Academic research community (GECIP)

When the human body senses germs, the immune system sends out a large army of forces to fight against infections. When these defences are weak, especially in the periods immediately after birth or in early childhood, babies and children are rendered helpless at the most critical time points in life. Severe and unusual infections, and other diseases in childhood can arise due to errors in the genetic blueprint. As a result, the development of major milestones like first steps, first words, or complex thoughts can be severely affected. In some cases, these genetic errors may even cause cancer or early ageing. The most crucial mechanisms in our body are found in replicating our genes ("genome stability") and recycling old material ("autophagy"). By analysing the genes in affected individuals and healthy family members, this project aims to uncover how the immune system protects the human brain. This will help both in genetic counselling and helping patients and families what to expect from their condition and how best to look after themselves.

The Ehlers-Danlos Syndromes (EDS) are a group of inherited disorders of the connective tissues. Connective tissues provide the scaffolding that makes up the structure of the body, and include many different tissue types such as bone, skin, muscle and tendon and blood vessels. There are still individuals and families with features suggestive of a rare EDS type for which a genetic cause has not yet been found, despite extensive genetic testing. This research project aims to identify the underlying genetic causes for this disease. We are one of the few groups doing this work within the NGRL at present..

To date, the analysis of the genome sequencing data in 100,000 Genomes Project (100KGP) has focused primarily on variants in coding regions of the genome (known as exons). However, variants in the non-coding regions of the genome (introns) are likely to contribute significantly to causation of disease and therefore identifying these will help to provide diagnoses for patients in the 100KGP who as yet have not received a genetic explanation for their condition. We propose to apply a range of custom algorithms to investigate these non-coding variants. We have developed algorithms that interrogate specific regions of the genome which are known to affect regulation of genes, in part because they affect the accessibility of the DNA to different proteins that are needed for gene expression. We have also developed algorithms that can interrogate how the coding regions (exons) of genes are joined together (or spliced) to make an alternative or aberrant form of a protein. The primary aim of this proposal is to provide diagnoses for patients who have not yet had a molecular diagnosis from the 100KGP (thereby increasing the diagnostic yield for 100KGP), but we also aim to understand more about the regulation of different genes and how that contributes to disease pathogenesis.

The hedgehog signalling pathway plays an essential role in early development of almost all mammals. The PTCH1 receptor acts as a negative regulator for this pathway, with PTCH1 variants being shown to cause aberrant hedgehog signalling leading to Gorlin syndrome (otherwise known as nevoid basal cell carcinoma syndrome). Heterozygous variation in PTCH1 (one mutated allele) is a well-documented cause of Gorlin syndrome, however, biallelic variation (two mutated alleles) is not well described. We wish to investigate the distribution and consequence of biallelic variation in PTCH1, particularly in the context of a rare disease known as craniosynostosis which results from the premature fusion of the skull sutures (gaps in the skull plates). Biallelic variants in other members of the hedgehog signalling pathway are associated with craniosynosostosis syndromes, notably Carpenter syndrome, but the role of PTCH1 remains unknown. To explore this, we shall investigate biallelic variants in the rare disease cohort in GE and, subsequently, the effect of such variation will be assessed experimentally considering the effect on the structure of PTCH1 and downstream hedgehog signalling.

For some patients with a rare genetic condition, the growth/maintenance of bones is impaired. In this study we will use data from the 100KGP to try and discover novel genetic causes for this group of skeletal conditions. More specifically, we will search for newly arising (“de novo”) variants and also for genetic variants that are predicted by computer algorithms to be highly deleterious. We will also compare our results to large databases of genetic variants seen in the general population. We anticipate that this work will lead to improvements in genetic diagnose rates for these group of patients and more generally a better understanding of bone development.

Astellas is a pharma company particularly intersted in cancer and in vision. It is looking for genetic variants which are responsible for symptoms and phenotypes in patients with rare diseases using genomic data and linked clinical record collected within the NGRL. We expect to find genes which are appropriate for therapeutic targets for these diseases and related disorders through the analysis.

This project will check how researchers working on craniosynostosis have liaised with the NHS Genomic Medicine Service and its referring clinicians, through the GECIP environment, to help get more diagnoses for patients enrolled into the 100,000 Genomes Project. The aim is to identify procedures to improve the diagnostic process from whole genome sequencing going forward.

