Large-scale whole-genome sequencing of the Icelandic population. Nat Genet. 2015;47:435-444. [PMID: 25807286 DOI: 10.1038/ng.3247]

Bi-allelic variants in POPDC2 cause an autosomal recessive syndrome presenting with cardiac conduction defects and hypertrophic cardiomyopathy

POPDC2 encodes the Popeye domain-containing protein 2, which has an important role in cardiac pacemaking and conduction, due in part to its cyclic AMP (cAMP)-dependent binding and regulation of TREK-1 potassium channels. Loss of Popdc2 in mice results in sinus pauses and bradycardia, and morpholino-mediated knockdown of popdc2 in zebrafish results in atrioventricular (AV) block. We identified bi-allelic variants in POPDC2 in four families with a phenotypic spectrum consisting of sinus node dysfunction, AV conduction defects, and hypertrophic cardiomyopathy. Using homology modeling, we show that the identified variants are predicted to diminish the ability of POPDC2 to bind cAMP. In in vitro electrophysiological studies, we demonstrated that, in contrast with wild-type POPDC2, variants found in affected individuals failed to increase TREK-1 current density. While muscle biopsy of an affected individual did not show clear myopathic disease, it showed significantly reduced abundance of both POPDC1 and POPDC2, suggesting that stability and/or membrane trafficking of the POPDC1-POPDC2 complex is impaired by pathogenic variants in either protein. Single-cell RNA sequencing from human hearts demonstrated that co-expression of POPDC1 and POPDC2 was most prevalent in AV node, AV node pacemaker, and AV bundle cells. Using population-level genetic data of more than 1 million individuals, we show that none of the familial variants were associated with clinical outcomes in heterozygous state, suggesting that heterozygous family members are unlikely to develop clinical manifestations and therefore might not necessitate clinical follow-up. Our findings provide evidence for bi-allelic variants in POPDC2 causing a Mendelian autosomal recessive cardiac syndrome.

Associations of APOE variants with sphingomyelin and cholesterol metabolites across the life-course in diverse populations

INTRODUCTION

Two alleles (ε2 and ε4) in the APOE gene are known to be strongly associated with lipid metabolism disorders, such as dyslipidemia, which are important risk factors for the development of cardiovascular diseases. While prior research has largely centered on adult populations, establishing APOE-lipid associations in infants, children, and adolescents-especially those from historically understudied groups-could inform earlier interventions and treatments.

OBJECTIVES

This study aimed to evaluate the dependence of the metabolome on the APOE variants using five diverse cohorts that span infancy through adulthood, comprising a total of over 190,000 individuals.

METHODS

We extracted the APOE variants (rs7412 and rs429358) from all cohorts-testing both the ε2 allele (rs7412-T and rs429358-T) and the ε4 allele (rs7412-C and rs429358-C)-and evaluated their associations with the global plasma metabolome which was measured by mass spectrometry-based (Metabolon or Broad Institute) or NMR-based (Nightingale) assays depending on the cohort, using a Bonferroni-corrected significance threshold.

RESULTS

Among 589 metabolites tested in our discovery population, only six including sphingomyelins and cholesterol were significantly associated with the rs7412/ε2 allele. Sphingomyelin (d18:1/22:0) and cholesterol were negatively associated with ε2 allele (β-value = -0.54 [-0.76, -0.32] p-value = 1.39 × 10-6 and - 0.55 [-0.77, -0.33]; p-value = 1.49 × 10-6, respectively). These relationships were replicated in the four additional cohorts without heterogeneity.

CONCLUSION

Our findings support the need for early intervention in lipid levels regardless of age, sex, and ethnicity and further investigations of the APOE variants on risk of various diseases in later life.

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.

Egypt Genome: Towards an African new genomic era

BACKGROUND

Studying the human genome is crucial to embrace precision medicine through tailoring treatment and prevention strategies to the unique genetic makeup and molecular information of individuals. After human genome project (1990-2003) generated the first full sequence of a human genome, there have been concerns towards Northern bias due to underrepresentation of other populations. Multiple countries have now established national genome projects aiming at the genomic knowledge that can be harnessed from their populations, which in turn can serve as a basis for their health care policies in the near future.

AIM OF REVIEW

The intention is to introduce the recently established Egypt Genome (EG) to delineate the genomics and genetics of both the modern and Ancient Egyptian populations. Leveraging genomic medicine to improve precision medicine strategies while building a solid foundation for large-scale genomic research capacity is the fundamental focus of EG.

KEY SCIENTIFIC CONCEPTS

EG generated genomic knowledge is predicted to enrich the existing human genome and to expand its diversity by studying the underrepresented African/Middle Eastern populations. The insightful impact of EG goes beyond Egypt and Africa as it fills the knowledge gaps in health and disease genomics towards improved and sustainable genomic-driven healthcare systems for better outcomes. Promoting the integration of genomics into clinical practice and spearheading the implementation of genomic-driven healthcare and precision medicine is therefore a key focus of EG. Mining into the wealth of Ancient Egyptian Genomics to delineate the genetic bridge between the contemporary and Ancient Egyptian populations is another excitingly unique area of EG to realize the global vision of human genome.

Bi-allelic variants in BRF2 are associated with perinatal death and craniofacial anomalies

BACKGROUND

Variants in genes encoding multiple subunits of the RNA Polymerase III complex which synthesizes rRNAs, tRNAs, and other small RNAs were previously associated with neurological disorders, such as syndromic hypomyelination leukodystrophies, pontocerebellar hypoplasia, and cerebellofaciodental syndrome. One new such candidate is BRF2, which encodes a TFIIB-like factor that recruits the RNA polymerase III complex to type 3 promoters to initiate transcription of U6, RnaseP, and 7SK RNAs.

METHODS

We combined sequencing with functional analyses to investigate the effects of BRF2 variants.

RESULTS

We observe that a previously reported significant underrepresentation of double transmission of a splice variant results in recessive lethality in three large Icelandic families with multiple perinatal losses. Using data aggregation, we identified an additional seven individuals worldwide from three unrelated families carrying biallelic variants in BRF2. Affected individuals present a variable phenotype ranging from severe craniofacial anomalies with early death to intellectual disability with motor and speech development. In silico 3D modelling and functional analyses showed functional impairment of the identified variants, e.g., differences in target loci occupancy. Zebrafish knocked down for the orthologous brf2 presented with abnormal escape response, reduced swimming velocity and head size, and craniofacial malformations. These defects were complemented by the human wild-type but not mutated BRF2 mRNA further demonstrating their deleteriousness.

CONCLUSIONS

Overall, our results support the association of biallelic BRF2 variants with a novel neurodevelopmental disease and provide an additional link between RNA polymerase III, its targets and craniofacial anomalies.

Translational genomics of osteoarthritis in 1,962,069 individuals

Osteoarthritis is the third most rapidly growing health condition associated with disability, after dementia and diabetes1. By 2050, the total number of patients with osteoarthritis is estimated to reach 1 billion worldwide2. As no disease-modifying treatments exist for osteoarthritis, a better understanding of disease aetiopathology is urgently needed. Here we perform a genome-wide association study meta-analyses across up to 489,975 cases and 1,472,094 controls, establishing 962 independent associations, 513 of which have not been previously reported. Using single-cell multiomics data, we identify signal enrichment in embryonic skeletal development pathways. We integrate orthogonal lines of evidence, including transcriptome, proteome and epigenome profiles of primary joint tissues, and implicate 700 effector genes. Within these, we find rare coding-variant burden associations with effect sizes that are consistently higher than common frequency variant associations. We highlight eight biological processes in which we find convergent involvement of multiple effector genes, including the circadian clock, glial-cell-related processes and pathways with an established role in osteoarthritis (TGFβ, FGF, WNT, BMP and retinoic acid signalling, and extracellular matrix organization). We find that 10% of the effector genes express a protein that is the target of approved drugs, offering repurposing opportunities, which can accelerate translation.

