Human Genomics

Abstract Background: Immune-mediated skin diseases frequently co-occur, but the molecular architecture connecting clinically distinct disorders, and the extent to which molecular proximity predicts shared therapeutic opportunity, remain incompletely defined. We constructed a multilayer skin diseasome integrating transcriptomic overlap, pathway enrichment, protein-interactome topology, curated disease associations, real-world clinical co-occurrence, and drug-perturbation signatures across psoriasis (PS), atopic dermatitis (AD), hidradenitis suppurativa (HS), vitiligo (VL), and chronic spontaneous urticaria (CSU), using sodium lauryl sulfate-induced irritant contact dermatitis (SLS-ICD) as a mechanistically distinct barrier-injury comparator. Methods: Differentially expressed genes (DEGs) were derived from publicly available NCBI Gene Expression Omnibus datasets and compared using exclusive pairwise and higher-order intersections. Gene Ontology biological-process enrichment characterized shared and condition-specific programs. Interactome-based network separation (S_AB) quantified the relative topological proximity of disease modules. DisGeNET enrichment generated candidate disease +associations, a selected subset of which was examined descriptively for patient co-occurrence in TriNetX. Candidate compounds were ranked by reversal of disease-associated expression signatures against LINCS L1000 perturbation profiles. Results: The largest exclusive DEG intersection occurred between PS and HS (2,060 genes), followed by AD-PS-HS (490), VL-PS (464), AD-PS (402), and VL-PS-HS (379). Fourteen genes were shared across PS, AD, HS, VL, and CSU but not SLS-ICD. Neutrophil-associated processes recurred across the immune-mediated conditions, whereas SLS-ICD was dominated by keratinization and epidermal-differentiation programs. PS and HS had the lowest observed network-separation value (S_AB = -0.594); SLS-ICD had positive S_AB values in all five comparisons, although this separation did not persist once module sizes were harmonized. DisGeNET linked the index conditions to diverse immune, cardiovascular, neurologic, and neoplastic categories; 42 of these candidate diseases were observed to co-occur with an index condition in the queried TriNetX cohorts. Drug-signature overlap was greatest between PS and CSU, despite their marginal interactome separation, indicating that interactome proximity and predicted pharmacologic reversal capture different dimensions of disease relatedness. mTOR/PI3K-pathway inhibitors were prominent among the psoriasis reversal candidates, while methotrexate and mycophenolate mofetil emerged from both the CSU signature and the curated gene set associated with HIV infection. Conclusion: Multilayer integration identified a connected molecular core among five immune-mediated skin diseases and a distinct SLS-ICD injury module. The discordance between interactome proximity and drug-signature overlap suggests that no single layer adequately defines disease relatedness. These findings provide a hypothesis-generating framework for prioritizing disease links and repurposing candidates, but controlled epidemiologic analyses and experimental validation are required before clinical or therapeutic inference.

Hypothyroidism has been associated with increased skin cancer risk, whereas greater genetic susceptibility to hypothyroidism is associated with lower risk. These opposing associations suggest that the average risk associated with hypothyroidism may conceal substantial heterogeneity among patients, and that genetic background could help identify those at highest risk. In this study, we analyzed more than 650,000 individuals across All of Us and FinnGen cohorts to determine whether a hypothyroidism polygenic risk score (H-PRS) stratifies skin cancer risk among patients with autoimmune hypothyroidism and whether integration of a skin cancer polygenic risk score (SC-PRS) further refines risk. In FinnGen, autoimmune hypothyroidism was associated with increased skin cancer hazard (hazard ratio [HR] = 1.10; 95% CI [1.06, 1.15]), whereas H-PRS was inversely associated with risk (HR=0.97 per 1-SD increase; 95% CI [0.95, 0.98]). The hypothyroidism x H-PRS interaction was also negative (HR=0.94; 95% CI [0.91, 0.98]), indicating greater hypothyroidism-associated risk at lower H-PRS. The hypothyroidism and H-PRS associations replicated in All of Us, and similar H-PRS risk gradients were observed for melanoma, basal cell carcinoma, and squamous cell carcinoma in both cohorts. Among hypothyroid patients, predicted 10-year risk increased with higher SC-PRS and lower H-PRS. Combined clinical-genetic profiles had HRs ranging from 2.32 at the 20th H-PRS/80th SC-PRS percentiles to 3.37 at the 5th/95th percentiles, exceeding published point estimates for the established dermatological risk factors. Among women aged 55, representing the more commonly affected sex at approximately the median age of diagnosis, 10-year risk of skin cancer was 14.9% (95% CI [8.4%, 20.9%]) in the highest-SC-PRS/lowest-H-PRS quartiles versus 2.8% (95% CI [1.0%, 4.7%]) in the opposite quartiles. Overall, these findings support PRS-guided risk stratification for targeted skin cancer prevention and surveillance.

