100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care - Preliminary Report

BACKGROUND

The U.K. 100,000 Genomes Project is in the process of investigating the role of genome sequencing in patients with undiagnosed rare diseases after usual care and the alignment of this research with health care implementation in the U.K. National Health Service. Other parts of this project focus on patients with cancer and infection.

METHODS

We conducted a pilot study involving 4660 participants from 2183 families, among whom 161 disorders covering a broad spectrum of rare diseases were present. We collected data on clinical features with the use of Human Phenotype Ontology terms, undertook genome sequencing, applied automated variant prioritization on the basis of applied virtual gene panels and phenotypes, and identified novel pathogenic variants through research analysis.

RESULTS

Diagnostic yields varied among family structures and were highest in family trios (both parents and a proband) and families with larger pedigrees. Diagnostic yields were much higher for disorders likely to have a monogenic cause (35%) than for disorders likely to have a complex cause (11%). Diagnostic yields for intellectual disability, hearing disorders, and vision disorders ranged from 40 to 55%. We made genetic diagnoses in 25% of the probands. A total of 14% of the diagnoses were made by means of the combination of research and automated approaches, which was critical for cases in which we found etiologic noncoding, structural, and mitochondrial genome variants and coding variants poorly covered by exome sequencing. Cohortwide burden testing across 57,000 genomes enabled the discovery of three new disease genes and 19 new associations. Of the genetic diagnoses that we made, 25% had immediate ramifications for clinical decision making for the patients or their relatives.

CONCLUSIONS

Our pilot study of genome sequencing in a national health care system showed an increase in diagnostic yield across a range of rare diseases. (Funded by the National Institute for Health Research and others.).

Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia

The occurrence of non-epileptic hyperkinetic movements in the context of developmental epileptic encephalopathies is an increasingly recognized phenomenon. Identification of causative mutations provides an important insight into common pathogenic mechanisms that cause both seizures and abnormal motor control. We report bi-allelic loss-of-function CACNA1B variants in six children from three unrelated families whose affected members present with a complex and progressive neurological syndrome. All affected individuals presented with epileptic encephalopathy, severe neurodevelopmental delay (often with regression), and a hyperkinetic movement disorder. Additional neurological features included postnatal microcephaly and hypotonia. Five children died in childhood or adolescence (mean age of death: 9 years), mainly as a result of secondary respiratory complications. CACNA1B encodes the pore-forming subunit of the pre-synaptic neuronal voltage-gated calcium channel Ca_v2.2/N-type, crucial for SNARE-mediated neurotransmission, particularly in the early postnatal period. Bi-allelic loss-of-function variants in CACNA1B are predicted to cause disruption of Ca²⁺ influx, leading to impaired synaptic neurotransmission. The resultant effect on neuronal function is likely to be important in the development of involuntary movements and epilepsy. Overall, our findings provide further evidence for the key role of Ca_v2.2 in normal human neurodevelopment.

Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome

EXTL3 regulates the biosynthesis of heparan sulfate (HS), important for both skeletal development and hematopoiesis, through the formation of HS proteoglycans (HSPGs). By whole-exome sequencing, we identified homozygous missense mutations c.1382C>T, c.1537C>T, c.1970A>G, and c.2008T>G in EXTL3 in nine affected individuals from five unrelated families. Notably, we found the identical homozygous missense mutation c.1382C>T (p.Pro461Leu) in four affected individuals from two unrelated families. Affected individuals presented with variable skeletal abnormalities and neurodevelopmental defects. Severe combined immunodeficiency (SCID) with a complete absence of T cells was observed in three families. EXTL3 was most abundant in hematopoietic stem cells and early progenitor T cells, which is in line with a SCID phenotype at the level of early T cell development in the thymus. To provide further support for the hypothesis that mutations in EXTL3 cause a neuro-immuno-skeletal dysplasia syndrome, and to gain insight into the pathogenesis of the disorder, we analyzed the localization of EXTL3 in fibroblasts derived from affected individuals and determined glycosaminoglycan concentrations in these cells as well as in urine and blood. We observed abnormal glycosaminoglycan concentrations and increased concentrations of the non-sulfated chondroitin disaccharide D0a0 and the disaccharide D0a4 in serum and urine of all analyzed affected individuals. In summary, we show that biallelic mutations in EXTL3 disturb glycosaminoglycan synthesis and thus lead to a recognizable syndrome characterized by variable expression of skeletal, neurological, and immunological abnormalities.

