Identifying phenotypic expansions for congenital diaphragmatic hernia plus (CDH+) using DECIPHER data

Congenital diaphragmatic hernia (CDH) can occur in isolation or in conjunction with other birth defects (CDH+). A molecular etiology can only be identified in a subset of CDH cases. This is due, in part, to an incomplete understanding of the genes that contribute to diaphragm development. Here, we used clinical and molecular data from 36 individuals with CDH+ who are cataloged in the DECIPHER database to identify genes that may play a role in diaphragm development and to discover new phenotypic expansions. Among this group, we identified individuals who carried putatively deleterious sequence or copy number variants affecting CREBBP, SMARCA4, UBA2, and USP9X. The role of these genes in diaphragm development was supported by their expression in the developing mouse diaphragm, their similarity to known CDH genes using data from a previously published and validated machine learning algorithm, and/or the presence of CDH in other individuals with their associated genetic disorders. Our results demonstrate how data from DECIPHER, and other public databases, can be used to identify new phenotypic expansions and suggest that CREBBP, SMARCA4, UBA2, and USP9X play a role in diaphragm development.

Novel de novo EEF1A2 missense mutations causing epilepsy and intellectual disability

BACKGROUND

Exome sequencing has led to the discovery of mutations in novel causative genes for epilepsy. One such gene is EEF1A2, encoding a neuromuscular specific translation elongation factor, which has been found to be mutated de novo in five cases of severe epilepsy. We now report on a further seven cases, each with a different mutation, of which five are newly described.

METHODS

New cases were identified and sequenced through the Deciphering Developmental Disabilities project, via direct contact with neurologists or geneticists, or recruited via our website.

RESULTS

All the mutations cause epilepsy and intellectual disability, but with a much wider range of severity than previously identified. All new cases share specific subtle facial dysmorphic features. Each mutation occurs at an evolutionarily highly conserved amino acid position indicating strong structural or functional selective pressure.

CONCLUSIONS

EEF1A2 should be considered as a causative gene not only in cases of epileptic encephalopathy but also in children with less severe epilepsy and intellectual disability. The emergence of a possible discernible phenotype, a broad nasal bridge, tented upper lip, everted lower lip and downturned corners of the mouth may help in identifying patients with mutations in EEF1A2.

How genetically heterogeneous is Kabuki syndrome?: MLL2 testing in 116 patients, review and analyses of mutation and phenotypic spectrum

MLL2 mutations are detected in 55 to 80% of patients with Kabuki syndrome (KS). In 20 to 45% patients with KS, the genetic basis remains unknown, suggesting possible genetic heterogeneity. Here, we present the largest yet reported cohort of 116 patients with KS. We identified MLL2 variants in 74 patients, of which 47 are novel and a majority are truncating. We show that pathogenic missense mutations were commonly located in exon 48. We undertook a systematic facial KS morphology study of patients with KS at our regional dysmorphology meeting. Our data suggest that nearly all patients with typical KS facial features have pathogenic MLL2 mutations, although KS can be phenotypically variable. Furthermore, we show that MLL2 mutation-positive KS patients are more likely to have feeding problems, kidney anomalies, early breast bud development, joint dislocations and palatal malformations in comparison with MLL2 mutation-negative patients. Our work expands the mutation spectrum of MLL2 that may help in better understanding of this molecule, which is important in gene expression, epigenetic control of active chromatin states, embryonic development and cancer. Our analyses of the phenotype indicates that MLL2 mutation-positive and -negative patients differ systematically, and genetic heterogeneity of KS is not as extensive as previously suggested. Moreover, phenotypic variability of KS suggests that MLL2 testing should be considered even in atypical patients.

Paediatric referral and attendance rates for the clinical genetics service in south-east Scotland--a comparison of a regional clinic with satellite clinics

BACKGROUND AND AIMS

In some studies the establishment of specialist satellite clinics nearer to the homes of patients has resulted in increased referral and attendance rates, particularly amongst populations in lower socio-economic groups. We investigated the effect on these rates of establishing satellite genetic counselling clinics for families with paediatric conditions in South East Scotland.

METHODS AND RESULTS

Families offered appointments at a clinic at the regional paediatric hospital were compared with those offered appointments at a satellite clinic at a local district general hospital. Both groups of families were more socially deprived than the general population (regional clinic p < 0.001, satellite clinics p < 0.05), and in both groups attendance rate at first appointment was 88% and inversely related to social deprivation. There was no evidence of greater attendance amongst more deprived patients at the satellite clinics compared to the regional clinic.

