Complex trait susceptibilities and population diversity in a sample of 4,145 Russians.

The population of Russia consists of more than 150 local ethnicities. The ethnic diversity and geographic origins, which extend from eastern Europe to Asia, make the population uniquely positioned to investigate the shared properties of inherited disease risks between European and Asian ancestries. We present the analysis of genetic and phenotypic data from a cohort of 4,145 individuals collected in three metro areas in western Russia. We show the presence of multiple admixed genetic ancestry clusters spanning from primarily European to Asian and high identity-by-descent sharing with the Finnish population. As a result, there was notable enrichment of Finnish-specific variants in Russia. We illustrate the utility of Russian-descent cohorts for discovery of novel population-specific genetic associations, as well as replication of previously identified associations that were thought to be population-specific in other cohorts. Finally, we provide access to a database of allele frequencies and GWAS results for 464 phenotypes.

An Lmx1b-miR135a2 regulatory circuit modulates Wnt1/Wnt signaling and determines the size of the midbrain dopaminergic progenitor pool.

MicroRNAs regulate gene expression in diverse physiological scenarios. Their role in the control of morphogen related signaling pathways has been less studied, particularly in the context of embryonic Central Nervous System (CNS) development. Here, we uncover a role for microRNAs in limiting the spatiotemporal range of morphogen expression and function. Wnt1 is a key morphogen in the embryonic midbrain, and directs proliferation, survival, patterning and neurogenesis. We reveal an autoregulatory negative feedback loop between the transcription factor Lmx1b and a newly characterized microRNA, miR135a2, which modulates the extent of Wnt1/Wnt signaling and the size of the dopamine progenitor domain. Conditional gain of function studies reveal that Lmx1b promotes Wnt1/Wnt signaling, and thereby increases midbrain size and dopamine progenitor allocation. Conditional removal of Lmx1b has the opposite effect, in that expansion of the dopamine progenitor domain is severely compromised. Next, we provide evidence that microRNAs are involved in restricting dopamine progenitor allocation. Conditional loss of Dicer1 in embryonic stem cells (ESCs) results in expanded Lmx1a/b+ progenitors. In contrast, forced elevation of miR135a2 during an early window in vivo phenocopies the Lmx1b conditional knockout. When En1::Cre, but not Shh::Cre or Nes::Cre, is used for recombination, the expansion of Lmx1a/b+ progenitors is selectively reduced. Bioinformatics and luciferase assay data suggests that miR135a2 targets Lmx1b and many genes in the Wnt signaling pathway, including Ccnd1, Gsk3b, and Tcf7l2. Consistent with this, we demonstrate that this mutant displays reductions in the size of the Lmx1b/Wnt1 domain and range of canonical Wnt signaling. We posit that microRNA modulation of the Lmx1b/Wnt axis in the early midbrain/isthmus could determine midbrain size and allocation of dopamine progenitors. Since canonical Wnt activity has recently been recognized as a key ingredient for programming ESCs towards a dopaminergic fate in vitro, these studies could impact the rational design of such protocols.

Presence of epilepsy-associated variants in large exome databases.

Mutations in more than 20 genes have been found to cause idiopathic epilepsies, and screening for these variants could facilitate the clinical diagnosis of epilepsy. However, many of the studies that reported putative pathogenic variants for epilepsy tested a relatively small number of control samples, making it more likely that a rare nonpathogenic variant could be mistaken as causal. To test the robustness of inferences based on small sample sizes, we investigated whether variants previously reported to cause epilepsy were present in the resequencing data from the large control populations of the 1000 Genomes Project and the National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project. A list of variants associated with epilepsy was compiled using a manual review of the literature for genes associated with epilepsy from a recent International League Against Epilepsy (ILAE) report and two comprehensive genetic studies. We checked for the presence of those variants in the 1000 Genomes Project database and the NHLBI Exome Variant Server (EVS). Of 208 epilepsy-associated variants that we identified from our literature review, only 7 were found among 17 thousand chromosomes across 1000 Genomes and the EVS. Consistent with recent published reports, we also found many variants with predicted pathogenicity in epilepsy-associated genes in the genomic databases. Our findings suggest that the 1000 Genomes and the EVS data sets may be a valuable resource of control data in research aimed at identifying genes for epilepsy specifically when the model predicts a highly penetrant allele. These databases also elucidate the array of genetic variation in putative epilepsy genes in the general population.