Genome-Wide Association Study Meta-Analysis of 9619 Cases With Tic Disorders

BACKGROUND

Despite the significant personal and societal burden of tic disorders (TDs), treatment outcomes remain modest, necessitating a deeper understanding of their etiology. Family history is the biggest known risk factor, and identifying risk genes could accelerate progress in the field.

METHODS

Expanding upon previous sample size limitations, we added 4800 new TD cases and 971,560 controls and conducted a genome-wide association study (GWAS) meta-analysis with 9619 cases and 981,048 controls of European ancestry. We attempted to replicate the results in an independent deCODE genetics GWAS (885 TD cases and 310,367 controls). To characterize GWAS findings, we conducted several post-GWAS gene-based and enrichment analyses.

RESULTS

A genome-wide significant hit (rs79244681, p = 2.27 × 10-8) within MCHR2-AS1 was identified, although it was not replicated. Post-GWAS analyses revealed a 13.8% single nucleotide polymorphism heritability and 3 significant genes: BCL11B, NDFIP2, and RBM26. Common variant risk for TD was enriched within genes preferentially expressed in the cortico-striato-thalamo-cortical circuit (including the putamen, caudate, nucleus accumbens, and Brodmann area 9) and 5 brain cell types (excitatory and inhibitory telencephalon neurons, inhibitory diencephalon and mesencephalon neurons, and hindbrain and medium spiny neurons). TD polygenic risk was enriched within loss-of-function intolerant genes (p = .0017) and high-confidence neurodevelopmental disorder genes (p = .0108). Of 112 genetic correlations, 43 were statistically significant, showing high positive correlations with most psychiatric disorders. Of the 2 single nucleotide polymorphisms previously associated with TDs, one (rs2453763) replicated in an independent subsample of our GWAS (p = .00018).

CONCLUSIONS

This GWAS was still underpowered to identify high-confidence, replicable loci, but the results suggest imminent discovery of common genetic variants for TDs.

A genome-wide association meta-analysis links hidradenitis suppurativa to common and rare sequence variants causing disruption of the Notch and Wnt/β-catenin signaling pathways

BACKGROUND

The contributions of genetic and environmental risk factors to hidradenitis suppurativa (HS) are both poorly understood.

OBJECTIVE

To identify sequence variants that associate with HS and determine the contribution of environmental risk factors and inflammatory diseases to HS pathogenesis.

METHODS

A genome-wide association meta-analysis of 4814 HS cases (Denmark: 1977; Iceland: 1266; Finland: 800; UK: 569; and US: 202) and 1.2 million controls, searching for sequence variants associated with HS.

RESULTS

We found 8 independent sequence variants associating with HS, 6 common and 2 rare (frequency <1%). Four associations point to candidate causal genes, NCSTN, PSENEN, WNT10A, and TMED10, that all map to the Notch and Wnt/β-catenin signaling pathways, involved in epidermal keratinization.

LIMITATIONS

Limited racial diversity may prevent identification of sequence variants of particular importance in non-Caucasian populations.

CONCLUSIONS

These findings demonstrate that genes and pathways involved in epidermal keratinization are the genetic backbone of HS pathology.

Rare loss-of-function variants in HECTD2 and AKAP11 confer risk of bipolar disorder

Bipolar disorder is a highly heritable psychiatric disorder; genome-wide association studies of bipolar disorder have yielded over 60 risk loci harboring common variants. To harness the information contained in rare loss-of-function (LOF) variants, holding promise for informing on the underlying biology, we performed a variant burden analysis for bipolar disorder using gene-based aggregation of LOF variants in whole-genome sequencing data from Iceland (4,197 cases, more than 200,000 controls) and the UK Biobank (1,881 cases, 426,622 controls). We found that HECTD2 was associated with bipolar disorder and confirmed it using the Bipolar Exome dataset. Meta-analysis with Bipolar Exome also revealed that LOF variants in AKAP11 were associated with bipolar disorder. Both associations with bipolar disorder are new, but AKAP11 has previously been associated with psychosis and schizophrenia. The products of AKAP11 and HECTD2 interact with GSK3β, a protein inhibited by lithium, the most effective mood stabilizer available to treat bipolar disorder.

Cell-free DNA from clinical testing as a resource of population genetic analysis

As a noninvasive biomarker, cell-free DNA (cfDNA) has achieved remarkable success in clinical applications. Notably, cfDNA is essentially DNA, and conducting whole-genome sequencing (WGS) can yield a wealth of genetic information. These invaluable data should not be confined to one-time use; instead, they should be leveraged for more comprehensive population genetic analysis, including genetic variation spectrum, population structure and genetic selection, and genome-wide association studies (GWASs), among others. Such research findings can, in turn, facilitate clinical practice, enabling more advanced and accurate disease predictions. This review explores the advantages, challenges, and current research areas of cfDNA in population genetics. We hope that this review can serve as a new chapter in the repurposing of cfDNA sequence data generated from clinical testing in population genetics.

Missense variants in FRS3 affect body mass index in populations of diverse ancestries

Obesity is associated with adverse effects on health and quality of life. Improved understanding of its underlying pathophysiology is essential for developing counteractive measures. To search for sequence variants with large effects on BMI, we perform a multi-ancestry meta-analysis of 13 genome-wide association studies on BMI, including data derived from 1,534,555 individuals of European ancestry, 339,657 of Asian ancestry, and 130,968 of African ancestry. We identify an intergenic 262,760 base pair deletion at the MC4R locus that associates with 4.11 kg/m2 higher BMI per allele, likely through downregulation of MC4R. Moreover, a rare FRS3 missense variant, p.Glu115Lys, only found in individuals from Finland, associates with 1.09 kg/m2 lower BMI per allele. We also detect three other low-frequency FRS3 missense variants that associate with BMI with smaller effects and are enriched in different ancestries. We characterize FRS3 as a BMI-associated gene, encoding an adaptor protein known to act downstream of BDNF and TrkB, which regulate appetite, food intake, and energy expenditure through unknown signaling pathways. The work presented here contributes to the biological foundation of obesity by providing a convincing downstream component of the BDNF-TrkB pathway, which could potentially be targeted for obesity treatment.

Equitable machine learning counteracts ancestral bias in precision medicine

Gold standard genomic datasets severely under-represent non-European populations, leading to inequities and a limited understanding of human disease. Therapeutics and outcomes remain hidden because we lack insights that could be gained from analyzing ancestrally diverse genomic data. To address this significant gap, we present PhyloFrame, a machine learning method for equitable genomic precision medicine. PhyloFrame corrects for ancestral bias by integrating functional interaction networks and population genomics data with transcriptomic training data. Application of PhyloFrame to breast, thyroid, and uterine cancers shows marked improvements in predictive power across all ancestries, less model overfitting, and a higher likelihood of identifying known cancer-related genes. Validation in fourteen ancestrally diverse datasets demonstrates that PhyloFrame is better able to adjust for ancestry bias across all populations. The ability to provide accurate predictions for underrepresented groups, in particular, is substantially increased. Analysis of performance in the most diverse continental ancestry group, African, illustrates how phylogenetic distance from training data negatively impacts model performance, as well as PhyloFrame's capacity to mitigate these effects. These results demonstrate how equitable artificial intelligence (AI) approaches can mitigate ancestral bias in training data and contribute to equitable representation in medical research.