Acknowledgement of Cilia’s reviewers in 2013

Contributing reviewers

Our thanks to Cilia’s reviewers

Contributing reviewers

We would like to thank all our reviewers for their contribution to the success of Cilia. Their voluntary participation has led to the launch of a new journal consistently publishing high quality articles and an intelligent peer review process for all our authors.

Chinius barbazanin. sp. de Thailande (Diptera : Psychodidae)

A new species of sandfly is described from limestone caves in Thailand. The inclusion of this species in the genus Chinius, which up until now was monospecific, is discussed. It is justified on the basis of characteristics of the head (eyes, pharynx, cibarium, complete interocular suture and length of the mouth pieces), thorax (rounded wings), abdomen (presence of trumpet glands on the tergites 4 and 5 of the male) and genitalia (morphology of the male genitalia and of the spermathecae in the female). Detailed descriptions and drawings are given. The wing of C. barbazani n. sp. lacks of vein R2 in both sexes. This anomaly, regarding to Phlebotominae, is discussed and considered as a probable autapomorphic regression. The differential diagnosis with Chinius junlianensis Leng, 1987, rests on a number of characteristics of the wing venation, antennal formula and the length of the male and female genital ducts, which are five times shorter in C. barbazani n. sp.

Nephrocystin-5, a ciliary IQ domain protein, is mutated in Senior-Loken syndrome and interacts with RPGR and calmodulin

Nephronophthisis (NPHP) is the most frequent genetic cause of chronic renal failure in children. Identification of four genes mutated in NPHP subtypes 1-4 (refs. 4-9) has linked the pathogenesis of NPHP to ciliary functions. Ten percent of affected individuals have retinitis pigmentosa, constituting the renal-retinal Senior-Loken syndrome (SLSN). Here we identify, by positional cloning, mutations in an evolutionarily conserved gene, IQCB1 (also called NPHP5), as the most frequent cause of SLSN. IQCB1 encodes an IQ-domain protein, nephrocystin-5. All individuals with IQCB1 mutations have retinitis pigmentosa. Hence, we examined the interaction of nephrocystin-5 with RPGR (retinitis pigmentosa GTPase regulator), which is expressed in photoreceptor cilia and associated with 10-20% of retinitis pigmentosa. We show that nephrocystin-5, RPGR and calmodulin can be coimmunoprecipitated from retinal extracts, and that these proteins localize to connecting cilia of photoreceptors and to primary cilia of renal epithelial cells. Our studies emphasize the central role of ciliary dysfunction in the pathogenesis of SLSN.

Energy metabolism in Bardet-Biedl syndrome

INTRODUCTION

Obesity is a consistent presenting feature of the Bardet-Biedl syndrome (BBS), a hereditary disorder caused by a single gene defect. This contrasts sharply with general obesity which, despite a strong hereditary component, has a multifactorial aetiology. For BBS, the phenotypic characterisation of the components of energy balance and the implications for their management remains relatively uninvestigated.

OBJECTIVE

A case-control study to determine whether energy metabolism in subjects with BBS differs from matched obese controls and to inform the clinical management of these patients.

METHODS

A total of 20 overweight and obese subjects with BBS (11 females, 9 males) matched for age, gender and BMI to 20 subjects without BBS. Resting metabolic rate (RMR) was measured by indirect calorimetry, physical activity by CSA accelerometry, body composition by the deuterium dilution technique and dietary intake by 7-day food records.

RESULTS

There was no significant difference between BBS and control subjects in body fat (male: % fat=38, s.d. 2.8 vs 34, s.d. 9.1, female: % fat=45, s.d. 5.9 vs 44, s.d. 8.1; P=0.46] or absolute RMR (male: 6.95, s.d. 1.55 MJ/day vs 7.19, s.d. 1.28 MJ/day; P=0.6). After adjustment for gender, age, fat-free mass and fat mass, there was no significant difference in RMR between BBS and control subjects (F(1, 30)=0.91; P=0.35). A lower level of physical activity was observed in BBS subjects (median cnts/min 259, IQR=153) compared to controls (median cnts/min=306, IQR=119, P=0.02). Reported energy intake, macronutrient composition and magnitude of under-reporting were comparable in both groups.

