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Nature Genetics

Springer Science and Business Media LLC

Preprints posted in the last 7 days, ranked by how well they match Nature Genetics's content profile, based on 240 papers previously published here. The average preprint has a 0.34% match score for this journal, so anything above that is already an above-average fit.

1
Genome-wide association and multi-omics functional screens reveal the genetic architecture of foveal development

Hunt, C.; Patil, M.; Syed, H.; Yoon, H.-J.; Yang, T.; Rodwell, V.; Tu, Z.; Maconachie, G. D.; Coley, K.; Lirio, A.; Shrine, N.; Packer, R.; Fassad, M.; SHENOY, R.; Allcock, N.; Lim, B.; Kuht, H. J.; Varma, G.; Karaer, I.; Injety, R.; Jakins, W.; Savant, R.; Sekhri, R.; Hisaund, M.; Han, J.; Teli, S.; Wang, J.; Zuo, Z.; Whittingham, J.; Douglas, G.; Sylvius, N.; Vasudevan, P. C.; Moshiri, A.; Zippin, J.; Brooks, B. P.; Montoliu, L.; Gottlob, I.; Chen, K.-F.; Yoshimatsu, T.; Tobin, M. D.; Norton, W. H.; Chen, R.; Batini, C.; Thomas, M. G.

2026-06-12 genetic and genomic medicine 10.64898/2026.06.11.26355452 medRxiv
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Foveal hypoplasia causes visual impairment across congenital eye disorders, yet the genetic programmes governing foveal development remain poorly characterised and no tractable model exists for foveal disease. In the first genome-wide association study of foveal hypoplasia, we identified 42 sentinel variants mapping to 54 effector genes supported by >= 2 criteria from a variant-to-gene framework incorporating developmental multi-omics. Disruption of six effector genes using mutant lines and CRISPR knockouts in the zebrafish high acuity zone recapitulates structural, functional, and ultrastructural hallmarks of foveal hypoplasia, establishing the first vertebrate disease model. Integration with human foetal single-cell and spatial transcriptomics reveals two temporal waves of effector gene expression and identifies Muller glia as critical mediators of foveal patterning. Phenome-wide analyses reveal foveal variants are pleiotropic with refractive, lenticular, and metabolic traits, connecting foveal development to anterior segment and systemic disease biology. These findings should inform mechanistic studies of macular disease.

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Distinct and shared genetics of kidney filtration function versus albuminuria revealed by multi-trait GWAS

de Hesselle, H. C.; Garben, B.-F.; Stark, K. J.; Warth, R.; Teumer, A.; Pattaro, C.; Heid, I. M.; Winkler, T. W.

2026-06-09 genetic and genomic medicine 10.64898/2026.06.08.26355141 medRxiv
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Chronic kidney disease is characterized by decreased glomerular filtration rate (eGFR, estimated from serum creatinine or cystatin C) or increased urinary albumin-to-creatinine-ratio (UACR). Genome-wide association studies provided the genetic make-up of these traits, but their overlap remained largely unknown. Our multi-trait GWAS (N=1M) identified 812 signals and multi-trait fine-mapping sharpened the identification of likely causal variants. Of 333 signals classified for filtration function or albuminuria, only 11 overlapped. Their effects on eGFR and UACR were directionally concordant, dominated by eGFR and independent of HbA1c or mean arterial pressure. Mapped genes pinpointed mechanisms related to glomerular filtration area (SHROOM3, EPB41L5) and sodium-mediated intraglomerular pressure (NRBP1, DPEP1/CHMP1A). Genetics of fluid intake resulted in shadow effects on UACR without albumin leakage into urine. Our multi-trait approach sharpened the identification of likely causal genes for kidney traits, demonstrated largely distinct genetics for filtration function versus albuminuria, and provided new biological insights into the overlap.

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Parental educational attainment polygenic scores contribute to phenotypic heterogeneity in offspring with autism

Gao, S.; Sui, Y.; Tian, P.; Rao, X.; Yan, C.; Xu, Y.; Wang, T.