Purpose A significant proportion of cases with rare inherited retinal disease (IRD) remain genetically unresolved following short-read whole genome sequencing (WGS). This study aimed to increase the diagnostic yield of two cohorts in a research setting. One cohort was previously screened by short-read WGS (n=120 cases), while the second cohort (n=28 cases) was not included in any previous short-read WGS studies. In contrast to the larger cohort, these cases only underwent either exome sequencing (ES) or single-molecule molecular inversion probe (smMIPs) sequencing as pre-screening in earlier studies. For all cases, we performed a stepwise, case by case reanalysis in which short-read WGS was generated (n=28 cases) and (re)analyzed short-read WGS data using an optimized approach. For a subset of cases (n=20) that remained unresolved, this was followed by long read WGS. Together, these steps aimed to improve the diagnostic yield in these cohorts. Methods Short-read WGS data of 148 IRD-cases were (re)analyzed using updated allele frequency databases, new variant caller and variant predictor tools, as well as updated and extended gene-panels to identify causal single nucleotide variants (SNVs) and structural variants (SVs). For 20 genetically unresolved cases with sufficient high-quality DNA available, long-read WGS was performed. Results The (re)analysis of short-read WGS data in the 120 previously WGS-screened unresolved cases resulted in a diagnostic yield of 15% (18/120). For the 28 individuals without prior WGS, performing WGS analysis within this study provided an additional yield of 32% (9/28). Furthermore, long-read WGS contributed two genetic diagnoses among the 20 long-read WGS-sequenced probands. Amongst other reasons, new genetic diagnoses were attributed to pathogenic variants in genes newly associated with IRDs and in genes that were not included in the gene panels applied in previous WGS studies. The Mobile Element Locator Tool facilitated the identification of two pathogenic Alu insertions in short-read WGS. Long-read WGS identified two additional pathogenic variants. Conclusion These results support periodic reanalysis of existing short-read WGS data as a key component of IRD genetic diagnostics, with selective long-read WGS representing a valuable additional approach for unresolved cases. Together, these complementary strategies offer a practical framework for improving molecular diagnosis and narrowing the remaining diagnostic gap in IRDs.

