Journal of Medical Genetics最新文献

Background: Autosomal dominant (AD) inheritance often arises through haploinsufficiency, dominant-negative or gain of function (GoF) effects, while autosomal recessive (AR) inheritance generally results from partial or complete loss of function (LoF). Yet, a subset of genes demonstrates both inheritance patterns. We aimed to curate a list of such 'AD/AR' genes and to propose additional candidates.

Methods: AD/AR genes were subcategorised based on genotype-phenotype correlations and disease mechanisms. Using bioinformatic analyses, we compared genes with AD, AR and AD/AR inheritance across various metrics, including gnomAD constraint values, exon count, protein length, quaternary structure and gene ontology terms. A machine learning-based metric was used to account for interdependence among features.

Results: Pathogenic variants in AD/AR genes can lead to distinct or similar phenotypes, depending on the molecular mechanism. AD/AR genes exhibit unique bioinformatic properties such as intermediate constraint scores, a combination of gene ontology terms, a greater average number of exons and an elevated propensity to form homomeric/heteromeric proteins. We identified homozygous LoF or clinically reported variants in nine genes previously classified as AD only.

Conclusion: Collectively, the data suggest that AD/AR genes possess distinctive features that likely underpin their dual inheritance modes. We propose nine candidate AD/AR genes and emphasise caution in filtering by inheritance type alone.

11β-hydroxylase deficiency (11βOHD) is the second most common cause (5%) of congenital adrenal hyperplasia (CAH). The CYP11B1 gene shares 95% of genomic sequence homology with CYP11B2, and therefore Sanger sequencing remains the gold standard. We present a case of 11βOHD due to an intragenic inversion in CYP11B1 that was missed by both the Sanger sequencing and massive parallel sequencing (MPS) methods. The child was born with virilised genitalia at Prader stage 4 and the biological findings showed a hydromineral retention pattern and a pathognomonic increase in steroid precursors suggestive of 11βOHD. Standard trio analysis revealed only one heterozygous pathogenic variation inherited from the father. The study using MPS showed similar outcomes. Careful observation of the alignment BAM files revealed breaks in sequencing depth, incomplete alignments and systematic paradoxical read-pairs orientation. A specifically designed amplification and Sanger protocol confirmed the novel NM_000497.4(CYP11B1):c.[892_1121+7 inv;1121+8_1121+9del]; p.(Glu298HisfsTer113) variant at heterozygous state in the proband and his mother, fulfilling the diagnosis. The present case reports the first short intragenic inversion in CAH and illustrates the pitfalls that must always be kept in mind when using sequencing methods. When the phenotype is unequivocal, a thorough investigation of the locus should be carried out with cross-use of different techniques.

In the UK, most patients receive publicly funded medical care through the National Health Service (NHS), which funds tumour and/or germline testing for eligible patients with cancer to inform clinical management.Testing on tumour-derived DNA may identify putative heritable variants, with implications for the proband and their wider family, but is not a reliable substitute for germline genetic testing when hereditary cancer predisposition is suspected.The likelihood that a variant identified through tumour testing is of germline origin depends on multiple clinical and technical factors. Certain genotypes significantly influence a patient's cancer risk, and intervention in those carriers may facilitate cancer prevention or early detection, while other genotypes are associated with lower cancer risk, and associated intervention in such cases have limited clinical utility.We convened a national meeting of clinical cancer genetics and scientific leads to rationalise germline follow-up testing of variants identified through tumour-based testing. After contrasting potential approaches, implementation of an NHS-contextualised 'intermediate conservative' approach was agreed and refined by the authors, with the final pathway recirculated to the UK clinical and scientific community for consensus agreement and publication.We outline relevant patient, genetic and technical considerations informing likely origin of variants, a review of current relevant guidance and NHS laboratory practices and a workflow for laboratory and clinical teams to triage tumour-detected variants requiring onward germline follow-up. This approach aims to direct limited resources towards identifying germline variants associated with the greatest potential clinical impact, with a view to supporting more efficient and equitable delivery of genomic medicine in oncology.

Background: Facioscapulohumeral muscular dystrophy 1 (FSHD1) is one of the most common autosomal dominant neuromuscular diseases. Genetic diagnosis of FSHD1 remains a challenge because of the long length and repetitive nature of D4Z4 repeats. Long-read sequencing is an effective method for detecting FSHD1, but sequencing depth remains a limitation.

Methods: We developed a long-read library adaptive sampling (LRL-AS) method based on Oxford Nanopore Technologies (ONT) sequencing to comprehensively detect FSHD1. Two patients were sequenced by adaptive sampling, followed by analyses of D4Z4 repeat units (RUs), methylation and haplotype.

Results: Compared with whole-genome sequencing, our LRL-AS method shows significant improvements in both sequencing depth and read length. LRL-AS can identify D4Z4 RUs contraction with accuracy comparable to optical genome mapping in both 4q35 and 10q26 regions. We also calculated methylation levels in the double homeobox 4 (DUX4) gene region. With the benefit of higher sequencing depth, allele-specific methylation can be calculated with greater precision. We also observed that, at different sequencing depths, ONT sequencing data consistently provide stable calculations of methylation levels. More importantly, we demonstrated that data from adaptive sampling can be effectively used to construct the haplotype of the pathogenic allele using single-nucleotide polymorphisms.

Conclusion: Our LRL-AS method is a comprehensive approach for FSHD1 detection, improving the accuracy of D4Z4 RUs and methylation detection while enabling allele-specific haplotype construction. It holds promising potential for clinical application.

