Genomics - Recent Highlights

Renal Genetics (FE Karet and RN Sandford)

The Renal Genetic and Tubular Disorders (RGTD) service at Addenbrooke's is a multidisciplinary NHS outpatient clinic serving those with inherited, heritable and tubular disorders.

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The Renal Genetic and Tubular Disorders (RGTD) service at Addenbrooke's is a multidisciplinary NHS outpatient clinic serving those with inherited, heritable and tubular disorders. From the research perspective, in addition to improving outcomes for our patients, our aims include

  • evaluating potential biomarkers for inherited renal disorders
  • investigating mechanisms of disease in renal tubular disorders
  • development and implementation of further specific diagnostic tests
  • development of improved care pathways for patients and their families

As examples, we have just completed an analysis of genotype-phenotype correlations in our cohort of 142 PKD patients, including in-house established PKD2 testing, to inform clinical guidelines for future genetic testing; we have identified and characterized a novel complex UMOD mutation in four large families that has allowed predictive testing for the first time; in collaboration with Clinical Biochemistry we have set up new urinary assays for UMOD protein and for retinol-binding protein (a marker of proximal tubular dysfunction); and we have assessed dipstick versus meter measurements of urinary pH, which is a necessary but underused part of the management of stone disease. In addition we have this year achieved Gene Dossier approval for a further three renal disease genes (PKD1, ATP6V1B1 and ATP6V0A4). Our NIHR portfolio study has registered over 200 patients.


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Medical Genetics Diagnostics (J Whittaker, I Simonic, DC Rubinsztein, J Todd, FL Raymond, H Firth)

The Department of Medical Genetics has been focusing on a number of projects aimed at translating local research expertise into new and novel clinical diagnostic assays. In the cytogenetics domain, we have been using NIHR BRC funding in order to test the potential of high resolution arrays for...

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The Department of Medical Genetics has been focusing on a number of projects aimed at translating local research expertise into new and novel clinical diagnostic assays. In the cytogenetics domain, we have been using NIHR BRC funding in order to test the potential of high resolution arrays for detecting small copy number variants associated with congenital abnormalities.

We identified several interesting abnormalities we are now following up. Since small copy number changes are frequent in normal individuals, it remains a major challenge to be able to infer causality for such variants. In other words, when a patient present with an abnormality, such as a structural cardiac defect and a small gene deletion (or duplication), then one needs to be able to answer the question if the genetic

abnormality is likely to be causal or an epiphenomenon. In order to address this issue, we have been testing whether we can use zebrafish as a model for this purpose. In order to generate proof-of-principle data, we have been knocking down expression of genes associated with defined congenital abnormalities, and then are testing whether the resulting zebrafish phenotypes mirror those seen in patients. Ultimately, we hope to be able to provide sufficient support for this approach to be able to apply it as a diagnostic adjunct for a range of phenotypes that are amenable to analysis in zebrafish.

In the molecular genetics diagnostic domain, we are defining the potential for next generation sequencing, initially using X-linked learning disability cases as a prototype condition, and the sequencing and bioinformatics of expertise of EASIH. The X-linked LD project has to date completed the sequence of the whole-exome complement of the X chromosome, accounting for over 700 genes, in 10 patient samples. Using 'first generation' sequencing approaches would have required approximately 5 years of NHS sequencing throughput, whereas with 'next generation' approaches this has been completed in less than 6 months. We have successfully developed the performance of both the sequencing platform and the data analysis tools required to validate the assay as fit for use in the diagnostic laboratory. This project will continue to validate a number of alternative strategies to allow the selective sequencing of genes relevant to X-linked learning disability, and will offer the assay as a diagnostic service UK wide within the next 6-8 months.


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X linked intellectual disability (L Raymond)

The NIHR funding was initially used to support the completion of high throughput Sanger sequencing on a cohort of families with X linked intellectual disability. We have screened >700 genes from the X chromosome in the research project and have identified 12 novel genes that cause disease....

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The NIHR funding was initially used to support the completion of high throughput Sanger sequencing on a cohort of families with X linked intellectual disability. We have screened >700 genes from the X chromosome in the research project and have identified 12 novel genes that cause disease. The NIHR BRC funding has also directly contributed to the translation of this research to providing a diagnostic service to the individuals who have a pathogenic mutation and the provision of testing for the extended family.

In 2009-10, the NIHR funding has supported the completion of the detailed analysis of the X chromosome with high resolution array technology and this led to resolution of the genetic defects in a further 13% of the families investigated. This has led to a diagnostic test for a further 25 families and have defined one further new gene and 3 further candidate genes for intellectual disability. More recently we have used NIHR BRC funding to develop non-invasive prenatal testing for X linked diseases with a view to translation of this method to clinical practice. We anticipate that we will deliver this test safely and reliably within the year.


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Genes to phenotypes and mechanisms in type 1 diabetes (John Todd)

We have continued our gene to phenotype studies in type 1 diabetes with several publications this year relating T1D-associated genotypes with phenotypes of immune cells in blood samples and purified immune cells. We have evidence the plasma protein soluble CD25 may be a biomarker of early...

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We have continued our gene to phenotype studies in type 1 diabetes with several publications this year relating T1D-associated genotypes with phenotypes of immune cells in blood samples and purified immune cells. We have evidence the plasma protein soluble CD25 may be a biomarker of early diagnosis of T1D; and that increased type 1 interferon production is associated with increased susceptibility to type 1 diabetes, by inheriting alleles of genes that promote this pathway and by viral infections (published in Nature). This information will underpin the identification of disease mechanisms that could be targets for therapeutic interventions.

