Narrowing the phenotype gap through vector embedding

Sparse data. Trying to match the growing body of genomic datasets with associated clinical data is difficult for a variety of reasons. Most importantly, while genomic data are standardized and can be generated at scale, clinical data are often unstructured and sparse, making it difficult to represent a phenotype fully through any type of abbreviated format. Quite frequently in our prior blog posts, we have discussed the Human Phenotype Ontology (HPO), a standardized dictionary where all phenotypic features can be mapped and linked. But these data also quickly become large and the question on how best to handle them remains. In a recent publication, we translated more than 53M patient notes using HPO and explored the utility of vector embedding, a method that currently forms the basis of many AI-based applications. Here is a brief summary on how these technologies can help us to better understand phenotypes. Continue reading

GRIA-related disorders – a different side of glutamate receptor dysfunction

GRIA genes. This is the first time we are describing GRIA genes on this blog. GRIA genes, which include GRIA1, GRIA2, GRIA3, and GRIA4, encode the AMPA receptor, one of the two key channels in the process of glutamate neurotransmission. While GRIN genes, which encode the NMDA receptor, have been characterized much more extensively in the literature, GRIAs remain relatively under-characterized, even though their protein products are involved in a similar molecular process in the post-synapse in modulating excitatory synaptic transmission. Here, we provide a brief overview of the genetic and phenotypic range of GRIA-related disorders.

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SYT1-related disorder: a neurodevelopmental SNAREopathy

SYT1. To continue our series on SNAREopathies—developmental disorders caused by genes encoding proteins involved in the SNARE complex—we next provide a brief overview of SYT1-related disorders. The gene SYT1 encodes synaptotagmin-1 (SYT1), which belongs to the group of synaptotagmin proteins that are essential for neurotransmission. Disease-causing mutations in SYT1 have a spectrum of clinical presentations ranging in severity and phenotypic complexity but also with certain unifying features, making SYT1-related disorders a complex neurodevelopmental SNAREopathy.

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The role of genetic counselors in the mystery, hope, and heartbreak of neurogenetics

Genetic counseling. This month, we celebrated DNA day, a successful fundraiser through Love for Liam, and the acceptance of our genetic counseling assistant (GCA), Rahma Ali, into the Emory University Genetic Counseling Training Program. On top of that, the Center for Epilepsy and Neurodevelopmental Disorders (ENDD) opens soon and we’ve been actively recruiting new GCAs and interviewing new genetic counselors (GCs). All of this has reminded our team of the vital function of our GCs both on our research and clinical teams. And, it has reminded our GC team of why we pursued this field and why we love neurogenetics in particular. As our lab expands, we are dedicating more blog posts to highlighting different team members and roles, and this week, we celebrate GCs as they share the greatest, hardest, and most exciting parts of being a GC, especially in neurology.

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The Queen of the Biorepositories

Biospecimens. From the first advents of clinical neuroscience, scientists have been fascinated by biospecimen classification and storage. The immortal images from Ramon y Cajal to the staining done by Golgi have illustrated that biospecimens are parallel to the discoveries seen in clinical neuroscience. As we move to the 21st century, we may not be all that different from the forbearers of Neurology. Here is a post starting from the origins of the biorepository and leading up to the relevance of biorepositories today.

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The human pangenome and the flavor of epilepsy variant interpretation

Reference. Today, the human pangenome was announced, the first reference of the human genome that systematically includes a cohort of genetically diverse individuals. The human genome, once thought to be a linear reference, is now a graph with nodes and edges. I came across the pangenome publications when I was thinking about a comment that I made earlier this week, when I was asked whether people on our team have their own flavor of variant interpretation. Let me share with you how both topics connect. Continue reading

Five novel concepts in epilepsy genetics you need to know in 2023

Framework. Neurogenetics is evolving, and so is the way we think about the connection between genes and seizures. Over the last few years, several new frameworks of thinking have entered the epilepsy genetics sphere that allow us to think about epilepsy genetics with more nuance. This blog post is dedicated to five known or emerging concepts that are evolving alongside our increased understanding of genetic epilepsies. Continue reading

Expanding the spectrum of SNAREopathies – STX1A in epilepsy and neurodevelopmental disorders

SNAREopathies. This post continues the series on SNAREopathies, a group of neurodevelopmental conditions caused by variants in genes encoding components that form the SNARE complex and regulatory proteins. As previously described, the SNARE complex is the molecular machinery driving synaptic vesicle release in the presynapse, which enables communication between neurons. Here, we expand the discussion to the second t-SNARE protein of the SNARE core complex, STX1A, and provide a brief review of the recent paper implicating STX1A in epilepsy and neurodevelopmental disorders.

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Love For Liam and the true driving force in epilepsy genetics

Fundraiser. Last Friday, our epilepsy genetics team participated in the Annual Love for Liam fundraiser, which was a golf tournament at the Northhampton Country Club, in Richboro, Pennsylvania. The Love For Liam Foundation was initiated by Heather and Kyle Johnson in memory of their baby boy, Liam, who passed away from a likely genetic epileptic encephalopathy. During the fundraiser, Heather gave one of the most passionate and powerful speeches in support of epilepsy genetics that I have ever heard. I had carried around a sense of “bittersweetness” all day that I had a hard time putting into words. And after Heather’s speech, it clicked: maybe we got it all wrong, maybe we should think about the real driving force in epilepsy genetics slightly differently.

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