Human Mutation最新文献

{"title":"Characterisation of a LINE-1 Insertion in the RP1 Gene by Targeted Adaptive Nanopore Sequencing in a Family with Retinitis Pigmentosa","authors":"Michael P. Backlund,&nbsp;Pauliina Repo,&nbsp;Harri Kangas,&nbsp;Kati Donner,&nbsp;Eeva-Marja Sankila,&nbsp;Julia Krootila,&nbsp;Maarjaliis Paavo,&nbsp;Kirmo Wartiovaara,&nbsp;Tero T. Kivelä,&nbsp;Joni A. Turunen","doi":"10.1155/2024/6580561","DOIUrl":"10.1155/2024/6580561","url":null,"abstract":"<p>Retinitis pigmentosa (RP) is a group of inherited degenerative retinal disorders affecting more than 1.5 million people worldwide. For 30-50% of individuals with RP, the genetic cause remains unresolved by current clinical diagnostic gene panels. It is likely explained by variants in novel RP-associated genes or noncoding regulatory regions, or by complex genetic alterations such as large structural variants. Recent developments in long-read sequencing techniques have opened an opportunity for efficient analysis of complex genetic variants. We analysed a Finnish family with dominantly inherited RP affecting six individuals in three generations. Two affected individuals underwent a comprehensive clinical examination in combination with a clinical diagnostic gene panel, followed by whole exome sequencing in our laboratory. They exhibited typical signs of RP, yet initial sequence analysis found no causative variants. Reanalysis of the sequencing data detected a LINE-1 (L1) retrotransposon insertion of unknown size in exon 4 of the RP1 axonemal microtubule-associated (<i>RP1</i>) gene. The large chimeric L1 insertion that segregated with the disease was further characterised using targeted adaptive nanopore sequencing of <i>RP1</i>, allowing us to identify a 5.6 kb L1 transposable element insertion in <i>RP1</i> as the cause of RP in this family with dominantly inherited RP.</p>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2024 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139790533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional Analysis of 3′UTR Variants at the LDLR and PCSK9 Genes in Patients with Familial Hypercholesterolemia","authors":"Javier Sanguino Otero,&nbsp;Carmen Rodríguez-Jiménez,&nbsp;Jose Mostaza Prieto,&nbsp;Carlos Rodríguez-Antolín,&nbsp;Ana Carazo Alvarez,&nbsp;Francisco Arrieta Blanco,&nbsp;Sonia Rodríguez-Nóvoa","doi":"10.1155/2024/9964734","DOIUrl":"10.1155/2024/9964734","url":null,"abstract":"<p>Familial hypercholesterolemia (FH) is an autosomal dominant disease with an estimated prevalence of 1 in 200-250 individuals. Patients with FH are at increased risk of premature coronary artery disease. Early diagnosis and treatment are essential for improving clinical outcomes. In many cases, however, the genetic diagnosis is not confirmed. At present, routine genetic testing does not analyze the 3^′UTR regions of <i>LDLR</i> and <i>PCSK9</i>. However, 3^′UTR-single nucleotide variants could be of interest because they can modify the target sequence of miRNAs that regulate the expression of these genes. Our study fully characterizes the 3^′UTR regions of <i>LDLR</i> and <i>PCSK9</i> in 409 patients with a suspected diagnosis of FH using next-generation sequencing. In 30 of the 409 patients, we found 21 variants with an allelic frequency of &lt;1%; 14 of them at 3^′UTR-<i>LDLR</i> and 8 at 3^′UTR-<i>PCSK9</i>. The variants’ pathogenicity was studied <i>in silico</i>; subsequently, a number of the variants were functionally validated using luciferase reporter assays. <i>LDLR</i>:c.^∗653G &gt; C showed a 41% decrease in luciferase expression, while <i>PCSK9</i>:c.^∗950C &gt; T showed a 41% increase in PCSK9 expression, results that could explain the hypercholesterolemia phenotype. In summary, the genetic analysis of the 3^′UTR regions of <i>LDLR</i> and <i>PCSK9</i> could improve the genetic diagnosis of FH.</p>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2024 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139792868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A De Novo Noncoding RARB Variant Associated with Complex Microphthalmia Alters a Putative Regulatory Element","authors":"Maria R. Replogle,&nbsp;Samuel Thompson,&nbsp;Linda M. Reis,&nbsp;Elena V. Semina","doi":"10.1155/2024/6619280","DOIUrl":"10.1155/2024/6619280","url":null,"abstract":"<p>Retinoic acid receptor beta (<i>RARB</i>) is a transcriptional regulator crucial for coordinating retinoic acid- (RA-) mediated morphogenic movements, cell growth, and differentiation during eye development. Loss- or gain-of-function <i>RARB</i> coding variants have