BRIP1 (OMIM: 605882), associated with hereditary ovarian cancer, has recently been described in association with central nervous system (CNS) tumours. Institutional germline database review identified 43 families with BRIP1 pathogenic germline variants (PGVs); 7 families (16.3%) reported 8 CNS tumours. Somatic database review identified 1143 individuals with CNS tumours who underwent somatic sequencing, of whom 7 had BRIP1 pathogenic variants (PVs) (0.6%); 1 of 2 germline-tested individuals had a BRIP1 PGV. Though BRIP1 PVs are rare in CNS tumours, a substantial proportion of BRIP1 carriers have a positive family history. Obtaining and documenting the clinical and pathological characteristics of reported CNS tumours in BRIP1 individuals and families is key to exploring a possible association.

Background: Duplication of the pituitary gland (DPG)-plus syndrome is an extremely rare developmental malformation of unknown aetiology.

Methods: Two unreported patients of DPG-plus syndrome are described. Underlying genetic defects were explored, including chromosomal microarray (CMA), whole exome sequencing (WES) and mRNA analysis. A literature review was presented.

Results: Patient 1 had DPG, palatal cleft, bifid tongue, intraoral teratoma, lingual hamartoma and duplicated basilar artery and odontoid process. Patient 2 had DPG, epignathus teratoma, a nasal mass, choanal atresia, cleft palate, bifid tongue, abnormal basilar artery and fused upper cervical spine. CMA yielded normal results. WES of patient 1 disclosed a novel splice site PTCH2 variant, c.1590+1G>A, leading to exon 12 skipping and an in-frame deletion of 44 amino acids. WES of patient 2 revealed no candidate variants. A literature review of 51 cases showed mostly reported in childhood and female sex (80%). The leading anomalies identified included DPG (100%), cleft palate (68.6%), anomalous cervical spine (56.9%), hypothalamic mass/enlargement (58.8%), intraoral teratoma (58.8%), basilar arterial abnormalities (43.1%) and bifid/trifid tongue (23.5%). Non-craniofacial anomalies were found in <10% of cases. Late complications included precocious puberty, all in female patients, and hypogonadotropic hypogonadism in a few patients.

Conclusions: Two new cases of DPG-plus syndrome were reported, with rare findings of epignathus and choanal atresia. We propose that DPG-plus syndrome may result from a double hit in one of the genes involved in SHH signalling, arising from a germline pathogenic variant with mosaicism for a somatic pathogenic variant or digenic/oligogenic inheritance of the SHH signalling-related genes.

The 22q11.2 deletion syndrome (22q11.2DS) results from a heterozygous deletion at chromosomal locus 22q11.2 and is associated with multisystem symptoms, including cardiovascular, psychiatric and palatal manifestations. Although congenital cardiovascular aberrations are frequent in patients with 22q11.DS, exact prevalence figures remain unclear. Literature was searched in August 2022 and updated in May 2024 using the databases PubMed, Web of Science and Cochrane library to retrieve studies in English and German focusing only on studies involving 22q11.2DS. Prevalence data for cardiovascular aberrations were arcsine transformed and summarised by random-effects models using Meta-XL. Evidence quality was assessed via the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. The systematic searches identified 4338 studies, of which 7 were included for the meta-analysis of prevalence using random-effects models and sensitivity analyses. The pooled prevalence for heart defects (mean; 95% CI) was found to be elevated for tetralogy of Fallot (20%; 0.17 to 0.23), ventricular septal defect (14%; 0.12 to 0.16), pulmonary atresia with ventricular septal defect (9%; 0.06; 0.12), interrupted aortic arch (10%; 0.06 to 0.15), truncus arteriosus communis (9%; 0.07 to 0.12) and atrial septal defect (3%; 0.01 to 0.04). The risk of bias of the included studies was low to moderate. This study, to our knowledge, represents the first systematic review and meta-analysis of prevalences for congenital cardiovascular aberrations in individuals with 22q11.2DS. The high frequencies observed underline the need for cardiovascular screening in patients with 22q11.2DS and genetic screening for 22q11.2DS in congenital heart disease.

Purpose: Williams-Beuren syndrome (WBS) is a well-known neurodevelopmental disorder caused by a copy-number loss at the 7q11.23 locus. Although the 1.5-1.8 Mb recurrent deletion carries several genes of interest, no single gene has been identified in which pathogenic variants cause a neurodevelopmental phenotype. At this locus, GTF2I, encoding the general transcription factor II-I, has been considered as the main candidate gene for the cognitive and behavioural phenotype of WBS, based on clinical observations of cases with atypical 7q.11.23 deletions and functional studies in humans and mice.

Methods: Individuals with a neurodevelopmental disorder were identified through a multicentre collaboration using GeneMatcher and the ERN-ITHACA network. They remained undiagnosed following genome/exome sequencing. Clinical evaluations were performed in each participating centre.

Results: We identified seven unrelated individuals with de novo variants in GTF2I (two non-sense, two splice-site, one missense, one indel and one intragenic deletion). We also identified one individual with a WBS phenotype and low GTF2I expression identified by RNA sequencing. All eight individuals presented with global developmental delay and facial dysmorphic features, with speech delay and/or autistic features in seven cases. The effect of the two splice-site variants was confirmed by RNA sequencing.

Conclusion: Pathogenic heterozygous GTF2I variants cause a neurodevelopmental disorder characterised by global developmental delay with facial dysmorphic features, partly resembling the phenotype observed in individuals affected with WBS.