CONCLUSION

This study reveals no evidence for systematic differences in energy metabolism in subjects with BBS relative to other obese individuals, suggesting that the genetic basis of BBS is not associated with specific abnormalities in energy metabolism. This is an important finding for clinical management and supports the use of energy prescriptions based on RMR for the general obese population plus an appropriate allowance for energy expended via physical activity. Further research is needed on physical activity in BBS.

Chromosome 11q13 and atopic asthma

Asthma is a complex syndrome in which bronchial inflammation and smooth muscle hyperactivity lead to labile airflow obstruction. The commonest form of asthma is that due to atopy, which is an immune disorder where production of IgE to inhaled antigens leads to bronchial mucosal inflammation. The ultimate origins of asthma are interactive environmental and genetic factors. The genetics is acknowledged to be heterogeneous, and one chromosomal region of interest and controversy has been 11q13. To clarify the nature of the chromosome 11q13 effect in atopy and asthma, we conducted a genetic association study in subjects with marked atopic asthma and matched controls, which incorporated the study of 13 genetic variants over a distance of 10-12 cM and which took account of detailed immune and clinical phenotyping. Association with high IgE levels was limited to the interval flanked by D11S1335 and CD20 in a 0.8-Mb interval and was greatest for variants of Fc epsilonRIbeta and HTm4; these variants also associated with asthma (recurrent wheeze with labile airflow obstruction and need for regular inhaler treatment). At the more telomeric marker, D11S480, variants associated with asthma, but not with high IgE levels. The data might support the possibility of multiple loci relevant to atopic asthma on chromosome 11q13.

Glutathione protects a human insulinoma cell line from tumor necrosis factor-alpha-mediated cytotoxicity

It is postulated that glutathione acting as a free oxygen radical scavenger may protect beta-cells from cytokine-mediated cytotoxicity in insulin-dependent diabetes. In this study the effect of glutathione in preventing the cytotoxic damage mediated by tumor necrosis factor-a in vitro towards a human beta-cell line (CM insulinoma) was investigated. CM cells were exposed in vitro to tumor necrosis factor-alpha, tumor necrosis factor-alpha plus glutathione or glutathione alone at different concentrations. The resulting cytotoxicity was measured using a colorimetric assay. Glutathione significantly reduced the cytotoxicity mediated by tumor necrosis factor-alpha in a dose-dependent fashion (P < 0.001). These results suggest a protective effect of glutathione on beta-cell cytotoxicity induced by tumor necrosis factor-alpha and encourage the use of glutathione in trials aimed at reducing the beta-cell damage occurring in insulin-dependent diabetes.

Normalization of the CD4/CD8 lymphocyte ratio and increased B lymphocytes in long standing diabetic patients following therapy with thymopentin

A double blind study with thymopentin (TP5) and placebo was performed in 49 patients affected by Type 1 and Type 2 diabetes of long duration characterized by a reduction of the CD4/CD8 (helper/suppressor) lymphocyte ratio. TP5 (50 mg) was administered subcutaneously 3 times weekly for 1 month. Total peripheral lymphocytes and functionally different cell subsets were measured throughout the course of the study. Data showed a statistically significant increase of the CD4/CD8 lymphocyte ratio (p less than 0.02) and of the percentage of B lymphocytes (p less than 0.001) only in the TP5 receiving group. No side effects were observed during the study and patients remained well controlled. These results suggests that TP5 may be administered safely to diabetic patients and by improving impaired cell mediated immune parameters TP5 may contribute to prevent the development of infections in these patients.