Expanding the spectrum of progressive familial intrahepatic cholestasis: A report of 3 cases

OBJECTIVES

Progressive familial intrahepatic cholestasis (PFIC) is a group of autosomal recessive disorders caused by defects in bile secretion or transport usually presenting as cholestasis in pediatric age. Herewith, we describe 3 PFIC cases with diagnostic challenges and highlight the role of genetic analysis.

METHODS

The clinical history, laboratory data, liver biopsy, and molecular analysis for each case were reviewed.

RESULTS

Case 1, a Hispanic male from Puerto Rico with hepatomegaly since age 2 months, was eventually diagnosed with PFIC3 following identification of a homozygous splice site variant in ATP binding cassette subfamily B member 4 (ABCB4) (c.2784-12T>C) at age 17 years by whole-exome sequencing (WES). Case 2 was a 37-year-old man with a history of alcoholism, abnormal liver function tests, and ductopenia on biopsy. Molecular testing revealed a pathogenic heterozygous ABCB4 mutation (c.1633C>T) variant leading to a diagnosis of PFIC3. Case 3 was a 2-year-old female initially presenting as a drug-induced liver injury but was diagnosed with PFIC10 following identification of a heterozygous frameshift mutation (p.Asp300Trpfs*19) and a heterozygous missense mutation (c.1357T>C) in myosin VB (MYO5B) by WES.

CONCLUSIONS

These PFIC cases highlight the heterogenous presentation and diagnostic challenges, and they emphasize the role of next-generation sequencing, particularly the utility of WES.

LGR4 (GPR48): The Emerging Inter-Bridge in Osteoimmunology

Leucine-rich repeat-containing G-protein-coupled receptor 4 (LGR4), a member of the G-protein-coupled receptor (GPCR) family, has been implicated in various regulatory functions across multiple differentiation stages and numerous target sites in bone diseases. Therefore, LGR4 is a potential regulator of nuclear factor-κB ligand (RANKL) during osteoclast differentiation. However, a comprehensive investigation of its functions and applications in bone immunology is lacking. This review discusses the molecular characteristics, signaling pathways, and role of LGR4 in osteoimmunology, with a particular focus on its interactions with RANKL during osteoclast differentiation, while identifying gaps that warrant further research.

Whole aorta imaging shows increased risk for thoracic aortic aneurysms and dilatations in relatives of abdominal aortic aneurysm patients

OBJECTIVE

For relatives of abdominal aortic aneurysm (AAA) patients, guidelines recommend abdominal imaging aimed at early detection and management of AAA, and do not include screening for thoracic aortic aneurysms (TAA). We aimed to investigate if TAA occur in undiagnosed relatives of patients with AAA without a known genetic susceptibility for aneurysms, similar to families with identified genetic susceptibilities for aneurysms like in Marfan and Loeys-Dietz syndrome, where both AAAs and TAAs occur.

METHODS

Relatives of patients with AAA were invited for noncontrast whole aorta computed tomography (CT) screening. Systematic measurements of the CT scans were used to detect aneurysms and dilatations. Classification into familial and nonfamilial was based on reported family histories. In addition, aneurysm gene panel testing of AAA index cases was used for the classification of high vs unknown genetic risk (high genetic risk: familial aneurysm or a pathogenic/likely pathogenic (P/LP) in an aneurysm gene; unknown genetic risk: no family history or P/LP).

RESULTS

Whole aorta imaging of 301 relatives of 115 index patients with AAA with noncontrast CT scans showed a 28-fold increase in TAAs in relatives (1.7% [P < .001] vs the age-adjusted population) and a high frequency of thoracic dilatations in 18% of the relatives. Thoracic aneurysms and dilatations in relatives occurred even when index patients were unaware of familial aneurysms. AAA was increased in the relatives compared with the age-adjusted population (8%; P < .001).

CONCLUSIONS

An increased risk for thoracic aneurysms and dilatations was detected by whole aorta imaging of relatives of index patients with AAA, even when index patients were unaware of familial aneurysms. These results indicate still unknown shared genetic susceptibilities for thoracic and abdominal aneurysms. Therefore, imaging of the whole aorta of relatives of all abdominal aneurysm patients, will improve early detection of aortic aneurysms in relatives of all patients with AAA.

Genetic architecture in Greenland is shaped by demography, structure and selection

Greenlandic Inuit and other indigenous populations are underrepresented in genetic research1,2, leading to inequity in healthcare opportunities. To address this, we performed analyses of sequenced or imputed genomes of 5,996 Greenlanders with extensive phenotypes. We quantified their historical population bottleneck and how it has shaped their genetic architecture to have fewer, but more common, variable sites. Consequently, we find twice as many high-impact genome-wide associations to metabolic traits in Greenland compared with Europe. We infer that the high-impact variants arose after the population split from Native Americans and thus are Arctic-specific, and show that some of them are common due to not only genetic drift but also selection. We also find that European-derived polygenic scores for metabolic traits are only half as accurate in Greenlanders as in Europeans, and that adding Arctic-specific variants improves the overall accuracy to the same level as in Europeans. Similarly, lack of representation in public genetic databases makes genetic clinical screening harder in Greenlandic Inuit, but inclusion of Greenlandic data remedies this by reducing the number of non-causal candidate variants by sixfold. Finally, we identify pronounced genetic fine structure that explains differences in prevalence of monogenic diseases in Greenland and, together with recent changes in mobility, leads to a predicted future reduction in risk for certain recessive diseases. These results illustrate how including data from Greenlanders can greatly reduce inequity in genomic-based healthcare.

Sequencing in over 50,000 cases identifies coding and structural variation underlying atrial fibrillation risk

Atrial fibrillation (AF) is a prevalent and morbid abnormality of the heart rhythm with a strong genetic component. Here, we meta-analyzed genome and exome sequencing data from 36 studies that included 52,416 AF cases and 277,762 controls. In burden tests of rare coding variation, we identified novel associations between AF and the genes MYBPC3, LMNA, PKP2, FAM189A2 and KDM5B. We further identified associations between AF and rare structural variants owing to deletions in CTNNA3 and duplications of GATA4. We broadly replicated our findings in independent samples from MyCode, deCODE and UK Biobank. Finally, we found that CRISPR knockout of KDM5B in stem-cell-derived atrial cardiomyocytes led to a shortening of the action potential duration and widespread transcriptomic dysregulation of genes relevant to atrial homeostasis and conduction. Our results highlight the contribution of rare coding and structural variants to AF, including genetic links between AF and cardiomyopathies, and expand our understanding of the rare variant architecture for this common arrhythmia.

Current approach to diagnosis and management of low-phospholipid associated cholelithiasis syndrome

PURPOSE OF REVIEW

Low phospholipid-associated cholelithiasis (LPAC) syndrome is a rare genetic form of intrahepatic cholesterol lithiasis, affecting mainly young adults. This review describes the recent advances in genetic and clinical characterization, diagnosis and management of LPAC syndrome.

RECENT FINDINGS

Recent publications report data from several retrospective cohorts. These cohorts describe the main clinical features, the most frequent radiological lesions, complications, the results of biliary endoscopic procedures and the prognosis associated with LPAC syndrome.