2026-06-08 genetic and genomic medicine 10.64898/2026.06.03.26354779 medRxiv
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Educational attainment-related polygenic scores have been implicated in autism spectrum disorder (ASD), but how parental polygenic scores shape offspring phenotypes remains unclear. Using genotyping and exome-sequencing data from 142,357 individuals (55,252 ASD cases) in a large ASD cohort, we dissected the direct and indirect genetic effects of educational attainment-related polygenic scores on ASD phenotypes. Trio-model analyses showed that parental polygenic scores for educational attainment (PGSEA ) were associated with milder core ASD symptoms, including social deficits and repetitive behaviors, predominantly through indirect genetic effects, whereas their associations with comorbidities were driven predominantly by direct genetic effects. PGSEA was also significantly negatively associated with rare variant burden and prenatal factors, although these factors contributed largely independently to most phenotypes. Adjustment for full-scale intelligence quotient (FSIQ) and socioeconomic status (SES) partially attenuated the indirect effects of PGSEA on offspring phenotypes. Finally, higher parental PGSEA was associated with later age at diagnosis in offspring, partly through its protective effects on ASD phenotypes. These findings indicate that indirect genetic effects of parentalPGSEA contribute substantially to phenotypic variation in ASD and highlight family-mediated pathways as an important component of ASD heterogeneity.

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An integrative multi-omics framework identifies epigenetic dysregulation of HAND2 as a potential primary driver of impaired enteric neural crest cell differentiation in Hirschsprung Disease

Mellein, S.; Paramasivam, N.; Gu, Z.; Roeth, R.; Mederer, T.; Kuzan, H.; Roessler, S.; Scheuerer, J.; Lasitschka, F.; Schwab, C.; Sahm, F.; Hamelmann, S.; Khasanov, R.; Tapia-Laliena, M. A.; Wessel, L.; Boettcher, M.; Carstensen, L.; Niesler, B.; Loescher, B.-S.; Franke, A.; Narci, K.; Huebschmann, D.; Rappold, G.; Schaaf, C.; Guenther, P.; Romero, P.

2026-06-12 gastroenterology 10.64898/2026.06.11.26354426 medRxiv
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Hirschsprung disease (HSCR) is a congenital neurodevelopmental disorder characterized by segmental aganglionosis due to impaired developmental processes of enteric neural crest cells (NCCs). Despite being the leading genetic cause of functional intestinal obstruction in early childhood, HSCR represents a paradigmatic challenge in precision medicine: its multifactorial etiology, complex gene-environment interactions and limited resolution of single-modality analyses have long hindered mechanistic understanding and therapeutic translation. Here, we applied an integrative multi-omics approach combining genetic, phenotypic, epigenomic and transcriptomic analyses of matched ganglionic and aganglionic formalin-fixed paraffin-embedded (FFPE) patient tissues, complemented by patient-specific in vitro models. Beyond established genetic contributors, our integrative approach reveals novel regulatory pathways predominantly affecting enteric NCC differentiation, with convergent evidence pointing to epigenetic dysregulation as a primary disease mechanism. Notably, we identified over 1,300 differentially methylated positions between ganglionic and aganglionic FFPE samples, with HAND2 emerging as a key candidate due to multiple hypermethylated sites and consistently reduced expression levels in aganglionic tissues and in vitro models, suggesting a potential role in HSCR pathophysiology. We propose that our multi-omics approach offers a powerful and comprehensive framework for dissecting disease mechanisms. Beyond advancing biological understanding, this strategy holds promise for paving the way for molecularly informed patient stratification and supporting the development of personalized treatment and postoperative management strategies.

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Multi-ancestry genome-wide association study and meta-analysis of stimulant use disorder reveals biology and relationships to other psychiatric disorders

Beck, S. E.; Deak, J. D.; Levey, D. F.; Ge, T.; Jeffries, P. W.; Lai, D.; Mallard, T. T.; Degenhardt, L.; Lind, P. A.; Tollerup Nielsen, T.; Tubbs, J. D.; Wetherill, L.; Johnson, E. C.; Hatoum, A. S.; The SUD Working Group of the Psychiatric Genomics Consortium, ; COGA Collaborators, ; Yale-Penn Collaboration, ; The VA Million Veteran Program, ; Borglum, A.; Demontis, D.; Medland, S. E.; Martin, N. G.; Nelson, E. C.; Smoller, J. W.; Kranzler, H. R.; Gaziano, J. M.; Stein, M. B.; Agrawal, A.; Edenberg, H. J.; Gelernter, J.