been associated with microphthalmia, coloboma, and anterior segment defects. We identified a <i>de novo</i> variant c.157+1895G&gt;A located within a conserved region (CR1) in the first intron of <i>RARB</i> in an individual with complex microphthalmia and significant global developmental delay. Based on the phenotypic overlap, we further investigated the possible effects of the variant on mRNA splicing and/or transcriptional regulation through <i>in silico</i> and functional studies. <i>In silico</i> analysis identified the possibility of alternative splicing, suggested by one out of three (HSF, SpliceAI, and MaxEntScan) splicing prediction programs, and a strong indication of regulatory function based on publicly available DNase hypersensitivity, histone modification, chromatin folding, and ChIP-seq data sets. Consistent with the predictions of SpliceAI and MaxEntScan, <i>in vitro</i> minigene assays showed no effect on <i>RARB</i> mRNA splicing. Evaluation of CR1 for a regulatory role using luciferase reporter assays in human lens epithelial cells demonstrated a significant increase in the activity of the <i>RARB</i> promoter in the presence of wild-type CR1. This activity was further significantly increased in the presence of CR1 carrying the c.157+1895G&gt;A variant, suggesting that the variant may promote <i>RARB</i> overexpression in human cells. Induction of <i>RARB</i> overexpression in human lens epithelial cells resulted in increased cell proliferation and elevated expression of <i>FOXC1</i>, a known downstream target of RA signaling and a transcription factor whose down- and upregulation is associated with ocular phenotypes overlapping the <i>RARB</i> spectrum. These results support a regulatory role for the CR1 element and suggest that the <i>de novo</i> c.157+1895G&gt;A variant affecting this region may alter the proper regulation of <i>RARB</i> and, as a result, its downstream genes, possibly leading to abnormal development.</p>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2024 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139592340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Macrocephaly and Digital Anomalies Expand the Phenotypic Spectrum of PGAP2 Variants in Hyperphosphatasia with Impaired Intellectual Development Syndrome 3 (HPMRS3)","authors":"Seda Susgun,&nbsp;Afif Ben-Mahmoud,&nbsp;Franz Rüschendorf,&nbsp;Bonsu Ku,&nbsp;Syeda Iqra Hussain,&nbsp;Solveig Schulz,&nbsp;Oliver Puk,&nbsp;Saskia Biskup,&nbsp;Jonathan D. J. Labonne,&nbsp;Dilan Wellalage Don,&nbsp;Vijay Gupta,&nbsp;Tae-Ik Choi,&nbsp;Saadullah Khan,&nbsp;Naveed Wasif,&nbsp;Yves Lacassie,&nbsp;Lawrence C. Layman,&nbsp;Sibel Aylin Ugur Iseri,&nbsp;Cheol-Hee Kim,&nbsp;Hyung-Goo Kim","doi":"10.1155/2024/5518289","DOIUrl":"10.1155/2024/5518289","url":null,"abstract":"<p>Glycosylphosphatidylinositols (GPIs) anchor over 150 proteins as GPI-anchored proteins (GPI-APs) with crucial roles in diverse biological processes. The highly conserved biosynthesis of GPI-APs involves precise steps with at least 21 genes, categorized as <i>PIG</i> and <i>PGAP</i> genes. Pathogenic variants in these genes are linked to human diseases, highlighting the importance of each biosynthesis step. <i>PGAP2</i> stands out among these genes due to its association with an expanded clinical spectrum of neurodevelopmental disorder (NDD) phenotypes with biallelic pathogenic variants. We present four patients from two families, one consanguineous and the other nonconsanguineous, each displaying distinct clinical presentations, including intellectual disability, hyperphosphatasia, hearing impairment, and epilepsy, as well as craniofacial and digital anomalies. Genetic analyses revealed homozygous and novel compound heterozygous missense variants in <i>PGAP2</i> in four affected individuals, confirming the molecular diagnosis of hyperphosphatasia with impaired intellectual development syndrome 3 (HPMRS3). Importantly, the three amino acids affected by missense variants exhibit complete conservation in 10 vertebrate species, illuminating their crucial role in the gene’s functionality. Protein modeling provided additional evidence for the pathogenicity of the three substitutions, demonstrating their detrimental impact on protein folding and putative protein-protein interactions, ultimately leading to impaired protein function. The four patients in our study displayed common phenotypic features, such as brachydactyly, camptodactyly, and syndactyly, which have not been previously documented in individuals with <i>PGAP2</i> variants. Notably, the occurrence of macrocephaly in two affected brothers from a consanguineous Pakistani family represents a novel finding. These previously unreported digital anomalies, along with macrocephaly and the identification of novel compound heterozygous variants, contribute to the expansion of the phenotypic and genotypic spectrum of HPMRS3 associated with <i>PGAP2</i> variants.