HGG Advances最新文献

{"title":"Uncovering the genetic architecture and evolutionary roots of androgenetic alopecia in African men.","authors":"Rohini Janivara, Ujani Hazra, Aaron Pfennig, Maxine Harlemon, Michelle S Kim, Muthukrishnan Eaaswarkhanth, Wenlong C Chen, Adebola Ogunbiyi, Paidamoyo Kachambwa, Lindsay N Petersen, Mohamed Jalloh, James E Mensah, Andrew A Adjei, Ben Adusei, Maureen Joffe, Serigne M Gueye, Oseremen I Aisuodionoe-Shadrach, Pedro W Fernandez, Thomas E Rohan, Caroline Andrews, Timothy R Rebbeck, Akindele O Adebiyi, Ilir Agalliu, Joseph Lachance","doi":"10.1016/j.xhgg.2025.100428","DOIUrl":"10.1016/j.xhgg.2025.100428","url":null,"abstract":"<p><p>Androgenetic alopecia is a highly heritable trait. However, much of our understanding about the genetics of male-pattern baldness comes from individuals of European descent. Here, we examined a dataset comprising 2,136 men from Ghana, Nigeria, Senegal, and South Africa that were genotyped using the Men of African Descent and Carcinoma of the Prostate Array. We first tested how genetic predictions of baldness generalize from Europe to Africa and found that polygenic scores from European genome-wide association studies (GWASs) yielded area under the curve statistics that ranged from 0.513 to 0.546, indicating that genetic predictions of baldness generalized poorly from European to African populations. Subsequently, we conducted an African GWAS of androgenetic alopecia, focusing on self-reported baldness patterns at age 45. After correcting for age at recruitment, population structure, and study site, we identified 266 moderately significant associations, 51 of which were independent (p < 10^-5, r² < 0.2). Most baldness associations were autosomal, and the X chromosome does not seem to have a large impact on baldness in African men. Although Neanderthal alleles have previously been associated with skin and hair phenotypes, within the limits of statistical power, we did not find evidence that continental differences in the genetic architecture of baldness are due to Neanderthal introgression. While most loci that are associated with androgenetic alopecia do not have large integrative haplotype scores or fixation index statistics, multiple baldness-associated SNPs near the EDA2R and AR genes have large allele frequency differences between continents. Collectively, our findings illustrate how population genetic differences contribute to the limited portability of polygenic predictions across ancestries.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100428"},"PeriodicalIF":3.3,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12000746/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Allele-specific silencing of a dominant SETX mutation in familial amyotrophic lateral sclerosis type 4.","authors":"Audrey Winkelsas, Athena Apfel, Brian Johnson, George Harmison, Kimberly Diaz Perez, Dongjun Li, Vivian G Cheung, Christopher Grunseich","doi":"10.1016/j.xhgg.2025.100435","DOIUrl":"10.1016/j.xhgg.2025.100435","url":null,"abstract":"<p><p>Amyotrophic lateral sclerosis 4 (ALS4) is an autosomal dominant motor neuron disease that is molecularly characterized by reduced R-loop levels and caused by pathogenic variants in senataxin (SETX). SETX encodes an RNA/DNA helicase that resolves three-stranded nucleic acid structures called R-loops. Currently, there are no disease-modifying therapies available for ALS4. Given that SETX is haplosufficient, removing the product of the mutated allele presents a potential therapeutic strategy. We designed a series of siRNAs to selectively target the RNA transcript from the ALS4 allele containing the c.1166T>C mutation (p.Leu389Ser). Transfection of HEK293 cells with siRNA and plasmids encoding either wild-type or mutant (Leu389Ser) epitope-tagged SETX revealed that three siRNAs specifically reduced mutant SETX protein levels while having minimal effect on the wild-type SETX protein. In ALS4 primary fibroblasts, siRNA treatment silenced the endogenous mutant SETX allele while sparing the wild-type allele and restored R-loop levels in patient cells. Our findings demonstrate that mutant SETX, differing from wild-type by a single nucleotide, can be effectively and specifically silenced by RNA interference.