SUMMARY

LPAC syndrome has been linked to a partial defect in the ATP binding cassette subfamily B member 4 ( ABCB4 ) gene encoding the canalicular phospholipid transporter multidrug resistance protein 3, but this mechanism would explain only half the cases, or even fewer. This syndrome is characterized by the appearance of cholelithiasis at an abnormally early age (before 40) and by the persistence of biliary symptoms after cholecystectomy. The diagnosis is usually confirmed by an ultrasound scan of the liver, which reveals the presence of intrahepatic microlithiasis, as evidenced by comet-tail images or microspots along the intrahepatic bile ducts. Ursodeoxycholic acid, at a daily dose of 5-15 mg/kg, is the reference treatment. If not performed prior to diagnosis, cholecystectomy should be avoided wherever possible. In complicated or refractory forms, endoscopic biliary intervention may be necessary.

2025 Heart Disease and Stroke Statistics: A Report of US and Global Data From the American Heart Association

BACKGROUND

The American Heart Association (AHA), in conjunction with the National Institutes of Health, annually reports the most up-to-date statistics related to heart disease, stroke, and cardiovascular risk factors, including core health behaviors (smoking, physical activity, nutrition, sleep, and obesity) and health factors (cholesterol, blood pressure, glucose control, and metabolic syndrome) that contribute to cardiovascular health. The AHA Heart Disease and Stroke Statistical Update presents the latest data on a range of major clinical heart and circulatory disease conditions (including stroke, brain health, complications of pregnancy, kidney disease, congenital heart disease, rhythm disorders, sudden cardiac arrest, subclinical atherosclerosis, coronary heart disease, cardiomyopathy, heart failure, valvular disease, venous thromboembolism, and peripheral artery disease) and the associated outcomes (including quality of care, procedures, and economic costs).

METHODS

The AHA, through its Epidemiology and Prevention Statistics Committee, continuously monitors and evaluates sources of data on heart disease and stroke in the United States and globally to provide the most current information available in the annual Statistical Update with review of published literature through the year before writing. The 2025 AHA Statistical Update is the product of a full year's worth of effort in 2024 by dedicated volunteer clinicians and scientists, committed government professionals, and AHA staff members. This year's edition includes a continued focus on health equity across several key domains and enhanced global data that reflect improved methods and incorporation of ≈3000 new data sources since last year's Statistical Update.

RESULTS

Each of the chapters in the Statistical Update focuses on a different topic related to heart disease and stroke statistics.

CONCLUSIONS

The Statistical Update represents a critical resource for the lay public, policymakers, media professionals, clinicians, health care administrators, researchers, health advocates, and others seeking the best available data on these factors and conditions.

Genotypes and different clinical variants between children and adults in progressive familial intrahepatic cholestasis: a state-of-the-art review

INTRODUCTION

Progressive Familial intrahepatic cholestasis (PFIC) are rare disorders of bile acid (BAs) secretion and transport with a genetic background. PFIC are paediatric manifestations, but the same variants causing PFIC can also cause cholestasis with a later paediatric onset or adult-onset cholestatic disease (AOCD). Pruritus is a symptom of cholestasis that can be so devastating that it requires a liver transplant (LT) in children; some PFIC types have been described as at risk of liver cancer development. Commonly prescribed medications for PFIC symptoms can partially relieve pruritus without changing the natural history of the disease. Recently, a therapy reducing the intestinal resorption of BAs has been approved; it is effective on both pruritus and cholestasis in PFIC, potentially being a disease-modifying intervention.

AREAS COVERED

The clinical and genetic characteristics of different PFIC and AOCD are summarized to provide a common background for geneticists and paediatric and adult hepatologists in diagnosis and management.

EXPERT OPINION

Collaboration between paediatric and adult hepatologists and geneticists will become crucial for cholestatic disease research and patient treatment. Therefore, adult hepatologists will need to learn more about FIC. This might enable the implementation of individualized surveillance in FIC patients and the evaluation of patient family histories.

Lynch syndrome screening in colorectal and endometrial cancers in Iceland

BACKGROUND AND PURPOSE

Screening for Lynch syndrome (LS) with mismatch repair (MMR) protein immunohistochemistry (IHC) in all patients with newly diagnosed colorectal (CRC) and endometrial cancer (EC) was implemented in Iceland in 2017. The aim of the study is to assess the accuracy of screening in 2020-2022 and compare it to 2017-2019 when screening was initiated.

PATIENTS/MATERIALS AND METHODS

All patients diagnosed with CRC and EC according to the Icelandic Cancer Registry in 2020-2022 were included. Screening results were crossmatched with a genotyping database from deCODE to calculate sensitivity and specificity for LS detection.   Results: In 2020-2022, 429 of 522 (82%) diagnosed CRCs were stained and 90 of 106 (85%) ECs, compared to 74% of CRCs and 82% of ECs in 2017-2019. The screening protocol was followed in 90% of cases for CRCs and 95% of cases for ECs compared to 89% and 68% during 2017-2019. The sensitivity of IHC as a screening method for LS was 70% and specificity 88% with a positive and negative predictive value of 8.4% and 99.4%, respectively.

INTERPRETATION

Three LS cases were missed with MMR IHC (1 MSH6 and 2 PMS2 carriers), it is possible these patients had sporadic cancers unrelated to their LS carrier status. MSH6 and PMS2 deficiency strongly predicts LS in Iceland.

Exploring the role of circulating proteins in multiple myeloma risk: a Mendelian randomization study

Multiple myeloma (MM) is an incurable blood cancer with unclear aetiology. Proteomics is a valuable tool in exploring mechanisms of disease. We investigated the causal relationship between circulating proteins and MM risk, using two of the largest cohorts with proteomics data to-date. We performed bidirectional two-sample Mendelian randomization (MR; forward MR = causal effect estimation of proteins and MM risk; reverse MR = causal effect estimation of MM risk and proteins). Summary statistics for plasma proteins were obtained from genome-wide association studies performed using SomaLogic (N = 35,559; deCODE) and Olink (N = 34,557; UK Biobank; UKB) proteomic platforms and for MM risk from a meta-analysis of UKB and FinnGen (case = 1649; control = 727,247) or FinnGen only (case = 1085; control = 271,463). Cis-SNPs associated with protein levels were used to instrument circulating proteins. We evaluated proteins for the consistency of directions of effect across MR analyses (with 95% confidence intervals not overlapping the null) and corroborating evidence from genetic colocalization. In the forward MR, 994 (SomaLogic) and 1570 (Olink) proteins were instrumentable. 440 proteins were analysed in both deCODE and UKB; 302 (69%) of these showed consistent directions of effect in the forward MR. Seven proteins had 95% confidence intervals (CIs) that did not overlap the null in both forward MR analyses and did not have evidence for an effect in the reverse direction: higher levels of dermatopontin (DPT), beta-crystallin B1 (CRYBB1), interleukin-18-binding protein (IL18BP) and vascular endothelial growth factor receptor 2 (KDR) and lower levels of odorant-binding protein 2b (OBP2B), glutamate-cysteine ligase regulatory subunit (GCLM) and gamma-crystallin D (CRYGD) were implicated in increasing MM risk. Evidence from genetic colocalization did not meet our threshold for a shared causal signal between any of these proteins and MM risk (h4 < 0.8). Our results highlight seven circulating proteins which may be involved in MM risk. Although evidence from genetic colocalization suggests these associations may not be robust to the effects of horizontal pleiotropy, these proteins may be useful markers of MM risk. Future work should explore the utility of these proteins in disease prediction or prevention using proteomic data from patients with MM or precursor conditions.

