Subarachnoid hemorrhage: tests of association with apolipoprotein E and elastin genes

<p>Abstract</p> <p>Background</p> <p>Apolipoprotein E (<it>APOE</it>) and elastin (<it>ELN</it>) are plausible candidate genes involved in the pathogenesis of stroke. We tested for association of variants in <it>APOE </it>and <it>ELN </it>with subarachnoid hemorrhage (SAH) in a population-based study. We genotyped 12 single nucleotide polymorphisms (SNPs) on <it>APOE </it>and 10 SNPs on <it>ELN </it>in a sample of 309 Caucasian individuals, of whom 107 are SAH cases and 202 are age-, race-, and gender-matched controls from the Greater Cincinnati/Northern Kentucky region. Associations were tested at genotype, allele, and haplotype levels. A genomic control analysis was performed to check for spurious associations resulting from population substructure.</p> <p>Results</p> <p>At the <it>APOE </it>locus, no individual SNP was associated with SAH after correction for multiple comparisons. Haplotype analysis revealed significant association of the major haplotype (Hap1) in <it>APOE </it>with SAH (<it>p </it>= 0.001). The association stemmed from both the 5' promoter and the 3' region of the <it>APOE </it>gene. <it>APOE </it>ε2 and ε 4 were not significantly associated with SAH. No association was observed for <it>ELN </it>at genotype, allele, or haplotype level and our study failed to confirm previous reports of <it>ELN </it>association with aneurysmal SAH.</p> <p>Conclusion</p> <p>This study suggests a role of the <it>APOE </it>gene in the etiology of aneurysmal SAH.</p

Quality assessment of buccal versus blood genomic DNA using the Affymetrix 500 K GeneChip

Abstract Background With the advent of genome-wide genotyping, the utility of stored buccal brushes for DNA extraction and genotyping has been questioned. We sought to describe the genomic DNA yield and concordance between stored buccal brushes and blood samples from the same individuals in the context of Affymetrix 500 K Human GeneChip genotyping. Results Buccal cytobrushes stored for ~7 years at -80°C prior to extraction yielded sufficient double stranded DNA (dsDNA) to be successfully genotyped on the Affymetrix ~262 K NspI chip, with yields between 536 and 1047 ng dsDNA. Using the BRLMM algorithm, genotyping call rates for blood samples averaged 98.4%, and for buccal samples averaged 97.8%. Matched blood samples exhibited 99.2% concordance, while matched blood and buccal samples exhibited 98.8% concordance. Conclusion Buccal cytobrushes stored long-term result in sufficient dsDNA concentrations to achieve high genotyping call rates and concordance with stored blood samples in the context of Affymetrix 500 K SNP genotyping. Thus, given high-quality collection and storage protocols, it is possible to use stored buccal cytobrush samples for genome-wide association studies.</p

Quantitative criteria for improving performance of buccal DNA for high-throughput genetic analysis

Abstract Background DNA from buccal brush samples is being used for high-throughput analyses in a variety of applications, but the impact of sample type on genotyping success and downstream statistical analysis remains unclear. The objective of the current study was to determine laboratory predictors of genotyping failure among buccal DNA samples, and to evaluate the successfully genotyped results with respect to analytic quality control metrics. Sample and genotyping characteristics were compared between buccal and blood samples collected in the population-based Genetic and Environmental Risk Factors for Hemorrhagic Stroke (GERFHS) study (https://gerfhs.phs.wfubmc.edu/public/index.cfm). Results Seven-hundred eight (708) buccal and 142 blood DNA samples were analyzed for laboratory-based and analysis metrics. Overall genotyping failure rates were not statistically different between buccal (11.3%) and blood (7.0%, p = 0.18) samples; however, both the Contrast Quality Control (cQC) rate and the dynamic model (DM) call rates were lower among buccal DNA samples (p  Conclusions We identified a buccal sample characteristic, a ratio of ds/total DNA <34%, which distinguished buccal DNA samples likely to fail high-throughput genotyping. Applying this threshold, the quality of final genotyping resulting from buccal samples is somewhat lower, but compares favorably to blood. Caution is warranted if cases and controls have different sample types, but buccal samples provide comparable results to blood samples in large-scale genotyping analyses.</p

EXPRESS: What is the Median Volume of Intracerebral Hemorrhage and is it Changing?

OBJECTIVES: Population-level estimates of the median intracerebral hemorrhage (ICH) volume would allow for the evaluation of clinical trial external validity and determination of temporal trends. We previously reported the median ICH volume in 1988. However, differences in risk factor management, neuroimaging and demographics may have affected ICH volumes. The goal of this study was to determine the median volume of ICH within a population-based cross-sectional study, including whether it has changed over time. METHODS: The Genetic and Environmental Risk Factors for Hemorrhagic Stroke study was a population-based study of ICH among residents of the Greater Cincinnati/Northern Kentucky region from 2008 through 2012. The current study utilizes those data and compares with ICH cases from the same region in 1988. Initial CT images of the head were reviewed, and ICH volumes were calculated using consistent methodology. RESULTS: From 2008 through 2012, we identified 1117 cases of ICH. The median volume of ICH was 14.0 mL and was lower in black (11.6) than in white (15.5) patients. Median volumes of lobar and deep ICH were 28·8 mL and 9.8 mL, respectively. Median ICH volume changed significantly from 1988 to 2008-2012, with age-and-race adjusted volume decreasing from 18.3 mL to 13.76 mL (p=0.025). CONCLUSIONS: Median volume of ICH was 13.76 mL, and this should be considered in clinical trial design. Median ICH volume has apparently decreased from 1988 to 2008-2012