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100435"},"PeriodicalIF":3.3,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12023877/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143812657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multidisciplinary stakeholder-informed identification of key characteristics for implementation of workplace genetic testing.","authors":"Elizabeth Charnysh, Kunal Sanghavi, Kerry A Ryan, Alyx Vogle, Alexandra Truhlar, Subhamoy Pal, Jonathan M Reader, J Scott Roberts, Charles Lee, Anya E R Prince, W Gregory Feero","doi":"10.1016/j.xhgg.2025.100458","DOIUrl":"10.1016/j.xhgg.2025.100458","url":null,"abstract":"<p><p>Workplace genetic testing (wGT) is an evolving model for genetic testing where employees are offered consumer genetic testing through employer-sponsored wellness programs. However, the potential harms, benefits, and key characteristics for best implementation practices for wGT have yet to be defined. To address this issue, we conducted a three-round modified Delphi process, including multiple rounds of survey and a virtual deliberative workshop, with purposely chosen wGT stakeholders (employees, employers, ethical, legal, and social implications [ELSI] professionals, genetic testing industry representatives, and healthcare professionals) to share their perspectives. From the modified Delphi process, we identified 12 key characteristics for the implementation of wGT that were perceived to increase the potential for benefit while reducing the risk of potential harms. Most participants agreed that privacy/security, voluntariness, transparency, understanding and education, anti-discrimination, employee control, and evidence-based testing measures were both important (>90%) and necessary (>75%) for the implementation of wGT. However, some participants also expressed a lack of confidence in the likelihood of achieving these characteristics in wGT programs. Overall, stakeholders expressed qualified support for wGT at the conclusion of the modified Delphi process. Their perspectives on the topic varied over the course of the process and were at least partially contingent on whether the aforementioned 12 key characteristics were met. These findings help inform the establishment of a normative framework for wGT assessment.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100458"},"PeriodicalIF":3.3,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12169765/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical features and molecular mechanisms of RP1L1 variants causing occult macular dystrophy.","authors":"Yang Pan, Daisuke Iejima, Kazutoshi Yoshitake, Kazushige Tsunoda, Takeshi Iwata","doi":"10.1016/j.xhgg.2025.100461","DOIUrl":"10.1016/j.xhgg.2025.100461","url":null,"abstract":"<p><p>Occult macular dystrophy (OMD) is an inherited retinopathy characterized by progressive bilateral vision loss despite normal findings on fundoscopic examination, fluorescein angiography, and full-field electroretinography. Its pathogenesis remains unknown, and no treatments are available. Here, we performed whole-exome sequencing on 133 samples from 78 OMD pedigrees to identify pathogenic variants, using filters for minor allele frequency, function prediction, and retinal expression. We identified the RP1L1 c.133C>T, p.Arg45Trp (R45W) mutation as the sole pathogenic variant in two families with dominantly inherited OMD. Additionally, we discovered five other potentially pathogenic RP1L1 variants. Together, these six variants accounted for 33.33% of pedigrees, with R45W being the most prevalent, at 16.6%. The R45W mutation correlated with earlier onset, more severe clinical phenotypes, and abnormal intracellular localization rather than altered expression levels. R45W disrupted the intracellular localization of RP1L1 and RP1, compromising cell viability. In induced photoreceptor-like cells derived from OMD patients carrying R45W, we observed downregulation of the long noncoding RNA MEG3 and the PI3K/Akt pathway, alongside upregulation of extracellular matrix organization. These findings validate the etiologic role of RP1L1 and offer insights into the pathogenesis of OMD, thereby facilitating future research and therapeutic development.