2026-06-10 genetic and genomic medicine 10.64898/2026.06.05.26354997 medRxiv
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Stimulant use disorder (StimUD) is a significant public health problem, but genetic studies have been limited by small sample sizes. We conducted genome-wide association studies (GWAS) of StimUD in the Million Veteran Program (MVP) and All of Us (AOU), followed by meta-analysis with FinnGen and 10 additional datasets, for a total of 709,369 individuals (Ncases=33,977, Ncontrols=675,392) in four broad ancestry groups: European (EUR) (Ncases=22,564, Ncontrols=624,672), African (AFR) (Ncases=7,574, Ncontrols=34,189), Admixed American (AMR) (Ncases=3,657, Ncontrols=15,698), and East Asian (EAS) (Ncases=182, Ncontrols=833). Population-specific SNP heritability was 6.1% in EUR and 2.4% in AFR. We discovered a total of 19 genome-wide-significant loci, six in EUR, including DRD2*rs5794864, P=7.32E-10, one in AFR, five in a multi-ancestry meta-analysis, including CHRNA5*rs55781567, P=3.27E-9, two in a male-only meta-analysis, including FTO*rs8057044, P=9.50E10-9, and five in a meta-analysis of sex-stratified results. In a hold-out AOU subsample (NEUR=18,841, NAFR=12,263, NAMR=9,739), ancestry-specific polygenic risk scores were significantly associated with StimUD in EUR (OR=3.28, 95% confidence interval (CI)=2.89-3.71) and AMR (OR=2.01, 95% CI=1.71-2.37). Transcriptome-wide association studies, fine-mapping, and colocalization analyses prioritized additional genes (e.g., GPX1, BSN). Genetic correlation, Mendelian randomization, and causal mixture analyses revealed relationships with other substance use and use disorder phenotypes, including cannabis use disorder (rg=0.94, P=5.43E-237) and opioid use disorder (rg=1.01, P=4.40E-107), and other psychiatric traits, including anxiety, depression, neuroticism, and attention-deficit/hyperactivity disorder. This is the first well-powered GWAS of StimUD, and it offers significant insights into disease biology.

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Host Genetic Regulation of NLRP3 Inflammasome Cytokines Reveals Immune and Vascular Pathways in HIV

Chung, R.; Chalasani, N. S.; Barbehenn, A. S.; Lundgren, E.; Savur, S.; Shome, S.; Sheikhzadeh, C. H.; Sarvadhavabhatla, S.; Donaire, M. S.; Pae, V.; Chu, X.; Winder, D.; Maguire, C. T.; Topal, S.; Ganesan, A.; Yabes, J. M.; Larson, D. T.; Lalani, T.; Ewers, E. C.; Colombo, R. E.; Dugan, E.; Rathore, U.; Marson, A.; Agan, B. K.; Tomalka, J. A.; Sekaly, R.-P.; Loannidis, N. M.; Lee, S. A.

2026-06-10 hiv aids 10.64898/2026.06.08.26355202 medRxiv
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People with HIV exhibit elevated inflammation and cardiovascular risk despite antiretroviral therapy. To define the genetic architecture of inflammasome-associated inflammation, we performed whole-genome sequencing and quantified plasma IL-6, IL-1{beta}, and IL-18 in 1,000 ART-suppressed PWH from the U.S. Military HIV Natural History Study. Genome-wide analyses identified 14 loci implicating antiviral defense (DDX17, DDX41, EEA1, BCL11A), lipid metabolism (ABCA1, ABCA12, ABCC1, AGMO), and vascular remodeling (KLHL29, RNF213, ETV1). Transcriptome-wide analyses across cardiovascular and immune tissues identified regulatory programs linking interferon signaling, immune activation, and vascular biology to circulating cytokine levels. Mendelian randomization analyses supported causal relationships between inflammasome-associated cytokines and vascular events. Functional integration with genome-wide CRISPR perturbation datasets in primary CD4 T cells linked cytokine-associated loci to HIV antiviral pathways and cytokine regulatory networks. External validation in cohorts without HIV demonstrated pathway-level convergence despite limited variant-level overlap. These findings define genetic mechanisms linking inflammasome signaling, antiviral defense, and cardiovascular risk.

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STELLAR: A flexible ensemble learning framework integrating rare variants to enhance polygenic risk prediction

Chen, T.; Li, X.; Mazumder, R.; Zhang, H.; Lin, X.

2026-06-09 genetic and genomic medicine 10.64898/2026.06.07.26355109 medRxiv
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Whole-exome and whole-genome sequencing technology has enabled the discovery of rare genetic variants associated with human health and diseases. However, existing statistical methods used for rare variant association testing are not well-suited for building genetic risk prediction models that jointly incorporate rare and common variants. We propose STELLAR, a flexible ensemble learning-based approach to compute rare variant polygenic risk scores (PRS) using association summary statistics to enhance conventional common variant PRS. Our method combines burden-based and penalty-based rare variant analysis and leverages functional annotation information to prioritize potentially causal variants within the prediction models. In simulation studies, PRS using STELLAR consistently showed the highest prediction accuracy compared to models using common variants alone or rare variant burdens. Applied to UK Biobank whole-exome sequencing data (n=310,831) across eight continuous and five binary traits, STELLAR significantly improved prediction accuracy, refined stratification of individuals at the highest genetic risk beyond common variants, and prioritized biologically relevant genes. STELLAR provides a scalable strategy to incorporate rare variants into PRS in addition to common variants, advancing precision risk prediction and enabling more comprehensive assessment of genetic contributions to complex diseases.

