor, or other DICER1-/DGCR8-related conditions and propose surveillance recommendations through research studies for individuals with DROSHA GPVs.

A Mendelian randomization study: causal relationship between immune cells and the risks of social phobia, specific phobia, and agoraphobia

BACKGROUND

Although phobia is a common psychiatric disorder, the underlying biological mechanisms have not been fully elucidated. Complex immune-brain interactions that affect neural development, survival, and function may have causal and therapeutic implications in psychiatric illnesses. In this study, the relationships between immune cell traits and phobia were analysed using Mendelian randomization to explore the biological mechanisms.

METHODS

Based on publicly-available genetic data, a two-sample MR analysis was used to determine the causal relationship between 731 immune cell traits and the risk of developing phobias. Sensitivity analyses were conducted to verify the robustness, heterogeneity, and horizontal pleiotropy of the results.

RESULTS

After forward and reverse analyses, false discovery rate (FDR) corrections were performed. No significant associations between phobias and immune cell traits were identified. After adjusting the FDR threshold, social phobia affected two immune cell traits: CD39 on granulocytes (β = 9.0347, 95% confidence interval (CI) = 4.4802-13.5891, P = 0.0001, FDR = 0.0738), and CD11c on granulocytes (β = 7.7976, 95% CI = 3.4616-12.1336, P = 0.0004, FDR = 0.1547). Three immune cell traits affected the risk of specific phobias: CD4 + CD8dim T cell %leukocyte (odds ratio (OR) = 0.9985, 95% CI = 0.9976-0.9993, P = 0.0006, FDR = 0.1373), CD45 on CD33 + HLA DR + CD14dim (OR = 0.9977, 95% CI = 0.9964-0.9990, P = 0.0004, FDR = 0.1373), and CD8 on CD28 + CD45RA + CD8br (OR = 0.9990, 95% CI = 0.9985-0.9996, P = 0.0003, FDR = 0.1373). Two immune cell traits affected the risk of agoraphobia: CD3 on CD39 + resting regulatory T cells (Tregs) (OR = 1.0010, 95 CI%=1.0005-1.0015, P = 0.0001, FDR = 0.0596) and HLA DR on CD33br HLA DR + CD14dim (OR = 0.9993, 95 CI%=0.9990-0.9997, P = 0.0002, FDR = 0.0596).

CONCLUSIONS

Immune cell traits closely related to phobias were screened out through genomics, which provides a reference for the subsequent research on the immune system-phobia interaction.

Actionable genetic variants in 4,198 Scottish participants from the Orkney and Shetland founder populations and implementation of return of results

The benefits of returning clinically actionable genetic results to participants in research cohorts are accruing, yet such a genome-first approach is challenging. Here, we describe the implementation of return of such results in two founder populations from Scotland. Between 2005 and 2015, we recruited >4,000 adults with grandparents from Orkney and Shetland into the Viking Genes research cohort. The return of genetic data was not offered at baseline, but in 2023, we sent invitations to participants for consent to return of actionable genetic findings. We generated exome sequence data from 4,198 participants and used the American College of Medical Genetics and Genomics (ACMG) v.3.2 list of 81 genes, ClinVar review, and pathogenicity status, plus manual curation, to develop a pipeline to identify potentially actionable variants. We identified 104 individuals (2.5%) with 108 actionable genotypes at 39 variants in 23 genes and validated these. Working with the NHS Clinical Genetics service, which provided genetic counseling and clinical verification of the research results, and after expert clinical review, we notified 64 consenting participants (or their next of kin) of their actionable genotypes. Ten actionable variants across seven genes (BRCA1, BRCA2, ATP7B, TTN, KCNH2, MUTYH, and GAA) have risen 50- to >3,000-fold in frequency through genetic drift in ancestral island localities. Viking Genes is one of the first UK research cohorts to return actionable findings, providing an ethical and logistical exemplar of return of results. The genetic structure in the Northern Isles of Scotland with multiple founder effects provides a unique opportunity for a tailored approach to disease prevention through genetic screening.

The contribution of coding variants to the heritability of multiple cancer types using UK Biobank whole-exome sequencing data

Genome-wide association studies have been highly successful at identifying common variants associated with cancer; however, they do not explain all the inherited risks of cancer. Family-based studies, targeted sequencing, and, more recently, exome-wide association studies have identified rare coding variants in some genes associated with cancer risk, but the overall contribution of these variants to the heritability of cancer is less clear. Here, we describe a method to estimate the genome-wide contribution of rare coding variants to heritability that fits models to the burden effect sizes using an empirical Bayesian approach. We apply this method to the burden of protein-truncating variants in over 15,000 genes for 11 cancers in the UK Biobank using whole-exome sequencing data on over 400,000 individuals. We extend the method to consider the overlap of genes contributing to pairs of cancers. We found ovarian cancer to have the greatest proportion of heritability attributable to protein-truncating variants in genes (46%). The joint cancer models highlight significant clustering of cancer types, including a near-complete overlap in susceptibility genes for breast, ovarian, prostate, and pancreatic cancer. Our results provide insights into the contribution of rare coding variants to the heritability of cancer and identify additional genes with strong evidence of susceptibility to multiple cancer types.