Structural variants (SVs) are larger genetic rearrangements such as deletions, duplications, and insertions and other forms of structural alterations. Given their large size, they can have an outsized effect on phenotype, however, the contribution of SVs to the genetic architecture of orofacial clefts (OFCs) is not well understood. In this study, we sought to better understand the contribution SVs to OFC risk by characterizing de novo SVs (dnSVs) in 1,549 probands with an OFC. Overall, we called 375 dnSVs in 307 probands (0.242 dnSVs per genome). The dnSV rate per genome was highest among individuals with cleft lip (CL, 0.29), followed by cleft lip and palate (CLP, 0.25) and cleft palate only (CP, 0.20), though differences across subtypes were not statistically significant. There were also no differences between sex or syndromic status, but we did identify a significant difference in the rate of duplications across OFC subtypes (p=0.005). Compared to CP (0.028), duplication rates were significantly higher for both CL (0.121; p = 0.003) and CLP (0.096; p = 0.002), suggesting a potential etiologic mechanism for CL/P. We systematically curated each dnSV to classify its potential for influencing OFC risk by examining the genes and regulatory elements disrupted by the SV and evidence for their role in craniofacial development or OFCs. We identified 22 dnSVs in regions associated with recurrent genomic disorders, including seven deletions and one duplication of the well-established OFC risk locus 22q11.2. Additionally, we identified 12 large (>1Mb) SVs, with eight meeting criteria for a likely pathogenic classification based on total gene involvement, and seven dnSVs disrupting well-known genes associated with autosomal dominant forms of OFC. The most notable was SATB2, for which we found four dnSVs, all in individuals with CP. Next, by combining evidence from recurrent dnSVs and de novo single nucleotide variants with Hi-C contact maps and predicted chromatin states from developing craniofacial tissues, we found new candidate genes for OFC risk including FHAD1, NBEA, NR3C2, and SPHKAP. Overall, dnSVs classified as likely pathogenic accounted for putative molecular diagnoses in approximately 1.67% of the cohort, with an additional 0.96% having variants of unknown significance with plausible risk for OFCs. Our results support dnSVs as an important component of OFC etiology and suggest their inclusion in analyses may improve diagnostic yield for affected individuals.

FBXO31 encodes the substrate receptor of an SCF (SKP1-CUL1-F-box) E3 ubiquitin ligase that recognizes C-terminal amide-bearing proteins (CTAPs) and targets them for proteasomal degradation, a function of particular importance in neurons. A recurrent de novo missense variant, c.1000G>A p.(Asp334Asn), reprograms FBXO31 substrate specificity and causes an autosomal-dominant neurodevelopmental disorder with spastic cerebral palsy through a neomorphic gain-of-function mechanism. By contrast, biallelic loss of function has tentatively been linked to a recessive disorder. Here we report a female patient, born to consanguineous parents, with moderate intellectual disability, developmental delay and dysmorphic features, who carries a homozygous 54.3 kb deletion removing exons 2-8 and the coding part of exon 9 of FBXO31. The deletion retains only the exon 1-encoded F-box domain, while removing the coding sequence for the entire C-terminal substrate-recognition region. It is predicted to result in loss of function. Segregation is consistent with autosomal-recessive inheritance, with both parents and three of five unaffected siblings being heterozygous carriers. Together with two previously reported recessive families and the experimentally established neomorphic action of p.(Asp334Asn), the homozygous deletion supports an FBXO31 allelic series comprising dominant gain of function and recessive biallelic loss of function.

Background: The inner ear is supplied by the labyrinthine artery, which is functionally close to an end artery with limited collateral reserve. Microvascular abnormalities have been implicated in sudden sensorineural hearing loss (SSNHL) and age-related hearing loss, yet inner-ear microvasculature cannot be assessed in vivo and current hearing genome-wide association studies (GWAS) are underpowered. We evaluated the shared genetic architecture of retinal arteriolar tortuosity (retina_AT) with blood pressure, cerebral small vessel disease (cSVD) and hearing phenotypes, and examined whether retinal microvasculature could serve as a candidate genetic window to inner-ear microvasculature. Methods: We used linkage-disequilibrium score regression (LDSC) to estimate SNP heritability for 19 phenotypes and genome-wide genetic correlations (rg) for 11 prespecified pairs. We ran approximate Bayes-factor colocalization (coloc.abf) between 19 independent retinal loci and systolic blood pressure (SBP), together with 95% credible-set fine-mapping, UCSC gene annotation, colocalization with GTEx aortic and tibial-artery expression QTL (eQTL) data and with white-matter hyperintensities (WMH), hearing-GWAS power calculations, and univariable and multivariable Mendelian randomization (MR) of blood pressure and heart rate on hearing. Results: Only retina_AT with SBP was significant genome-wide (rg = 0.10, P = 4.2x10, FDR q = 0.00042). The strongest retinal locus, 13q34, did not colocalize (PP.H3 = 0.996; peaks about 267 kb apart; allelic heterogeneity), whereas two secondary loci colocalized strongly--CSK at 15q24 (PP.H4 = 0.98; 3/3 credible variants within CSK) and PAWR at 12q21 (PP.H4 = 0.99; 3/5 within PAWR)--supported by tissue-matched, moderate eQTL evidence (PP.H4 = 0.71-0.75). At 13q34, retina_AT with WMH was an adequately powered null (PP.H4 = 0.019; only this region and phenotype were tested). On the hearing side, sharing of the blood-pressure magnitude (rg {approx} 0.10) was a near-powered null (about 1.5-fold larger sample needed for 80% power under that assumption, versus about 15-fold for weak rg {approx} 0.03 sharing), and rg [≥] 0.12 was excluded; MR found no robust causal effect. Conclusions: Retinal arteriolar tortuosity shows limited, distributed genetic sharing with blood pressure at the vascular-tone genes CSK and PAWR; no sharing with WMH was observed at 13q34 (only this region was tested). Retinal microvasculature may serve as a candidate genetic window to inner-ear microvasculature, but this analogy awaits direct testing by larger, vessel-oriented hearing GWAS and inner-ear tissue functional studies.

