Journal of Medical Genetics最新文献

Background: Familial exudative vitreoretinopathy (FEVR) is an inherited eye disease characterised by the incomplete development of the retinal vasculature. Over 10 genes have been associated with FEVR, but there are still a substantial number of genetically unsolved cases. The aim of this study was to analyse whole genome sequencing (WGS) data from the FEVR cases in the Genomics England (GEL) 100 000 genomes project to identify the causative variants.

Methods: WGS was performed by GEL and accessed within the GEL Research Environment. FEVR cases were identified using LabKey and candidate variants were extracted using the 'gene-variant workflow' and 'CNV/SV workflow' and by using BCFtools in unfiltered VCF files.

Results: Fifty-nine FEVR probands were submitted to GEL. We found six novel and eight previously reported pathogenic variants in six genes known to underlie FEVR (TSPAN12, LRP5, FZD4, CTNNB1, KIF11 and NDP), as well as structural variants in TSPAN12 and KIF11. These accounted for 15/59 (25.4%) of FEVR cases. We also found candidate heterozygous variants in CTNND1 in three unsolved FEVR cases. Expanding the list of genes examined to include all genes reported to be mutated in ocular disorders likely solved a further four cases, indicating that these individuals may be misclassified as FEVR in GEL.

Conclusion: By performing bespoke reanalysis of the FEVR GEL cohort, this study has highlighted additional heterozygous variants in CTNND1 in FEVR cases and increased the diagnostic yield from 20% solved by the GEL analysis pipeline to 37% (22/59), but the majority of FEVR cases remain without a molecular diagnosis.

Background: Mitochondrial diseases are genetic disorders arising from pathogenic variants in nuclear or mitochondrial DNA (mtDNA) characterised by respiratory chain dysfunction. Clinical manifestations are diverse, and treatment is mostly symptomatic. Mitochondria are maternally inherited, but new reproductive technologies may prevent the transmission of pathogenic mtDNA. We decided to investigate the pregnancies of women with the m.3243A>G mtDNA variant.

Methods: 16 women with m.3243A>G were included in this retrospective, observational cohort study. Medical records were screened for pregnancies managed at Oulu University Hospital (Oulu, Finland) during the years 1960-2020. Main outcomes were obstetric complications as well as maternal and neonatal morbidity. All eligible pregnancies (n=38) were reviewed for the course of pregnancy and delivery as well as maternal and neonatal health.

Results: The median of maternal m.3243A>G load in muscle or buccal epithelium was 59% (range 30-76%). There were 30 deliveries and 31 born children. Among singleton pregnancies, gestational diabetes was present in seven (24%), gestational hypertension or pre-eclampsia in three (10%) and preterm delivery in two (7%). Mean birth weight was 3537 g (1020-5310 g), with a z-score of 0.80±1.37 for girls and 0.77±1.05 for boys. Seven newborns (12%) were treated in the neonatal intensive care unit.

Conclusion: Women harbouring m.3243A>G may have an elevated risk for obstetric complications, such as gestational diabetes and gestational hypertension. Their babies may have an elevated risk of preterm birth and need for intensive care. Pregnancies of women with m.3243A>G should be followed carefully.

Background: The BRCA2 c.8351G>A p.(Arg2784Gln) variant has long been classified as a variant of uncertain significance (VUS) due to conflicting evidence used in variant classification. This study aims to clarify its pathogenicity and associated risks for breast and ovarian cancer.

Methods: This study was conducted by the international Evidence-based Network for the Interpretation of Germline Mutant Alleles consortium. We collected data from 29 informative families with this variant. Co-segregation likelihood ratios (LRs) were calculated using the full-likelihood method to assess pathogenicity, and cancer risks were estimated with modified segregation analysis.

Results: Co-segregation analysis using a grid search across scaled penetrance levels for BRCA2 truncating variants yielded the strongest evidence in favour of pathogenicity, with LR maximised at approximately 20% of full penetrance (LR=11.026). Furthermore, estimated breast cancer risks were markedly higher for early onset breast cancer; women diagnosed at <50 years had a HR of 4.5, compared with a HR of 1.65 for women diagnosed at ≥50 years. The estimated lifetime risks were 25% for breast cancer and 6% for ovarian cancer.Evidence of pathogenicity was also supported by the presence of the variant allele in two patients with Fanconi anaemia.