CONCLUSION

Our study found no evidence that the establishment of satellite clinics for genetic counselling in South East Scotland increases attendance by families with paediatric conditions in lower socio-economic groups. This suggests that factors other than clinic location determine referral and attendance rates, and these may include understanding of the reason for referral and the advantage of attendance.

Uptake of testing for BRCA1/2 mutations in South East Scotland

We investigated the uptake of genetic testing by 54 families in South East Scotland with a BRCA1/2 mutation. At a median of 37 months since identification of the mutation, the overall rate of uptake of testing in 269 eligible family members was 32%. First-degree relatives were significantly (P<0.05) less likely to be referred for genetic counselling in more, compared to less, socioeconomically deprived families (46 versus 68%). Among relatives who attended for genetic counselling, females were more likely to be tested than males (76 versus 53%; P<0.05) and relatives with children more than those without children (82 versus 53%; P<0.001). Tested relatives were older than relatives who did not undergo testing (mean 41.9 versus 36.8 years, P<0.05) but did not differ in degree of relationship to the index case or in socioeconomic deprivation. Our results confirm the findings from other studies of substantially lower rates of uptake of genetic testing for BRCA1/2 mutations than anticipated in earlier predictions. Relatives in more socioeconomically deprived families were less likely to be referred for genetic counselling, which is a matter of concern. This may be partly the result of a lack of understanding of the testing process. Cascading currently does not work in breast cancer families and further work is required to investigate intrafamilial communication patterns, testing behaviour and counselling strategies.

Inequality of use of cancer genetics services by members of breast, ovarian and colorectal cancer families in South East Scotland

Some studies have found a deficiency of male, younger and more socially deprived individuals amongst referrals to and/or attendees at cancer genetics clinics. We investigated this inequality of use of genetics services from data on 4,178 Scottish patients with a family history of breast and/or ovarian cancer (BOC) or colorectal cancer (CRC) referred from 2000--2006. Some 98% BOC and 60% CRC referrals were female. Median age of female referrals was greater in the CRC than the BOC group (45.3 vs. 38.7 years, P < 0.001). Both groups of referrals were less socially deprived than the general population (P < 0.001) and the CRC less deprived than the BOC group (P < 0.001). Some 88% patients attended the first appointment offered. Attendance was greater in the CRC group (P < 0.001) and in older patients (P < 0.001) and in the BOC group was highly significantly lower in more socially deprived patients (P < 0.001). Male relatives may feel counselling is less relevant and relatives of both sexes may delay counselling until approaching the age of onset of cancer in a relative. We suggest that medical professionals and the general public may have more knowledge about the genetics of BOC than of CRC. Thus relatives in CRC families seeking counselling are likely to be those with access to more information. The lower attendance amongst more deprived relatives in BOC families may result from poor understanding of the reason for referral. These findings confirm the need to provide male, younger and more socially deprived relatives with more helpful information on cancer genetics.

Further evidence of the increased risk for malignant peripheral nerve sheath tumour from a Scottish cohort of patients with neurofibromatosis type 1

A recent study, looking at the lifetime risk of developing malignant peripheral nerve sheath tumour (MPNST) in patients with neurofibromatosis type 1 (NF1), estimated the risk to be 8-13%. Prior to this, longitudinal studies had shown that patients with NF1 had a risk of 4-5% of developing MPNST, and cross-sectional studies had found that only 1-2% of patients with NF1 had MPNST. The aim of this study was to estimate the lifetime risk of MPNST in patients with NF1 in southern Scotland, using patient records obtained from the Edinburgh and Glasgow Genetic Units and Scottish Cancer Register. In the period 1993-2002, 14 patients with NF1 were diagnosed with MPNST in a population of 3.5 million. The lifetime risk of MPNST in the Scottish patients with NF1 was calculated to be 5.9-10.3%. This provides further evidence that patients with NF1 are at greater risk of developing MPNST than was previously estimated, and emphasises the importance of educating patients about suspicious symptoms, which may need an urgent medical opinion. The mean age at diagnosis of MPNST (p<0.05) and 5-year survival (p<0.01) were significantly lower in patients with NF1 than in unaffected individuals. This may be due to patients with NF1 presenting later, because the tumour is mistaken for a neurofibroma, or due to MPNST having a more aggressive course in NF1.