Radial dysplasia is characterised by a variable shortening or absence of the larger of the two bones in the forearm and is present at birth. It may be caused by spontaneous variants (without an obvious cause), drugs that may interfere with fetal development or genetic syndromes (where a mutation causes radial dysplasia associated with an abnormality in another body system(s)). This project aims to identify novel genetic causes of radial dysplasia (either alone or as part of a wider genetic syndrome) by interrogating whole genome sequencing data in the NGRL in order to uncover novel biological mechanisms underlying forearm patterning defects.

The Mediator complex is an evolutionarily conserved, multi-subunit complex that regulates gene expression in all eukaryotes. Regulation of Mediator activity is, in part, achieved by the reversible association of a four-subunit kinase module (“Module”) comprising cyclin C (encoded by CCNC) and either cyclin-dependent kinase 8 (CDK8), MED12, and MED13 or their respective paralogs CDK19, MED12L, and MED13L. variants in CDK8, MED12, MED12L, MED13, and MED13L have been previously identified in syndromic developmental disorders with overlapping phenotypes, supporting the general concept of a Module-related syndrome (Calpena et al., AJHG [2019]). It was recently demonstrated that FBXL19 can recruit the Mediator-Module complex to chromatin via recognition of CpG islands, where the complex plays an important role in supporting normal developmental gene expression (Dimitrova et al., eLife [2018]). Interestingly, removal of the FBXL19 ZF-CxxC domain (responsible for the CpG island-recognition/binding) leads to perturbed development and embryonic lethality in mice. We have recently identified two cases with de novo missense variants affecting the FBXL19 ZF-CxxC domain that may affect the targeting of the Mediator-Module complex. In collaboration with Prof. Robert Klose’s group (University of Oxford), we are conducting functional assays to provide additional evidence for pathogenicity. Through a GeneMatcher collaboration, we have identified further cases with de novo FBXL19 variants. The intention of this Project is to provide additional genetic evidence supporting that variants in FBXL19 gene (missense o/e = 0.46, pLoF o/e = 0, gnomAD constraints) are responsible for a developmental disorder in humans. This will involve the analysis of FBXL19 variants within the Rare Disease cohort (Research Environment). Our preliminary analysis (release v7) has already revealed a number of potentially pathogenic FBXL19 variants. Such FBXL19 variants will be reported on Contact Referring Clinician forms. We would like to collaborate with the clinicians who submitted these families to fully characterise the associated phenotype. This work will help to demonstrate whether FBXL19 is a novel disease gene and investigate if variants affecting this gene are responsible for a syndromic developmental disorder compatible with the concept of a Module-related syndrome.

Multiple Epiphyseal Dysplasia (M.E.D) is a rare heterogenous condition, with both recessive and dominant forms, resulting in short stature and joint dysfunction. Over 20% cases are without molecular confirmation. We plan to interrogate the data of the 42 patients with M.E.D enrolled into the 100,000 genome project to look for novel gene causes and new variants for existing genes.

The 100,000 Genomes Project provides an unprecedented opportunity to explore the genetic basis for complex diseases. Our approach focus on specific regions of the genome which regulate the expression of individual genes. We will use information from various databases as well as develop bioinformatic approaches and use experimental data to pinpoint regions of the genome for detailed interrogation. We will test experimental genes in the lab using various model systems.

Genomic technologies have shown promise for stratifying disease management, identifying patients with rare disorders and identifying the causes of infections, all of which could improve both health and non-health outcomes in patients. The 100,000 Genomes Project (100KGP) presents both an ideal opportunity to systematically collect high-quality cost and health outcome data within the largest genome sequencing programme in the UK, in an NHS setting. This data, when used in the context of economic evaluations will be able to provide information on where the use of whole genome sequencing (WGS) is most likely to represent value for money for the NHS. This analysis will include the examination of both appropriate diagnostic points in the care pathway and the downstream consequences of testing (such as the use of targeted drug therapies). The 100KGP also provides a fantastic opportunity to address a range of methodological challenges facing health economists in this area.

We think we have identified a novel disease gene that when mutated may lead to a condition that comprises small head, short stature, learning disability as well as potentially other features. By collaborating with other scientists through the GeneMatcher website we hope to confirm our findings and publish our results so that this information may be useful for other clinical geneticists across the world

We previously identified and published heterozygous point variants of ERF in patients with craniosynostosis, and concluded that these variants were associated with haploinsufficiency. Although heterozygous deletions would be predicted to be associated with a similar pathogenic effect, none has previously been published (to our knowledge). Here, we wish to identify and analyse the phenotypes of deletions that include ERF and have been identified within the 100,000 Genomes Project (100kG).