Rare variant associations with birth weight identify genes involved in adipose tissue regulation, placental function and insulin-like growth factor signalling

Investigating the genetic factors influencing human birth weight may lead to biological insights into fetal growth and long-term health. We report analyses of rare variants that impact birth weight when carried by either fetus or mother, using whole exome sequencing data in up to 234,675 participants. Rare protein-truncating and deleterious missense variants are collapsed to perform gene burden tests. We identify 9 genes; 5 with fetal-only effects on birth weight, 1 with maternal-only effects, 3 with both, and observe directionally concordant associations in an independent sample. Four of the genes were previously implicated by GWAS of birth weight. IGF1R and PAPPA2 (fetal and maternal-acting) have known roles in insulin-like growth factor bioavailability and signalling. PPARG, INHBE and ACVR1C (fetal-acting) are involved in adipose tissue regulation, and the latter two also show associations with favourable adiposity patterns in adults. We highlight the dual role of PPARG (fetal-acting) in adipocyte differentiation and placental angiogenesis. NOS3 (fetal and maternal-acting), NRK (fetal), and ADAMTS8 (maternal-acting) have been implicated in placental function and hypertension. To conclude, our analysis of rare coding variants identifies regulators of fetal adipose tissue and fetoplacental angiogenesis as determinants of birth weight, and further evidence for the role of insulin-like growth factors.

Population Genomics of Japanese Macaques (Macaca fuscata): Insights Into Deep Population Divergence and Multiple Merging Histories

The influence of long-term climatic changes such as glacial cycles on the history of living organisms has been a subject of research for decades, but the detailed population dynamics during the environmental fluctuations and their effects on genetic diversity and genetic load are not well understood on a genome-wide scale. The Japanese macaque (Macaca fuscata) is a unique primate adapted to the cold environments of the Japanese archipelago. Despite the past intensive research for the Japanese macaque population genetics, the genetic background of Japanese macaques at the whole-genome level has been limited to a few individuals, and the comprehensive demographic history and genetic differentiation of Japanese macaques have been underexplored. We conducted whole-genome sequencing of 64 Japanese macaque individuals from 5 different regions, revealing significant genetic differentiation and functional variant diversity across populations. In particular, Japanese macaques have low genetic diversity and harbor many shared and population-specific gene loss, which might contribute to population-specific phenotypes. Our estimation of population demography using phased haplotypes suggested that, after the strong population bottleneck shared among all populations around 400 to 500 kya, the divergence among populations initiated around 150 to 200 kya, but there has been the time with strong gene flow between some populations after the split, indicating multiple population split and merge events probably due to habitat fragmentation and fusion during glacial cycles. These findings not only present a complex population history of Japanese macaques but also enhance their value as research models, particularly in neuroscience and behavioral studies. This comprehensive genomic analysis sheds light on the adaptation and evolution of Japanese macaques, contributing valuable insights to both evolutionary biology and biomedical research.

Adipose tissue eQTL meta-analysis highlights the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits

Complete characterization of the genetic effects on gene expression is needed to elucidate tissue biology and the etiology of complex traits. In the present study, we analyzed 2,344 subcutaneous adipose tissue samples and identified 34,774 conditionally distinct expression quantitative trait locus (eQTL) signals at 18,476 genes. Over half of eQTL genes exhibited at least two eQTL signals. Compared with primary eQTL signals, nonprimary eQTL signals had lower effect sizes, lower minor allele frequencies and less promoter enrichment; they corresponded to genes with higher heritability and higher tolerance for loss of function. Colocalization of eQTLs with genome-wide association study (GWAS) signals for 28 cardiometabolic traits identified 1,835 genes. Inclusion of nonprimary eQTL signals increased discovery of colocalized GWAS-eQTL signals by 46%. Furthermore, 21 genes with ≥2 colocalized GWAS-eQTL signals showed a mediating gene dosage effect on the GWAS trait. Thus, expanded eQTL identification reveals more mechanisms underlying complex traits and improves understanding of the complexity of gene expression regulation.

Genetic and Molecular Underpinnings of Atrial Fibrillation

Atrial fibrillation (AF), the most common sustained arrhythmia, increases stroke and heart failure risks. Here we review genes linked to AF and mechanisms by which they alter AF risk. We highlight gene expression differences between atrial and ventricular cardiomyocytes, regulatory mechanisms responsible for these differences, and their potential contribution to AF. Understanding AF mechanisms through the lens of atrial gene regulation is crucial to improving AF treatment.

Enhancement of erythropoietic output by Cas9-mediated insertion of a natural variant in haematopoietic stem and progenitor cells

Some gene polymorphisms can lead to monogenic diseases, whereas other polymorphisms may confer beneficial traits. A well-characterized example is congenital erythrocytosis-the non-pathogenic hyper-production of red blood cells-that is caused by a truncated erythropoietin receptor. Here we show that Cas9-mediated genome editing in CD34+ human haematopoietic stem and progenitor cells (HSPCs) can recreate the truncated form of the erythropoietin receptor, leading to substantial increases in erythropoietic output. We also show that combining the expression of the cDNA of a truncated erythropoietin receptor with a previously reported genome-editing strategy to fully replace the HBA1 gene with an HBB transgene in HSPCs (to restore normal haemoglobin production in cells with a β-thalassaemia phenotype) gives the edited HSPCs and the healthy red blood cell phenotype a proliferative advantage. Combining knowledge of human genetics with precise genome editing to insert natural human variants into therapeutic cells may facilitate safer and more effective genome-editing therapies for patients with genetic diseases.

Genome-wide meta-analysis of myasthenia gravis uncovers new loci and provides insights into polygenic prediction

Myasthenia gravis (MG) is a rare autoantibody-mediated disease affecting the neuromuscular junction. We performed a genome-wide association study of 5708 MG cases and 432,028 controls of European ancestry and a replication study in 3989 cases and 226,643 controls provided by 23andMe Inc. We identified 12 independent genome-wide significant hits (P < 5e-8) across 11 loci. Subgroup analyses revealed two of these were associated with early-onset (at age <50) and four with late-onset MG (at age ≥ 50). Imputation of human leukocyte antigen alleles revealed inverse effect sizes for late- and early-onset, suggesting a potential modulatory influence on the time of disease manifestation. We assessed the performance of polygenic risk scores for MG, which significantly predicted disease status in an independent target cohort, explaining 4.21% of the phenotypic variation (P = 5.12e-9). With this work, we aim to enhance our understanding of the genetic architecture of MG.

Sequence variants associated with BMI affect disease risk through BMI itself

Mendelian Randomization studies indicate that BMI contributes to various diseases, but it's unclear if this is entirely mediated by BMI itself. This study examines whether disease risk from BMI-associated sequence variants is mediated through BMI or other mechanisms, using data from Iceland and the UK Biobank. The associations of BMI genetic risk score with diseases like fatty liver disease, knee replacement, and glucose intolerance were fully attenuated when conditioned on BMI, and largely for type 2 diabetes, heart failure, myocardial infarction, atrial fibrillation, and hip replacement. Similar attenuation was observed for chronic kidney disease and stroke, though results varied. Findings were consistent across sexes, except for myocardial infarction. Residual effects may result from temporal BMI changes, pleiotropy, measurement error, non-linear relationships, non-collapsibility, or confounding. The attenuation extent of BMI genetic risk score on disease associations suggests the potential impact of reducing BMI on disease risk.

Gene-based burden tests of rare germline variants identify six cancer susceptibility genes

Discovery of cancer risk variants in the sequence of the germline genome can shed light on carcinogenesis. Here we describe gene burden association analyses, aggregating rare missense and loss of function variants, at 22 cancer sites, including 130,991 cancer cases and 733,486 controls from Iceland, Norway and the United Kingdom. We identified four genes associated with increased cancer risk; the pro-apoptotic BIK for prostate cancer, the autophagy involved ATG12 for colorectal cancer, TG for thyroid cancer and CMTR2 for both lung cancer and cutaneous melanoma. Further, we found genes with rare variants that associate with decreased risk of cancer; AURKB for any cancer, irrespective of site, and PPP1R15A for breast cancer, suggesting that inhibition of PPP1R15A may be a preventive strategy for breast cancer. Our findings pinpoint several new cancer risk genes and emphasize autophagy, apoptosis and cell stress response as a focus point for developing new therapeutics.

