Papers of the week – 15q11 duplications, Olig1 & Automated decision-making


A productive week in epilepsy genetics.  Scientists and editors were certainly busy this week reporting novel variants and deletions as well the experimental and statistical advances for their interpretation.

A de novo GRIN2A missensmutation in early-onset epileptic encephalopathy. We and others have associated variants affecting the GRIN2A gene with a range of childhood focal epilepsy syndromes. Continue reading

2013 in review: top three lists and the gene finding of the year

Gene of the year. Let’s take a minute to look back at the very busy year of 2013. There were major advances in many areas of epilepsy genetics. First and foremost, massive (and I mean massive) progress has been made in the genetics of the epileptic encephalopathies, where de novo mutations have been identified as a major source of genetic morbidity. Secondly, the new technologies have made it possible to identify several novel genes for various epilepsy types. Out of these genes, we have again selected the most important finding in 2013. And the gene finding of the year is… Continue reading

Beneath the surface – the role of small inherited CNVs in autism

Grey zone. Structural genomic variants or copy number variations (CNV) can be reliably assessed using array comparative genomic hybridization (array CGH) or Single Nucleotide Polymorphism (SNP) arrays.  However, for deletions or duplications smaller than 50-100 kB, these technologies have a poor detection rate with many false positive and false negative findings unless platforms are used that target specific candidate regions. Exome analysis, on the other hand, is capable of assessing genetic variation reliably on the single base-pair level. Between both technologies, there is a grey zone of structural genomic variants that are difficult to detect; CNVs smaller than 50 kB are often difficult to assess, and the extent and pathogenic role of these small CNVs is unclear. Now, a recent paper in the American Journal of Human Genetics manages to detect small CNVs through exome data. Their analysis in patients with autism, parents, and unaffected siblings suggests a contribution of small inherited CNVs to the overall autism risk. Continue reading

Identifying core phenotypes – epilepsy, ID and recurrent microdeletions

Triad. There are three microdeletions in particular that increase the risk for the Idiopathic/Genetic Generalized Epilepsies (IGE/GGE). This triad includes microdeletions at 15q13.3, 16p13.11 and 15q11.2, which are hotspot deletions arising from the particular architecture of the human genome. While the association of these microdeletions with epilepsy and other neurodevelopmental disorders including autism, intellectual disability and schizophrenia is well established, the core phenotype of these variants remains elusive, including the question whether such a core phenotype actually exists. In a recent paper in Neurology, Mullen and collaborators zoom in on a possible core phenotype of these microdeletions. The authors investigate a phenotype in which these microdeletions are particularly enriched: generalized epilepsy with intellectual disability. Continue reading

Transmission of rare variants in parent-offspring trios – power or no power?

My untested assumption. Recently, I have boasted quite a bit about the power of the trio design, i.e. the inclusion of patients and parents in the analysis of rare genetic variants. Rare variants, in contrast to monogenic variants that arise de novo, are usually transmitted from unaffected parents and are the big unknown of modern day genetic studies. Much of the missing heritability may be accounted for by rare variants, but identifying these variants from genomic noise is difficult. Power calculations for association studies usually suggest that thousands, if not tens of thousands, of patients are necessary to identify these variants with sufficient statistical certainty, a sample size that the field of epilepsy research may never arrive at. So what about switching to parent-offspring trios? Would this help us? Follow me on a brief statistical journey through the land of rare variants. Continue reading

16p13.11 microdeletions and the male bias

The enigmatic deletion. Amongst the various microdeletions implicated in human epilepsy, the 16q13.11 microdeletion is one of the structural variations that poses significant difficulties in understanding its associated risk and phenotypes. Now a recent paper in PLOS One investigates a large cohort of patients with various neurodevelopmental disorders for microdeletions in the 16p13.11 region. And particularly the finding regarding the sex distribution of symptomatic deletion carriers is remarkable.   Continue reading

How human evolution has shaped epilepsy genes

Man and ape. Comparative genomics is relating the differences between species in the genome to the phenotype. When the first comparisons between human and chimpanzee were published in 2005, neuroscientists were  excited that this comparison would show what makes our brain human. A glance at the genes clusters that rapidly evolved during human-specific evolution was sobering. Many of the genes that rapidly evolved are immune-regulatory genes, highlighting  our constant struggle with some parasites, bacteria and viruses and our arrangement with the microbiome, the cloud of microbes contribute ten times as many cells to our bodies than we do. Prominent genes such as FOXP2, a gene found to be disrupted in patients with developmental language problems, and most other brain genes barely show up as a group in comparative genomics.

