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Effects of copy number variable regions on local gene expression in white blood cells of Mexican Americans.

ABSTRACT: Only few systematic studies on the contribution of copy number variation to gene expression variation have been published to date. Here we identify effects of copy number variable regions (CNVRs) on nearby gene expression by investigating 909 CNVRs and expression levels of 12059 nearby genes in white blood cells from Mexican-American participants of the San Antonio Family Heart Study. We empirically evaluate our ability to detect the contribution of CNVs to proximal gene expression (presumably in cis) at various window sizes (up to a 10 Mb distance) between the gene and CNV. We found a ~1-Mb window size to be optimal for capturing cis effects of CNVs. Up to 10% of the CNVs in this study were found to be significantly associated with the expression of at least one gene within their vicinity. As expected, we find that CNVs that directly overlap gene sequences have the largest effects on gene expression (compared with non-overlapping CNVRs located nearby), with positive correlation (except for a few exceptions) between estimated genomic dosage and expression level. We find that genes whose expression level is significantly influenced by nearby CNVRs are enriched for immunity and autoimmunity related genes. These findings add to the currently limited catalog of CNVRs that are recognized as expression quantitative trait loci, and have implications for future study designs as well as for prioritizing candidate causal variants in genomic regions associated with disease.

SUBMITTER: Blackburn A

PROVIDER: S-EPMC4538210 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundThe association between stroke and dementia is well established. Less is known about this association in underrepresented ethnic groups. In a large ethnically diverse cohort, we examined whether history of stroke was associated with cognitive impairment, and whether this relationship differed by ethnicity (Mexican American [MA] versus non-Hispanic White).MethodsThis was a population-based cohort study conducted in Nueces County, TX, a biethnic community with a large and primarily nonimmigrant MA population. Residents aged ≥65 were recruited door-to-door or by telephone between May 2018 and December 2021. The primary exposure was history of stroke, obtained by self-report. Demographic, medical, and educational histories were also obtained. The primary outcome was the Montreal Cognitive Assessment (MoCA), a scale that evaluates multiple domains of cognitive performance. Scores were divided into 3 ordinal categories, roughly corresponding to normal cognition (MoCA 26-30), mild cognitive impairment (MoCA 20-25), or probable dementia (MoCA 0-19).ResultsOne thousand eight hundred one participants completed MoCA screening (55% female; 50% MA, 44% Non-Hispanic White, 6% other), of whom 12.4% reported history of stroke. Stroke prevalence was similar across ethnicities (X2 2.1; P=0.34). In a multivariable cumulative logit regression model for the ordinal cognition outcome, a stroke by ethnicity interaction was observed (P=0.01). Models stratified by ethnicity revealed that stroke was associated with cognitive impairment across ethnicities, but had greater impact on cognition in non-Hispanic Whites (cumulative odds ratio=3.81 [95% CI, 2.37-6.12]) than in MAs (cumulative odds ratio=1.58 [95% CI, 1.04-2.41]). Increased age and lower educational attainment were also associated with cognitive impairment, regardless of ethnicity.ConclusionsHistory of stroke was associated with increased odds of cognitive impairment after controlling for other factors in both MA and Non-Hispanic White participants. The magnitude of the impact of stroke on cognition was less in MA than in Non-Hispanic White participants.

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Effects of copy number variable regions on local gene expression in white blood cells of Mexican Americans.

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