Polygenic Interactions With Environmental Exposures in Blood Pressure Regulation: The HUNT Study

BACKGROUND

The essential hypertension phenotype results from an interplay between genetic and environmental factors. The influence of lifestyle exposures such as excess adiposity, alcohol consumption, tobacco use, diet, and activity patterns on blood pressure (BP) is well established. Additionally, polygenic risk scores for BP traits are associated with clinically significant phenotypic variation. However, interactions between genetic and environmental risk factors in hypertension morbidity and mortality are poorly characterized.

METHODS AND RESULTS

We used genotype and phenotype data from up to 49 234 participants from the HUNT (Trøndelag Health Study) to model gene-environment interactions between genome-wide polygenic risk scores for systolic BP and diastolic BP and 125 environmental exposures. Among the 125 environmental exposures assessed, 108 and 100 were independently associated with SBP and DBP, respectively. Of these, 12 interactions were identified for genome-wide PRSs for systolic BP and 4 for genome-wide polygenic risk scores for diastolic BP, 2 of which were overlapping (P < 2 × 10-4). We found evidence for gene-dependent influence of lifestyle factors such as cardiorespiratory fitness, dietary patterns, and tobacco exposure, as well as biomarkers such as serum cholesterol, creatinine, and alkaline phosphatase on BP.

CONCLUSIONS

Individuals that are genetically susceptible to high BP may be more vulnerable to common acquired risk factors for hypertension, but these effects appear to be modifiable. The gene-dependent influence of several common acquired risk factors indicates the potential of genetic data combined with lifestyle assessments in risk stratification, and gene-environment-informed risk modeling in the prevention and management of hypertension.

Developmental language disorder - heritability and genetic correlations with other disorders affecting language

Developmental language disorder (DLD) is a neurodevelopmental disorder primarily affecting language in the absence of a known biomedical condition, which may have a large impact on a person's life and mental health. Family-based studies indicate a strong genetic component in DLD, but genetic studies of DLD are scarce. In this study we estimated the heritability of DLD and its genetic correlations with related disorders and traits in sample of >25,000 individuals from the Danish Blood Donor Study for whom we had both genotype data and questionnaire data on language disorder and language support. We estimated SNP-based heritabilities for DLD and genetic correlations with disorders which may involve spoken language deficits and traits related to spoken language. We found significant heritability estimates for DLD ranging from ∼27 % to ∼52 %, depending on the method used. We found no significant evidence for genetic correlation with the investigated disorders or traits, although the strongest effect was observed for a negative genetic correlation between DLD and nonword repetition ability. To our knowledge, this study reports the first significant heritability estimate for DLD from molecular genetic data.

Sequence variants influencing the regulation of serum IgG subclass levels

Immunoglobulin G (IgG) is the main isotype of antibody in human blood. IgG consists of four subclasses (IgG1 to IgG4), encoded by separate constant region genes within the Ig heavy chain locus (IGH). Here, we report a genome-wide association study on blood IgG subclass levels. Across 4334 adults and 4571 individuals under 18 years, we discover ten new and identify four known variants at five loci influencing IgG subclass levels. These variants also affect the risk of asthma, autoimmune diseases, and blood traits. Seven variants map to the IGH locus, three to the Fcγ receptor (FCGR) locus, and two to the human leukocyte antigen (HLA) region, affecting the levels of all IgG subclasses. The most significant associations are observed between the G1m (f), G2m(n) and G3m(b*) allotypes, and IgG1, IgG2 and IgG3, respectively. Additionally, we describe selective associations with IgG4 at 16p11.2 (ITGAX) and 17q21.1 (IKZF3, ZPBP2, GSDMB, ORMDL3). Interestingly, the latter coincides with a highly pleiotropic signal where the allele associated with lower IgG4 levels protects against childhood asthma but predisposes to inflammatory bowel disease. Our results provide insight into the regulation of antibody-mediated immunity that can potentially be useful in the development of antibody based therapeutics.

Emerging drugs for the treatment of progressive familial intrahepatic cholestasis: a focus on phase II and III trials

INTRODUCTION

Progressive familial intrahepatic cholestasis (PFIC) is a group of disorders characterized by inappropriate bile formation, causing hepatic accumulation of bile acids and, subsequently, liver injury. Until recently, no approved treatments were available for these patients.

AREAS COVERED

Recent clinical trials for PFIC treatment have focused on intestine-restricted ileal bile acid transporter (IBAT) inhibitors. These compounds aim to reduce the pool size of bile acids by interrupting their enterohepatic circulation. Other emerging treatments in the pipeline include systemic IBAT inhibitors, synthetic bile acid derivatives, compounds targeting bile acid synthesis via the FXR/FGF axis, and chaperones/potentiators that aim to enhance the residual activity of the mutated transporters.

EXPERT OPINION

Substantial progress has been made in drug development for PFIC patients during the last couple of years. Although data concerning long-term efficacy are as yet only scarcely available, new therapies have demonstrated robust efficacy in a considerable fraction of patients at least on the shorter term. However, a substantial fraction of PFIC patients do not respond to these novel therapies and thus still requires surgical treatment, including liver transplantation before adulthood. Hence, there is still an unmet medical need for long-term effective medical, preferably non-surgical, treatment for all PFIC patients.

GGTyper: genotyping complex structural variants using short-read sequencing data

MOTIVATION

Complex structural variants (SVs) are genomic rearrangements that involve multiple segments of DNA. They contribute to human diversity and have been shown to cause Mendelian disease. Nevertheless, our abilities to analyse complex SVs are very limited. As opposed to deletions and other canonical types of SVs, there are no established tools that have explicitly been designed for analysing complex SVs.

RESULTS

Here, we describe a new computational approach that we specifically designed for genotyping complex SVs in short-read sequenced genomes. Given a variant description, our approach computes genotype-specific probability distributions for observing aligned read pairs with a wide range of properties. Subsequently, these distributions can be used to efficiently determine the most likely genotype for any set of aligned read pairs observed in a sequenced genome. In addition, we use these distributions to compute a genotyping difficulty for a given variant, which predicts the amount of data needed to achieve a reliable call. Careful evaluation confirms that our approach outperforms other genotypers by making reliable genotype predictions across both simulated and real data. On up to 7829 human genomes, we achieve high concordance with population-genetic assumptions and expected inheritance patterns. On simulated data, we show that precision correlates well with our prediction of genotyping difficulty. This together with low memory and time requirements makes our approach well-suited for application in biomedical studies involving small to very large numbers of short-read sequenced genomes.

AVAILABILITY AND IMPLEMENTATION

Source code is available at https://github.com/kehrlab/Complex-SV-Genotyping.

Rare coding variant analysis for human diseases across biobanks and ancestries

Large-scale sequencing has enabled unparalleled opportunities to investigate the role of rare coding variation in human phenotypic variability. Here, we present a pan-ancestry analysis of sequencing data from three large biobanks, including the All of Us research program. Using mixed-effects models, we performed gene-based rare variant testing for 601 diseases across 748,879 individuals, including 155,236 with ancestry dissimilar to European. We identified 363 significant associations, which highlighted core genes for the human disease phenome and identified potential novel associations, including UBR3 for cardiometabolic disease and YLPM1 for psychiatric disease. Pan-ancestry burden testing represented an inclusive and useful approach for discovery in diverse datasets, although we also highlight the importance of ancestry-specific sensitivity analyses in this setting. Finally, we found that effect sizes for rare protein-disrupting variants were concordant between samples similar to European ancestry and other genetic ancestries (βDeming = 0.7-1.0). Our results have implications for multi-ancestry and cross-biobank approaches in sequencing association studies for human disease.