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100461"},"PeriodicalIF":3.3,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12206149/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144226964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitochondrial DNA variant detection in over 6,500 rare disease families by the systematic analysis of exome and genome sequencing data resolves undiagnosed cases.","authors":"Sarah L Stenton, Kristen Laricchia, Nicole J Lake, Sushma Chaluvadi, Vijay Ganesh, Stephanie DiTroia, Ikeoluwa Osei-Owusu, Lynn Pais, Emily O'Heir, Christina Austin-Tse, Melanie O'Leary, Mayada Abu Shanap, Chelsea Barrows, Seth Berger, Carsten G Bönnemann, Kinga M Bujakowska, Dean R Campagna, Alison G Compton, Sandra Donkervoort, Mark D Fleming, Lyndon Gallacher, Joseph G Gleeson, Goknur Haliloglu, Eric A Pierce, Emily M Place, Vijay G Sankaran, Akiko Shimamura, Zornitza Stark, Tiong Yang Tan, David R Thorburn, Susan M White, Maha S Zaki, Eric Vilain, Monkol Lek, Heidi L Rehm, Anne O'Donnell-Luria","doi":"10.1016/j.xhgg.2025.100441","DOIUrl":"10.1016/j.xhgg.2025.100441","url":null,"abstract":"<p><p>Variants in the mitochondrial genome (mtDNA) cause a diverse collection of mitochondrial diseases and have extensive phenotypic overlap with Mendelian diseases encoded on the nuclear genome. The mtDNA is not always specifically evaluated in patients with suspected Mendelian disease, resulting in overlooked diagnostic variants. Here, we analyzed a cohort of 6,660 rare disease families (5,625 genetically undiagnosed [84%]) from the Genomics Research to Elucidate the Genetics of Rare diseases (GREGoR) Consortium, as well as other rare disease cohorts. Using dedicated pipelines to address the technical challenges posed by the mtDNA-circular genome, variant heteroplasmy, and nuclear misalignment-we called single nucleotide variants, small insertions/deletions, and large mtDNA deletions from exome and/or genome sequencing data, in addition to RNA sequencing data when available. Diagnostic mtDNA variants were identified in 10 previously genetically undiagnosed families (1 large deletion, 8 reported pathogenic variants, and 1 previously unreported likely pathogenic variant), as well as candidate diagnostic variants in a further 11 undiagnosed families. In one additional undiagnosed proband, detection of >900 heteroplasmic variants provided functional evidence of pathogenicity to a de novo variant in the nuclear gene POLG (DNA polymerase gamma), responsible for mtDNA replication and repair. Overall, mtDNA variant calling from data generated by exome and genome sequencing-primarily for nuclear variant analysis-resulted in a genetic diagnosis for 0.2% of undiagnosed families affected by a broad range of rare diseases, as well as the identification of additional promising candidates in 0.2%.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":"6 3","pages":"100441"},"PeriodicalIF":3.3,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12278631/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144050879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing polygenic scores for cardiometabolic traits through tissue- and cell-type-specific functional annotations.","authors":"Kristjan Norland, Daniel J Schaid, Iftikhar J Kullo","doi":"10.1016/j.xhgg.2025.100427","DOIUrl":"10.1016/j.xhgg.2025.100427","url":null,"abstract":"<p><p>Functional genomic annotations can improve polygenic scores (PGS) within and between genetic ancestry groups. While general annotations are commonly used in PGS development, tissue- and cell-type-specific annotations derived from open chromatin and gene expression experiments may further enhance PGS for cardiometabolic traits. We developed PGS for 14 cardiometabolic traits in the UK Biobank using SBayesRC. We integrated GWAS summary statistics from FinnGen and GLGC with three annotation sources: (1) Baseline-LD model version 2.2 (general annotations), (2) cell-type-specific snATAC-seq peaks, and (3) tissue-specific eQTLs/sQTLs. We created PGS using two EUR LD reference panels (1.2 million [1.2M] HapMap3 variants and 7M imputed variants). Tissue- and cell-type-specific annotations showed stronger heritability enrichment than Baseline-LD annotations on average, particularly coronary snATAC-seq peaks and fine-mapped eQTLs. Without annotations, HapMap3 and 7M variant PGS performed similarly. However, with all annotations, 7M variant PGS outperformed HapMap3 variant PGS (8% average increase in relative performance in EUR). Compared to using no annotations, modeling Baseline-LD annotations improved performance by 5% for HapMap3 and 11% for 7M variant PGS, while modeling all annotations yielded improvements of 5% and 13%, respectively. Although annotations provided greater relative improvement for cross-ancestry prediction, they did not decrease the disparity in PGS performance between genetic ancestry groups. In conclusion, functional annotations improved PGS for cardiometabolic traits. Despite strong heritability enrichment, tissue- and cell-type-specific snATAC-seq and eQTL annotations provided marginal performance gains beyond general genomic annotations.