Background: Short-rib polydactyly syndrome type IV (Beemer-Langer syndrome) is a lethal skeletal ciliopathy that can result from biallelic pathogenic variants in KIAA0586 (TALPID3). Earlier clinical observations suggested an unusually high occurrence of this phenotype in Romani families from the Carpathian Basin. Methods: Whole-exome sequencing was performed in affected individuals from five independent families, and the frequency of KIAA0586 c.1815G>A was assessed in a Hungarian Romani genetic database of 500 individuals. Results: The affected individuals were homozygous for c.1815G>A, a splice-disrupting variant previously shown to cause exon 14 skipping. Four families self-identified as Roma from Hungary and one affected individual was from Turkey. Six heterozygous carriers were identified among 500 individuals in the Hungarian Romani cohort, corresponding to an allele frequency of 0.6%. This was markedly higher than the frequencies cited from ALFA (0.01%) and gnomAD (0.0014%). The Hungarian-Romani and Turkish affected individuals also shared genotypes at informative markers flanking the variant, supporting a shared ancestral haplotype. Conclusions: These observations strengthen evidence that KIAA0586 c.1815G>A is a founder allele enriched in at least some Romani populations. The data support consideration of ancestry-informed carrier testing in appropriately counseled families. Historical admixture may explain the occurrence of the same haplotype in a Turkish case, but this remains a hypothesis requiring broader population-genomic confirmation.

Abstract INTRODUCTION Despite major advances in genomic sequencing and analytical pipelines for rare disorders, more than 50% of affected individuals remain without a molecular diagnosis. One challenge is the interpretation of inherited variants exhibiting incomplete penetrance (IP). MATERIALS AND METHODS We developed a pipeline to systematically investigate inherited variants as the cause of rare disease in 4,325 families, consisting of affected probands and unaffected parents, from the Broad Center for Mendelian Genomics, part of the GREGoR Consortium. As a proof-of-concept of further omics follow-up, epigenomic and transcriptomic analyses were performed in one family harboring an inherited disease-causing frameshift variant in CHD8. RESULTS We identified 81 families where the affected proband harbored a putative disease-causing variant inherited from a reportedly unaffected parent. Clinical re-evaluation identified 30 families in which an inherited variant was considered diagnostic, including six previously missed diagnoses. In this cohort, inherited IP variants account for 1.6% of the diagnosed cases, with an overall diagnostic yield of 0.4% in the cohort. Methylation analysis of the CHD8 family confirmed a positive CHD8 clinical episignature in the male proband, but also in the reportedly unaffected mother. Transcriptomic analysis showed that despite similar CHD8 haploinsufficiency, the proband and mother displayed divergent downstream transcriptional effects. DISCUSSION This study highlights the importance of considering parentally inherited IP variants in rare disease, with at least 1 in 60 diagnostic variants inherited from a reportedly unaffected parent, and demonstrates the potential of integrating omics evaluation to improve variant interpretation.