A continuing strategic development has been major continued efforts in the Cambridge BioResource. This year we have enrolled a further 3,800 local volunteers onto the BioResource panel bringing the total now to over 9,500 volunteers and over 400 existing CBR volunteers have participated in Phase 2 research studies. Individuals from the Cambridge, and now, wider regions, who have volunteered to participate in this resource, have provided samples for DNA extraction to enable genotyping for (disease-associated) polymorphisms of interest. Individuals can be approached on the basis of their genotype to undertake detailed phenotyping studies, including cellular assays. Samples of DNA, plasma and serum have been deposited in a dedicated biorepository, lifestyle information has been collected and stored in a purpose-designed database, and full blood counts have been determined.

One of the major phase 2 studies, 'An investigation into genes and mechanisms based on genotypephenotype correlations in type 1 diabetes and related diseases using peripheral blood mononuclear cells from volunteers that are part of the Cambridge BioResource' by John Todd and Linda Wicker in the Department of Medical Genetics, continued, in 2009-2010, recruiting 356 subjects for our immunophenotyping studies. A new BRC facility has been set up this year, funded jointly by the NIHR BRC, the University, and an award from the MRC: the Eastern Sequence and Informatics Hub (EASIH; director, John Todd), which in addition to supporting several projects, is developing next generation sequencing in X-linked intellectual disability diagnostic testing, with Lucy Raymond and Howard Martin; and also HLA typing with Cristina Navarrete at the NHS Blood and Transplant at Colindale. Both these projects could have near-term impact on patients.

Core funding for the Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory (director, John Todd) for the next five years was renewed recently (£10M). The laboratory has also helped in the establishment of state-of-the-art, cross-campus flow cytometric phenotyping facilities, which are essential in the path from disease susceptibility genes to disease mechanisms and pathways, towards primary prevention of this major disease of childhood and its increasing population incidence.


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Understanding how drugs regulate autophagy and impact on disease (DC Rubinsztein)

(Macro) autophagy is a bulk degradation process that mediates the clearance of long-lived proteins and organelles. Autophagy is initiated by double-membraned structures, which engulf portions of cytoplasm. The resulting autophagosomes ultimately fuse with lysosomes, where their contents are...

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(Macro) autophagy is a bulk degradation process that mediates the clearance of long-lived proteins and organelles. Autophagy is initiated by double-membraned structures, which engulf portions of cytoplasm. The resulting autophagosomes ultimately fuse with lysosomes, where their contents are degraded. Initially, we discovered that autophagy is a key regulator of the levels of intracytoplasmic aggregate-prone proteins that cause neurodegenerative diseases. We have shown that autophagy-upregulating drugs enhance the clearance of mutant huntingtin, mutant ataxin 3 (that causes spinocerebellar ataxia), and mutant and wild-type forms of tau in a range of in vivo models (flies, zebrafish and mice) and attenuate the toxicities of these proteins in these in vivo models.

When we initiated our studies, the only known pharmacological way of inducing autophagy chronically was with rapamycin. Although rapamycin is designed for long-term use, it has side effects which may make it unattractive to patients who may need to take the drug for decades. Thus, we have embarked on a series of studies to identify novel autophagy-upregulating compounds and have discovered pathways that are independent of the target of rapamycin. We have shown that drugs acting on such pathways are protective in fly, zebrafish and mouse models of Huntington's disease. We are about to embark on a safety trial with one of these drugs, rilmenidine, in Huntington's disease patients, in collaboration with Dr Roger Barker (Clinical Neurosciences).

Importantly, our studies have also revealed that antioxidants, which are widely believed to be protective in neurodegenerative disease, impair autophagy and worsen the phenotype in various Huntington's disease models. This provides a new insight into possible side effects of such drugs and may explain their lack of efficacy in trials in Huntington's disease patients, to date.


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Type I Diabetes and the Cambridge BioResource - Professor John Todd

The recent revolution in the genetic dissection of the common diseases has catalysed the study of physiology in human subjects. In order to identify phenotypes, some of which might be precursors of disease that might be targetable in future clinical trials, we are correlating disease-associated...

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The recent revolution in the genetic dissection of the common diseases has catalysed the study of physiology in human subjects. In order to identify phenotypes, some of which might be precursors of disease that might be targetable in future clinical trials, we are correlating disease-associated genotypes with immune phenotypes in human blood samples in the ongoing investigation of mechanisms in the autoimmune disease type 1 diabetes (Diabetes and Inflammation Laboratory).

To achieve this we need two major clinical resources, healthy volunteers and families with diabetes. Therefore we have created the NIHR Biomedical Research Centre Cambridge BioResource (cambridgebioresource.org.uk), a panel of 9,000 local research volunteers who have agreed to be approached for medical research projects and who can be recalled based on specific genotypes. This project provides direct access to study human physiology in health and diseases. Hundreds of volunteers have already participated in several projects. The Cambridge BioResource also provides a major opportunity for outreach and education of the general public in medical research. In type 1 diabetes we have also initiated a major collection of unaffected siblings in families with type 1 diabetes in order to help detect and characterise the earliest, inherited events in the disease (Diabetes ' Genes, Autoimmunity and Prevention).

See Medical Genetics Key Publications


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