Homozygosity for a stop-gain variant in CCDC201 causes primary ovarian insufficiency

Age at menopause (AOM) has a substantial impact on fertility and disease risk. While many loci with variants that associate with AOM have been identified through genome-wide association studies (GWAS) under an additive model, other genetic models are rarely considered1. Here through GWAS meta-analysis under the recessive model of 174,329 postmenopausal women from Iceland, Denmark, the United Kingdom (UK; UK Biobank) and Norway, we study low-frequency variants with a large effect on AOM. We discovered that women homozygous for the stop-gain variant rs117316434 (A) in CCDC201 (p.(Arg162Ter), minor allele frequency ~1%) reached menopause 9 years earlier than other women (P = 1.3 × 10-15). The genotype is present in one in 10,000 northern European women and leads to primary ovarian insufficiency in close to half of them. Consequently, homozygotes have fewer children, and the age at last childbirth is 5 years earlier (P = 3.8 × 10-5). The CCDC201 gene was only found in humans in 2022 and is highly expressed in oocytes. Homozygosity for CCDC201 loss-of-function has a substantial impact on female reproductive health, and homozygotes would benefit from reproductive counseling and treatment for symptoms of early menopause.

Genetic links between ovarian ageing, cancer risk and de novo mutation rates

Human genetic studies of common variants have provided substantial insight into the biological mechanisms that govern ovarian ageing1. Here we report analyses of rare protein-coding variants in 106,973 women from the UK Biobank study, implicating genes with effects around five times larger than previously found for common variants (ETAA1, ZNF518A, PNPLA8, PALB2 and SAMHD1). The SAMHD1 association reinforces the link between ovarian ageing and cancer susceptibility1, with damaging germline variants being associated with extended reproductive lifespan and increased all-cause cancer risk in both men and women. Protein-truncating variants in ZNF518A are associated with shorter reproductive lifespan-that is, earlier age at menopause (by 5.61 years) and later age at menarche (by 0.56 years). Finally, using 8,089 sequenced trios from the 100,000 Genomes Project (100kGP), we observe that common genetic variants associated with earlier ovarian ageing associate with an increased rate of maternally derived de novo mutations. Although we were unable to replicate the finding in independent samples from the deCODE study, it is consistent with the expected role of DNA damage response genes in maintaining the genetic integrity of germ cells. This study provides evidence of genetic links between age of menopause and cancer risk.

Loss-of-function variants in ITSN1 confer high risk of Parkinson's disease

Parkinson's disease (PD) is a debilitating neurodegenerative disorder and its rising global incidence highlights the need for the identification of modifiable risk factors. In a gene-based burden test of rare variants (8647 PD cases and 777,693 controls) we discovered a novel association between loss-of-function variants in ITSN1 and PD. This association was further supported with burden data from the Neurodegenerative Disease Knowledge Portal and the Accelerating Medicines Partnership Parkinson's Disease Knowledge Platform. Our findings show that Rho GTPases and disruptions in synaptic vesicle transport may be involved in the pathogenesis of PD, pointing to the possibility of novel therapeutic approaches.

Deciphering the genetics and mechanisms of predisposition to multiple myeloma

Multiple myeloma (MM) is an incurable malignancy of plasma cells. Epidemiological studies indicate a substantial heritable component, but the underlying mechanisms remain unclear. Here, in a genome-wide association study totaling 10,906 cases and 366,221 controls, we identify 35 MM risk loci, 12 of which are novel. Through functional fine-mapping and Mendelian randomization, we uncover two causal mechanisms for inherited MM risk: longer telomeres; and elevated levels of B-cell maturation antigen (BCMA) and interleukin-5 receptor alpha (IL5RA) in plasma. The largest increase in BCMA and IL5RA levels is mediated by the risk variant rs34562254-A at TNFRSF13B. While individuals with loss-of-function variants in TNFRSF13B develop B-cell immunodeficiency, rs34562254-A exerts a gain-of-function effect, increasing MM risk through amplified B-cell responses. Our results represent an analysis of genetic MM predisposition, highlighting causal mechanisms contributing to MM development.

Progress and Implications from Genetic Studies of Bipolar Disorder

With the advancements in gene sequencing technologies, including genome-wide association studies, polygenetic risk scores, and high-throughput sequencing, there has been a tremendous advantage in mapping a detailed blueprint for the genetic model of bipolar disorder (BD). To date, intriguing genetic clues have been identified to explain the development of BD, as well as the genetic association that might be applied for the development of susceptibility prediction and pharmacogenetic intervention. Risk genes of BD, such as CACNA1C, ANK3, TRANK1, and CLOCK, have been found to be involved in various pathophysiological processes correlated with BD. Although the specific roles of these genes have yet to be determined, genetic research on BD will help improve the prevention, therapeutics, and prognosis in clinical practice. The latest preclinical and clinical studies, and reviews of the genetics of BD, are analyzed in this review, aiming to summarize the progress in this intriguing field and to provide perspectives for individualized, precise, and effective clinical practice.

The correlation between CpG methylation and gene expression is driven by sequence variants

Gene promoter and enhancer sequences are bound by transcription factors and are depleted of methylated CpG sites (cytosines preceding guanines in DNA). The absence of methylated CpGs in these sequences typically correlates with increased gene expression, indicating a regulatory role for methylation. We used nanopore sequencing to determine haplotype-specific methylation rates of 15.3 million CpG units in 7,179 whole-blood genomes. We identified 189,178 methylation depleted sequences where three or more proximal CpGs were unmethylated on at least one haplotype. A total of 77,789 methylation depleted sequences (~41%) associated with 80,503 cis-acting sequence variants, which we termed allele-specific methylation quantitative trait loci (ASM-QTLs). RNA sequencing of 896 samples from the same blood draws used to perform nanopore sequencing showed that the ASM-QTL, that is, DNA sequence variability, drives most of the correlation found between gene expression and CpG methylation. ASM-QTLs were enriched 40.2-fold (95% confidence interval 32.2, 49.9) among sequence variants associating with hematological traits, demonstrating that ASM-QTLs are important functional units in the noncoding genome.

Whole-Exome Analysis for Polish Caucasian Patients with Retinal Dystrophies and the Creation of a Reference Genomic Database for the Polish Population

We present the results of the first study of a large cohort of patients with inherited retinal dystrophies (IRD) performed for the Polish population using whole-exome sequencing (WES) in the years 2016-2019. Moreover, to facilitate such diagnostic analyses and enable future application of gene therapy and genome editing for IRD patients, a Polish genomic reference database (POLGENOM) was created based on whole-genome sequences of healthy Polish Caucasian nonagenarians and centenarians. The newly constructed database served as a control, providing a comparison for variant frequencies in the Polish population. The diagnostic yield for the selected group of IRD patients reached 64.9%. The study uncovered the most common pathogenic variants in ABCA4 and USH2A in the European population, along with several novel causative variants. A significant frequency of the ABCA4 complex haplotype p.(Leu541Pro; Ala1038Val) was observed, as well as that of the p.Gly1961Glu variant. The first VCAN causative variant NM_004385.5:c.4004-2A>G in Poland was found and described. Moreover, one of the first patients with the RPE65 causative variants was identified, and, in consequence, could receive the dedicated gene therapy. The availability of the reference POLGENOM database enabled comprehensive variant characterisation during the NGS data analysis, confirming the utility of a population-specific genomic database for enhancing diagnostic accuracy. Study findings suggest the significance of genetic testing in elder patients with unclear aetiology of eye diseases. The combined approach of NGS and the reference genomic database can improve the diagnosis, management, and future treatment of IRDs.