An Alternatively Translated Isoform of PPARG Suggests AF-1 Domain Inhibition as an Insulin Sensitization Target

ARTICLE HIGHLIGHTS

Genetic screens were performed across PPARG to study how disruptive mutations across the full coding sequence affect function. An alternative translational start site in PPARG generates a truncated isoform, peroxisome proliferator-activated receptor γ (PPARγ) M135, which lacks the N-terminal activation function 1 (AF-1) domain and shows increased agonist-induced transactivation of target genes. In human carriers of rare PPARG variants, AF-1 domain-disrupting genetic variants increase agonist-induced PPARγ activity and decrease metabolic syndrome severity. Targeting the AF-1 domain is a potential therapeutic strategy for insulin sensitization.

Mendelian randomization study investigating the relationship between nutrients and polycystic ovary syndrome

OBJECTIVE

Polycystic ovary syndrome (PCOS) affects many women and is linked to nutrient intake, but the causal role of nutrients is unclear. Our study used Mendelian randomization (MR) to explore this relationship.

METHODS

We employed two-sample MR to investigate the causal effects of four macronutrients (carbohydrates, fats, sugars, proteins) and 12 micronutrients (vitamin A [retinol], folate, vitamin B6, vitamin B12, vitamin C [ascorbic acid], vitamin D, vitamin E [alpha-tocopherol], magnesium, calcium, iron, selenium, and zinc) on the risk of PCOS based on their circulating levels. We conducted analyses using the inverse variance-weighted method (IVW), MR-Egger regression, weighted median method, and simple model approach, with IVW as the primary method. To correct for multiple testing, the false discovery rate (FDR) method was applied. The reliability and potential bias of the results were assessed by sensitivity analysis and F-statistics.

RESULTS

From a genetic standpoint, higher circulating vitamin A (retinol) levels were found to be a protective factor for PCOS and closely associated with the risk of PCOS, consistent with recent research findings. The inverse variance-weighted (IVW) estimation indicated a protective effect of vitamin A (retinol) on PCOS (IVWOR = 0.97, 95% CI: 0.95-0.99, P = 0.002, FDR_P = 0.03). However, no causal relationship was found between other nutrients and PCOS. In addition, MR-PRESSO and MR-Egger regression showed that our results were not affected by horizontal pleiotropy (P > 0.05). Finally, leave-one-out sensitivity analysis confirmed the robustness of MR Results.

CONCLUSION

Our findings suggest that circulating vitamin A (retinol) levels influence the risk of PCOS, but further research is needed.

Clonal Hematopoiesis of Indeterminate Potential and Risk of Microvascular Complications Among Individuals With Type 2 Diabetes: A Cohort Study

ARTICLE HIGHLIGHTS

Clonal hematopoiesis of indeterminate potential (CHIP) is an age-related disorder that is associated with macrovascular diseases, such as coronary artery disease and stroke. However, the effects of CHIP on microvascular complication have not been explored in individuals with type 2 diabetes. We wanted to determine whether CHIP is associated with diabetic microvascular complications (DMCs). CHIP was associated with a high risk of DMCs, specifically, diabetic retinopathy and diabetic kidney disease, but not diabetic neuropathy. Gene-specific analyses suggested that some driver genes were associated with risk of developing DMCs. These findings indicated that CHIP may represent a novel risk factor for DMCs among individuals with type 2 diabetes, distinct from traditional risk factors, which may have implications for prevention and management of DMCs.

Endothelium Piezo1 deletion alleviates experimental varicose veins by attenuating perivenous inflammation

Previous large-scale genetic studies have prioritized the causal genes piezo type mechanosensitive ion channel component 1 (PIEZO1) and castor zinc finger 1 (CASZ1) associated with varicose veins (VVs). This study aims to evaluate their roles in both clinical and experimental VVs. In this study, we investigated abundance of PIEZO1 and CASZ1 in both varicose and normal veins from the same patients. Yoda1 (a selective PIEZO1 agonist, 2.6 mg/kg/day) or vehicle was administered intraperitoneally for 3 weeks to evaluate the effect of PIEZO1 activation on experimental VVs. Subsequently, endothelial Piezo1 deletion mice (Piezo1iΔEC mice) were generated to explored the role of endothelial PIEZO1 on VVs. Laser speckle imaging, flow cytometry, cell tracing with Evans blue or rhodamine-6G, and histopathological staining were utilized to evaluate the pathophysiology of VVs. Our results showed that mRNA expression of PIEZO1, but not CASZ1, was abundant and increased in clinical VVs. The Piezo1tP1-td mice revealed endothelium-specific expression of PIEZO1 in mice veins. By establishing iliac vein ligation-induced VVs in mice, Yoda1 exacerbated experimental VVs with increased inflammatory cell infiltration. Subsequently, endothelial Piezo1 deletion (Piezo1iΔEC mice) alleviated experimental VVs and vascular remodeling by directly reducing vascular permeability and leukocyte-endothelium interactions compared to the control (Piezo1fl/fl mice). PIEZO1 is highly expressed in clinical VVs, meanwhile, activation or inhibition of PIEZO1 exerts a remarkable effect on experimental VVs. Furthermore, Piezo1 may constitute a potential therapeutic approach for the medical treatment of VVs.

