Journal of Medical Genetics最新文献

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Pathogenic mobile element insertion in the MEN1 gene mimicking a deletion in MLPA: characterisation by long-read sequencing. MEN1基因中模仿MLPA缺失的致病性移动元件插入:通过长读测序表征。
IF 3.4 2区 医学
Journal of Medical Genetics Pub Date : 2026-07-23 DOI: 10.1136/jmg-2025-111230
Aleksandra Pfeifer, Jadwiga Zebracka-Gala, Agnieszka Pawlaczek, Artur Zajkowicz, Agata Abramowicz, Karolina Tecza, Agnieszka Kotecka-Blicharz, Hanna Langer-Maciol, Marta Cieslicka, Dagmara Rusinek, Malgorzata Porc, Renata Cyplinska, Malgorzata Oczko-Wojciechowska
{"title":"Pathogenic mobile element insertion in the <i>MEN1</i> gene mimicking a deletion in MLPA: characterisation by long-read sequencing.","authors":"Aleksandra Pfeifer, Jadwiga Zebracka-Gala, Agnieszka Pawlaczek, Artur Zajkowicz, Agata Abramowicz, Karolina Tecza, Agnieszka Kotecka-Blicharz, Hanna Langer-Maciol, Marta Cieslicka, Dagmara Rusinek, Malgorzata Porc, Renata Cyplinska, Malgorzata Oczko-Wojciechowska","doi":"10.1136/jmg-2025-111230","DOIUrl":"10.1136/jmg-2025-111230","url":null,"abstract":"<p><strong>Background: </strong>Mobile element insertions (MEIs) disrupting coding sequences are rare but clinically significant mutations that are often missed by standard next-generation sequencing (NGS) workflows. Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant tumour predisposition syndrome caused by pathogenic variants in the <i>MEN1</i> gene.</p><p><strong>Methods: </strong>Patients included in this study were referred for genetic testing of hereditary cancer syndromes. In a validation of our NGS-based copy number variant detection pipeline, four cases showed discrepancies between NGS and multiplex ligation-dependent probe amplification (MLPA) results. Further investigation using soft-clipped read analysis and the MEI detection tool Scramble revealed an Alu insertion in the <i>MEN1</i> gene. Long-read whole genome sequencing (LR-WGS) was used for validation and complete characterisation of the variant. Additionally, 2014 retrospective NGS samples were analysed with Scramble. Relatives of probands were tested with MLPA and PCR. Positive samples were analysed with Sanger sequencing.</p><p><strong>Results: </strong>The apparent exon 2 deletion detected by MLPA was shown to be a false positive caused by an Alu insertion within the probe binding site. LR-WGS confirmed the pathogenic variant (<i>MEN1</i>:c.143_144insAlu) and resolved its complete sequence. Screening of the retrospective cohort revealed no additional MEIs. Altogether, we identified 10 affected individuals from two Polish families carrying hereditary <i>MEN1</i>:c.143_144insAlu, which segregates with MEN1 syndrome.</p><p><strong>Conclusion: </strong>We report a novel pathogenic Alu insertion in the <i>MEN1</i> gene, which is associated with MEN1 syndrome. Our findings underscore the importance of incorporating MEI detection into routine diagnostics. It also emphasises the necessity of interpreting single-exon MLPA deletions cautiously, as recommended in the MLPA protocol.</p>","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"527-536"},"PeriodicalIF":3.4,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13479647/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147774010","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}
引用次数: 0
Uterine serous carcinoma and germline genetic testing: patterns of referral, completion and pathogenic variant detection. 子宫浆液癌和种系基因检测:转诊模式,完成和致病变异检测。
IF 3.4 2区 医学
Journal of Medical Genetics Pub Date : 2026-07-23 DOI: 10.1136/jmg-2025-111285
Lauren Tostrud, Simge Bagci Turkmen, Jiaqi Zhang, Rachel Hodan, Kerry Kingham, Oliver Dorigo, James M Ford, Allison W Kurian, Talayeh S Ghezelayagh