Ultrastructure of lymphocyte subsets and of activated lymphocytes in type 1 diabetes as defined by monoclonal antibodies and the immunogold technique

The ultrastructure of peripheral blood lymphocyte subsets and activated lymphocytes from 5 patients with recent onset insulin-dependent diabetes as identified by monoclonal antibodies (CD4, CD8 and 4F2) and labelled with gold coupled goat anti-mouse IgG are described and depicted. Electron microscopy revealed no differences in appearance between investigated lymphocyte subsets at the single cell level. Activated lymphocytes as defined by an early activation antigen (4F2) do not always have a characteristic appearance nor do they show morphological signs of activation in all cases. We would conclude that it is not possible to recognize different lymphocyte subsets based only on their ultrastructure.

Inhibition of the receptor for interleukin-2 induced by carbimazole: relevance for the therapy of autoimmune thyroid disease

Evidence has been accumulated that the anti-thyroid drugs used in the treatment of Graves' disease may have immunosuppressive properties but the exact mechanism of action is still unclear. In the present study, we have investigated the in vitro effect of carbimazole (CBZ) on the expression of lymphocyte differentiation antigens and on suppressor cell activity. The incorporation of radiolabelled methimazole (35S-MMI, the active metabolite of CBZ) by resting and mitogen stimulated lymphocytes was also investigated. CBZ at concentrations of 60 microM significantly inhibited the expression of the receptor for interleukin-2 (as defined by the anti-TAC monoclonal antibody [MoAb]) by lymphocytes stimulated with phytohaemagglutinin. The expression of an early activation antigen (as characterized by the 4F2 MoAb) was not affected. Twenty-four hour pre-incubation of cells with different concentrations of CBZ or medium alone did not change the lymphocyte response to mitogenic stimulation, thus suggesting no effect of the compound on suppressor cell function. Finally, there were no significant differences in the uptake of 35S-MMI between resting and stimulated lymphocytes. These data suggest that the immunosuppressive effect of CBZ may be due to its effect of reducing the expression of the receptor for interleukin-2 on lymphocytes undergoing full activation. This property of CBZ could be of relevance in the therapy of autoimmune thyroid diseases (not only Graves' disease) which are characterised by the presence of activated T cells in the thyroid and in circulation.

In vitro inhibition of insulin release mediated by sera with complement-fixing islet cell antibodies belonging to normal first degree relatives of patients with type 1 diabetes

Islet cell antibodies (ICA) are present in the sera of most patients with Type 1 diabetes at diagnosis and in some of their genetically susceptible, but otherwise normal, first degree relatives. In this study we have investigated basal and stimulated insulin release by mouse islets following preincubation with human sera (with or without the addition of guinea pig complement) belonging to: 15 normal first degree relatives of diabetic probands; 7 patients with Type 1 diabetes; 7 control subjects with no history of diabetes. All sera had been previously screened for conventional (IgG), complement fixing (CF) and surface (S) ICA. Basal insulin release was not altered by any of the sera. The response to stimulus after incubation with ICA negative and IgG-ICA positive (but CF-ICA negative) sera was similar whether complement was present or not. Stimulated insulin release was significantly inhibited by complement and sera from 2 relatives and 3 diabetic patients. These sera were CF-ICA positive, the sera of the 2 relatives being also ICSA positive. One relative developed Type 1 diabetes 14 months later. This study demonstrates for the first time that sera containing CF-ICA and belonging to individuals susceptible to Type 1 diabetes, can impair insulin release in vitro. It is therefore likely that antibody-dependent, complement-mediated mechanisms are involved in the pathogenesis of Type 1 diabetes.

Labelling of lymphocytes with indium 111 oxine: effect on cell surface phenotype and antibody-dependent cellular cytotoxicity

Indium 111 oxine is currently used to label peripheral lymphocytes in order to study the kinetics of these cells in vivo. Since the quantity of radioisotope for labelling is still a matter of controversy, we have investigated in vitro the effect of increasing the concentration of indium 111 oxine on the lymphocyte surface phenotype and the antibody-dependent cellular cytotoxicity (ADCC) using lymphocytes from normal subjects. The cell surface phenotype, as evaluated by 2 monoclonal antibodies, was not affected whereas ADCC, at any of the doses used, was significantly reduced compared to the baseline value. The implications of these results for the use of indium 111 oxine for the in vivo studies are discussed.