</p>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2024 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139381426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Disruption of OVOL2 Distal Regulatory Elements as a Possible Mechanism Implicated in Corneal Endothelial Dystrophy","authors":"Lubica Dudakova,&nbsp;Lenka Noskova,&nbsp;Stanislav Kmoch,&nbsp;Martin Filipec,&nbsp;Ales Filous,&nbsp;Alice E. Davidson,&nbsp;Vasileios Toulis,&nbsp;Jana Jedlickova,&nbsp;Pavlina Skalicka,&nbsp;Hana Hartmannova,&nbsp;Viktor Stranecky,&nbsp;Jana Drabova,&nbsp;Drahuse Novotna,&nbsp;Marketa Havlovicova,&nbsp;Zdenek Sedlacek,&nbsp;Petra Liskova","doi":"10.1155/2024/4450082","DOIUrl":"10.1155/2024/4450082","url":null,"abstract":"<p>The genetic architecture of corneal endothelial dystrophies remains unknown in a substantial number of affected individuals. The proband investigated in the current study was diagnosed in the neonatal period with bilateral corneal opacification due to primary endothelial cell dysfunction. Neither his parents nor his sister had signs of corneal disease. Conventional karyotyping revealed a <i>de novo</i> translocation involving chromosomes 3 and 20, t(3;20)(q25;p11-12). Following genome and targeted Sanger sequencing analysis, the breakpoints were mapped at the nucleotide level. Notably, the breakpoint on chromosome 20 was identified to lie within the same topologically associated domain (TAD) as corneal endothelial dystrophy-associated gene <i>OVOL2</i>, and it is predicted to disrupt distal enhancers. The breakpoint at chromosome 3 is located within intron 2 of <i>PFN2</i>, which is currently not associated with any human disease. Further interrogation of the proband’s genome failed to identify any additional potentially pathogenic variants in corneal endothelial dystrophy-associated genes. Disruption of a candidate <i>cis</i>-regulatory element and/or positional effects induced by translocation of <i>OVOL2</i> to a novel genomic context may lead to an aberrant <i>OVOL2</i> expression, a previously characterized disease mechanism of corneal endothelial dystrophy. Further research is necessary to explore how disruption of regulatory elements may elucidate genetically unsolved corneal endothelial dystrophies.</p>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2024 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139386823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Compendium of Clinical Variant Classification for 2,246 Unique ABCA4 Variants to Clarify Variant Pathogenicity in Stargardt Disease Using a Modified ACMG/AMP Framework","authors":"Stéphanie S. Cornelis,&nbsp;Miriam Bauwens,&nbsp;Lonneke Haer-Wigman,&nbsp;Marieke De Bruyne,&nbsp;Madhulatha Pantrangi,&nbsp;Elfride De Baere,&nbsp;Robert B. Hufnagel,&nbsp;Claire-Marie Dhaenens,&nbsp;Frans P. M. Cremers","doi":"10.1155/2023/6815504","DOIUrl":"10.1155/2023/6815504","url":null,"abstract":"<div>\u0000 <p>Biallelic variants in <i>ABCA4</i> cause Stargardt disease (STGD1), the most frequent heritable macular disease. Determination of the pathogenicity of variants in <i>ABCA4</i> proves to be difficult due to (1) the high number of benign and pathogenic variants in the gene; (2) the presence of many rare <i>ABCA4</i> variants; (3) the presence of complex alleles for which phasing data are absent; (4) the extensive variable expressivity of this disease and (5) reduced penetrance of hypomorphic variants. Therefore, the classification of many variants in <i>ABCA4</i> is currently of uncertain significance. Here, we complemented the <i>ABCA4</i> Leiden Open Variation Database (LOVD) with data from ~11,000 probands with <i>ABCA4</i>-associated inherited retinal diseases from literature up to the end of 2020. We carefully adapted the ACMG/AMP classifications to <i>ABCA4</i> incorporating ClinGen recommendations and assigned these classifications to all 2,246 unique variants from the <i>ABCA4</i> LOVD to increase the knowledge of pathogenicity. In total, 1,248 variants were categorized with a likely pathogenic or pathogenic classification, whereas 194 variants were categorized with a likely benign or benign classification. This uniform and improved structured reclassification, incorporating the largest dataset of <i>ABCA4</i>-associated retinopathy cases so far, will improve both the diagnosis as well as genetic counselling for individuals with <i>ABCA4</i>-associated retinopathy.