Common-variant and rare-variant genetic architecture of heart failure across the allele-frequency spectrum

Heart failure is a complex trait, influenced by environmental and genetic factors, affecting over 30 million individuals worldwide. Here we report common-variant and rare-variant association studies of all-cause heart failure and examine how different classes of genetic variation impact its heritability. We identify 176 common-variant risk loci at genome-wide significance in 2,358,556 individuals and cluster these signals into five broad modules based on pleiotropic associations with anthropomorphic traits/obesity, blood pressure/renal function, atherosclerosis/lipids, immune activity and arrhythmias. In parallel, we uncover exome-wide significant associations for heart failure and rare predicted loss-of-function variants in TTN, MYBPC3, FLNC and BAG3 using exome sequencing of 376,334 individuals. We find that total burden heritability of rare coding variants is highly concentrated in a small set of Mendelian cardiomyopathy genes, while common-variant heritability is diffusely spread throughout the genome. Finally, we show that common-variant background modifies heart failure risk among carriers of rare pathogenic truncating variants in TTN. Together, these findings discern genetic links between dysregulated metabolism and heart failure and highlight a polygenic component to heart failure not captured by current clinical genetic testing.

Functional interrogation of cellular Lp(a) uptake by genome-scale CRISPR screening

BACKGROUND AND AIMS

An elevated level of lipoprotein(a), or Lp(a), in the bloodstream has been causally linked to the development of atherosclerotic cardiovascular disease and calcific aortic valve stenosis. Steady state levels of circulating lipoproteins are modulated by their rate of clearance, but the identity of the Lp(a) uptake receptor(s) has been controversial.

METHODS

We performed a genome-scale CRISPR screen to functionally interrogate all potential Lp(a) uptake regulators in HuH7 cells. Screen validation was performed by single gene disruption and overexpression. Direct binding between purified lipoproteins and recombinant protein was tested using biolayer interferometry. An association between human genetic variants and circulating Lp(a) levels was analyzed in the UK Biobank cohort.

RESULTS

The top positive and negative regulators of Lp(a) uptake in our screen were LDLR and MYLIP, encoding the LDL receptor and its ubiquitin ligase IDOL, respectively. We also found a significant correlation for other genes with established roles in LDLR regulation. No other gene products, including those previously proposed as Lp(a) receptors, exhibited a significant effect on Lp(a) uptake in our screen. We validated the functional influence of LDLR expression on HuH7 Lp(a) uptake, confirmed in vitro binding between the LDLR extracellular domain and purified Lp(a), and detected an association between loss-of-function LDLR variants and increased circulating Lp(a) levels in the UK Biobank cohort.

CONCLUSIONS

Our findings support a central role for the LDL receptor in mediating Lp(a) uptake by hepatocytes.

Tracing the Evolution of Human Immunity Through Ancient DNA

Infections have imposed strong selection pressures throughout human evolution, making the study of natural selection's effects on immunity genes highly complementary to disease-focused research. This review discusses how ancient DNA studies, which have revolutionized evolutionary genetics, increase our understanding of the evolution of human immunity. These studies have shown that interbreeding between modern humans and Neanderthals or Denisovans has influenced present-day immune responses, particularly to viruses. Additionally, ancient genomics enables the tracking of how human immunity has evolved across cultural transitions, highlighting strong selection since the Bronze Age in Europe (<4,500 years) and potential genetic adaptations to epidemics raging during the Middle Ages and the European colonization of the Americas. Furthermore, ancient genomic studies suggest that the genetic risk for noninfectious immune disorders has gradually increased over millennia because alleles associated with increased risk for autoimmunity and inflammation once conferred resistance to infections. The challenge now is to extend these findings to diverse, non-European populations and to provide a more global understanding of the evolution of human immunity.

Causal relationship between bladder cancer and gut microbiota contributes to the gut-bladder axis: A two-sample Mendelian randomization study

BACKGROUND

Recent studies have underscored a potential link between gut microbiota and urological tumors, yet the causal relationship with bladder cancer (BCa) and the role of metabolic pathways remain unclear.

METHODS

Instrumental variables (IVs) for gut microbiota were obtained from genome-wide association studies (GWAS) conducted by the MiBioGen consortium (n = 18,340). GWAS data for BCa were sourced from a comprehensive genome-wide meta-analysis encompassing 23 cohorts. Mendelian randomization (MR) was employed to investigate the causal relationship between gut microbiota and BCa, utilizing inverse variance weighted (IVW) as the primary MR method. Additionally, metabolic pathways associated with these microbiota were analyzed to understand their functional roles in BCa pathogenesis. Sensitivity analyses were conducted to validate all MR results.

RESULTS

The MR analysis identified five gut microbiota taxa with a causal association with BCa, with the genus Bilophila notably promoting BCa. Metabolic pathway analysis revealed significant associations between specific pathways and BCa, suggesting that changes in amino acid and NAD metabolism might influence BCa development. Sensitivity analyses indicated no significant heterogeneity or horizontal pleiotropy among the IVs.