Segmental duplications and human evolution. Recent human evolution did not only leave traces at the single-base pair level that allows for the discovery of individual sequence differences but also larger structural genomic variants including segmental duplications. Recurrent microdeletions such as the 15q13.3, 16p13.11 or 15q11.2 microdeletions occur relatively frequently because the genomic sequence of these deletions is located between segmental duplications (Figure 1). These segmental duplications are so similar that the DNA replication machinery sometimes mistakes one duplication for the other (e.g. the “right flanking duplication” for the “left flanking duplication”). Thereby, the intervening sequence is either deleted or duplicated. Segmental duplications are relatively human-specific, for example a paralogue region for the 15q13.3 microdeletion is not present in rodents. Even in chimpanzees, the segmental duplications that give rise to Prader-Willi-Syndrome, Williams-Syndrome or Spinal Muscular Atrophy are not present, indicating that something very human-specific must have happened here that resulted in these segmental duplications, which give rise to so-called genomic disorders. While many of the epilepsy genes identified through family studies including SCN1A or GABRG2 are conserved in animals, microdeletions are not.

Figure 1. The human genome is a complicated meshwork of duplications and deletions that are lineage-specific, i.e. only occuring in human. One example of this is the genetic architecture of human chromosome 16. When comparing baboon and man, the human chromosome 16 is a complicated puzzle of deletions, duplication, duplications-within-duplications etc. This is the reason why there are at least five different microdeletions syndromes on chromosome 16, resulting from accidental genomic rearrangements between these duplications. This image is modified from a figure on the web page of the Eichler lab.

The SRGAP2 story. Two recent publications on the SRGAP2 gene illustrate the problems with reasoning around the human-specific changes. Saitsu and colleagues describe a female patient with epileptic encephalopathy and a balanced translocation in SRGAP2, a  gene highly expressed in the developing forebrain. Balanced translocations are very rare  and might provide insight into monogenic epilepsy syndromes. The function of SRGAP2 is still unknown. The second paper by Dennis and collaborators describes the evolution of the SRGAP2 family, hypothesizing that the evolution paralleled neocortical expansion at the transition of Australopithecus to Homo.

How human is our SRGAP2?  While the suggestion that disruption of a human-specific gene results in West Syndrome carries some appeal, comes with an almost philosophical flaw. Epileptic encephalopathy, a severe neurodevelopmental disease, may be conceptualized as a disruption of basic cellular or network processes, e.g. large malformations, neurometabolic disorders or fundamental disruptions of synaptic function rather than defects in the subtle differences between man and ape that make us human. In fact, the Toronto Database of Genomic Variants lists several intragenic deletions and duplications in SRGAP2, suggesting that disruptions of this gene may be seen in apparently healthy individuals. Possibly, the genetic architure in SRGAP2 might predispose to deletions, duplications or more complicated rearrangements that even result in balanced translocations. Evolution has merely generated a complex human-specific gene prone to recombination events rather than a genuine epilepsy gene.

Evolutionary genomics and EuroEPINOMICS. So-called hotspot microdeletions including variants at 15q13.3, 16p13.11, 15q11.2 are the immediate result of recent genomic changes that allowed us to be human. Segmental duplications rather than changes on the base-pair level might have been the main driver for human evolution, and the occurence of microdeletions may be conceptualized as a “trade-off” for the fragile human genomic architecture. Microdeletions already help us explain approximately 3% of cases of epilepsy. It can be hypothesized that similar effects on a smaller genomic level are still to be discovered and may help explain additional genetic findings seen in epilepsy patients.