Journal of Medical Genetics最新文献

{"title":"Heterozygous <i>COL17A1</i> variants are a frequent cause of amelogenesis imperfecta.","authors":"Tero T Kivelä, Walter Lisch, Jayne E Weiss","doi":"10.1136/jmg-2024-110310","DOIUrl":"10.1136/jmg-2024-110310","url":null,"abstract":"","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"982"},"PeriodicalIF":3.5,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142108226","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":"From onset to blindness: a comprehensive analysis of <i>RPGR</i>-associated X-linked retinopathy in a large cohort in China.","authors":"Jiawen Wu, Junfeng Li, Daowei Zhang, Hongli Liu, Ting Li, Ping Xu, Yingke Zhao, Chenchen Li, Fangyuan Hu, Qian Li, Shenghai Zhang, Ji-Hong Wu","doi":"10.1136/jmg-2024-110088","DOIUrl":"10.1136/jmg-2024-110088","url":null,"abstract":"<p><strong>Background: </strong>Variants in the <i>RPGR</i> are the leading cause of X-linked retinopathies (XLRPs). Further in-depth investigation is needed to understand the natural history.</p><p><strong>Methods: </strong>Review of all case records, molecular genetic testing results, best-corrected visual acuity (BCVA), retinal imaging data (including fundus autofluorescence imaging and optical coherence tomography (OCT)), static visual field (VF) assessments and full-field electroretinogram.</p><p><strong>Results: </strong>Genetic testing was conducted on 104 male patients from 89 family pedigrees, identifying 22 novel variants and 1 de novo variant. The initial symptoms appeared in 78.2% of patients at a median age of 5 years. BCVA declined at a mean rate of 0.02 (IQR, 0-0.04) logarithm of the minimum angle of resolution per year, with a gradual, non-linear decrease over the first 40 years. Autofluorescence imaging revealed macular atrophy at a median age of 36.1 (IQR, 29.9-43.2) years. Patients experienced blindness at a median age of 42.5 (IQR, 32.9-45.2) years according to WHO visual impairment categories. OCT analysis showed a mean ellipsoid zone narrowing rate of 23.3 (IQR, -1.04-22.29) µm/month, with an accelerated reduction in the first 40 years (p<0.01). The median age at which ERG no longer detected a waveform was 26.5 (IQR, 20.5-32.8) years. Comparison by variant location indicated faster progression in patients with exon 1-14 variants during the initial two decades, while those with ORF15 variants showed accelerated progression from the third decade.</p><p><strong>Conclusions: </strong>We provide a foundation for determining the treatment window and an objective basis for evaluating the therapeutic efficacy of gene therapy for XLRP.</p>","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"973-981"},"PeriodicalIF":3.5,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141995905","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":"Germline testing for breast cancer patients in England: illogical to prioritise grade 1 breast cancer aged 30-39 over grade 3 aged 40-49 years?","authors":"D Gareth Evans, Sacha J Howell, George J Burghel, Claire Forde, Fiona Lalloo, Miriam J Smith, Anthony Howell, Ashu Gandhi, Emma Roisin Woodward","doi":"10.1136/jmg-2024-110183","DOIUrl":"10.1136/jmg-2024-110183","url":null,"abstract":"","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"935-936"},"PeriodicalIF":3.5,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141759252","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":"The PS4-likelihood ratio calculator: flexible allocation of evidence weighting for case-control data in variant classification.","authors":"Charlie F Rowlands, Alice Garrett, Sophie Allen, Miranda Durkie, George J Burghel, Rachel Robinson, Alison Callaway, Joanne Field, Bethan Frugtniet, Sheila Palmer-Smith, Jonathan Grant, Judith Pagan, Trudi McDevitt, Terri P McVeigh, Helen Hanson, Nicola Whiffin, Michael Jones, Clare Turnbull","doi":"10.1136/jmg-2024-110034","DOIUrl":"10.1136/jmg-2024-110034","url":null,"abstract":"<p><strong>Background: </strong>The 2015 American College of Medical Genetics/Association of Molecular Pathology (ACMG/AMP) variant classification framework specifies that case-control observations can be scored as 'strong' evidence (PS4) towards pathogenicity.