CONCLUSION

This study revealed the significant causal relationship between gut microbiota and BCa, particularly identifying Bilophila as a key pathogenic initiator. These findings elucidated the potential impact of metabolic pathways, especially amino acid and NAD metabolism, on the pathogenesis of BCa. They not only laid the foundation for innovative therapeutic strategies but also highlighted the immense potential of microbiota-based interventions in the prevention and treatment of BCa, paving the way for new directions in precision medicine.

Reassessing the role of the p.(Arg304Gln) missense AIP variant in pituitary tumorigenesis

OBJECTIVE

Heterozygous germline loss-of-function variants in AIP are associated with young-onset growth hormone and/or prolactin-secreting pituitary tumours. However, the pathogenic role of the c.911G > A; p.(Arg304Gln) (R304Q) AIP variant has been controversial. Recent data from public exome/genome databases show this variant is not infrequent. The objective of this work was to reassess the pathogenicity of R304Q based on clinical, genomic, and functional assay data.

DESIGN

Data were collected on published R304Q pituitary neuroendocrine tumour cases and from International Familial Isolated Pituitary Adenoma Consortium R304Q cases (n = 38, R304Q cohort). Clinical features, population cohort frequency, computational analyses, prediction models, presence of loss-of-heterozygosity, and in vitro/in vivo functional studies were assessed and compared with data from pathogenic/likely pathogenic AIP variant patients (AIPmut cohort, n = 184).

RESULTS

Of 38 R304Q patients, 61% (23/38) had growth hormone excess, in contrast to 80% of AIPmut cohort (147/184, P < .001). R304Q cohort was older at disease onset and diagnosis than the AIPmut cohort (median [quartiles] onset: 25 y [16-35] vs 16 y [14-23], P < .001; median [quartiles] diagnosis: 36 y [24-44] vs 21 y [15-29], P < .001). R304Q is present in gnomADv2.1 (0.31%) and UK Biobank (0.16%), including three persons with homozygous R304Q. No loss-of-heterozygosity was detected in four R304Q pituitary neuroendocrine tumour samples. In silico predictions and experimental data were conflicting.

CONCLUSIONS

Evidence suggests that R304Q is not pathogenic for pituitary neuroendocrine tumour. We recommend changing this variant classification to likely benign and do not recommend pre-symptomatic genetic testing of family members or follow-up of already identified unaffected individuals with the R304Q variant.

Update on the genetics of allergic diseases

The field of genetic etiology of allergic diseases has advanced significantly in recent years. Shared risk loci reflect the contribution of genetic factors to the sequential development of allergic conditions across the atopic march, while unique risk loci provide opportunities to understand tissue specific manifestations of allergic disease. Most identified risk variants are noncoding, indicating that they likely influence gene expression through gene regulatory mechanisms. Despite recent advances, challenges persist, particularly regarding the need for increased ancestral diversity in research populations. Further, while polygenic risk scores show promise for identifying individuals at higher genetic risk for allergic diseases, their predictive accuracy varies across different ancestries and can be difficult to translate to an individual's absolute risk of developing a disease. Methodologies, including "nearest gene," 3D chromatin interaction analysis, expression quantitative trait locus analysis, experimental screens, and integrative bioinformatic models, have established connections between genetic variants and their regulatory targets, enhancing our understanding of disease risk and phenotypic variability. In this review, we focus on the state of knowledge of allergic sensitization and 5 allergic diseases: asthma, atopic dermatitis, allergic rhinitis, food allergy, and eosinophilic esophagitis. We summarize recent progress and highlight opportunities for advancing our understanding of their genetic etiology.

Rare damaging CCR2 variants are associated with lower lifetime cardiovascular risk

BACKGROUND

Previous work has shown a role of CCL2, a key chemokine governing monocyte trafficking, in atherosclerosis. However, it remains unknown whether targeting CCR2, the cognate receptor of CCL2, provides protection against human atherosclerotic cardiovascular disease.

METHODS

Computationally predicted damaging or loss-of-function (REVEL > 0.5) variants within CCR2 were detected in whole-exome-sequencing data from 454,775 UK Biobank participants and tested for association with cardiovascular endpoints in gene-burden tests. Given the key role of CCR2 in monocyte mobilization, variants associated with lower monocyte count were prioritized for experimental validation. The response to CCL2 of human cells transfected with these variants was tested in migration and cAMP assays. Validated damaging variants were tested for association with cardiovascular endpoints, atherosclerosis burden, and vascular risk factors. Significant associations were replicated in six independent datasets (n = 1,062,595).

RESULTS

Carriers of 45 predicted damaging or loss-of-function CCR2 variants (n = 787 individuals) were at lower risk of myocardial infarction and coronary artery disease. One of these variants (M249K, n = 585, 0.15% of European ancestry individuals) was associated with lower monocyte count and with both decreased downstream signaling and chemoattraction in response to CCL2. While M249K showed no association with conventional vascular risk factors, it was consistently associated with a lower risk of myocardial infarction (odds ratio [OR]: 0.66, 95% confidence interval [CI]: 0.54-0.81, p = 6.1 × 10-5) and coronary artery disease (OR: 0.74, 95%CI: 0.63-0.87, p = 2.9 × 10-4) in the UK Biobank and in six replication cohorts. In a phenome-wide association study, there was no evidence of a higher risk of infections among M249K carriers.