{"title":"Uterine serous carcinoma and germline genetic testing: patterns of referral, completion and pathogenic variant detection.","authors":"Lauren Tostrud, Simge Bagci Turkmen, Jiaqi Zhang, Rachel Hodan, Kerry Kingham, Oliver Dorigo, James M Ford, Allison W Kurian, Talayeh S Ghezelayagh","doi":"10.1136/jmg-2025-111285","DOIUrl":"10.1136/jmg-2025-111285","url":null,"abstract":"<p><strong>Background: </strong>Current guidelines recommend consideration of germline genetic testing for patients with uterine serous carcinoma (USC) but real-world data are limited on completion rates of testing and pathogenic variant (PV) identification. This study aimed to evaluate the rate of genetic testing referral and completion in a cohort of patients with USC, determine the prevalence of clinically meaningful PVs found on testing and explore factors associated with genetics referral and testing completion.</p><p><strong>Methods: </strong>We retrospectively examined the medical records of all individuals diagnosed with USC between 2019 and 2024 seen at a single academic cancer centre. Outcomes of interest included referral for germline genetic testing, completion of testing and testing results.</p><p><strong>Results: </strong>Of 131 individuals included, 5 (3.8%) had prior genetic testing and only 45 (34.4%) were recommended to undergo genetic testing or referred to cancer genetics. Younger individuals and those with a personal history of cancer other than USC or family history of breast or ovarian cancer were more likely to be referred. Nine (26.5%) of 34 individuals who completed germline testing had a PV identified in a cancer-related gene, including <i>BRCA1</i>, <i>BRCA2</i>, <i>BRIP1</i>, <i>CHEK2</i>, <i>MSH6</i>, <i>PMS2</i> and <i>ATM</i>. Only a personal history of cancer other than USC was independently associated with the discovery of a PV on germline genetic testing. In those without a prior personal history of cancer, the PV prevalence was 5.6%.</p><p><strong>Conclusions: </strong>Given the high prevalence of PVs in this population, germline genetic testing for all patients diagnosed with USC can provide clinically meaningful benefit but is currently underused in practice.</p>","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"537-542"},"PeriodicalIF":3.4,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13479625/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147773070","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}
引用次数: 0
Optical genome mapping identifies previously undetected causal variants in early-onset developmental epileptic encephalopathies. 光学基因组图谱确定了早发性发育性癫痫性脑病中以前未被发现的因果变异。
IF 3.4 2区 医学
Journal of Medical Genetics Pub Date : 2026-07-23 DOI: 10.1136/jmg-2026-111485
Sanem Yilmaz, Enise Avci Durmusalioglu, Dilara Ece Toprak Dogan, Seda Kanmaz, Tahir Atik, Mehmet Burak Mutlu, Uluç Yiş, Unsal Yilmaz, Aycan Unalp, Sarenur Gökben, Hasan Baş, Arman Rostamlou, Nur Selvi Gunel, Cumhur Gunduz, Hasan Tekgul, Esra Isik
{"title":"Optical genome mapping identifies previously undetected causal variants in early-onset developmental epileptic encephalopathies.","authors":"Sanem Yilmaz, Enise Avci Durmusalioglu, Dilara Ece Toprak Dogan, Seda Kanmaz, Tahir Atik, Mehmet Burak Mutlu, Uluç Yiş, Unsal Yilmaz, Aycan Unalp, Sarenur Gökben, Hasan Baş, Arman Rostamlou, Nur Selvi Gunel, Cumhur Gunduz, Hasan Tekgul, Esra Isik","doi":"10.1136/jmg-2026-111485","DOIUrl":"10.1136/jmg-2026-111485","url":null,"abstract":"<p><strong>Background: </strong>Optical genome mapping (OGM) is a novel technology that enables high-resolution detection of structural variants. This study aimed to evaluate the diagnostic contribution of OGM in early-onset developmental epileptic encephalopathies (DEEs) with unresolved genetic causes.</p><p><strong>Materials and methods: </strong>A total of 38 children with early-onset DEEs (aged 0-18 years) who remained undiagnosed despite conventional karyotyping, chromosomal microarray analysis (CMA) and whole-exome sequencing (WES) were included. All patients underwent detailed phenotypic reassessment and WES reanalysis. One patient received a definitive molecular diagnosis following WES reanalysis. Four patients subsequently withdrew consent, and one patient was excluded due to inadequate DNA quality for OGM. OGM was therefore performed in the remaining 32 patients. Potential OGM findings were validated using appropriate laboratory techniques.