Citations

Abstract Pathogenic variants in cardiomyopathy genes confer substantial disease risk, yet clinical penetrance varies widely. The population-level prevalence, age-specific penetrance, and the extent to which polygenic susceptibility modifies disease risk across diverse ancestries remain poorly defined. This population-based cohort study leveraged genome sequencing and linked electronic health record data from the All of Us Research Program (n=414,830). This study found that P/LP variants in cardiomyopathy-associated genes were present in 0.91% of participants (95% CI, 0.88%–0.94%), with similar prevalence across ancestry groups. Compared with non-carriers, variant carriers had significantly higher odds of all-cause heart failure (ACHF, OR, 2.58; 95% CI, 2.31–2.89), non-ischemic heart failure (NIHF, OR, 2.74; 95% CI, 2.42–3.10), and non-ischemic cardiomyopathy (NICM, OR, 4.99; 95% CI, 4.44–5.63). Among carriers, by age 50 years, 24.5% (95% CI, 14.5%–33.4%) developed ACHF, 17.2% (95% CI, 8.8%–24.8%) developed NIHF, and 30.1% (95% CI, 19.5%–40.2%) developed NICM. Higher polygenic risk for heart failure was independently associated with increased risk of ACHF (OR, 1.81; 95% CI, 1.74–1.89), NIHF (OR, 1.66; 95% CI, 1.58–1.75), and NICM (OR, 1.69; 95% CI, 1.59–1.80). Among carriers with elevated polygenic risk, odds of disease were substantially higher than among non-carriers at average polygenic risk (ACHF: OR, 4.71; 95% CI, 4.17–5.32; NIHF: OR, 4.56; 95% CI, 3.99–5.22; NICM: OR, 8.51; 95% CI, 7.44–9.73). Results showed that P/LP variants in cardiomyopathy genes were relatively common in this large, ancestrally diverse cohort, and conferred increased risk of cardiomyopathy and HF, with incomplete but clinically meaningful penetrance. Polygenic risk for HF independently and additively increased disease risk across ancestries. Integrating both may improve risk stratification and enable more precise, equitable care.

ABSTRACT Polyglucosan body myopathy type 2 (PGBM2; OMIM #616199) is an autosomal recessive myopathy caused by biallelic variants in GYG1 , which encodes glycogenin‐1. It is characterized by progressive muscle weakness and PAS‐positive, diastase‐resistant polyglucosan inclusions on muscle biopsy. We report a 64‐year‐old woman who developed progressive proximal weakness beginning in her early 50s, with polyglucosan bodies identified on muscle histopathology. Genome sequencing (GS) detected a single heterozygous pathogenic splice‐site variant, NM_004130.4( GYG1 ):c.143+3G>C. Given strong histopathologic evidence of PGBM2, GS data were reanalyzed, revealing an additional rare deep intronic variant, NM_004130.4( GYG1 ):c.7+992T>G, predicted to activate a cryptic exon. RNA sequencing (RNA‐seq) confirmed aberrant splicing from both variants, demonstrating exon 2 skipping associated with c.143+3G>C and cryptic exon inclusion caused by c.7+992T>G. Variant phasing posed a diagnostic challenge due to unavailable parental DNA, and long‐range PCR results were inconclusive. Long‐read GS definitively demonstrated that the two variants were in trans , establishing compound heterozygosity and confirming the molecular diagnosis. These findings enabled reclassification of the deep intronic variant as likely pathogenic. This case highlights the diagnostic limitations of conventional phasing approaches in adult‐onset recessive disorders and demonstrates the clinical utility of integrating genome reanalysis, RNA‐seq, and long‐read GS for resolving complex phasing challenges.

