Deciphering the phenotypic code – AP2M1 in epileptic encephalopathies

Synaptic. Identifying the genetic changes underlying severe childhood epilepsies is one of the key steps for predicting outcomes and developing better treatments. However, while our ability to analyze genetic data at scale allows us to simultaneously query tens of thousands of exomes or genomes, our understanding of large phenotypic data has been limited. This limitation, the “phenotypic bottleneck”, is often frustrating, especially as many developmental and epileptic encephalopathies present with unusual and very complex phenotypic features that we would like to better understand for our clinical decision making. The lack of concepts and methods to handle large amounts of phenotypic data has been one of the main contributing factors to this shortcoming. In a new publication in the American Journal of Human Genetics, we aim to overcome this problem by identifying a measurement for phenotypic similarity, using a computational approach to determine how similar patients are to each other based on Human Phenotype Ontology terms. When combined with exome sequencing data, we identified AP2M1, a gene that caused such a similar phenotype that it stood out from the remainder of the cohort. It is the first epilepsy-associated gene identified not from a genetic association, but from phenotypic similarity. Continue reading

ICK, Juvenile Myoclonic Epilepsy, and the burden of proof

Pathogenic or benign. In 2018, ICK, coding for Intestinal-Cell Kinase, was reported as a novel causative gene in Juvenile Myoclonic Epilepsy (JME) in the New England Journal of Medicine. JME is one of the most common epilepsy syndromes, and the authors suggested that up to 7% of JME in their study may be explained by pathogenic variants in this gene, suggesting that, if applicable to all individuals with JME, it may provide a genetic diagnosis for an expected 500,000 individuals worldwide. In a reply to the initial study, the investigators of the EuroEPINOMICS-CoGIE, EpiPGX, Epi4K, and EPGP Consortia attempted to replicate these initial findings, but could not find any evidence in for a role of ICK in JME and indicated that the initial results may have arisen by chance and due to methodological issues. Given the potential implications for future research and therapy development in a relatively common epilepsy, the controversial ICK story is a good example to highlight why it is important to revisit the current consensus on when we consider a candidate a true disease gene and why a category mistake confusing variant pathogenicity for gene validity may result in false positive findings. Continue reading

The Epilepsy Genetics Initiative – novel diagnoses through exome re-analysis

The negative exome. Despite writing a lot about the power of next generation sequencing technologies to provide a genetic diagnosis in individuals with severe epilepsies, it is important to remember that most exome tests performed in a diagnostic setting are negative. Even the most optimistic studies do not find a diagnostic yield that exceeds 40%. However, what can be done about the 60-70% of patients who had undergone exome sequencing, the current gold-standard diagnostic testing, but have received a negative test result? A systematic re-analysis after 12-24 months is currently considered one possibility to make sense of existing exome data. In a current publication, the Epilepsy Genetics Initiative (EGI) reports their results of a systematic research-based re-analysis in 166 individuals with epilepsy. In eight individuals, a novel diagnosis could be achieved, including novel genes not known at the time of the initial report and novel mechanisms such as alternative exons. With a diagnostic rate of 6%, this study provides a unique benchmark of what can be expected when exomes initially come back as negative. Continue reading

V is for valine – VARS mutations in epileptic encephalopathy

Transfer RNAs. A critical step in translating a cDNA into proteins involves transfer RNAs (tRNAs) that deliver a specific amino acid to the ribosome based on a specific codon in the messenger RNA. Thereby, tRNAs establish the physical link between the mRNA and the amino acid sequence of the growing protein, an essential cellular function. In order for tRNAs to be loaded with the appropriate amino acids, the organism has developed enzymes specific for the individual amino acids that are referred to as tRNA ligases or, more precisely, aminoacyl tRNA synthetases (aaRS). Despite the ubiquitous role of aaRS in the cell, pathogenic variants in genes coding for specific aaRS result primarily in neurological phenotypes, ranging from peripheral neuropathy to early-onset epileptic encephalopathies. In two recent back-to-back publications, bi-allelic pathogenic variants in VARS are described as a novel cause for epileptic encephalopathy, adding VARS to the list of aaRS genes linked to human disease and solving an almost decade-old mystery. Continue reading

Constrained coding regions and genetic causes for epilepsy that we might have missed

