A Workflow for Selection of Single Nucleotide Polymorphic Markers for Studying of Genetics of Ischemic Stroke Outcomes

Abstract

In this paper we propose a workflow for studying the genetic architecture of ischemic stroke outcomes. It develops further the candidate gene approach. The workflow is based on the animal model of brain ischemia, comparative genomics, human genomic variations, and algorithms of selection of tagging single nucleotide polymorphisms (tagSNPs) in genes which expression was changed after ischemic stroke. The workflow starts from a set of rat genes that changed their expression in response to brain ischemia and results in a set of tagSNPs, which represent other SNPs in the human genes analyzed and influenced on their expression as well.

Examination of Genetic Variants Revealed from a Rat Model of Brain Ischemia in Patients with Ischemic Stroke: A Pilot Study

“…The risk of IS was generally correlated with the prevalence of heterozygous genotypes in our patients. Similar direction of the association was demonstrated in the study of Melegy et al [ 38 ], who tested the association of SNP rs2305619 with AMI (SNP rs2305619 was in strong linkage disequilibrium (LD; r 2 = 0.97) with our SNP rs2316710 in CEU test population from 1000 Genomes Project [ 15 ]). At the same time, no such correlations were observed in the larger study of Barbati et al [ 39 ], who explored the influence of PTX3 polymorphisms on the risk of AMI and pentraxin-3 plasma levels (the SNPs tested were in strong LD with our SNPs rs2316710 and rs7634847, but not with rs62278647 ( r 2 = 0.47–0.69), in CEU test population [ 15 ]).…”

“…Similar direction of the association was demonstrated in the study of Melegy et al [ 38 ], who tested the association of SNP rs2305619 with AMI (SNP rs2305619 was in strong linkage disequilibrium (LD; r 2 = 0.97) with our SNP rs2316710 in CEU test population from 1000 Genomes Project [ 15 ]). At the same time, no such correlations were observed in the larger study of Barbati et al [ 39 ], who explored the influence of PTX3 polymorphisms on the risk of AMI and pentraxin-3 plasma levels (the SNPs tested were in strong LD with our SNPs rs2316710 and rs7634847, but not with rs62278647 ( r 2 = 0.47–0.69), in CEU test population [ 15 ]). Given that PTX3 is a marker for prognosis after AMI and IS, and following Barbati et al [ 39 ], we propose that the lack of correlations between PTX3 polymorphisms and IS outcome is because the PTX3 level itself is not a causal factor for IS outcome.…”

“…DNA was isolated from peripheral blood cells by proteinase K treatment, followed by extraction with phenol–chloroform [ 21 ]. The principles of the selection of polymorphic markers analyzed in the study were described in our recently developed protocol [ 15 ]. They included the following main steps: (1) Selection of rat genes that showed the most significant changes in their expression in the brain in response to temporal artery occlusion; (2) Identification of the human orthologues of these rat genes; (3) Identification of SNPs within human genes and revealing among them any informative SNPs with a high degree of linkage disequilibrium (tagSNPs).…”

“…Although the creation of more perfect animal models of the diseases has been declared as one method of improving the translation, relevant results can be obtained through the development of approaches based on careful selection and cross-species multi-omic data validation [ 13 , 14 ]. Following similar principles, we have recently developed a bioinformatics protocol to search for genomic markers that could affect IS outcome [ 15 ]. The protocol bears certain similarities with the method of Pasterkamp et al [ 16 ] that was used for the human validation of atherosclerosis-causing genes studied in knockout and transgenic mice.…”

Genome-Wide RNA-Sequencing Reveals Massive Circular RNA Expression Changes of the Neurotransmission Genes in the Rat Brain after Ischemia–Reperfusion

“…Moreover, annotated DECs contained coding exons predominantly. Previously, we identified the human orthologues for a number of rat genes, which expression was changed after ischaemic stroke ( Adora2a, Bcl3, Ccl22, Ccr1, Cd14, Gpr6, Gpr88, Rgs9, and other genes) [ 57 ]. Those results gave us the basis for examination of genetic variants revealed from a rat model of brain ischemia in patients with ischemic stroke.…”