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Polygenic risk scores associate with asthma phenotypes and proteomic analyses implicate IL1R1 in two family-based studies

Lee, S.; Moll, M.; Mendez, K.; Prince, N.; Lasky-Su, J.; Lutz, S. M.; Weiss, S. T.; Lange, C.; Kelly, R. S.; Hecker, J.

2026-06-11 genetic and genomic medicine 10.64898/2026.06.06.26355045 medRxiv
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Despite its high prevalence and the discovery of hundreds of genetic associations, the genetic determinants and heterogeneous manifestations of asthma remain incompletely understood. Incorporating polygenic risk scores (PRS) into asthma research offers a powerful approach to quantify inherited susceptibility, refine risk profiles, and advance mechanistic understanding of disease development. For this study, we leveraged whole-genome sequencing (WGS) data from two family-based cohorts of childhood asthma - the Genetics of Asthma in Costa Rica Study (GACRS) and the Childhood Asthma Management Program (CAMP) - to examine the transmission profiles of externally derived asthma PRS and their associations with clinical phenotypes in children with asthma. To further elucidate molecular mechanisms, we integrated large-scale external genome-wide association study (GWAS) summary statistics and genetic prediction models of protein abundance in a two-step proteome-wide association study (PWAS) of asthma. Our findings provide robust evidence supporting the validity of externally derived asthma PRS (asthma PRS association p-value p={10}^{-24} [GACRS and CAMP trios combined] for the Global Biobank Meta-analysis Initiative [GBMI]) and reveal consistent associations with spirometry measures and atopy markers across both studies, as 13 of 21 traits (62%) were significantly associated with the GBMI-PRS in the meta-analysis after multiple-testing correction. Moreover, the results of the integrative proteomic analysis implicate IL-1 signaling in the etiology of asthma, reinforcing the candidacy of IL1R1 antagonists for drug repurposing.

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Polygenic risk of cardiovascular disease manifests in cardiac structure and function

Felici, B.; Ritchie, S. C.; Khullar, S.; Foguet, C.; Persyn, E.; Manikpurage, H. D.; Liu, Y.; Lambert, S. A.; Ip, S.; Rudd, J. H. F.; Inouye, M.

2026-06-08 cardiovascular medicine 10.64898/2026.06.07.26354998 medRxiv
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Cardiovascular diseases (CVDs) are highly heritable, but pathogenesis at the organ and physiological level is still poorly defined. Polygenic risk scores (PRSs), which estimate individual genetic susceptibility to a disease, may allow for the identification of associated abnormal organ structures. Ultimately, identifying where cardiovascular polygenic risk manifests can guide early interventions, shape mechanistic hypotheses, and motivate prevention trials for cardiac remodelling. This study investigated the association between PRSs for five common CVDs [heart failure (HF), coronary artery disease (CAD), atrial fibrillation (AF), abdominal aortic aneurysm (AAA) and ischaemic stroke (IS)] and 28 imaging-derived phenotypes (IDPs) from cardiac magnetic resonance imaging of ~62,000 participants in UK Biobank. To investigate the cardiac features associated with elevated polygenic risk of CVDs, we tested CVD PRSs against cardiac IDPs and identified 97 significant associations (FDR [≤] 0.05). We further identified 32 significant putative mediators between CVD PRSs and incident disease events, revealing that across CVDs, polygenic risk manifested as distinct patterns in cardiac structures. HF implicated all cardiac chambers, including left ventricular and left atrial dysfunction alongside enlarged aorta. AF was characterised by biatrial enlargement and reduced ejection fractions, most prominently in the left atrium but also involving left ventricular wall thickness. IS exhibited left ventricular hypertrophy and left atrial dysfunction, while CAD predominantly involved left ventricular hypertrophy. AAA was primarily characterised by enlarged descending aorta. Overall, cardiac IDPs mediated a substantial proportion of polygenic risk for CVDs, in particular for HF. Taken together, our results show that cardiac structure and function lie on the pathway between polygenic risk and cardiovascular events.

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Deconvolution-based cell-type specific DNA methylation-wide and transcriptome-wide association studies identify risk CpG sites and genes associated with colorectal cancer risk

Li, Q.; Xu, L.; Wang, J.; Li, C.; Wen, W.; Shu, X.; Yang, Y.; Shu, X.-o.; Cai, Q.; Long, J.; Singh, B.; Lau, K. S.; Yin, Z.; Casey, G.; Song, M.; Peters, U.; Zheng, W.; Guo, X.

