What is the genomic blind spot?

Beneath the surface. Even though the comprehensiveness of next generation sequencing technologies may suggest that we can capture all the variation in the human genome, there is an entire gray zone of small rearrangements that current technologies are blind to. In a recent publication in the American Journal of Human Genetics, Brand and collaborators now use a novel technology to explore the twilight zone of genomics, the realm of small deletions, duplication, inversions and cryptic complex rearrangements. Continue reading

SETBP1, ZMYND11, and the power of joint exome and CNV analysis

Parallel worlds. There are two fields of genetics for neurodevelopmental disorders that currently produce large amounts of data – the field of copy number variation analysis and the field of exome sequencing. When assigning pathogenicity, information from both genetic technologies are rarely considered jointly. A recent study in Nature Genetics now performs a combined analysis of a large CNV and exome datasets in intellectual disability and autism. Interestingly, this method produces robust results, highlighting novel causative genes. Continue reading

The common variants in our genome that predispose to epilepsy – the ILAE GWAS

ILAE GWAS. This is one of the rare occasions when I can write on behalf of the ILAE Genetics Commission and discuss a recent publication. Earlier this week, the ILAE Consortium on complex epilepsies came online in Lancet Neurology. This study is a large meta-analysis of almost 9,000 patients and 26,000 controls looking at common genetic variants predisposing to common epilepsies, including the Idiopathic/Genetic Generalized Epilepsies and focal epilepsies. In a nutshell, when looking for common variants predisposing to the epilepsies, the answer is surprisingly simple. Continue reading

Typical versus atypical: exome sequencing in pediatric epilepsies

Exome mining. Trio exome sequencing is both easy and difficult at the same time. If you manage to identify a plausible de novo mutation, the job is pretty much done. However, if no plausible de novo is found, things can become complex very quickly. Some of the known genes for recessive disorders are quite variable and therefore difficult to interpret. Also, we know little about the overall spectrum of the recessive disorders and the plausibility of atypical cases. A recent paper in Clinical Genetics takes a comprehensive approach to the genetic basis of pediatric epilepsies by exome sequencing. The authors include the analysis of recessive and compound heterozygous variants, and they follow up on some of the biomarkers that establish the diagnosis. There are some surprising findings. Continue reading

Critical brain-expressed exons and de novo mutations in autism

Selection. De novo mutations in neurodevelopmental disorders including autism, schizophrenia, and intellectual disability raise an important question: are the mutations identified in patients pathogenic or are they simply genomic noise? A recent study in Nature Genetics tries to answer this question by looking at expression of particular exons in the brain and the overall mutational burden in these exons. They come up with critical exons, which seem to be particularly vulnerable in Autism Spectrum Disorder. Continue reading

Twisting DNA and seizures: TDP2 mutations in neurodegeneration with epilepsy

Torsional stress. The DNA double helix has one major problem that we know from telephone cords: it is difficult to untangle. However, our DNA is constantly twisted and untangled for gene transcription. This constant twisting and untwisting produces torsional stress that is relieved by topoisomerases. A recent publication in Nature Genetics now identified a human neurological phenotype that is caused by faulty activity of this mechanism: neurodegeneration with epileptic encephalopathy. However, there are some features of the phenotype that are not easily explained by erroneous DNA twisting. Continue reading

Three things about 16p11.2 duplications in Rolandic Epilepsy that surprised us

In depth. Last week, we briefly mentioned the publication by Reinthalter and collaborators on 16p11.2 duplications in Benign Rolandic Epilepsy. At first glance, you might think that Eva’s publication may just be another description of a microdeletion in another type of epilepsy. However, nothing could be further from the truth. It’s a game changer. Here are three reasons why. Continue reading

Switching inhibition on – SLC12A5/KCC2 variants in human epilepsy

Inhibition. We usually like to think of GABA as an inhibitory neurotransmitter, which counteracts the excitatory and potentially epileptogenic effects of glutamate. However, this is not always true during brain development. Initially, GABA is a powerful excitatory neurotransmitter. The excitatory effect of GABA has been shown to be important for brain development and the formation of dendritic spines – and the switch from excitation to inhibition is due to a single ion channel: KCC2, encoded by SLC12A5. Two recent publications in EMBO Reports now implicate genetic variation in SLC12A5 in human epilepsy. Continue reading

What neuronal membranes are made of – CERS1 in progressive myoclonus epilepsy

Ceramide. Sphingolipids are a major component of neuronal membranes and help neurons in intracellular signaling and trafficking. Ceramide is one of the basic building blocks of sphingolipids. In a recent publication in Annals of Neurology, mutations in CERS1, coding for ceramide synthetase, are identified in a family with progressive myoclonus epilepsy – and provides an unexpected linked between a group of storage disorders such as Niemann-Pick disease and Tay-Sachs disease and progressive myoclonus epilepsies. Continue reading

SLC25A22, migrating seizures and mitochrondial glutamate deficiency

MPSI. Migrating partial seizures of infancy (MPSI) are a catastrophic form of infantile epilepsy that was entirely unexplained until de novo mutations in KCNT1 were identified in a subset of sporadic cases in 2012. For familial MPSI, however, the genetic basis remained unknown. In a recent publication in Annals of Neurology, Poduri and collaborators identify mutations in SCL25A22 in a family with recessive MPSI. Their study sheds light on the genetic basis of catastrophic epilepsies and the phenotypic range of mitochondrial glutamate starvation. Continue reading