Abstract Introduction Mature T-cell lymphomas, including aggressive nodal PTCL, advanced stage CTCL, and extranodal cytotoxic lymphomas, are associated with poor outcomes. While karyotype (KT) abnormalities are frequently detected in these diseases, limited data exist on their prognostic significance. We evaluated the impact of KT abnormalities, including complex KT and specific chromosomal lesions, along with clinical and demographic factors, on overall survival (OS) in a single-center cohort. Methods We retrospectively reviewed 189 patients (pts) diagnosed with T-cell lymphoma who had successful metaphase KT at diagnosis from peripheral blood (PB), bone marrow (BM), or tumor tissue. T-cell lymphomas were classified according to WHO 2022 into nodal, extranodal/cytotoxic, and cutaneous subtypes. CTCLs were stratified into indolent (Early-stage CTCL, IA–IB) and aggressive (Sézary syndrome, transformed mycosis fungoides). KTs classified as normal, abnormal, and complex (≥3 abnormalities), and recurrent abnormalities were recorded. Baseline clinical and lab data were collected. OS was estimated using the Kaplan-Meier (KM) method with 95% confidence intervals (CI). Univariate Cox proportional hazards (CPH) model identified factors associated with OS, and significant variables were entered into multivariate CPH models. Results The median age was 66 years (IQR 55-74); 65% were male and 35% were female. Overall, 58% of pts were alive at analysis. Nodal PTCL was the most common subtype (113 pts, 60%), followed by early CTCL (30, 16%), aggressive CTCL (24, 13%), and extranodal lymphomas (22, 12%). KT was obtained from 166 BM (86%), 26 PB (13%), and 2 tissue (1%) specimens. Among abnormal KTs, 63% were from BM, 35% from PB, and 2% from tissue. Specific abnormalities included gain of chr1 (5%), gain of chr3 (5%), gain of chr7 (5%), gain of chr8 (5%), monosomy 5 or del(5q) (4%), monosomy 9 or del(9q13q22) (4%), Monosomy 10 (4%), loss of chrY (5%), and presence of marker chromosomes (5%).Of the 189 pts, 48 (25%) had an abnormal KT, while 141 (75%) had a normal KT. Complex KT was observed in 31 (16%) pts. Abnormal non-complex and complex KTs were seen respectively in: aggressive CTCL (8%, 42%), nodal PTCL (4%, 13%), extranodal (9%, 14%), and early CTCL (27%, 10%). KM survival analysis showed a median OS for the entire cohort of 95 months (95% CI: 65-245). Pts with a normal KT had a median OS of 143 months (95% CI: 81-inf) compared with 34 months (95% CI: 18-83) for those with an abnormal KT. Pts without a complex KT had a median OS of 144 months (95% CI: 85-inf), whereas those with a complex KT had 14 months (95% CI: 4-25). For specific abnormalities, pts with gain of chr7 had OS of 3 months, gain of chr8 had 19 months, monosomy 5 or del(5q) had 4 months, loss of chrY had 30 months, gain of chr1 had 4.5 months, gain of chr3 had 7.5 months, monosomy 9 or del(9q13q22) had 2 months, monosomy 10 had 17 months, and marker chromosome presence had 5.5 months. Univariate CPH identified complex KT (HR = 3.9, p < 0.001), gain of chr1 (HR = 5.7, p < 0.001), gain of chr3 (HR = 4.6, p < 0.001), monosomy 5 or del(5q) (HR = 4.6, p < 0.001), gain of chr7 (HR = 4.2, p < 0.001), gain of chr8 (HR = 3.3, p < 0.001), monosomy 9 or del(9q13q22) (HR = 4.9, p < 0.001), monosomy 10 (HR = 2.8, p = 0.008), and marker chromosomes (HR = 4.6, p < 0.001) as adverse factors. Higher platelet count was protective (HR = 0.9, p < 0.001), while greater number of abnormalities increased hazard (HR = 1.1, p < 0.001). In multivariate CPH model, complex KT (HR = 3.1, 95% CI: 1.2-8.2, p = 0.019), monosomy 9 or del(9q13q22) (HR = 4.4, 95% CI: 1.2-15.4, p = 0.022), gain of chr1 (HR = 3.5, 95% CI: 1.1-11.8, p = 0.042), and low platelet count (HR = 0.98, 95% CI: 0.97-0.99, p = 0.006) remained independent predictors of poor OS. Conclusion: We demonstrate that cytogenetic abnormalities detected in PB or BM, most notably complex KTs, confer a markedly poor prognosis in aggressive T-cell lymphomas. The integration of KT data with clinical parameters, such as platelet count, offers a powerful approach to refine risk stratification, identify biologically high-risk subgroups, and potentially guide personalized therapeutic strategies in this challenging disease spectrum. To our knowledge, this is one of the largest single-center studies assessing the prognostic significance of KT in mature T-cell lymphomas, providing novel insights into the role of specific chromosomal lesions in patient outcomes.

DNA methylation is an essential epigenetic modification that plays a crucial role in regulating gene expression and maintaining genomic stability. With the advancement in sequencing technology, methylation studies have provided valuable insights into the diagnosis of rare diseases through the various identification of episignatures, epivariation, epioutliers, and allele-specific methylation. However, current methylation studies are not without limitations. This mini-review explores the current understanding of DNA methylation in rare diseases, highlighting the key mechanisms and diagnostic potential, and emphasizing the need for advanced methodologies and integrative approaches to enhance the understanding of disease progression and design more personable treatment for patients, given the nature of rare diseases.