2026-06-12 genetic and genomic medicine 10.64898/2026.06.11.26355460 medRxiv
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Bulk tissue-based DNA methylation-wide (MWAS) and transcriptome-wide association studies (TWAS) have identified CpG sites and genes associated with colorectal cancer (CRC) risk, but do not account for cellular heterogeneity. To address this, we developed a deconvolution-informed framework to infer cell-type specific DNA methylation and gene expression profiles from bulk normal colon tissues using reference single-cell epigenomic and transcriptomic datasets. We performed cell-type specific MWAS (ctMWAS) using deconvoluted DNA methylation data from 293 normal colon samples and conducted cell-type specific TWAS (ctTWAS) using deconvoluted gene expression data from 707 normal colon samples. Genetically predicted methylation and expression models were integrated with CRC GWAS summary statistics (78,473 cases and 107,143 controls) to identify risk-associated CpG sites and genes. Through ctMWAS, ctTWAS, and colocalization analyses, we identified 178 significant cell-type-specific CpG sites in 106 loci and 68 risk genes in 40 loci, including 26 previously unreported loci. Through additional integrative methylation-gene analysis, we prioritized 132 candidate risk genes, the majority of which were supported by multi-omics evidence and stage-specific dysregulation across the adenoma-carcinoma and serrated-carcinoma progression pathways. Pathway enrichment analyses implicated pathways involved in DNA double-strand break repair, TP53 regulation, TGF-{beta} signaling, and innate immune responses. Among prioritized genes, 14 were identified as putative druggable targets linked to 90 FDA-approved or clinical-stage drugs. Experimental validation supports an oncogenic role for SF3A3. These findings demonstrate that deconvolution-informed integrative analyses enable cell-type-resolved identification of epigenetic and transcriptional mechanisms underlying CRC susceptibility and provide insights into disease biology, prevention, and therapeutic target discovery.

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Disentangling Confounders from Pathology in Long-COVID Trajectory Prediction for Women: An Interpretable Large-Language-Model Approach

Wang, J.; Galis, Z.; Zhang, T.; Luo, Y.; Sra, A.; Niu, X.; Shen, J.; Xie, Q.; Weiss, J. C.

2026-06-12 infectious diseases 10.64898/2026.06.10.26355420 medRxiv
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Objective. Post-acute sequelae of SARS-CoV-2 infection (PASC, "Long COVID") dispropor- tionately affects women, in whom hallmark symptoms--insomnia, fatigue, palpitations, cogni- tive difficulty--overlap with comorbidities and hormonal transitions such as menopause. This diagnostic overlap is a confounding problem: models that forecast future symptom severity risk attributing baseline physiological noise to viral pathology. We ask whether an interpretable, causally disentangled language model can separate true pathological signal from such con- founders while remaining competitive with strong predictors of future PASC severity

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Decoding the Genetic Architecture of Autistic Traits in the Aging Population

Tian, P.; Rao, X.; Sui, Y.; Gao, S.; Meng, Y.; Han, X.; Wang, T.

2026-06-11 genetic and genomic medicine 10.64898/2026.06.10.26355340 medRxiv
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Autism research has mostly focused on diagnostic frameworks in childhood. However, autistic traits including social skills, communication, attention switching, attention to detail, and imagination may also vary in many undiagnosed individuals beyond childhood, and the genetic architecture of autistic traits in undiagnosed aging adults remains poorly understood. Here, we performed an exome-wide association study of autistic traits in adults aged >=40 from the UK Biobank (n = 161,269) and independently validated key findings in the SPARK cohort (n = 142,357). We identified exome-wide significance at 17q21.31, represented by a lead variant associated with social skills (rs199533, beta = 0.081, P = 2.04e-11). In addition, we identified an independent signal for communication (rs12632110, beta = 0.042, P = 3.07e-12) and two independent signals for attention switching (rs690733, beta = 0.046, P = 4.26e-12; rs2164272, beta = -0.047, P = 1.73e-12). Gene-based analyses further implicated loss-of-function variation in ZSCAN2 (beta = 1.00, P = 2.44e-6), which was associated with communication differences. Enrichment analyses revealed preferential expression of implicated genes in the cerebral cortex, while phenotypic and neuroimaging analyses linked those variants to cortical brain structure and regional volume. Taken together, these findings delineate the genetic architecture of autistic traits in the aging population and link genetic variation to downstream molecular and neuroanatomical mechanisms.

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Topological Deep Learning Identifies Polygenic Variant Clusters Across Familial Multimorbid Disorders

Vomo-Donfack, K. L.; Bousquet, G.; Falgarone, G.; Ginot, G.; Morilla, I.