Conclusions: Our results indicate that BRCA2 c.8351G>A p.(Arg2784Gln) has a disease-causing effect, with reduced penetrance, similar to other pathogenic variants in moderate risk breast cancer genes such as ATM and CHEK2. We also provide risk-adapted recommendations for clinical management. Importantly, one should be aware of a reduced penetrance as the underlying reason for conflicting results among pieces of evidence used for variant classification.

Whole-genome sequencing (WGS) for every UK newborn is hailed as a leap towards lifelong personalised medicine, yet policymakers have scarcely examined the informatics iceberg beneath the initiative: where, and at what cost, will millions of genomes be stored? This perspective contends that the research-era reflex of keeping raw reads and alignments in high-performance 'hot' cloud storage is incompatible with NHS budgets and net-zero targets. Drawing on the National Genomic Research Library's current practice (~80 GB per child), I estimate the UK government's 10-year rollout would accumulate more than 0.5 exabytes and incur ~£620 million in standard S3 fees-exceeding NICE's entire core budget over the same period-while driving up data-centre energy demand. By contrast, automatically migrating files to deep-archive tiers 3 months after newborn screening preserves future utility but cuts lifetime storage costs by 91% to about £18 per child and reduces operational power by an order of magnitude; 12-24 hour restore latencies remain clinically acceptable for episodic re-analysis. I argue that newborn sequencing is primarily a logistics challenge rather than a scientific one, and that a national 'screen-then-archive' policy, anchored by a retrieval service-level agreement, would safeguard public funds, support workforce expansion and honour NHS carbon commitments while allowing consent-based re-analysis at adolescence or adulthood. Embedding cold storage economics now will prevent the programme from sinking under an exabyte scale liability.

Background: Whole genome sequencing (WGS) has recently been introduced as a diagnostic test for patients with particular rare diseases in the National Health Service (NHS) in England. Little is known about the process of communicating results from WGS to families in practice.

Methods: We audio-recorded clinicians and parents discussing the results of WGS for their child's rare disease diagnosis as part of a larger mixed-methods evaluation of the implementation of the NHS Genomic Medicine Service during its early years.

Results: 10 consultations were audio-recorded across four NHS Trusts. Clinical indications for WGS were related to neurological and developmental disorders. Seven parents received a genetic diagnosis for their child's condition, two received a variant of uncertain significance, and one received a no primary finding result. One parent also received an incidental finding for their child. Challenges in discussing results included (1) explaining a diagnosis when the genotype was established before detailed phenotyping, (2) navigating follow-up for an adult-onset condition identified in childhood, (3) disclosing an unexpected diagnosis for a parent from trio testing and (4) conveying a diagnosis with an uncertain prognosis.

Conclusion: This study illustrates some of the issues that can arise from unexpected and uncertain information when returning results from broad-scope genomic testing for paediatric neurological and developmental disorders. Further study of actual interactions between clinicians and families discussing results from WGS across different specialities and conditions is needed to inform guidance on communication of results within this rapidly evolving area of medicine.

Background: Myotonic dystrophy type 1 (DM1) is a multisystem disorder with autosomal dominant inheritance, caused by the abnormal expansion of the CTG triplet in the DMPK gene. Biomarker discovery in DM1 is crucial for monitoring disease progression.

Methods: We performed RNA sequencing on blood, skin and muscle samples from the same patients to assess splicing events. Mis-splicing events were identified using the Mann-Whitney U rank-sum test, and per cent spliced in for exons was correlated with repeat expansion size using Spearman's correlation. We also examined the relationship between mis-splicing and disease severity through Fisher's exact test and correlation analyses.

Results: We identified 937, 384 and 1216 mis-splicing events in muscle, blood and skin, respectively. Of these, 52 exons in muscle and 10 in blood correlated with estimated progenitor allele length (false discovery rate (FDR) <0.1), but none in skin. Notably, nine exons in blood correlated with total muscle mis-splicing (FDR<0.05), suggesting their potential as biomarkers of severity.