Genetic architecture. Our reference dataset for genetic variation in humans has become so large that we can increasingly ask the question whether the distribution of genetic variants tells us something about genes and regions within genes without knowing anything about what these genes actually do. For example, it is well established that genes with fewer protein-truncating variants than expected are much more likely to be causative genes for epilepsy and neurodevelopmental disorders than genes that have an average number of these variants. A recent publication in Nature Genetics takes this approach one step further by looking at specific regions within genes rather than entire genes, a somewhat interesting approach that the authors introduce by discussing bullet damage to airplanes in World War II. Continue reading

The second ILAE GWAS or why 30% of genetic generalized epilepsy is explained

Genome-wide association. While most of the neurogenetics community was focused on exome sequencing and the discovery of novel monogenic forms of epilepsy in the last few years, something quite remarkable had happened in the background. Common variants and genome-wide association studies have made a remarkable comeback. The ILAE Consortium for Complex Epilepsy had slowly worked on increasing sample sizes over time, and the second analysis of common variants in common epilepsies was published in late 2018. Sample sizes have almost doubled since the first study in 2014, and as a result, the number of genome-wide significant loci has tripled. However, the most intriguing finding was something that completely caught me by surprise – more than 30% of the heritability of the genetic generalized epilepsies is explained through common variants, approaching the numbers we see in epileptic encephalopathies explained by monogenic causes. This is one more reason to discuss the recent ILAE GWAS in more detail. Continue reading

STXBP1-related disorders – one or two disease mechanisms?

Haploinsufficiency. STXBP1-related disorders are one of the most common neurodevelopmental disorders due to pathogenic variants in a single gene. Haploinsufficiency is the proposed disease mechanism and a significant number of individuals have deletions or protein-truncating variants. However, there are also recurrent missense variants in STXBP1, which is often seen in diseases that have a different disease mechanism. In a recent publication in Nature Communications, some of the recurrent variants in STXBP1 are suggested to have an additional disease mechanism, a dominant-negative effect. In this blog post, I want to discuss how we can reconcile both observations and whether STXBP1-related disorders are a single entity with a common disease mechanism. Continue reading

Big data, ontologies, and the phenotypic bottle neck in epilepsy research

Unconnected data. Within the field of biomedicine, large datasets are increasingly emerging. These datasets include the genomic, imaging, and EEG datasets that we are somewhat familiar with, but also many large unstructured datasets, including data from biomonitors, wearables, and the electronic medical records (EMR). It appears that the abundance of these datasets makes the promise of precision medicine tangible – achieving an individualized treatment that is based on data, synthesizing available information across various domains for medical decision-making. In a recent review in the New England Journal of Medicine, Haendel and collaborators discuss the need in the biomedical field to focus on the development of terminologies and ontologies such as the Human Phenotype Ontology (HPO) that help put data into context. This review is a perfect segue to introduce the increasing focus on computational phenotypes within our group in order to overcome the phenotypic bottleneck in epilepsy genetics. Continue reading

A critical step towards precision medicine – the ClinGen epilepsy gene curation

Clinical relevance. Pathogenic variants in more than 80 genes have been reported in childhood epilepsies over the last two decades. Developing precision therapies that target the underlying genetic changes is a major research focus and holds the promise to positively influence the lives of thousands of people with individually rare, but collectively common genetic epilepsies. However, in order to develop novel therapies, a formal, unbiased framework is needed to define whether the association between certain gene and disease is in fact valid and that a specific variant is truly pathogenic. This task has proven to be much more difficult than initially expected. Within the larger framework of the ClinGen Consortium, our epilepsy expert panel assesses the clinical validity of genes and variants for human epilepsies, starting with gene curation. In the recently published Human Mutation Special Issue on ClinGen/ClinVar, our panel reports our pilot data and reviews what it takes to connect two increasingly separate fields: the domain of traditional clinical epileptology and the rapidly evolving area of diagnostic genetic testing. Brace yourself: 50% of the alleged gene-disease associations evaluated in our pilot phase did not meet the criteria to be considered clinically valid. Continue reading

A polygenic trickle of common variants in neurodevelopmental disorders

Common variants. In addition to the gradual increase in gene discovery due to exome sequencing, there is a field of human genetics developing in parallel that we have not paid much attention to recently. The role of common genetic variants or Single Nucleotide Polymorphisms (SNP) was initially limited to genome-wide association studies, looking at single variants individually. However, more recently, common variants have been assessed jointly in various diseases, resulting in so-called polygenic scores. In a recent publication in Nature, the polygenic contribution to neurodevelopmental disorders is evaluated. Interestingly, there seems to be a very robust contribution of common variants in neurodevelopmental disorders, even in patients with known de novo variants. Here is a brief discussion on why common variants start getting interesting for the neurogenetics field again. Continue reading