CONCLUSIONS

Carriers of an experimentally confirmed damaging CCR2 variant are at a lower lifetime risk of myocardial infarction and coronary artery disease without carrying a higher risk of infections. Our findings provide genetic support for the translational potential of CCR2-targeting as an atheroprotective approach.

Reduced Penetrance is Common Among Predicted Loss-of-Function Variants and is Likely Driven by Residual Allelic Activity

Loss-of-function genetic variants (LoFs) often result in severe phenotypes, including autosomal dominant diseases driven by haploinsufficiency. Due to low carrier frequencies, their penetrance is generally unknown but typically variable. Here, we investigate the penetrance of >6,000 predicted LoFs (pLoFs) linked to 91 haploinsufficient diseases using a cohort of ≈24,000 carriers with linked electronic health record data. We find evidence for widespread reduced penetrance, which persisted after accounting for variant annotation artifacts, missed diagnoses, and incomplete clinical data. We thus hypothesized that many pLoFs have incomplete penetrance, which may be driven by residual allelic activity. To test this, we trained machine learning models to predict pLoF penetrance using variant-specific genomic features that may correlate with incomplete loss-of-function. The models were predictive of pLoF penetrance across a range of diseases and variant types, including those with prior clinical evidence for pathogenicity. This suggests that many pLoFs have incomplete penetrance due to residual allelic activity, complicating disease prognostication in asymptomatic carriers.

Functional variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene are associated with increased risk of colorectal cancer

BACKGROUND

Individuals with cystic fibrosis (CF; a recessive disorder) have an increased risk of colorectal cancer (CRC). Evidence suggests individuals with a single CFTR variant may also have increased CRC risk.

METHODS

Using population-based studies (GECCO, CORECT, CCFR, and ARIC; 53 785 CRC cases and 58 010 controls), we tested for an association between the most common CFTR variant (Phe508del) and CRC risk. For replication, we used whole exome sequencing data from UK Biobank (UKB; 5126 cases and 20 504 controls matched 4:1 based on genetic distance, age, and sex), and extended our analyses to all other heterozygous CFTR variants annotated as CF-causing.

RESULTS

In our meta-analysis of GECCO-CORECT-CCFR-ARIC, the odds ratio (OR) for CRC risk associated with Phe508del was 1.11 (P = 0.010). In our UKB replication, the OR for CRC risk associated with Phe508del was 1.28 (P = 0.002). The sequencing data from UKB also revealed an association between the presence of any other single CF-causing variant (excluding Phe508del) and CRC risk (OR = 1.33; P = 0.030). When stratifying CFTR variants by functional class, class I variants (no protein produced) had a stronger association (OR = 1.77; p = 0.002), while class II variants (misfolding and retention of the protein in the endoplasmic reticulum) other than Phe508del (OR = 1.75; p = 0.107) had similar effect size as Phe508del, and variants in classes III-VI had non-significant ORs less than 1.0 and/or were not present in cases.

CONCLUSIONS

CF-causing heterozygous variants, especially class I variants, are associated with a modest but statistically significant increased CRC risk. More research is needed to explain the biology underlying these associations.

Interactive and evolutionary effect of CASZ1 gene variants on varicose veins susceptibility in South Asian Indians

BACKGROUND

Varicose veins (VV) are spectrum of common vascular diseases having complex genetic etiology. The Castor Zinc Finger 1 (CASZ1) gene has been involved in vascular development and its variant has shown association with VV in various ethnicities, but CASZ1 susceptibility to VV risk is unexplored in the South Asian Indian population. The objective of this study was to estimate the association of the CASZ1 gene variations and VV susceptibility in the South Asian Indians, and to examine the evolutionary patterns of these variants compared to other populations.

METHODOLOGY

Population based case control analysis was conducted on all CASZ1 variants present in the Global Screening Array, including the established VV variant rs11121615 with a focus on validating and identification of both novel and established genetic markers to capture a full spectrum of population-specific genetic markers unique to studied population group. Linkage disequilibrium patterns and cumulative variant effects were also analyzed, followed by selection pressure assessment using neutrality tests.

RESULTS

Three CASZ1 variants rs72860191 (OR 1.58, 95% CI 1.07-2.32, p = 0.01), rs7519604 (OR 1.43, 95% CI 1.05-1.94, p = 0.01), and rs11121615 (OR 0.69, 95% CI 0.50-0.95, p = 0.02) were observed to be significantly associated with VV. Haplotype analysis identified unique haplotype structure of South Asian Indians compared to other global populations. Moreover, the cumulative OR was observed to be higher than the independently estimated values (OR = 2.41, 95% CI 1.48-3.94), indicating genotypic epistasis of VV associated variants. The neutrality tests revealed balancing selection within CASZ1 in the studied population compared to other populations, CONCLUSION: The present study identified CASZ1 variants and their epistatic interactions is associated with VV susceptibility supported with evidence of balancing selection, provides crucial insights into the genetic architecture of VV in studied group, highlighting the impact of evolutionary forces on disease susceptibility.