Ancestry-related genomic variation may contribute to phenotypic diversity. However, its cellular consequences remain difficult to evaluate. To address this, we developed a human induced pluripotent stem cell (hiPSC)-based framework for investigating such phenotypes. We used the Japanese population as a model of Jomon-related and continental East Asian ancestry admixture. Jomon ancestry, estimated using the Jomon allele score (JAS), was associated with clinical measures, including renal-related traits and serum triglycerides in 34,152 Tohoku Medical Megabank participants. Peripheral blood mononuclear cell transcriptomics of donors from the upper and lower extremes of the JAS distribution (n = 10) suggested group-level differences in immune-related gene expression. To test whether the serum triglyceride association coincided with hepatic cellular phenotypes, we differentiated hiPSCs from these donors into hepatocyte-like cells. Neither intracellular triglycerides nor lipid-related gene expression differed between groups. These findings highlight the value of a genetically characterized hiPSC-based framework for investigating ancestry-associated phenotypes across cellular contexts.

Introduction: Killer-cell immunoglobulin-like receptor (KIR) gene content shapes natural killer-cell responses and varies substantially among populations. We examined whether worldwide KIR diversity reflects regional structure, isolation by distance, serial founder effects, or latitudinal gradients. Data and methods: Carrier frequencies for 11 variable KIR genes were obtained from the Allele Frequency Net Database. The primary analysis included 189 locally sampled, non-diaspora, non-mixed populations from 70 countries, comprising 25,469 individuals; 161 populations had complete 11-gene profiles. Diversity indices, ordination, clustering, permutation-based variance decomposition, Mantel tests, and regression models were used to characterize geographic structure. Serial founder effects were evaluated using four distance measures from East Africa, both globally and within the Old World. Models of latitude incorporated spatial autocorrelation. Prespecified sensitivity analyses evaluated alternative population sets, gene panels, geographic classifications, weighting schemes, and multivariate outlier exclusion. Results: Geographic region explained 53.5% of variation in KIR profiles, substantially exceeding the permutation-null expectation of 6.9%, although multivariate dispersion differed among regions. Twenty-five of 28 pairwise regional comparisons remained significant after false-discovery-rate correction. Isolation by distance was modest (Mantel r=0.3003) and weakened after controlling for region (r=0.1557). KIR diversity did not decline with distance from East Africa globally but decreased strongly within the Old World (expected heterozygosity {beta}=-0.0066 and standardized gene content {beta}=-0.0789). B-content decreased nominally with absolute latitude, but latitude was collinear with region and the association survived neither spatial modelling nor sensitivity analyses. Regional differentiation remained robust across analytical specifications, whereas the Old World decline was carried by gene content once standard errors were clustered by country. Conclusion: Worldwide KIR gene-content variation shows pronounced regional differentiation, modest isolation by distance, and no independent latitudinal gradient. Diversity declines with distance from East Africa across the Old World, supporting serial founder effects, but not once the Americas and Oceania are included.

CBX1-related syndrome is characterized by developmental delay, hypotonia, autistic features, and mild dysmorphic features. This syndrome is caused by heterozygous missense variants in CBX1, which encodes heterochromatin protein 1 beta (HP1{beta}). These variants are situated within the chromodomain of HP1{beta}, a critical region that mediates the interaction between HP1{beta} and trimethylated H3K9. While a prior study identified three individuals with pathogenic CBX1 variants, the variant and clinical spectrum of CBX1-related syndrome remains largely unknown. Here we report three patients with novel de novo heterozygous variants in CBX1. Patients with CBX1 p.(Leu40Pro) and p.(Cys60Arg) manifested with global developmental delay, while the patient with CBX1 p.(Cys60Gly) primarily exhibited speech delay without concurrent motor developmental delay. All variants reside within chromodomain of the HP1{beta} protein. Interestingly, in vitro cellular assays revealed that CBX1 p.(Cys60Gly) variant showed an intermediate cellular phenotype between the wild type and the CBX1 p.(Leu40Pro) and p.(Cys60Arg) variants, suggesting a possible genotype-phenotype correlation. This report provides further evidence that missense variants within the chromodomain of HP1{beta} cause a syndromic neurodevelopmental disorder, CBX1-related syndrome.