</p><p><strong>Methods: </strong>We developed the PS4-likelihood ratio calculator (PS4-LRCalc) for quantitative evidence assignment based on the observed variant frequencies in cases and controls. Binomial likelihoods are computed for two models, each defined by prespecified OR thresholds. Model 1 represents the hypothesis of association between variant and phenotype (eg, OR≥5) and model 2 represents the hypothesis of non-association (eg, OR≤1).</p><p><strong>Results: </strong>PS4-LRCalc enables continuous quantitation of evidence for variant classification expressed as a likelihood ratio (LR), which can be log-converted into log LR (evidence points). Using PS4-LRCalc, observed data can be used to quantify evidence towards either pathogenicity or benignity. Variants can also be evaluated against models of different penetrance. The approach is applicable to balanced data sets generated for more common phenotypes and smaller data sets more typical in very rare disease variant evaluation.</p><p><strong>Conclusion: </strong>PS4-LRCalc enables flexible evidence quantitation on a continuous scale for observed case-control data. The converted LR is amenable to incorporation into the now widely used 2018 updated Bayesian ACMG/AMP framework.</p>","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"983-991"},"PeriodicalIF":3.5,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11503184/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125964","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":"Developmental dysplasia of the hip caused by homozygous <i>TRIM33</i> pathogenic variant affecting downstream BMP pathway.","authors":"Maya Gombosh, Regina Proskorovski-Ohayon, Yuval Yogev, Marina Eskin-Schwartz, Noam Hadar, Sarit Aharoni, Vadim Dolgin, Eugen Cohen, Ohad S Birk","doi":"10.1136/jmg-2024-109928","DOIUrl":"10.1136/jmg-2024-109928","url":null,"abstract":"<p><strong>Background: </strong>Developmental dysplasia of the hip (DDH), formerly termed congenital dislocation of the hip, is the most common congenital disease of the musculoskeletal system in newborns. While familial predilection to DDH has been well documented, the molecular genetics/pathways of this common disorder are poorly understood.</p><p><strong>Methods: </strong>Linkage analysis and whole exome sequencing; real-time PCR studies of skin fibroblasts.</p><p><strong>Results: </strong>Consanguineous Bedouin kindred presented with DDH with apparent autosomal recessive heredity. Linkage analysis and whole exome sequencing delineated a single 3.2 Mbp disease-associated chromosome 1 locus (maximal multipoint Logarithm of the Odds score 2.3), containing a single homozygous variant with a relevant expression pattern: addition of threonine in TRIM33 (NM_015906.4); c.1648_1650dup. <i>TRIM33</i> encodes a protein that acts both in the TGF-β and the BMP pathways; however, it has been mostly studied regarding its function in the TGF-β pathway. Since BMPs are known to act in bone formation, we focused on the BMP pathway, in which TRIM33 functions as a transcription factor, both an activator and repressor. Skin fibroblasts of two affected girls and a heterozygous <i>TRIM33</i> variant carrier were assayed through reverse-transcription PCR for expression of genes known to be downstream of TRIM33 in the BMP pathway: fibroblasts of affected individuals showed significantly reduced expression of <i>DLX5</i>, significantly increased expression of <i>BGLAP</i>, increased expression of <i>ALPL</i> and no change in expression of <i>RUNX2</i> or of <i>TRIM33</i> itself.</p><p><strong>Conclusions: </strong>DDH can be caused by a biallelic variant in <i>TRIM33</i>, affecting the BMP pathway.</p>","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"959-965"},"PeriodicalIF":3.5,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141759251","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":"Is renal cell carcinoma associated with <i>MITF</i> c.952G>A (p.E318K)?","authors":"Philip Harraka, Fiona Bruinsma, Tu Nguyen-Dumont, Susan Jordan, Graham G Giles, Ingrid M Winship, Kathy Tucker, Melissa C Southey","doi":"10.1136/jmg-2024-109984","DOIUrl":"10.1136/jmg-2024-109984","url":null,"abstract":"","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"937-938"},"PeriodicalIF":3.5,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141875105","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":"Genotype-phenotype correlation of <i>SQSTM1</i> variants in patients with amyotrophic lateral sclerosis.","authors":"Shichan Wang, Qirui Jiang, Xiaoting Zheng, Qianqian Wei, Junyu Lin, Tianmi Yang, Yi Xiao, Chunyu Li, Huifang Shang","doi":"10.1136/jmg-2023-109569","DOIUrl":"10.1136/jmg-2023-109569","url":null,"abstract":"<p><strong>Background: </strong>Several variants of sequestosome 1 (<i>SQSTM1</i>) were screened in patients with amyotrophic lateral sclerosis (ALS), while the pathogenicity and genotype-phenotype correlation remains unclear.