Hyperopia may exert a protective effect against senile cataracts: Evidence from a Mendelian randomization study

Myopia has been extensively documented as a significant risk factor for cataracts; however, the relationship between hyperopia and cataract development remains poorly understood. Given the distinct refractive profiles of myopia and hyperopia, hyperopia may confer a protective effect against cataracts. In this study, we employed Mendelian randomization (MR) to examine the causal association between hyperopia and cataracts. A 2-sample MR framework was utilized to examine the causal relationship between hyperopia and cataracts, with multivariable MR implemented to account for potential confounding variables. The inverse variance weighted (IVW) method served as the primary analytical tool, complemented by multiple sensitivity analyses to ensure the robustness and reliability of the findings. Enrichment analyses were conducted to elucidate the underlying biological pathways, while Bayesian colocalization analysis pinpointed shared genetic loci that influence both hyperopia and cataracts. In our study, we found that hyperopia may exert a protective effect against cataracts (IVW odds ratio, 0.920 [95% confidence interval, 0.872-0.972]; P = .0029) and cataract surgery (IVW odds ratio, 0.811 [95% confidence interval, 0.754-0.873]; P < .0001). Multivariable MR, adjusting for confounding factors such as smoking, glaucoma, and diabetes, confirmed hyperopia's protective association with cataracts. Bayesian colocalization identified rs12193446 as a high-probability shared causal variant, while enrichment analyses revealed potential biological mechanisms linking hyperopia to cataract development. Genetic evidence suggests that higher levels of hyperopia are associated with a reduced risk of age-related nuclear cataracts, cataract extraction, and lens implants. Given the opposite refractive states of myopia and hyperopia and their opposite effects on cataracts, these findings provide new insights into the pathogenesis of age-related cataracts.

Prevalence of deleterious cardiomyopathy variants in early-onset atrial fibrillation

Background

Atrial fibrillation (AF) is a common cardiac arrhythmia associated with an increased risk of stroke, heart failure, and death. Recent studies suggests that individuals with early onset of AF could be at increased risk of developing heart failure and dilated cardiomyopathy. This study aimed to identifying genetic variants in a broad panel of cardiomyopathy genes among early-onset AF individuals.

Methods

We conducted targeted genetic sequencing of 29 cardiomyopathy-associated genes in 478 individuals with AF onset below 45 years of age from a Danish cohort. Additionally, we analyzed whole exome sequencing data in 374,289 individuals from the UK Biobank, including 29,108 individuals with AF. The cohort was stratified by age at AF diagnosis, and individuals with pre-existing cardiomyopathy were excluded. We focused on rare, truncating variants predicted to lead to loss of function, and potentially deleterious missense variants in the UK Biobank.

Results

In the Danish cohort, 42 (8.8%) individuals with early-onset AF had truncating genetic variants in known cardiomyopathy genes. The UK Biobank analysis showed an inverse dose-response-like relationship between age of AF onset and prevalence of truncating variants, ranging from 3.8% in the AF onset <45 years group to 1.4% in the group without AF diagnosis. The prevalence of rare missense variants showed a similar pattern.

Conclusions

We identified a high prevalence of deleterious variants in cardiomyopathy-associated genes among individuals with early-onset AF. This supports recent guideline suggestions and indicates that genetic testing and surveillance for cardiomyopathy could be relevant in selected individuals with an early AF diagnosis.

Comprehensive causal analysis between autoimmune diseases and glioma: A Mendelian randomization study

The causal association between the autoimmune disease and the development of glioma and its subtypes remains unclear. We performed a comprehensive Mendelian randomization (MR) to clarify their causal association from genetic perspective. We obtained the summary-level datasets for autoimmune diseases from recently published genome-wide association studies in the UK Biobank (UKB) and the FinnGen consortium. Additionally, we collected summary statistics datasets related to glioma and its subtypes from a comprehensive meta-analysis genome-wide association study, which included 12,488 cases and 18,169 controls. We primarily used inverse variance weighting method, supplemented by Bonferroni correction to account for multiple tests to reduce the probability of false positive results. We also performed sensitivity analyses to address potential pleiotropy and strengthen the reliability of the results. After meta-analysis, pernicious anemia may decrease the risk of glioblastoma (GBM) (UKB: odds ratio (OR) = 0.01, 95% confidence interval (CI) = 0.01-0.02, P = 1.01E-12; FinnGen: OR = 0.86, 95% CI = 0.79-0.93, P = .0002; Meta: OR = 0.04, 95% CI = 0.03-0.04). In reverse MR analysis, GBM decreased the risk of celiac disease (UKB: OR = 0.96, 95% CI = 0.95-0.98, P = .0000; FinnGen: OR = 0.89, 95% CI = 0.84-0.94, P = .0001; Meta: OR = 0.95, 95% CI = 0.94-0.97). Heterogeneity and pleiotropy analyses, and reverse analysis, confirmed the robustness of these results. From the genetic perspective, our MR study uncovered that pernicious anemia may decrease the risk of GBM. Conversely, GBM appeared to mitigate the risk of celiac disease. Future studies are required to validate the causal association and illuminate the underlying mechanisms.