Psoriasis is a chronic skin disease characterized by red, scaly plaques mainly driven by dysregulated T cells that induce keratinocytes (KCs) proliferation and inflammation. Despite significant advancements in disease management through biologics and topical therapies, these treatments offer only temporary relief and fail to prevent disease recurrence. Considering the current therapeutic needs, we described herein a novel small molecule TEM1657, derived from 3,5-dicaffeoylquinic acid with anti-inflammatory potency in imiquimod-induced psoriasis mouse model as well as in Th17-stimulated KCs. Mechanistically, its action is mediated through modulation of mitochondrial dynamics, specifically via OPA1, an inner mitochondrial membrane protein that alters mitochondrial calcium influx, and further impacts cellular bioenergetics. Moreover, TEM1657 rapidly suppresses transcription of NFKBIZ and various other psoriasis-associated genes. These observations highlighted a pathway that represents an innovative target in psoriasis and other NFKBIZ-related disorders.

Type 1 diabetes (T1D) is a complex autoimmune disease characterized by the destruction of insulin-producing pancreatic {beta} cells. Both genetic susceptibility and epigenetic dysregulation contribute to T1D risk. Recent studies have reported {beta}-cell dysfunction before disease onset, suggesting that {beta}-cell-intrinsic mechanisms contribute to pathogenesis. However, the mechanistic link between disease-associated variants and {beta}-cell dysfunction remains poorly understood. We hypothesized that a subset of T1D-associated variants directly influences cell type-specific candidate cis-regulatory elements (cCREs) by disrupting transcription factor (TF) binding and altering gene expression. To define cell type-specific cCREs in human islets, we integrated publicly available epigenomic datasets, including bulk histone modification profiles and single-cell multiomic data from human pancreatic islets. We combined these data with T1D genome-wide association study (GWAS) variants to identify disease-associated SNPs located within enhancer regions. Using multiomic datasets from PANC-DB, we characterized cell type-specific chromatin accessibility in nondiabetic and T1D islets and identified regulatory regions that may control gene expression in {beta} cells and other islet cell types. We then applied ChromBPNet, a deep learning model that predicts base-pair-resolution chromatin accessibility from scATAC-seq data, to evaluate how specific variants may alter local regulatory activity. In parallel, we used TF footprinting to nominate TFs likely to bind these variant-containing regions. These analyses identified several T1D-associated SNPs predicted to alter chromatin accessibility at candidate TF binding sites, suggesting mechanisms by which noncoding variants may contribute to {beta}-cell dysfunction and T1D susceptibility. Our findings link T1D-associated variants to cell type-specific enhancer activity and regulatory pathways and provide candidates for future mechanistic studies.

Sebum lipids are one of the key ecological determinants of skin microbiome composition, where sebaceous sites are enriched with sebum utilising microbes such as Cutibacterium acnes. While sebaceous gland (SG) activation and sebogenesis are classically viewed as host-regulated processes, the association of C. acnes expansion with sebum production in the skin suggests a possible bidirectional host-microbe regulation. Using bacterial supernatants, we combined image-based lipid quantification, GC-FID metabolite profiling, lipid secretion quantification, and transcriptomic analysis to determine the metabolic drivers of the interaction between C. acnes and sebocytes. We found that C. acnes secretome significantly increased lipid droplet accumulation in sebocytes and propionate as the primary driver of this lipogenic response. Mechanistically, propionate reprogrammed the central carbon metabolism, redirecting carbon flux toward energy production and generation of precursors for lipid biosynthesis. Propionate also promoted lipid assembly pathways and modulated the composition of the secreted lipids from the treated sebocytes. We further show that propionate promotes expression of late sebocyte differentiation markers associated with holocrine secretion. Together, these findings redefine the relationship between microbiome and sebaceous glands, and identify C. canes as an active regulator promoting both sebogenesis and holocrine secretion for the release of lipids in the pilosebaceous unit.