</p>\u0000 </div>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2023 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2023/6815504","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139155220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"REVEL Is Better at Predicting Pathogenicity of Loss-of-Function than Gain-of-Function Variants","authors":"Jasmin J. Hopkins,&nbsp;Matthew N. Wakeling,&nbsp;Matthew B. Johnson,&nbsp;Sarah E. Flanagan,&nbsp;Thomas W. Laver","doi":"10.1155/2023/8857940","DOIUrl":"https://doi.org/10.1155/2023/8857940","url":null,"abstract":"<div>\u0000 <p>In silico predictive tools can help determine the pathogenicity of variants. The 2015 American College of Medical Genetics and Genomics (ACMG) guidelines recommended that scores from these tools can be used as supporting evidence of pathogenicity. A subsequent publication by the ClinGen Sequence Variant Interpretation Working Group suggested that high scores from some tools were sufficiently predictive to be used as moderate or strong evidence of pathogenicity. REVEL is a widely used metapredictor that uses the scores of 13 individual in silico tools to calculate the pathogenicity of missense variants. Its ability to predict missense pathogenicity has been assessed extensively; however, no study has previously tested whether its performance is affected by whether the missense variant acts via a loss-of-function (LoF) or gain-of-function (GoF) mechanism. We used a highly curated dataset of 66 confirmed LoF and 65 confirmed GoF variants to evaluate whether this affected the performance of REVEL. 98% of LoF and 100% of GoF variants met the author-recommended REVEL threshold of 0.5 for pathogenicity, while 89% of LoF and 88% of GoF variants exceeded the 0.75 threshold. However, while 55% of LoF variants met the threshold recommended for a REVEL score to count as strong evidence of pathogenicity from the ACMG guidelines (0.932), only 35% of GoF variants met this threshold (<i>P</i> = 0.0352). GoF variants are therefore less likely to receive the highest REVEL scores which would enable the REVEL score to be used as strong evidence of pathogenicity. This has implications for classification with the ACMG guidelines as GoF variants are less likely to meet the criteria for pathogenicity.</p>\u0000 </div>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2023 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2023/8857940","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143248403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating the Utility of REVEL and CADD for Interpreting Variants in Amyotrophic Lateral Sclerosis Genes","authors":"Michael R. Fiorini,&nbsp;Allison A. Dilliott,&nbsp;Sali M. K. Farhan","doi":"10.1155/2023/8620557","DOIUrl":"10.1155/2023/8620557","url":null,"abstract":"<div>\u0000 <p>Amyotrophic lateral sclerosis (ALS) is a debilitating neurodegenerative disease affecting approximately two per 100,000 individuals globally. While there are many benefits to offering early genetic testing to people with ALS, this has also led to an increase in the yield of novel variants of uncertain significance in ALS-associated genes. Computational (<i>in silico</i>) predictors, including REVEL and CADD, are widely employed to provide supporting evidence of pathogenicity for variants in conjunction with clinical, molecular, and other genetic evidence. However, <i>in silico</i> predictors are developed to be broadly applied across the human genome; thus, their ability to evaluate the consequences of variation in ALS-associated genes remains unclear. To resolve this ambiguity, we surveyed 20 definitive and moderate ClinGen-defined ALS-associated genes from two large, open-access ALS sequencing datasets (total people with ALS = 8,230; controls = 9,671) to investigate REVEL and CADD’s ability to predict which variants are most likely to be disease-causing in ALS. While our results indicate a predetermined pathogenicity threshold for REVEL that could be of clinical value for classifying variants in ALS-associated genes, an accurate threshold was not evident for CADD, and both <i>in silico</i> predictors were of limited value for resolving which variants of uncertain significance (VUS) may be likely pathogenic in ALS. Our findings allow us to provide important recommendations for the use of REVEL and CADD scores for variants and indicate that both tools should be used with caution when attempting to evaluate the pathogenicity of VUSs in ALS genetic testing.