Pulling the Strands Together: MEGA Steps to Drive European Genomics and Personalised Medicine.

The increasing understanding of the genome is recognised as being one of the main determinants of future improvement in healthcare. The availability of genetic data from a large number of individuals increases the ability to investigate questions across many rare and common diseases and in different populations, and also provides more information for understanding clinical care outcomes for an individual. A number of large scale genome sequencing initiatives have been launched in the last few years to try and capitalise on this potential. Within Europe, the UK has led the way with the 100,000 Genomes Project. This project looks at the genome sequences of patients with rare diseases or cancer. More recently France announced plans to invest EUR 670 million in a genomics and personalised medicine programme. In the US, the Precision Medicine Initiative aims at large-scale research by gathering one million or more volunteers to extend precision medicine to all diseases. Meanwhile, China has announced plans to invest nearly USD 10 billion in its own precision medicine initiative. These projects demonstrate the commitment at a national level and raise the question "What benefits would be realised by undertaking a million genome initiative in a coordinated effort across European countries?" A coordinated, pan-European MEGA project would garner crucial genetic information that could have an immeasurable benefit when it comes to the health of current and future EU citizens.

Next generation sequencing for molecular diagnosis of neurological disorders using ataxias as a model.

Many neurological conditions are caused by immensely heterogeneous gene mutations. The diagnostic process is often long and complex with most patients undergoing multiple invasive and costly investigations without ever reaching a conclusive molecular diagnosis. The advent of massively parallel, next-generation sequencing promises to revolutionize genetic testing and shorten the 'diagnostic odyssey' for many of these patients. We performed a pilot study using heterogeneous ataxias as a model neurogenetic disorder to assess the introduction of next-generation sequencing into clinical practice. We captured 58 known human ataxia genes followed by Illumina Next-Generation Sequencing in 50 highly heterogeneous patients with ataxia who had been extensively investigated and were refractory to diagnosis. All cases had been tested for spinocerebellar ataxia 1-3, 6, 7 and Friedrich's ataxia and had multiple other biochemical, genetic and invasive tests. In those cases where we identified the genetic mutation, we determined the time to diagnosis. Pathogenicity was assessed using a bioinformatics pipeline and novel variants were validated using functional experiments. The overall detection rate in our heterogeneous cohort was 18% and varied from 8.3% in those with an adult onset progressive disorder to 40% in those with a childhood or adolescent onset progressive disorder. The highest detection rate was in those with an adolescent onset and a family history (75%). The majority of cases with detectable mutations had a childhood onset but most are now adults, reflecting the long delay in diagnosis. The delays were primarily related to lack of easily available clinical testing, but other factors included the presence of atypical phenotypes and the use of indirect testing. In the cases where we made an eventual diagnosis, the delay was 3-35 years (mean 18.1 years). Alignment and coverage metrics indicated that the capture and sequencing was highly efficient and the consumable cost was ∼£400 (€460 or US$620). Our pathogenicity interpretation pathway predicted 13 different mutations in eight different genes: PRKCG, TTBK2, SETX, SPTBN2, SACS, MRE11, KCNC3 and DARS2 of which nine were novel including one causing a newly described recessive ataxia syndrome. Genetic testing using targeted capture followed by next-generation sequencing was efficient, cost-effective, and enabled a molecular diagnosis in many refractory cases. A specific challenge of next-generation sequencing data is pathogenicity interpretation, but functional analysis confirmed the pathogenicity of novel variants showing that the pipeline was robust. Our results have broad implications for clinical neurology practice and the approach to diagnostic testing.

Primary lymphedema with coarctation of the aorta: possible new syndrome or variant of Irons-Bianchi syndrome?

We present a boy with congenital lymphedema, a congenital heart defect (coarctation of the aorta), and mild dysmorphic features. Clinical impression and targeted investigations ruled out Noonan syndrome and Milroy syndrome, but it was not clear whether or not he had Irons-Bianchi syndrome. We discuss the genomic and lymphoscintigraphy evaluation of this case, and review whether the small number of current case reports represent the original Irons-Bianchi syndrome or variants. We anticipate that ongoing molecular investigations such as Next Generation Sequencing will delineate a currently clinically defined phenotypic spectrum.

De novo nonsense mutations in ASXL1 cause Bohring-Opitz syndrome.

Bohring-Opitz syndrome is characterized by severe intellectual disability, distinctive facial features and multiple congenital malformations. We sequenced the exomes of three individuals with Bohring-Opitz syndrome and in each identified heterozygous de novo nonsense mutations in ASXL1, which is required for maintenance of both activation and silencing of Hox genes. In total, 7 out of 13 subjects with a Bohring-Opitz phenotype had de novo ASXL1 mutations, suggesting that the syndrome is genetically heterogeneous.

Bohring-Opitz (Oberklaid-Danks) syndrome: clinical study, review of the literature, and discussion of possible pathogenesis.

Bohring-Opitz syndrome (BOS) is a rare congenital disorder of unknown etiology diagnosed on the basis of distinctive clinical features. We suggest diagnostic criteria for this condition, describe ten previously unreported patients, and update the natural history of four previously reported patients. This is the largest series reported to date, providing a unique opportunity to document the key clinical features and course through childhood. Investigations undertaken to try and elucidate the underlying pathogenesis of BOS using array comparative genomic hybridization and tandem mass spectrometry of cholesterol precursors did not show any pathogenic changes responsible.

Mardini-Nyhan association (lung agenesis, congenital heart, and thumb anomalies): three new cases and possible recurrence in a sib-is there a distinct recessive syndrome?

In 1985, Mardini and Nyhan described three patients from consanguineous families with unilateral complete/partial lung agenesis, congenital cardiac defects, and ipsilateral thumb anomalies. Although there have been many reports of lung agenesis with other malformations, especially hemifacial microsomia and radial ray anomalies, very few demonstrate this triad of defects. We describe three patients with the Mardini-Nyhan association which may represent a distinct entity, although this remains uncertain at present. A fourth patient is also described, the sister of one of the other patients, with complex congenital cardiac disease and bilateral lung lobation abnormalities. This is the first reported incidence of a possible recurrence within a family and suggests, together with the consanguinity observed by Mardini and Nyhan, that recessive inheritance should be considered in genetic counseling for this disorder.

Dysmorphology of Barth syndrome.

Barth syndrome is an X-linked recessive condition caused by defective remodelling of cardiolipins in mitochondrial membranes because of mutations in the tafazzin (TAZ1/G4.5) gene located at Xq28. The cardinal features of Barth syndrome are cardiac and skeletal myopathy and neutropaenia, reported in the initial description of this condition by Barth et al. (J Neurol Sci 62:327-355) in 1983. Many features of the Barth phenotype have been described but there is no published comment on the facial appearance of these boys, which is consistent and characteristic of this condition.