</p><p><strong>Methods: </strong>We screened variants of <i>SQSTM1</i> gene in 2011 Chinese patients with ALS and performed a burden analysis focusing on the rare variants. Furthermore, we conducted a comprehensive analysis of patients with variants of <i>SQSTM1</i> gene in patients with ALS from our cohort and published studies.</p><p><strong>Results: </strong>In our cohort, we identified 32 patients with 25 different <i>SQSTM1</i> variants with a mutant frequency of 1.6%. Notably, 26% (5/19) of the patients with ALS with <i>SQSTM1</i> variant in our cohort had comorbid cognitive impairment and 43% (3/7) of them had behavioural variant frontotemporal dementia (FTD). Our meta-analysis found a total frequency of <i>SQSTM1</i> variants in 7183 patients with ALS was 2.4%; burden analysis indicated that patients with ALS had enrichment of ultra-rare (minor allele frequency<0.01%) probably pathogenic variants in <i>SQSTM1</i>. Most variants were missense variants and distributed in various domains of p62 protein, some of which might be related to comorbidities of Paget's disease of bone and FTD.</p><p><strong>Conclusion: </strong>Our study established the largest cohort of patients with ALS with <i>SQSTM1</i> variants, expanded the mutation spectrum and investigated the genotype-phenotype correlations of <i>SQSTM1</i> variants.</p>","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"966-972"},"PeriodicalIF":3.5,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141912979","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":"Long-read sequencing identifies an SVA_D retrotransposon insertion deep within the intron of <i>ATP7A</i> as a novel cause of occipital horn syndrome.","authors":"Naoko Yano, Pin Fee Chong, Kenji K Kojima, Tomoichiro Miyoshi, Ahmad Luqman-Fatah, Yu Kimura, Kengo Kora, Taisei Kayaki, Kanako Maizuru, Takahiro Hayashi, Atsushi Yokoyama, Masahiko Ajiro, Masatoshi Hagiwara, Teruyuki Kondo, Ryutaro Kira, Junko Takita, Takeshi Yoshida","doi":"10.1136/jmg-2024-110056","DOIUrl":"10.1136/jmg-2024-110056","url":null,"abstract":"<p><strong>Background: </strong>SINE-VNTR-Alu (SVA) retrotransposons move from one genomic location to another in a 'copy-and-paste' manner. They continue to move actively and cause monogenic diseases through various mechanisms. Currently, disease-causing SVA retrotransposons are classified into human-specific young SVA_E or SVA_F subfamilies. In this study, we identified an evolutionarily old SVA_D retrotransposon as a novel cause of occipital horn syndrome (OHS). OHS is an X-linked, copper metabolism disorder caused by dysfunction of the copper transporter, ATP7A.</p><p><strong>Methods: </strong>We investigated a 16-year-old boy with OHS whose pathogenic variant could not be detected via routine molecular genetic analyses.</p><p><strong>Results: </strong>A 2.8 kb insertion was detected deep within the intron of the patient's <i>ATP7A</i> gene. This insertion caused aberrant mRNA splicing activated by a new donor splice site located within it. Long-read circular consensus sequencing enabled us to accurately read the entire insertion sequence, which contained highly repetitive and GC-rich segments. Consequently, the insertion was identified as an SVA_D retrotransposon. Antisense oligonucleotides (AOs) targeting the new splice site restored the expression of normal transcripts and functional ATP7A proteins. AO treatment alleviated excessive accumulation of copper in patient fibroblasts in a dose-dependent manner. Pedigree analysis revealed that the retrotransposon had moved into the OHS-causing position two generations ago.</p><p><strong>Conclusion: </strong>This is the first report of a human monogenic disease caused by the SVA_D retrotransposon. The fact that the evolutionarily old SVA_D is still actively transposed, leading to increased copy numbers may make a notable impact on rare genetic disease research.