CACNA1A-related disorders arise from altered function of the P/Q-type calcium channel Cav2.1 and encompass a broad spectrum of neurological phenotypes, including developmental and epileptic encephalopathy, familial hemiplegic migraine type 1 and episodic ataxia type 2. Although loss-of-function and gain-of-function mechanisms have both been implicated, interpretation of rare CACNA1A missense variants remains challenging because clinical presentation is heterogeneous and many variants identified through diagnostic sequencing remain classified as variants of uncertain significance. To generate clinically interpretable functional evidence, we developed a calibrated high-throughput automated patch-clamp assay to assess the CACNA1A variants. Twenty-six curated benign/likely benign and 30 curated pathogenic/likely pathogenic missense variants were expressed in Flp-In HEK293 cells with CACNB4 and CACNA2D1. We quantified current density, {Lambda}V0.5 activation,{Lambda}V0.5 inactivation and recovery from inactivation (T0.5 RFI), and used benign controls to define parameter-specific normal ranges with {+/-}3 Z-score thresholds. This multi-parameter framework classified all benign controls as functionally normal and 29 of 30 pathogenic controls as abnormal, yielding 100% specificity and 96.7% sensitivity. Current density identified 19 pathogenic controls with loss of function, while gating and recovery from inactivation identified additional abnormal variants with preserved or partially preserved current density. The assay generated likelihood ratios of 0.033 for normal function and 25.13 for abnormal function, supporting BS3 and PS3 functional evidence, respectively. Application to 23 CACNA1A variants identified in Australian patients showed abnormal function in all four variants already classified as pathogenic or likely pathogenic. Among 19 variants of uncertain significance, 11 were functionally abnormal and nine were reclassified as likely pathogenic after integration of PS3 evidence with other ACMG/AMP criteria. These data show that CACNA1A missense variants can produce loss-of-function, gain-of-function or mixed effects, and that multi-parameter functional assessment is required for accurate interpretation. This calibrated automated patch-clamp framework provides clinically interpretable evidence for refining CACNA1A variant classification in diagnostic practice.

Background: Pancreatic ductal adenocarcinoma (PDAC) is projected to become the second leading cause of cancer-related mortality, with an increasing incidence and dismal 10% survival at 5 years despite best available care. PDAC is characterized by low tumour cellularity, recurrent driver mutation alterations, and substantial inter and intra-tumoural heterogeneity. The influence of individual genetic features such as sex and ancestry on tumour heterogeneity remains poorly understood. Methods: We assembled a cohort of PDAC across five datasets for a total of 7,527 tumours. Measures of genomic instability were assessed across sex and ancestry on a global level (SNV density and percent genome altered by copy number events), and at a gene level for recurrent events. KRAS variant frequencies, ploidy and mRNA abundance were also evaluated. Ancestry was assigned using ADMIXTURE from germline genotypes where available, and patient reported otherwise. Results: We observed ancestry-specific mutation patterns in global point mutation density, with higher SNV burden in African PDAC tumours and lower SNV burden in Asian PDAC tumours as compared to European tumours. We also identified an ancestry bias in the driver gene, GNAS, in which driver SNVs in GNAS was detected more frequently in those of Asian ancestry, and less frequently in those of African ancestry. No sex- or ancestry-associations were found for KRAS, but individual KRAS variants showed a trend towards ancestry-related variation. Conclusions: These findings demonstrate that ancestry contributes to the genomic heterogeneity of PDAC, shaping both global and gene-specific mutation patterns. This work underscores the importance of including diverse ancestries in PDAC molecular profiling efforts which may inform the development of tailored molecular diagnostics and targeted therapies.