2026-06-09 health informatics 10.64898/2026.06.03.26354242 medRxiv
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Whole-genome sequencing comprehensively captures coding, non-coding and structural variation in families with suspected inherited disorders, yet its clinical utility remains constrained by an interpretation bottleneck: selecting a handful of relevant variants from millions of candidates. Current rule-based pipelines, anchored in ACMG/AMP criteria, excel at identifying highly penetrant Mendelian alleles but frequently miss variants of low-to-moderate penetrance, non-coding alterations and germline-somatic interactions. Here we introduce PolyCLIP-T, a topology-guided multimodal framework that transforms variant selection from a classification problem into a geometric discovery task. By contrastively aligning DNA-sequence embeddings with functional annotations, PolyCLIP-T constructs a unified latent space in which the displacement between reference and alternate embeddings quantifies the molecular perturbation induced by each variant. Persistent homology then identifies stable topological components - coherent variant groups shared among affected relatives - that transcend single-variant scoring logic. Applied to six families with multi-morbid cancer, autoimmune and cardiovascular disease, PolyCLIP-T recovered non-coding and structural candidates overlooked by conventional pipelines and revealed pleiotropic networks spanning disease categories. This approach provides an interpretable, scalable solution for genome-first investigations of disorders driven by polygenic architectures that evade single-variant analysis. The framework was developed and benchmarked on deeply characterised familial cohorts selected for transgenerational multimorbidity; validation in larger, independent populations will be essential to establish its generalisability. An interactive web tool is freely available at https://www.polyclip-t.uma.es/.

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Two modes of aversive control in suicidality: joint computational modelling exposes regime-specific clinical signatures invisible to symptom-based stratification

Laessing, P.; Karvelis, P.; Rashid-Cocker, A. S.; Ruocco, A. C.; Koudys, J. W.; Kennedy, J. L.; Zai, C. C.; Dayan, P.; Diaconescu, A.

2026-06-11 psychiatry and clinical psychology 10.64898/2026.06.09.26355278 medRxiv
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Suicidal thoughts and behaviours (STBs) are heterogeneous in their proximal dynamics, planning, and stress-sensitivity, yet most subtyping efforts remain symptom-driven and rarely validated across independent datasets. Computational mixture modelling offers a principled alternative: by fitting explicit models of learning and action selection and partitioning individuals by their latent parameter profiles, it can identify mechanistically distinct control strategies invisible to cross-sectional symptom measurement. We applied this approach to aversive Go/NoGo performance, jointly clustering two independently collected STB-enriched samples (N = 50 and N = 184) using tasks with the same structure but different duration, reversal timing, and clinical instrumentation. Two recurrent behavioural regimes emerged: a fast/adaptive regime characterised by rapid policy updating and elevated feedback reactivity, and a slow/perseverative regime characterised by slow updating, high choice determinism, and a pronounced cost following contingency reversal. These regimes were stable across initialisations, recovered more parsimoniously in joint than independent solutions, and were largely orthogonal to symptom-based stratification. Critically, stratification by regime exposed clinical-computational coupling structures substantially attenuated in pooled analyses. Pooled, population-level associations were modest and anchored by a broad affective burden axis. Within the slow/perseverative regime, coupling reorganised around learning dynamics and internalizing burden (depression, hopelessness, and active suicidal ideation) with markedly larger effect sizes. Within the fast/adaptive regime, a dissociation between anxious-compulsive and antisocial-disinhibitory profiles emerged along the same computational axis, invisible at the population level. These findings support a view of suicidality heterogeneity in which clinically similar individuals differ in the control strategies they recruit under aversive uncertainty - variation that symptom measurement alone cannot capture.

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Dissecting the functional landscape of rare diseases through genomic variation in a heterogeneous cohort of 11,000 patients

Uria-Regojo, G.; Fernandez-Caballero, L.; Lopez-Alcojor, A.; Lopez-Lopez, L.; Benitez, Y.; Rodilla, C.; Avila Fernandez, A.; Trujillo-Tiebas, M. J.; Osorio, A.; Corton, M.; Almoguera, B.; Ayuso, C.; Minguez, P.