Conclusion: This is the first study to identify splicing dysregulation in blood and skin in patients with DM1 and identify novel potential blood-based mis-splicing biomarkers for disease severity. The correlation between several blood exons and the muscle splicing dysregulation indicates that blood-based biomarkers can be valuable for assessing disease severity, monitoring disease progression and evaluating treatment efficacy. Larger sample sizes may be necessary to clarify the relationship between mis-splicing and disease severity.

Comprehensive genomic testing in routine cancer care pathways has created the need to interpret the consequences of somatic (acquired) genomic variants beyond the currently well-characterised driver variants in cancer gene hotspots. While several guidelines have been published to determine the oncogenicity of somatic cancer gene variants, they lack a comprehensive and flexible approach that encompasses all available lines of evidence. Individual UK laboratories have developed local approaches to standardise somatic variant interpretation, often based on different sets of published guidelines, but a comprehensive national standardised framework is lacking. The absence of standardisation in approaches to somatic variant interpretation highlights a significant gap in the field of genomic medicine within the UK healthcare system. Key stakeholders from across the UK cancer genomics diagnostic community formed the UK Somatic Variant Interpretation Group (SVIG-UK) in September 2018 to develop a consensus approach for interpretation of somatic variants identified through genomic testing in patients with solid tumours and haematological malignancies. SVIG-UK scientists conducted a review of existing somatic variant interpretation classification systems and although they mostly agreed on evidence sources for variant interpretation, differences were identified in how the evidence should be used, weighted and combined. The SVIG-UK team subsequently developed a single, standardised UK-wide approach to somatic variant interpretation which encompassed both solid tumour and haematological cancer genomic testing. This framework was shared with stakeholders across the UK alongside variants for preliminary testing. Outcomes were then reviewed and following engagement sessions across the community, the variant interpretation recommendations were updated and ratified by the UK Association of Clinical Genomics Sciences. We present herein the SVIG-UK framework and recommendations, which provide a standardised, comprehensive and flexible approach for classifying the oncogenicity of somatic variants in cancer genes.

Despite the identification of many genes involved in developmental eye phenotypes, a large percentage of families lack genetic diagnoses, suggesting novel mechanisms remain to be discovered. Large deletions of 16p11.2, 3p14 or 19p13.11 regions involving transcription factors MAZ, FOXP1 and SIN3B, correspondingly, along with other genes, have been previously reported in individuals with neurodevelopmental and variable other features, including ocular coloboma and/or microphthalmia; recently, intragenic variants in FOXP1 and SIN3B have also been shown to cause neurodevelopmental phenotypes, with developmental eye defects reported in a small number of individuals with FOXP1 variants. Through exome sequencing analysis we identified novel splicing variants in MAZ and SIN3B, and a recurrent nonsense allele in FOXP1 in unrelated families affected with colobomatous microphthalmia, all with predicted loss-of-function effects; additionally, we report two new families with coloboma and 16p11.2 genomic deletions including MAZ, one de novo and another inherited from an affected parent. These findings provide further support for a role for FOXP1 in structural eye phenotypes, expanding its spectrum to include colobomatous microphthalmia, and suggest a role for MAZ and SIN3B in human eye development and disease.

Neuroendocrine tumours (NETs) are increasingly associated with Lynch syndrome (LS). In this autosomal dominant cancer predisposition syndrome, a somatic mutation in addition to a germline pathogenic variant is required for tumour development. We describe the case of a middle-aged female patient with LS with a known germline MLH1 mutation who was diagnosed with Cushing's syndrome. An ectopic adrenocorticotropic hormone (ACTH) producing carcinoid tumour of the lung with lymph node metastases was found and resected. Immunohistochemical analysis showed loss of MLH1/PMS2 expression, and genetic analysis confirmed a deletion of the entire MLH1 gene, acting as the second hit for tumour formation. This provides unequivocal evidence of the tumour's association with LS. Only 30 cases of NETs in LS have been described in the literature, most of them of gastrointestinal origin. We describe the first bronchopulmonary NET in a patient with LS, broadening the spectrum of LS tumours, and the first ACTH-producing tumour in LS.