There is one previous report of an association between a translocation of SOX6 and craniosynostosis. Preliminary analysis indicates that the GEL dataset includes additional SOX6 variants of potential clinical significance. This project aims to share information with clinicians who have also identified potentially significant SOX6 variants, to gain a broader picture of whether these variants are likely to be causative of the associated phenotypes.

Cleft lip and palate despite collectively being one of the most common birth defects, it is highly heterogeneous and remains poorly understood. This is in large part due to its cause being attributed to a complex interaction between genetic and environmental risk factors. In this project, we set out to study 100K data in a select cohort of families with multiple affected individuals with cleft lip and palate. The pattern of inheritance implicates a strong genetic influence and therefore provides the opportunity to better identify the causal genetic risk factors.

Craniosynostosis, the premature fusion of one or more of the cranial sutures of the skull, affects approximately 1 in 2000 children and requires a multidisciplinary approach to management. About one quarter of children with craniosynostosis is currently known to be caused by a damaging change to a single gene or chromosomal region, but the true proportion might be up to one third. This study will seek to identify new genetic causes of craniosynostosis by looking for clusters of variants or chromosome rearrangements in GEL sequence data and integrating the findings with those from our own sequencing programme in the Genetics of Craniofacial Malformations study.

Congenital talipes equinovarus (iCTEV), also known as clubfoot, is generally categorised as idiopathic or syndromic. Syndromic congenital talipes equinovarus is diagnosed when the condition presents with another inborn disease. On the other hand, the idiopathic version is described when the presentation occurs in the absence of another congenital disease. Affecting 1 in every 1000 live births, it is the most common newborn deformity. It is generally treated soon after birth using the non-invasive Ponseti method (based on manipulation and stretching of the affected foot). However, the underlying cause of of iCTEV is unknown. Initially, we will look at the characteristics associated with iCTEV. Following this, a bioinformatics-based approach will be used, to examine the genomic variation in previously identified genes of affected individuals compared to their parents and controls. It is hoped that identification of genetic variants will allow development of improved management of individuals affected with iCTEV.

Camptodactyly is a condition that causes one or more fingers to be permanently bent. It is a rare condition that occurs in less than 1% of the general population. Previously, in a Brazilian family of Japanese ancestry with camptodactyly, we identified a variant that may be associated with their camptodactyly. The current project aims to replicate our finding in additional patients with a similar condition.

Endocrine and metabolic disorders are common and may be caused by excess hormone production associated with tumours, or hormone deficiency due to inherited conditions affecting certain organs. These disorders can occur sporadically or be genetically inherited, however often the underlying biology causing these conditions is poorly understood. The control of calcium within the body involves a balance between the amounts absorbed from the gut, deposited into bone and into cells, and excreted from the kidney. This fine balance is controlled by parathyroid hormone (PTH) produced in the parathyroid glands in the neck, and an active metabolite of vitamin D synthesised by the kidney. PTH over-secretion is the major cause of increased blood calcium concentrations and may lead to kidney stones, kidney failure, bone fractures, lack of energy, feeling sick, ulcers and constipation. A lack of PTH leading to a fall in blood calcium concentration, may be associated with epilepsy, seizures, cataracts, bone malformations and abnormal teeth. Similarly, kidney defects are associated with high levels of calcium in urine and can lead to kidney stones. Bone disorders, which may be associated with short stature and arthritis, may also lead to abnormal calcium metabolism. Moreover, over- or under-activity of other hormone producing organs may also affect calcium and bone metabolism.

Disorders affecting the balance of calcium with the body may be caused by mutations to genes encoding proteins that are expressed in the parathyroid glands, bone and kidney. For example, mutations in genes encoding proteins involving in sensing blood calcium concentrations can affect PTH secretion. In this project we aim to look for mutations in genes associated with disorders of calcium homeostasis that may affect multiple organ systems including parathyroid, bone and kidney. Once these candidates have been selected we will undertake laboratory studies to determine what the effect of such mutations will be. Overall, we aim to aid in genetic diagnosis and facilitate the development of new treatments based on improved understanding of the mechanisms of these disorders.