</p><p><strong>Results: </strong>Among the 32 patients who underwent OGM, three candidate structural variants were identified. Two variants (2/32, 6.3%), ogm[GRCh38] ins(X;?)(q27.3;?) and ogm[GRCh38] 6p24.1 (13083829_13279761)x1, were confirmed using orthogonal validation methods, resulting in the molecular diagnoses of Fragile X syndrome and <i>PHACTR1-</i>related DEE, respectively.</p><p><strong>Conclusion: </strong>OGM contributed to the identification of clinically relevant structural variants in genetically undiagnosed early-onset DEEs. These findings support the complementary role of OGM in the genetic evaluation of complex neurodevelopmental disorders.</p>","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"487-493"},"PeriodicalIF":3.4,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147698909","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}
引用次数: 0
VHL gene fragment analysis: large inversion detection in Alu region for clinical applications. VHL基因片段分析:Alu区大反转检测临床应用
IF 3.4 2区 医学
Journal of Medical Genetics Pub Date : 2026-07-23 DOI: 10.1136/jmg-2026-111493
Ryan N Baugher, Stephanie D Mellott, Kristen M Pike, Todd B Young, Heidi E Lawhorn, Stephen M Hewitt
{"title":"<i>VHL</i> gene fragment analysis: large inversion detection in <i>Alu</i> region for clinical applications.","authors":"Ryan N Baugher, Stephanie D Mellott, Kristen M Pike, Todd B Young, Heidi E Lawhorn, Stephen M Hewitt","doi":"10.1136/jmg-2026-111493","DOIUrl":"10.1136/jmg-2026-111493","url":null,"abstract":"<p><p>von Hippel-Lindau (VHL) is an autosomal-dominant tumour susceptibility disorder associated with pathogenic germline variants in the <i>VHL</i> gene that put patients at increased risk of developing benign and malignant tumours within various organs. While current CLIA (Clinical Laboratory Improvement Amendments) genetic tests demonstrate a high detection rate of pathogenic <i>VHL</i> variants, clinical manifestations of VHL with atypical germline alteration undetectable by established genetic tests have been reported by Vocke <i>et al</i>, indicating the need for bespoke methods confirming germline alterations. We CLIA-validated a test using PCR and fragment analysis that evaluates a pathogenic inversion of 291 kb found within intron 2 of <i>VHL</i> and the 3' UTR of <i>TTLL</i>3 in patients with canonical VHL manifestations and no conventional germline alterations. Validation results matched as expected by achieving 100% concordance. Although clinical diagnosis of VHL is possible in the absence of conclusive pathogenic cause, this report demonstrates bespoke CLIA methodologies are essential for managing hereditary diseases and promoting early symptom detection. Our CLIA assay allows for greater confidence in diagnosis for families dealing with complex structural germline alterations and may aid in future efforts at corrective therapies to ease patient suffering. This work was performed in our CLIA-certified laboratory (CLIA ID # 21D0947274).</p>","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"511-513"},"PeriodicalIF":3.4,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13416925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147773709","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}
引用次数: 0
Clinical characteristics and prognosis of SDHD pathogenic variant carriers: a systematic review and meta-analysis. sdd致病变异携带者的临床特征和预后:系统回顾和荟萃分析。
IF 3.4 2区 医学
Journal of Medical Genetics Pub Date : 2026-07-23 DOI: 10.1136/jmg-2025-111235
Xinquan Lian, Liping Shen, Jiayin Song, Mengqi Pang, Yunmeng Zhong, Han Zhang, Yadong Xing, Tao-Hsin Tung, Bo Shen