Pontocerebellar hypoplasia (PCH) is a group of ultrarare, neurodegenerative disorders characterized by cerebellar and pontine hypoplasia. Genetic analysis over the last two decades has revealed an increasing number of pathogenic variants in a wide range of broadly expressed genes functioning in RNA processing, tRNA metabolism, and translation. However, the mechanisms linking these ubiquitous processes to brain region-specific vulnerability are unknown. Here, we established a multi-level variant-to-function in silico framework to predict the molecular consequences of PCH-associated variants in TSEN complex genes. These variants were predicted to have heterogeneous effects on diverse protein properties, including stability, subcellular localization, and degradation, supporting variant-specific rather than uniform disease mechanisms. Complementary transcriptomic analyses showed that PCH-associated genes were not globally enriched in the prenatal cerebellum. Instead, their expression was coordinated in a stage- and cell type-specific manner during cerebellar development. We therefore hypothesize that multiple PCH-associated genes are regulated by a common set of transcription factors, providing an explanation of the selective vulnerability of the cerebellum and to the phenotypic convergence of genetically diverse PCH subtypes. In summary, this study prioritizes candidate variants for biochemical, cellular, and in vivo validation, and identifies regulatory programs, cell lineages, and developmental windows for targeted, mechanistically informed disease modelling.

Psoriasis is associated with increased cardiovascular morbidity, but the extent and structure of the shared genetic architecture remain incompletely understood. We integrated large-scale European-ancestry genome-wide summary statistics for psoriasis and seven cardiovascular diseases to quantify genetic overlap, model shared liability and prioritize candidate mechanisms. Psoriasis showed modest genetic correlations with all cardiovascular outcomes, but mixture modelling estimated that more than half of psoriasis-associated non-zero variants were shared with five cardiovascular diseases. Genomic structural equation modelling of a latent psoriasis-CVD factor identified 167 independent risk loci, including 50 not genome-wide significant in any component trait. Multimodal prioritization nominated 473 candidate genes and 90 approved compounds with therapeutic relevance, including shared targets involving PDE4B, GLP1R, KEAP1 and PRDM16. Mediation and Mendelian randomization analyses implicated cardiometabolic traits, although no single trait accounted for more than half of the shared liability. These results prioritize genetic mechanisms and pharmacological hypotheses for psoriasis-associated cardiovascular multimorbidity.

Identifying inherited cancer predisposition genes remains challenging. We leveraged the skin's high UV-mutagenic burden to discover susceptibility genes by studying patients with high frequency of basal cell carcinomas (hfBCC). We found that hfBCC patients had three-fold higher internal malignancy prevalence and identified a novel candidate EPHB2 cancer susceptibility mutation associated with BCC and prostate cancer. These findings demonstrate the skin's potential as a powerful platform for discovering cancer predisposition variants.

The prognostic relevance of peritumoral SULF1 transcript signal in oral squamous cell carcinoma (OSCC) is unclear. We assembled a retrospective cohort of 133 patients with 218 primary-site tissue-microarray cores; 131 patients had evaluable boundary features. Multiplex fluorescence imaging combined RNAscope SULF1, CK-pan, and DAPI. Tumor-stroma boundaries were annotated with the SULF1 channel hidden. We screened 50 exported boundary features across cumulative stromal bands of 35-300 um against recurrence-free survival (RFS), overall survival (OS), and disease-specific survival (DSS), with false-discovery-rate correction. The strongest DSS association was signal SD within 150 um (n = 107; 23 disease-specific deaths; HR = 2.20 per SD; 95% CI, 1.64-2.94; q = 2.1 x 10^-6). In 50 repeated 5-fold cross-validations with feature selection repeated within training folds, adding a boundary feature to AJCC stage increased mean held-out DSS c-index from 0.613 to 0.754 (delta C = +0.141; 2.5th-97.5th percentiles across repeats, +0.105 to +0.192). These percentiles describe split variability, not confidence intervals. The 150-um SD feature was selected in 39.2% of DSS training folds. The DSS association persisted after adjustment for mean signal, although the measurements were strongly correlated. Peritumoral SULF1 signal dispersion was associated with outcome beyond an ordinal AJCC-stage model; independent validation is required.