Decreased cholesterol synthesis as a possible aetiological factor in malformations of trisomy 18

We report a series of neonates and foetuses with trisomy 18 and abnormally low cholesterol levels and propose that down regulation of cholesterol synthesis in trisomy 18 is, in part, responsible for its phenotype. Cholesterol is a major structural lipid of cell membranes, as well as the precursor of steroid hormones and bile acids. Several human malformation syndromes have been identified biochemically as disorders of cholesterol biosynthesis. Trisomy 18, a multi-system malformation syndrome, has clinical features that overlap with those of disorders of cholesterol biosynthesis and dysregulation of this pathway may have a role in the developmental pathology.

Insights into the biochemical and genetic basis of glucokinase activation from naturally occurring hypoglycemia mutations

Glucokinase (GCK) is a key regulatory enzyme in the pancreatic beta-cell and catalyzes the rate-limiting step for beta-cell glucose metabolism. We report two novel GCK mutations (T65I and W99R) that have arisen de novo in two families with familial hypoglycemia. Insulin levels, although inappropriately high for the degree of hypoglycemia, remain regulated by fluctuations in glycemia, and pancreatic histology was normal. These mutations are within the recently identified heterotropic allosteric activator site in the theoretical model of human beta-cell glucokinase. Functional analysis of the purified recombinant glutathionyl S-transferase fusion proteins of T65I and W99R GCK revealed that the kinetic changes result in a relative increased activity index (a measure of the enzyme's phosphorylating potential) of 9.81 and 6.36, respectively, compared with wild-type. The predicted thresholds for glucose-stimulated insulin release using mathematical modeling were 3.1 (T65I) and 2.8 (W99R) mmol/l, which were in line with the patients' fasting glucose. In conclusion, we have identified two novel spontaneous GCK-activating mutations whose clinical phenotype clearly differs from mutations in ATP-sensitive K(+) channel genes. In vitro studies confirm the validity of structural and functional models of GCK and the putative allosteric activator site, which is a potential drug target for the treatment of type 2 diabetes.

Analysis of germline CDKN1C (p57KIP2) mutations in familial and sporadic Beckwith-Wiedemann syndrome (BWS) provides a novel genotype-phenotype correlation

Beckwith-Wiedemann syndrome (BWS) is a human imprinting disorder with a variable phenotype. The major features are anterior abdominal wall defects including exomphalos (omphalocele), pre- and postnatal overgrowth, and macroglossia. Additional less frequent complications include specific developmental defects and a predisposition to embryonal tumours. BWS is genetically heterogeneous and epigenetic changes in the IGF2/H19 genes resulting in overexpression of IGF2 have been implicated in many cases. Recently germline mutations in the cyclin dependent kinase inhibitor gene CDKN1C (p57KIP2) have been reported in a variable minority of BWS patients. We have investigated a large series of familial and sporadic BWS patients for evidence of CDKN1C mutations by direct gene sequencing. A total of 70 patients with classical BWS were investigated; 54 were sporadic with no evidence of UPD and 16 were familial from seven kindreds. Novel germline CDKN1C mutations were identified in five probands, 3/7 (43%) familial cases and 2/54 (4%) sporadic cases. There was no association between germline CDKN1C mutations and IGF2 or H19 epigenotype abnormalities. The clinical phenotype of 13 BWS patients with germline CDKN1C mutations was compared to that of BWS patients with other defined types of molecular pathology. This showed a significantly higher frequency of exomphalos in the CDKN1C mutation cases (11/13) than in patients with an imprinting centre defect (associated with biallelic IGF2 expression and H19 silencing) (0/5, p<0.005) or patients with uniparental disomy (0/9, p<0.005). However, there was no association between germline CDKN1C mutations and risk of embryonal tumours. No CDKN1C mutations were identified in six non-BWS patients with overgrowth and Wilms tumour. These findings (1) show that germline CDKN1C mutations are a frequent cause of familial but not sporadic BWS, (2) suggest that CDKN1C mutations probably cause BWS independently of changes in IGF2/H19 imprinting, (3) provide evidence that aspects of the BWS phenotype may be correlated with the involvement of specific imprinted genes, and (4) link genotype-phenotype relationships in BWS and the results of murine experimental models of BWS.