{"title":"Clinical characteristics and prognosis of <i>SDHD</i> pathogenic variant carriers: a systematic review and meta-analysis.","authors":"Xinquan Lian, Liping Shen, Jiayin Song, Mengqi Pang, Yunmeng Zhong, Han Zhang, Yadong Xing, Tao-Hsin Tung, Bo Shen","doi":"10.1136/jmg-2025-111235","DOIUrl":"10.1136/jmg-2025-111235","url":null,"abstract":"<p><strong>Background: </strong>Germline pathogenic variants (PVs) of succinate dehydrogenase subunit D (<i>SDHD</i>) are major genetic causes of pheochromocytomas and paragangliomas. Existing studies have reported inconsistent findings and lack a comprehensive synthesis regarding penetrance, multifocality and metastatic risk in carriers of <i>SDHD</i> PVs.</p><p><strong>Objective: </strong>To systematically assess age-specific penetrance (in all carriers) and the proportions of multifocality, metastatic disease and mortality among affected carriers, and explore potential genotype-phenotype associations through a systematic review and meta-analysis.</p><p><strong>Methods: </strong>Eligible observational studies were selected from PubMed, MEDLINE and EMBASE that reported age-specific penetrance (in all carriers) and the proportions of multifocality, metastatic disease and mortality among affected carriers (those with tumours). Additionally, data on specific <i>SDHD</i> variants associated with tumour multifocality or metastatic behaviour were collected. Following independent data extraction and quality assessment by two reviewers, these proportions were meta-analysed using random-effects models or fixed-effect model to generate pooled estimates with 95% CIs and prediction intervals.</p><p><strong>Results: </strong>Age-specific penetrance increased from 20% at 20 years of age (95% CI 16% to 25%) to 58% at 40 years (95% CI 48% to 67%) and 82% at 60 years (95% CI 75% to 90%). Among the affected <i>SDHD</i> PV carriers, the pooled proportions were 75% (95% CI 72% to 79%) for multifocal tumours, 3% (95% CI 2% to 4%) for metastatic disease and 1% (95% CI 1% to 2%) for mortality.</p><p><strong>Conclusion: </strong><i>SDHD</i> PV carriers exhibit increasing age-specific penetrance, with a high proportion of patients having multifocal tumours but low proportions of metastatic disease and mortality, providing partial evidence for the need for lifelong monitoring of <i>SDHD</i> PV carriers. However, evidence linking specific variants to these phenotypes is limited and requires further investigation.</p><p><strong>Prospero registration number: </strong>CRD420251060752.</p>","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"467-473"},"PeriodicalIF":3.4,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13479636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147690497","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}
引用次数: 0
Rare missense variants in MYO7A and OTOP2 genes in a South Korean Meniere's disease cohort. 韩国梅尼埃氏病队列中MYO7A和OTOP2基因的罕见错义变异
IF 3.4 2区 医学
Journal of Medical Genetics Pub Date : 2026-07-23 DOI: 10.1136/jmg-2025-111426
Mai T Pham, Pablo Cruz-Granados, Prathamesh T Nadar-Ponniah, Han Chow Chua, Seung Hyun Jang, Heon Yung Gee, Jinsei Jung, Jae Young Choi, Sung Huhn Kim, Jose A Lopez-Escamez
{"title":"Rare missense variants in <i>MYO7A</i> and <i>OTOP2</i> genes in a South Korean Meniere's disease cohort.","authors":"Mai T Pham, Pablo Cruz-Granados, Prathamesh T Nadar-Ponniah, Han Chow Chua, Seung Hyun Jang, Heon Yung Gee, Jinsei Jung, Jae Young Choi, Sung Huhn Kim, Jose A Lopez-Escamez","doi":"10.1136/jmg-2025-111426","DOIUrl":"10.1136/jmg-2025-111426","url":null,"abstract":"<p><strong>Background: </strong>Meniere's disease (MD) is a polygenic condition defined by episodes of vertigo associated with sensorineural hearing loss and tinnitus. Genetic studies in familial MD in East Asian populations are limited, and the potential MD genes remain to be established in non-Finnish European populations.</p><p><strong>Methods: </strong>By exome sequencing and rare variant analysis, we have searched for existing and novel genes associated with MD in a South Korean cohort of 16 MD individuals with bilateral sensorineural hearing loss.