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100427"},"PeriodicalIF":3.3,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12059674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143721703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A variant in RNF212B may contribute to female infertility and recurrent pregnancy loss.","authors":"Michelle E Darko, Michelle Kappy, Daniel Rabizadeh, Chaim Jalas, Eric J Forman, Paula Brady, Zev Williams","doi":"10.1016/j.xhgg.2025.100443","DOIUrl":"10.1016/j.xhgg.2025.100443","url":null,"abstract":"<p><p>Women with genetic causes of infertility are more likely to experience recurrent pregnancy loss (RPL). Advances in whole-genome sequencing (WGS) have allowed for the improved detection of such genes. One reproductively young patient with a history of RPL underwent 5 in vitro fertilization cycles with nearly complete arrest of blastocyst development and ubiquitous aneuploidy of maternal origin in arrested embryos. Here, we present the discovery of a gene variant, RNF212B, as a potential genetic cause of female infertility and RPL. DNA was extracted and submitted for WGS. After filtering out variants with Genome Aggregation Database allele frequencies exceeding 0.25%, we identified 87 unique variants and conducted a literature search to identify potential associations with infertility. PGT-A analysis of arrested embryos revealed extensive aneuploidies affecting many chromosomes in all embryos. Maternal WGS revealed a homozygous stop-gain mutation in the RNF212B gene. RNF212 has been shown to interact with proteins involved in meiotic recombination, including DMC1 and DNA repair protein RAD51. This homozygous nonsense mutation in the RNF212B gene may be responsible for the presence of aberrant oogonium and for disrupting the meiotic recombination process, thereby contributing to female infertility and RPL.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":"6 3","pages":"100443"},"PeriodicalIF":3.3,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12134597/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143999769","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Common genetic modifiers influence cardiomyopathy susceptibility among the carriers of rare pathogenic variants.","authors":"Samantha J Klasfeld, Katherine A Knutson, Melissa R Miller, Eric B Fauman, Joanne Berghout, Rob Moccia, Hye In Kim","doi":"10.1016/j.xhgg.2025.100460","DOIUrl":"10.1016/j.xhgg.2025.100460","url":null,"abstract":"<p><p>Cardiomyopathy presents a significant medical burden due to frequent hospitalizations and invasive interventions. While cardiomyopathy is considered a rare monogenic disorder caused by rare pathogenic variants in a few genes, emerging evidence suggests that common genetic modifiers influence disease penetrance and clinical variability. Quantifying the interplay between common genetic modifiers and rare pathogenic variants is challenging due to the rarity of subjects with cardiomyopathy and pathogenic variant carriers. In this study, we utilized large-scale genetic and phenotypic data from the UK Biobank to refine the genetic architecture of hypertrophic and dilated cardiomyopathies. Using ClinVar annotations and variant effect prediction tools, we first identified known and predicted pathogenic variants and evaluated their association with disease risk, age of diagnosis, and quantitative cardiac phenotypes that reflect disease progression. We next examined the impact of polygenic risk scores on disease in the combined sets of known and predicted pathogenic variant carriers. Indeed, the polygenic risk scores were significantly associated with increased disease risk, with rare pathogenic variant carriers in the top 20% of polygenic risk having 5.7 and 2.3 times higher risk than those in the bottom 20% for hypertrophic and dilated cardiomyopathies, respectively. We observed stronger associations in the carrier sets that included predicted pathogenic variant carriers, suggesting improved statistical power. In summary, our study adds to the evidence that common genetic modifiers influence the cardiomyopathy disease risk among rare pathogenic variant carriers and illustrates the benefits and limitations of incorporating variant effect predictions to examine the polygenic influence in rare disease variant carriers.