2026-06-11 genetic and genomic medicine 10.64898/2026.06.10.26355349 medRxiv
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Rare diseases (RDs) remain a major diagnostic challenge. Genetic and phenotypic heterogeneity, incomplete knowledge of disease mechanisms, and limitations in variant clinical interpretation leave many patients without a molecular diagnosis. Meanwhile, the growing volume of genomic data generated in clinical practice offers an opportunity to develop data-driven methodologies for exploring disease mechanisms and improving the reanalysis of unsolved cases. We aggregated real-world genomic data from 11,084 unrelated patients with suspected RD. Patients were clinically classified into 122 diseases. We built a multi-disease genomic variant frequency database (FJD-DB), which enabled the development of variant and gene-disease association scores by means of case-control subcohort comparisons across 32 disease groups. Functional enrichment analyses were then used to highlight disease-associated protein domains, pathways, biological processes, and phenotypes. Finally, the resulting knowledge was integrated into a data-driven framework for the guided reanalysis of unsolved RD patients applied to Inherited Retinal Dystrophies (IRD) patients as first use case. FJD-DB contained more than 45 million unique variants, including ~185,000 potentially pathogenic variants. Disease-specific analyses identified disease-associated pathogenic variants and highlighted both established and candidate disease genes. We detected 179 significantly enriched protein domains across 23 diseases, 124 Human Phenotype Ontology terms across 13 diseases, 79 Reactome pathways across 10 diseases, and 72 Gene Ontology biological processes across 8 diseases, revealing highly disease-specific functional signatures. Integration of disease-specific variant, gene, and functional association signals enabled the development of a data-driven framework for guided reanalysis of unsolved RD cases. Applied to more than 1,100 unsolved IRD cases, the framework generated clinically relevant findings in 26 patients, including four molecular diagnoses, seven candidate diagnoses, and 15 cases upgraded from non-informative findings to variants of uncertain significance. Aggregated real-world genomic data can be leveraged to identify disease-associated molecular signals generating novel biological hypotheses. A unified analytical framework provides a scalable strategy for knowledge discovery and guided reanalysis, facilitating the identification of overlooked and potentially novel genetic causes of RDs.

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A canary in the mind: A single baseline brain scan predicts adolescent depression and anxiety one year later

Deco, G.; Sanz Perl, Y.; Vohryzek, J.; Garcia-Guzman, E.; Pizzagalli, D. A.; Laukkonen, R.; Chandaria, S.; Kringelbach, M. L.

2026-06-10 psychiatry and clinical psychology 10.64898/2026.06.08.26355206 medRxiv
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Mood and anxiety disorders emerge predominantly in adolescence, yet they are usually identified only once symptoms have consolidated, when intervention can only be reactive. A marker that registers the loss of healthy brain function before symptoms crystallise would allow earlier and more targeted treatment, much as caged canaries once warned miners of danger before it became apparent. Here we report such a marker using a single baseline resting-state functional MRI scan in 150 adolescents in the Human Connectome Project Boston Adolescent Neuroimaging of Depression and Anxiety (HCP BANDA) cohort, allowing us to prospectively predict depression and anxiety symptoms one year later in held-out participants at r = 0.60, substantially above the effect-size ceiling reported for functional connectivity in the same data. The marker is not computed from raw functional connectivity but read out from a whole-brain generative model fitted to each individual's dynamics, which gives access to interference structure that covariance-based features cannot represent. The regions driving the prediction, including precuneus, ventromedial prefrontal and anterior cingulate cortices, are among those previously implicated in internalising disorders, and the same signature tracks cognitive variation in healthy participants and is mechanistically linked to the efficiency of task-related computation. These findings establish a mechanistically interpretable and prospectively predictive marker of adolescent mental health and define a clear path towards external validation and clinical use.

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Genetic basis of dynamic brain states reveals cellular and disease associations

Ebneabbasi, A.; Whiteside, D. J.; Gu, Y.; Bethlehem, R. A. I.; Warrier, V.; Rittman, T.

2026-06-12 genetic and genomic medicine 10.64898/2026.06.10.26355409 medRxiv
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Dynamic resting-state fMRI captures the time-varying patterns of brain activity that are obscured by static approaches. Hidden Markov Models (HMMs) characterise these dynamics as recurring whole-brain states and quantify their fractional occupancy (FO), the proportion of time spent in each state, yet the biological basis of inter-individual variation in FO remains unclear. Using data from 52,335 White UK Biobank participants, with replication in East and South Asian subsamples, this study examined the heritability, cellular and neurotransmitter basis of brain states, and their links with complex phenotypes. FO was significantly heritable and enriched for neuronal populations, particularly glutamatergic and GABAergic signalling. Analyses identified shared and state-specific loci and revealed genetic correlations, colocalisation, and potential causal relationships between FO and several phenotypes, including educational attainment, sleep duration, and disease risk. These findings establish dynamic brain states as biologically grounded intermediate phenotypes, linking genetic variation to neural dynamics, diseases and traits.

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ECG-derived age deviation predicts cardiovascular diseases across lead configurations and cohorts

Aydogdu, D.; Gaber, F.; Sorooshmehr, A.; Akalin, A.