</p>","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"950-958"},"PeriodicalIF":3.5,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141498188","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":"Shared germline genomic variants in two patients with double primary gastrointestinal stromal tumours (GISTs).","authors":"David S Moura, Daniel López López, Davide di Lernia, Marta Martin-Ruiz, Maria Lopez-Alvarez, Rafael Ramos, Jose Merino, Joaquin Dopazo, Jose Lopez-Guerrero, Jose L Mondaza-Hernandez, Pablo Romero, Nadia Hindi, Jesus Garcia-Foncillas, Javier Martin-Broto","doi":"10.1136/jmg-2024-110109","DOIUrl":"10.1136/jmg-2024-110109","url":null,"abstract":"<p><strong>Background: </strong>Gastrointestinal stromal tumours (GISTs) are prevalent mesenchymal tumours of the gastrointestinal tract, commonly exhibiting structural variations in <i>KIT</i> and <i>PDGFRA</i> genes. While the mutational profiling of somatic tumours is well described, the genes behind the susceptibility to develop GIST are not yet fully discovered. This study explores the genomic landscape of two primary GIST cases, aiming to identify shared germline pathogenic variants and shed light on potential key players in tumourigenesis.</p><p><strong>Methods: </strong>Two patients with distinct genotypically and phenotypically GISTs underwent germline whole genome sequencing. CNV and single nucleotide variant (SNV) analyses were performed.</p><p><strong>Results: </strong>Both patients harbouring low-risk GISTs with different mutations (<i>PDGFRA</i> and <i>KIT</i>) shared homozygous germline pathogenic deletions in both <i>CFHR1</i> and <i>CFHR3</i> genes. CNV analysis revealed additional shared pathogenic deletions in other genes such as <i>SLC25A24</i>. No particular pathogenic SNV shared by both patients was detected.</p><p><strong>Conclusion: </strong>Our study provides new insights into germline variants that can be associated with the development of GISTs, namely, <i>CFHR1</i> and <i>CFHR3</i> deep deletions. Further functional validation is warranted to elucidate the precise contributions of identified germline mutations in GIST development.</p>","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"927-934"},"PeriodicalIF":3.5,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141995906","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":"Development and internal validation of a clinical risk score to predict incident renal and pulmonary tumours in people with tuberous sclerosis complex.","authors":"Frédéric Loubert, Andrew A House, Catherine Larochelle, Philippe Major, Mark R Keezer","doi":"10.1136/jmg-2023-109717","DOIUrl":"10.1136/jmg-2023-109717","url":null,"abstract":"<p><strong>Objective: </strong>This study aims to develop and internally validate a clinical risk score to predict incident renal angiomyolipoma (AML) and pulmonary lymphangioleiomyomatosis (LAM) in people with tuberous sclerosis complex (TSC).</p><p><strong>Study design: </strong>Data from 2420 participants in the TSC Alliance Natural History Database were leveraged for these analyses. Logistic regression was used to predict AML and LAM development using 10 early-onset clinical manifestations of TSC as potential predictors, in addition to sex and genetic mutation. For our models, we divided AML into three separate outcomes: presence or absence of AML, unilateral or bilateral and whether any are ≥3 cm in diameter. The resulting regression models were turned into clinical risk scores which were then internally validated using bootstrap resampling, measuring discrimination and calibration.</p><p><strong>Results: </strong>The lowest clinical risk scores predicted a risk of AML and LAM of 1% and 0%, while the highest scores predicted a risk of 99% and 73%, respectively. Calibration was excellent for all three AML outcomes and good for LAM. Discrimination ranged from good to strong. C-statistics of 0.84, 0.83, 0.83 and 0.92 were seen for AML, bilateral AML, AML with a lesion≥3 cm and LAM, respectively.</p><p><strong>Conclusion: </strong>Our work is an important step towards identifying individuals who could benefit from preventative strategies as well as more versus less frequent screening imaging. We expect that our work will allow for more personalised medicine in people with TSC. External validation of the risk scores will be important to confirm the robustness of our findings.</p>","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"943-949"},"PeriodicalIF":3.5,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141558892","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}