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100460"},"PeriodicalIF":3.3,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12278620/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Long-read sequencing is required for precision diagnosis of incontinentia pigmenti.","authors":"Monica H Wojcik, Robin D Clark, Abdallah F Elias, Casie A Genetti, Jill A Madden, Dana Simpson, Linda Golkar, Miranda P G Zalusky, Angela L Miller, Araceli Rodriguez, Joy Goffena, Camille A Dash, Nikhita Damaraju, Sophia B Gibson, Sophie H R Storz, Zachary B Anderson, Jonas A Gustafson, Isabelle Thiffault, Emily G Farrow, Tomi Pastinen, Jasmine Lin, Jennifer T Huang, Alan H Beggs, Pankaj B Agrawal, David T Miller, Danny E Miller","doi":"10.1016/j.xhgg.2025.100468","DOIUrl":"10.1016/j.xhgg.2025.100468","url":null,"abstract":"<p><p>Incontinentia pigmenti (IP) is caused by loss-of-function variants in IKBKG, with molecular genetic diagnosis complicated by a pseudogene. We describe seven individuals from three families with IP but negative clinical genetic testing in whom long-read sequencing identified causal variants, including one family with the common exon 4-10 deletion not identified by conventional clinical genetic testing. Concurrent methylation analysis explained disease severity in one individual who died from neurologic complications, identified a mosaic variant in an individual with an atypical presentation, and confirmed skewed X chromosome inactivation in an XXY individual.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100468"},"PeriodicalIF":3.3,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12256307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144294994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targeted long-read cDNA sequencing reveals novel splice-altering pathogenic variants causing retinal dystrophies.","authors":"Dalila Capasso, Roberta Zeuli, Gavin Arno, Michael Kwint, Raoul Timmermans, Karla A Ruiz-Ceja, Marianthi Karali, Francesca Simonelli, Sabrina Signorini, Enza Maria Valente, Frans P M Cremers, Sandro Banfi, Susanne Roosing, Daan M Panneman, Suzanne E de Bruijn","doi":"10.1016/j.xhgg.2025.100442","DOIUrl":"10.1016/j.xhgg.2025.100442","url":null,"abstract":"<p><p>Splice-altering variants are suggested to be responsible for part of the missing heritability of inherited retinal diseases (IRDs). The interpretation of these variants is challenging as functional evidence is required to validate pathogenicity. We explored the diagnostic value of a targeted long-read cDNA sequencing (lrcDNA-seq) approach to investigate IRD-associated splicing defects. For each affected individual, RNA was isolated from blood, and for each candidate gene, cDNA amplicons, spanning the complete open reading frame or multiple exons, were generated and subjected to long-read sequencing. We validated our approach by assessing previously described pathogenic splice-altering variants in IRD-associated genes. Next, we investigated six genetically unexplained affected individuals, each carrying pathogenic variant(s) in NMNAT1. In two probands, we provided functional validation for previously identified variants of uncertain significance present on the second allele. In four other subjects, lrcDNA-seq revealed the partial inclusion of an SVA_F retrotransposon in the NMNAT1 mRNA, predicted to introduce a premature stop codon. We showed that targeted lrcDNA-seq is effective in characterizing splice defects and in identifying novel splice-altering variants and uncovered the IRD genetic basis for six previously unexplained subjects. We believe that the implementation of this technique has the potential to contribute to an increased diagnostic rate of IRDs.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":"6 3","pages":"100442"},"PeriodicalIF":3.3,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12099450/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144015315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}