</p>\u0000 </div>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2023 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2023/8620557","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136349044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating the Utility of a New Pathogenicity Predictor for Pediatric Cardiomyopathy","authors":"Alyssa L. Rippert,&nbsp;Sarah Trackman,&nbsp;Danielle Burstein,&nbsp;J. William Gaynor,&nbsp;Heather Griffis,&nbsp;Christine Seymour,&nbsp;Rebecca Ahrens-Nicklas","doi":"10.1155/2023/8892833","DOIUrl":"10.1155/2023/8892833","url":null,"abstract":"<div>\u0000 <p>Pediatric cardiomyopathy (CM) has significant childhood morbidity and mortality which is caused by both genetic and environmental factors. Previous research has focused on identifying genetic variants in pediatric CM for diagnostic purposes, but not for risk stratification. The current study was modeled after previous work which showed an association between CardioBoost-classified disease-causing variants and an increased risk for severe clinical outcomes in adults with CM to assess if the same association is true in pediatric CM. This was a retrospective, single-center cohort study that evaluated outcomes in pediatric CM patients who were evaluated by the Children’s Hospital of Philadelphia (CHOP). CardioBoost (CB) scores were generated for these patients, and scores were categorized as ≤0.1, 0.1-0.9, and ≥0.9. Composite endpoint was freedom from a major adverse cardiac event (MACE). 104 patients were included in the final analysis. 32 (31%) had DCM, 45 (43%) had HCM, and 27 (26%) had other CM. There was no significant association between CB score and clinical outcome in pediatric CM patients. Overall, this study highlights the continued deficits in variant interpretation for pediatric CM. We recommend using caution when applying this tool to stratify clinical outcomes in the pediatric population.</p>\u0000 </div>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2023 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2023/8892833","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136233996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical SMN1 and SMN2 Gene-Specific Sequencing to Enhance the Clinical Sensitivity of Spinal Muscular Atrophy Diagnostic Testing","authors":"Cecelia R. Miller,&nbsp;Jin Fang,&nbsp;Pamela Snyder,&nbsp;Susan E. Long,&nbsp;Thomas W. Prior,&nbsp;Dan Jones,&nbsp;Matthew R. Avenarius","doi":"10.1155/2023/6436853","DOIUrl":"10.1155/2023/6436853","url":null,"abstract":"<div>\u0000 <p><i>Purpose</i>. Therapeutic advances in the treatment of spinal muscular atrophy (SMA) prompt the need for robust and efficient molecular diagnosis of this disease. Approximately five percent of SMA cases are attributable to one copy of <i>SMN1</i> with a hypomorphic or inactivating variant in <i>trans</i> with a deleted or converted allele. These intragenic variants are challenging to definitively localize to <i>SMN1</i> due to its sequence homology with the <i>SMN2</i> gene. To enhance the clinical sensitivity of SMA diagnostic testing, we present an optimized gene-specific sequencing assay to localize variants to either <i>SMN1</i> or <i>SMN2</i>. <i>Methods</i>. <i>SMN1</i> and <i>SMN2</i> genes are independently amplified by long-range allele-specific PCR. Long-range products are used in subsequent nested PCR reactions to amplify the coding exons of <i>SMN1</i> and <i>SMN2</i>. The resulting products are sequenced using standard Sanger-based methodologies and analyzed for disease-associated alterations. <i>Results</i>. 83 probands suspicious for a clinical diagnosis of SMA with a nondiagnostic <i>SMN</i> dosage result were sequenced for intragenic variants in the <i>SMN1</i> gene. Gene-specific sequencing revealed likely disease-associated variants in <i>SMN1</i> in 42 cases (50.6%). Of the 42 variants, 27 are unique including 16 loss-of-function variants, 9 missense variants, 1 in-frame deletion variant, and 1 splice site variant. <i>Conclusions</i>. Herein, we describe an optimized assay for clinical sequencing of the full coding region of <i>SMN1</i> and <i>SMN2</i>. This assay uses standard techniques and equipment readily available to most molecular diagnostic laboratories.</p>\u0000 </div>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2023 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2023/6436853","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135728878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}