</p><p><strong>Results: </strong>We have found one individual with two rare missense variants in the <i>OTOP2</i> gene, a new candidate gene for MD and three heterozygous variants in the <i>MYO7A</i> gene, supporting the hypothesis of biallelic inheritance. Wild-type and mutated protein models were compared, and currents were measured in the human proton channel OTOP2 expressed in <i>Xenopus laevis</i> oocytes to further elucidate functional consequences. Structural changes in the T364M or H435Q OTOP2 variants were not associated with changes in measured currents, regardless of pH or Ca<sup>2+</sup> concentrations.</p><p><strong>Conclusion: </strong>The <i>OTOP2</i> gene is a novel candidate for the audiovestibular dysfunction observed in MD. Furthermore, rare variants in the <i>MYO7A</i> gene, previously associated with European MD, have been found in the South Korean cohort. The OTOP2 protein was found in the basal cells of the stria vascularis, spiral ganglion neurons and inner hair cells in the organ of Corti, suggesting a dual role in endolymphatic homeostasis and neural signal transmission.</p>","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"494-504"},"PeriodicalIF":3.4,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147773970","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}
引用次数: 0
Biallelic variants in DNAH10 are associated with skeletal developmental abnormalities and ciliary dysfunction. DNAH10双等位基因变异与骨骼发育异常和纤毛功能障碍有关。
IF 3.4 2区 医学
Journal of Medical Genetics Pub Date : 2026-07-23 DOI: 10.1136/jmg-2025-111109
Rui Zheng, Xinrong Du, Jierui Yan, Gelin Huang, Zhuoyao Guo, Wei Li, Hanyun Que, Yuting Wen, Fei Yan, Daijuan Chen, Li Dai, Yu Shi, Weicheng Chen, Wenming Xu
{"title":"Biallelic variants in <i>DNAH10</i> are associated with skeletal developmental abnormalities and ciliary dysfunction.","authors":"Rui Zheng, Xinrong Du, Jierui Yan, Gelin Huang, Zhuoyao Guo, Wei Li, Hanyun Que, Yuting Wen, Fei Yan, Daijuan Chen, Li Dai, Yu Shi, Weicheng Chen, Wenming Xu","doi":"10.1136/jmg-2025-111109","DOIUrl":"10.1136/jmg-2025-111109","url":null,"abstract":"<p><strong>Background: </strong>Primary cilia are essential for skeletal development by coordinating key signalling pathways in osteoblasts and chondrocytes. While pathogenic variants in approximately 40 genes have been linked to skeletal ciliopathies, additional causative genes remain to be identified. Although DNAH10 is well characterised in motile cilia, its role in primary cilia remains unclear.</p><p><strong>Methods: </strong>Whole-exome sequencing was performed in two individuals with skeletal developmental abnormalities and identified biallelic <i>DNAH10</i> variants. In vitro assays were used to assess the effects of these variants on DNAH10 protein abundance. <i>Dnah10</i> knockout mice were generated to investigate the associated skeletal phenotypes and underlying mechanisms.</p><p><strong>Results: </strong>Biallelic <i>DNAH10</i> variants were identified in two individuals with skeletal developmental abnormalities. In vitro, these missense variants were associated with reduced DNAH10 protein abundance. <i>Dnah10</i>-deficient mice recapitulated key skeletal features, including polydactyly, impaired cartilage development and abnormal ossification. Mechanistically, <i>Dnah10</i> loss was associated with abnormal primary cilia morphology, attenuated Hedgehog signalling, impaired osteoblast differentiation and defective chondrocyte maturation.</p><p><strong>Conclusion: </strong>Our findings support <i>DNAH10</i> as a candidate gene associated with skeletal developmental abnormalities and ciliary dysfunction and suggest a previously underappreciated role for DNAH10 in primary cilia-related skeletal development beyond its established role in motile cilia.</p>","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"474-486"},"PeriodicalIF":3.4,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147839129","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}