On ARGs, pedigrees, and genetic relatedness matrices

Genetic relatedness is a central concept in genetics, underpinning studies of population and quantitative genetics in human, animal, and plant settings. It is typically stored as a genetic relatedness matrix (GRM), whose elements are pairwise relatedness values between individuals. This relatedness has been defined in various contexts based on pedigree, genotype, phylogeny, coalescent times, and, recently, ancestral recombination graph (ARG). ARG-based GRMs have been found to better capture the structure of a population and improve association studies relative to the genotype GRM. However, calculating GRMs and further operations with them is fundamentally challenging due to inherent quadratic time and space complexity. Here, we first discuss the different definitions of relatedness in a unifying context, making use of the additive model of a quantitative trait to provide a definition of "branch relatedness" and the corresponding "branch GRM". We explore the relationship between branch relatedness and pedigree relatedness through a case study of French-Canadian individuals that have a known pedigree. Through the tree sequence encoding of an ARG, we then derive an efficient algorithm for computing products between the branch GRM and a general vector, without explicitly forming the branch GRM. This algorithm leverages the sparse encoding of genomes with the tree sequence and hence enables large-scale computations with the branch GRM. We demonstrate the power of this algorithm by developing a randomized principal components algorithm for tree sequences that easily scales to millions of genomes. All algorithms are implemented in the open source tskit Python package. Taken together, this work consolidates the different notions of relatedness as branch relatedness and by leveraging the tree sequence encoding of an ARG it provides efficient algorithms that enable computations with the branch GRM that scale to mega-scale genomic datasets.

Systematic Evaluation of the Impact of a Wide Range of Dietary Habits on Myocardial Infarction: A Two-Sample Mendelian Randomization Analysis

BACKGROUND

Myocardial infarction is a cardiovascular disease that significantly contributes to global morbidity and disability. Given the significant role of diet in the pathogenesis and prevention of cardiovascular diseases, this study rigorously investigates the causal relationship between dietary habits and myocardial infarction.

METHODS AND RESULTS

This study used large-scale genome-wide association studies with pooled UK Biobank data to explore associations between 9 dietary categories (83 types) and myocardial infarction. A 2-sample Mendelian randomization approach was applied to assess these associations, while multivariate Mendelian randomization and mediation analyses investigated the role of lipids in mediating the effects of diet on myocardial infarction. Univariate Mendelian analyses revealed genetic associations among 9 categories of dietary habits (83 types) and myocardial infarction. Notably, robust evidence indicates the "tablespoons of cooked vegetables per day" as the most significant risk factor for myocardial infarction development. "Coffee consumption(cups per day)" and "frequency of adding salt to food" were also identified as supplementary risk factors. In contrast, "overall alcohol intake" showed a protective effect, potentially by increasing high-density lipoprotein cholesterol (4.48% mediation) and reducing triglycerides (6.24% mediation). Cereal category, particularly "cereal consumption (bowls per week)" was associated with reduced myocardial infarction risk, contributing by raising high-density lipoprotein cholesterol (3.69% mediation) and lowering total cholesterol (8.33% mediation). Additionally, "overall cheese consumption" was also protective against myocardial infarction.

CONCLUSIONS

Our findings elucidate the influence of dietary habits on myocardial infarction, showing underlying genetic mechanisms and emphasizing the regulatory role of lipids as an intermediate.

Allele age estimators designed for whole genome datasets show only a moderate reduction in performance when applied to whole exome datasets

Personalized genomics in the healthcare system is becoming increasingly accessible as the costs of sequencing decreases. With the increase in the number of genomes, larger numbers of rare variants are being discovered, leading to important initiatives in identifying the functional impacts in relation to disease phenotypes. One way to characterize these variants is to estimate the time the mutation entered the population. However, allele age estimators such as those implemented in the programs Relate, Genealogical Estimator of Variant Age (GEVA), and Runtc, were developed based on the assumption that datasets include the entire genome. We examined the performance of each of these estimators on simulated exome data under a neutral constant population size model, as well as under population expansion and background selection models. We found that each provides usable estimates of allele age from whole-exome datasets. Relate performs the best amongst all three estimators with Pearson coefficients of 0.83 and 0.73 (with respect to true simulated values, for neutral constant and expansion population model, respectively) with a 12 percent and 20 percent decrease in correlation between whole genome and whole exome estimations. Of the three estimators, Relate is best able to parallelize to yield quick results with little resources, however, Relate is currently only able to scale to thousands of samples making it unable to match the hundreds of thousands of samples being currently released. While more work is needed to expand the capabilities of current methods of estimating allele age, these methods show a modest decrease in performance in the estimation of the age of mutations.