Genome-wide association meta-analysis identifies five loci associated with postpartum hemorrhage

Bleeding in early pregnancy and postpartum hemorrhage (PPH) bear substantial risks, with the former closely associated with pregnancy loss and the latter being the foremost cause of maternal death, underscoring the severe impact on maternal-fetal health. We identified five genetic loci linked to PPH in a meta-analysis. Functional annotation analysis indicated candidate genes HAND2, TBX3 and RAP2C/FRMD7 at three loci and showed that at each locus, associated variants were located within binding sites for progesterone receptors. There were strong genetic correlations with birth weight, gestational duration and uterine fibroids. Bleeding in early pregnancy yielded no genome-wide association signals but showed strong genetic correlation with various human traits, suggesting a potentially complex, polygenic etiology. Our results suggest that PPH is related to progesterone signaling dysregulation, whereas early bleeding is a complex trait associated with underlying health and possibly socioeconomic status and may include genetic factors that have not yet been identified.

EASL Clinical Practice Guidelines on genetic cholestatic liver diseases

Genetic cholestatic liver diseases are caused by (often rare) mutations in a multitude of different genes. While these diseases differ in pathobiology, clinical presentation and prognosis, they do have several commonalities due to their cholestatic nature. These Clinical Practice Guidelines (CPGs) offer a general approach to genetic testing and management of cholestatic pruritus, while exploring diagnostic and treatment approaches for a subset of genetic cholestatic liver diseases in depth. An expert panel appointed by the European Association for the Study of the Liver has created recommendations regarding diagnosis and treatment, based on the best evidence currently available in the fields of paediatric and adult hepatology, as well as genetics. The management of these diseases generally takes place in a tertiary referral centre, in order to provide up-to-date approaches and expertise. These CPGs are intended to support hepatologists (for paediatric and adult patients), residents and other healthcare professionals involved in the management of these patients with concrete recommendations based on currently available evidence or, if not available, on expert opinion.

Obesity Variants in the GIPR Gene Are not Associated With Risk of Fracture or Bone Mineral Density

CONTEXT

It is not clear if antagonizing the GIP (glucose-dependent insulinotropic polypeptide) receptor (GIPR) for treatment of obesity is likely to increase the risk of fractures, or to lower bone mineral density (BMD) beyond what is expected with rapid weight loss.

OBJECTIVE

The objective of this study was to investigate the risk of fracture and BMD of sequence variants in GIPR that reduce the activity of the GIP receptor and have been associated with reduced body mass index (BMI).

METHODS

We analyzed the association of 3 missense variants in GIPR, a common variant, rs1800437 (p.Glu354Gln), and 2 rare variants, rs139215588 (p.Arg190Gln) and rs143430880 (p.Glu288Gly), as well as a burden of predicted loss-of-function (LoF) variants with risk of fracture and with BMD in a large meta-analysis of up to 1.2 million participants. We analyzed associations with fractures at different skeletal sites in the general population: any fractures, hip fractures, vertebral fractures and forearm fractures, and specifically nonvertebral and osteoporotic fractures in postmenopausal women. We also evaluated associations with BMD at the lumbar spine, femoral neck, and total body measured with dual-energy x-ray absorptiometry (DXA), and with BMD estimated from heel ultrasound (eBMD).

RESULTS

None of the 3 missense variants in GIPR was significantly associated with increased risk of fractures or with lower BMD. Burden of LoF variants in GIPR was not associated with fractures or with BMD measured with clinically validated DXA, but was associated with eBMD.

CONCLUSION

Missense variants in GIPR, or burden of LoF variants in the gene, are not associated with risk of fractures or with lower BMD.

Start codon variant in LAG3 is associated with decreased LAG-3 expression and increased risk of autoimmune thyroid disease

Autoimmune thyroid disease (AITD) is a common autoimmune disease. In a GWAS meta-analysis of 110,945 cases and 1,084,290 controls, 290 sequence variants at 225 loci are associated with AITD. Of these variants, 115 are previously unreported. Multiomics analysis yields 235 candidate genes outside the MHC-region and the findings highlight the importance of genes involved in T-cell regulation. A rare 5'-UTR variant (rs781745126-T, MAF = 0.13% in Iceland) in LAG3 has the largest effect (OR = 3.42, P = 2.2 × 10-16) and generates a novel start codon for an open reading frame upstream of the canonical protein translation initiation site. rs781745126-T reduces mRNA and surface expression of the inhibitory immune checkpoint LAG-3 co-receptor on activated lymphocyte subsets and halves LAG-3 levels in plasma among heterozygotes. All three homozygous carriers of rs781745126-T have AITD, of whom one also has two other T-cell mediated diseases, that is vitiligo and type 1 diabetes. rs781745126-T associates nominally with vitiligo (OR = 5.1, P = 6.5 × 10-3) but not with type 1 diabetes. Thus, the effect of rs781745126-T is akin to drugs that inhibit LAG-3, which unleash immune responses and can have thyroid dysfunction and vitiligo as adverse events. This illustrates how a multiomics approach can reveal potential drug targets and safety concerns.

Biallelic variants in POPDC2 cause a novel autosomal recessive syndrome presenting with cardiac conduction defects and variable hypertrophic cardiomyopathy

POPDC2 encodes for the Popeye domain-containing protein 2 which has an important role in cardiac pacemaking and conduction, due in part to its cAMP-dependent binding and regulation of TREK-1 potassium channels. Loss of Popdc2 in mice results in sinus pauses and bradycardia and morpholino knockdown of popdc2 in zebrafish results in atrioventricular (AV) block. We identified bi-allelic variants in POPDC2 in 4 families that presented with a phenotypic spectrum consisting of sinus node dysfunction, AV conduction defects and hypertrophic cardiomyopathy. Using homology modelling we show that the identified POPDC2 variants are predicted to diminish the ability of POPDC2 to bind cAMP. In in vitro electrophysiological studies we demonstrated that, while co-expression of wild-type POPDC2 with TREK-1 increased TREK-1 current density, POPDC2 variants found in the patients failed to increase TREK-1 current density. While patient muscle biopsy did not show clear myopathic disease, it showed significant reduction of the expression of both POPDC1 and POPDC2, suggesting that stability and/or membrane trafficking of the POPDC1-POPDC2 complex is impaired by pathogenic variants in any of the two proteins. Single-cell RNA sequencing from human hearts demonstrated that co-expression of POPDC1 and 2 was most prevalent in AV node, AV node pacemaker and AV bundle cells. Sinoatrial node cells expressed POPDC2 abundantly, but expression of POPDC1 was sparse. Together, these results concur with predisposition to AV node disease in humans with loss-of-function variants in POPDC1 and POPDC2 and presence of sinus node disease in POPDC2, but not in POPDC1 related disease in human. Using population-level genetic data of more than 1 million individuals we showed that none of the familial variants were associated with clinical outcomes in heterozygous state, suggesting that heterozygous family members are unlikely to develop clinical manifestations and therefore might not necessitate clinical follow-up. Our findings provide evidence for POPDC2 as the cause of a novel Mendelian autosomal recessive cardiac syndrome, consistent with previous work showing that mice and zebrafish deficient in functional POPDC2 display sinus and AV node dysfunction.

GRAPHICAL ABSTRACT