引用次数: 0
Best practice recommendations for bioinformatics approaches applied to high-throughput sequencing for rare disease and cancer diagnosis within the UK National Health Service. 生物信息学方法应用于罕见疾病和癌症诊断的高通量测序的最佳实践建议在英国国家卫生服务。
IF 3.4 2区 医学
Journal of Medical Genetics Pub Date : 2026-07-23 DOI: 10.1136/jmg-2025-111289
Jamie M Ellingford, Erik Waskiewicz, Ashley J Pritchard, Javier Lopez, Rebecca Morgan, Emily Ley, Matt Lyon, Alona Sosinsky, Dalia Kasperaviciute, Joo Wook Ahn
{"title":"Best practice recommendations for bioinformatics approaches applied to high-throughput sequencing for rare disease and cancer diagnosis within the UK National Health Service.","authors":"Jamie M Ellingford, Erik Waskiewicz, Ashley J Pritchard, Javier Lopez, Rebecca Morgan, Emily Ley, Matt Lyon, Alona Sosinsky, Dalia Kasperaviciute, Joo Wook Ahn","doi":"10.1136/jmg-2025-111289","DOIUrl":"10.1136/jmg-2025-111289","url":null,"abstract":"<p><strong>Background: </strong>Establishing best practice recommendations helps to increase consistency, equity and innovation in clinical genomics services. Bioinformatics approaches are a core component of clinical genomics services that use high-throughput genomic sequencing applied in the diagnosis of rare disorders and cancer. While a broad range of international recommendations exist for genomic diagnostic testing and genetic variant classification, the current UK-specific best practice recommendations for bioinformatics approaches applied in this context are outdated.</p><p><strong>Methods: </strong>We assembled a team of bioinformaticians and scientists with diverse expertise in rare disease and cancer genomics applied in clinical diagnostics within the UK National Health Service. Through structured discussion, polls and surveys, we developed an updated set of best practice recommendations for bioinformatics approaches applied to high-throughput genomic sequencing in clinical genomic testing.</p><p><strong>Results: </strong>We provide best practice recommendations across the spectrum of activities within a clinical genomics bioinformatics pipeline, including quality control, primary, secondary and tertiary analysis approaches and shared knowledge bases. We also comment on issues related to software development and maintenance. The recommendations can be applied to multiple sequencing technologies and encompass both targeted and whole genome sequencing approaches applied to germline and tumour DNA samples.</p><p><strong>Conclusion: </strong>The best practice recommendations outlined in this study provide a national framework for adoption and innovation of bioinformatics approaches across diverse clinical genomic testing strategies in the UK National Health Service.</p>","PeriodicalId":16237,"journal":{"name":"Journal of Medical Genetics","volume":" ","pages":"514-526"},"PeriodicalIF":3.4,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13479684/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147773943","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}
引用次数: 0
Long-read genome sequencing increases diagnostic yield in a short-read sequencing unsolved developmental epileptic encephalopathy (DEE) cohort. 长读基因组测序增加了短读测序未解决的发展性癫痫性脑病(DEE)队列的诊断率。
IF 3.4 2区 医学
Journal of Medical Genetics Pub Date : 2026-07-23 DOI: 10.1136/jmg-2026-111514
Chanatjit Cheawsamoot, Rungroj Thangpong, Wanna Chetruengchai, Songphon Kanlayaprasit, Wuttichart Kamolvisit, Phawin Kor-Anantakul, Adjima Assawapitaksakul, Ponghatai Boonsimma, Sathida Poonmaksatit, Krisnachai Chomtho, Tayard Desudchit, Vorasuk Shotelersuk
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引用次数: 0
Diagnostic inversion in prenatal genomics: counselling, governance and the expanded role of clinical genetics. 产前基因组学诊断反转:咨询,治理和扩大作用的临床遗传学。
IF 3.4 2区 医学
Journal of Medical Genetics Pub Date : 2026-07-21 DOI: 10.1136/jmg-2026-111759
Himanshu Goel
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引用次数: 0
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