Human CD33 deficiency is associated with mild alteration of circulating white blood cell counts

The single pass transmembrane protein CD33 is enriched in phagocytic and hematopoietic cell types, such as monocytes. CD33 is thought to be associated with immune cell function, susceptibility to Alzheimer's disease, and rare leukemias. Antagonism or genetic ablation of CD33 has been proposed to treat Alzheimer's disease, hematological cancers, and as a selection mechanism for enriching genetically altered blood cells. To understand the impact of chronic CD33 loss or ablation, we describe individuals who we confirmed to be missing CD33 due to germline loss of function variants. Through PheWAS-based approaches using existing whole exome biobanks and bespoke phenotyping using recall-by-genotype (RBG) studies, we show that CD33 loss of function alters circulating white blood cell counts and distributions, albeit mildly and with no overt clinical pathology. These findings indicate that chronic CD33 antagonism/ablation is likely to be safe in humans.

Rare variant association studies: Significance, methods, and applications in chronic pain studies

Rare genetic variants, characterized by their low frequency in a population, have emerged as essential components in the study of complex disease genetics. The biology of rare variants underscores their significance, as they can exert profound effects on phenotypic variation and disease susceptibility. Recent advancements in sequencing technologies have yielded the availability of large-scale sequencing data such as the UK Biobank whole-exome sequencing (WES) cohort empowered researchers to conduct rare variant association studies (RVASs). This review paper discusses the significance of rare variants, available methodologies, and applications. We provide an overview of RVASs, emphasizing their relevance in unraveling the genetic architecture of complex diseases with special focus on chronic pain and Arthritis. Additionally, we discuss the strengths and limitations of various rare variant association testing methods, outlining a typical pipeline for conducting rare variant association. This pipeline encompasses crucial steps such as quality control of WES data, rare variant annotation, and association testing. It serves as a comprehensive guide for researchers in the field of chronic pain diseases interested in rare variant association studies in large-scale sequencing datasets like the UK Biobank WES cohort. Lastly, we discuss how the identified variants can be further investigated through detailed experimental studies in animal models to elucidate their functional impact and underlying mechanisms.

Genome-wide association testing beyond SNPs

Decades of genetic association testing in human cohorts have provided important insights into the genetic architecture and biological underpinnings of complex traits and diseases. However, for certain traits, genome-wide association studies (GWAS) for common SNPs are approaching signal saturation, which underscores the need to explore other types of genetic variation to understand the genetic basis of traits and diseases. Copy number variation (CNV) is an important source of heritability that is well known to functionally affect human traits. Recent technological and computational advances enable the large-scale, genome-wide evaluation of CNVs, with implications for downstream applications such as polygenic risk scoring and drug target identification. Here, we review the current state of CNV-GWAS, discuss current limitations in resource infrastructure that need to be overcome to enable the wider uptake of CNV-GWAS results, highlight emerging opportunities and suggest guidelines and standards for future GWAS for genetic variation beyond SNPs at scale.

Genetic and epigenetic factors shape phenotypes and outcomes in systemic lupus erythematosus - focus on juvenile-onset systemic lupus erythematosus

PURPOSE OF REVIEW

Systemic lupus erythematosus (SLE) is a severe autoimmune/inflammatory disease. Patients with juvenile disease-onset and those of non-European ancestry are most severely affected. While the exact pathophysiology remains unknown, common and rare gene variants in the context of environmental exposure and epigenetic alterations are involved. This manuscript summarizes the current understanding of genetic and epigenetic contributors to SLE risk, manifestations and outcomes.

RECENT FINDINGS

Though SLE is a mechanistically complex disease, we are beginning to understand the impact of rare and common gene variants on disease expression and associated outcomes. Recent trans -ancestral and multigenerational studies suggest that differential genetic and environmental impacts shape phenotypic variability between age-groups and ancestries. High genetic burden associates with young age at disease-onset, organ involvement, and severity. Additional epigenetic impact contributes to disease-onset and severity, including SLE-phenotypes caused by rare single gene variants. Studies aiming to identify predictors of organ involvement and disease outcomes promise future patient stratification towards individualized treatment and care.

SUMMARY

An improved understanding of genetic variation and epigenetic marks explain phenotypic differences between age-groups and ancestries, promising their future exploitation for diagnostic, prognostic and therapeutic considerations.

Exome sequencing identifies novel genes associated with cerebellar volume and microstructure

Proteins encoded by exons are critical for cellular functions, and mutations in these genes often result in significant phenotypic effects. The cerebellum is linked to various heritable human disease phenotypes, yet genome-wide association studies have struggled to capture the effects of rare variants on cerebellar traits. This study conducts a large-scale exome association analysis using data from approximately 35,000 UK Biobank participants, examining seven cerebellar traits, including total cerebellar volume and white matter microstructure. We identify 90 genes associated with cerebellar traits, 60 of which were previously unreported in genome-wide association studies. Notable findings include the discovery of genes like PRKRA and TTK, as well as RASGRP3, linked to cerebellar volume and white matter microstructure. Gene enrichment analysis reveals associations with non-coding RNA processing, cognitive function, neurodegenerative diseases, and mental disorders, suggesting shared biological mechanisms between cerebellar phenotypes and neuropsychiatric diseases.