2026-06-08 cardiovascular medicine 10.64898/2026.06.05.26354974 medRxiv
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Cardiovascular diseases (CVDs) remain the primary global health burden, motivating the search for robust, non-invasive risk biomarkers. We harness a foundation model pretrained on over 10 million recordings, to evaluate ECG-derived age deviation as a cross-cohort biomarker of CVD burden. A predictive model, trained exclusively on healthy subjects, achieved accurate age prediction. Diseased subjects exhibited significant positive age acceleration across multiple categories, with structural and ischemic heart diseases showing the largest effects. External validation in a hospital-based cohort (n=160,493) confirmed that age acceleration independently predicts all-cause mortality, with the strongest prognostic value in patients under 65 years. Furthermore, we demonstrated that disease discrimination and mortality prediction are preserved across 6-lead and single-lead configurations, supporting potential deployment in wearable or mobile devices. Our analysis also revealed a striking morphological confound from the complete left bundle branch block, leading us to propose absolute age deviation as a more robust, universal risk marker. These findings establish ECG-derived biological age deviation as a highly generalizable and clinically actionable biomarker for assessing cardiovascular risk. We have also developed a web application at https://bioinformatics.mdc-berlin.de/ECGage that allows users to easily test our framework.

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Human genetic evidence links serine biosynthesis to diabetic peripheral neuropathy

Fridman, V.; Kakar, A.; Jensen, A.; Van de Vondel, L.; Wheeler, A.; Phillips, L. S.; Zhou, J.; Zuchner, S.; Reusch, J.; Raghavan, S.

2026-06-10 genetic and genomic medicine 10.64898/2026.06.09.26355286 medRxiv
Top 3%
2.4%
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Diabetic peripheral neuropathy (DPN) is a common and disabling condition for which no disease-modifying therapies are available. Glycemic and metabolic drivers do not fully explain why only a subset of individuals with diabetes develop DPN, and genetic contributors remain poorly defined. We aimed to perform a multi-population genome-wide association study (GWAS) of DPN to highlight potential new etiological pathways and therapeutic targets. Methods We performed a multi-population GWAS of neuropathy in people with and without diabetes using the VA Million Veteran Program and UK Biobank, followed by replication in the All of Us Research Program (AoU), and gene-based and gene-set analyses to identify implicated pathways. Causal relationships between circulating serine levels and DPN were further tested using two sample Mendelian randomization. To further evaluate pathogenic potential, we analyzed rare, high impact variants in GWAS implicated genes among individuals with unresolved inherited neuropathies using the GENESIS platform. Findings Among individuals with type 2 diabetes, we identified seven genome wide significant loci (p<5x10-): PHGDH and PSPH (key serine synthesis genes), TEAD1, CYP4F11, LARGE1, FTO, and COBLL1. No loci were significant in individuals without diabetes or with type 1 diabetes. Four loci (PHGDH, TEAD1, FTO and CYP4F11) replicated in AoU (p <0.05). Mendelian randomization demonstrated that higher genetically predicted serine levels were associated with lower DPN risk, consistent with a causal role of serine metabolism in disease pathogenesis. Rare-variant burden analyses revealed associations of predicted deleterious variants with inherited neuropathy case status in PHGDH (odds ratio [OR] 12.7 [95% CI 7.9, 20.4]), PSPH (OR 8.5 [7.2, 10.2]), PHKG1 (OR 4.8 [3.7, 6.3]), and LARGE1 (OR 0.007 [0.0004, 0.1]). Interpretation Convergent genetic evidence across common and rare variation implicates serine synthesis as a key pathway in DPN. These findings link diabetic and inherited neuropathies through a shared metabolic mechanism, identifying serine metabolism as a potential therapeutic target.

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Global Health Injustice From Climate Change Driven By Consumption

Rupcic, L.; Yoo, D.; Levasseur, A.; Alexandre, C.; Laurent, A.; Jolliet, O.

2026-06-12 public and global health 10.64898/2026.06.10.26355381 medRxiv
Top 4%
1.7%
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Climate change imposes unequal health burdens from heat and cold, disproportionately harming vulnerable nations least responsible for emissions. A framework to quantitatively attribute this damage to different countries' consumption patterns has been missing. We developed a global framework linking consumption-based greenhouse gas emissions to country-specific health burdens, measured in Disability-Adjusted Life Years (DALYs). Our results quantify the profound scale of this externalized harm. For example, average North American consumption imposes a global health burden of 34 days of healthy life per person per year, without net damage suffered. In contrast, Sub-Saharan Africa endures 25 days per person per year despite minimal emissions. The resulting Health Injustice Index provides a powerful instrument for climate accountability, reframing responsibility in terms of tangible human health impacts.