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Mapping the genetic variation of regional brain volumes as explained by all common SNPs from the ADNI study.

ABSTRACT: Typically twin studies are used to investigate the aggregate effects of genetic and environmental influences on brain phenotypic measures. Although some phenotypic measures are highly heritable in twin studies, SNPs (single nucleotide polymorphisms) identified by genome-wide association studies (GWAS) account for only a small fraction of the heritability of these measures. We mapped the genetic variation (the proportion of phenotypic variance explained by variation among SNPs) of volumes of pre-defined regions across the whole brain, as explained by 512,905 SNPs genotyped on 747 adult participants from the Alzheimer's Disease Neuroimaging Initiative (ADNI). We found that 85% of the variance of intracranial volume (ICV) (p?=?0.04) was explained by considering all SNPs simultaneously, and after adjusting for ICV, total grey matter (GM) and white matter (WM) volumes had genetic variation estimates near zero (p?=?0.5). We found varying estimates of genetic variation across 93 non-overlapping regions, with asymmetry in estimates between the left and right cerebral hemispheres. Several regions reported in previous studies to be related to Alzheimer's disease progression were estimated to have a large proportion of volumetric variance explained by the SNPs.

SUBMITTER: Bryant C

PROVIDER: S-EPMC3756017 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Mapping the genetic variation of regional brain volumes as explained by all common SNPs from the ADNI study.

Bryant Christopher C Giovanello Kelly S KS Ibrahim Joseph G JG Chang Jing J Shen Dinggang D Peterson Bradley S BS Zhu Hongtu H

PloS one 20130828 8

Typically twin studies are used to investigate the aggregate effects of genetic and environmental influences on brain phenotypic measures. Although some phenotypic measures are highly heritable in twin studies, SNPs (single nucleotide polymorphisms) identified by genome-wide association studies (GWAS) account for only a small fraction of the heritability of these measures. We mapped the genetic variation (the proportion of phenotypic variance explained by variation among SNPs) of volumes of pre- ...[more]

PMID: 24015190

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Project description:BackgroundGenome-wide association studies can have limited power to identify QTL, partly due to the stringent correction for multiple testing and low linkage-disequilibrium between SNPs and QTL. Regional Heritability Mapping (RHM) has been advanced as an alternative approach to capture underlying genetic effects. In this study, RHM was used to identify loci underlying variation in the 16(th) QTLMAS workshop simulated traits.MethodsThe method was implemented by fitting a mixed model where a genomic region and the overall genetic background were added as random effects. Heritabilities for the genetic regional effects were estimated, and the presence of a QTL in the region was tested using a likelihood ratio test (LRT). Several region sizes were considered (100, 50 and 20 adjacent SNPs). Bonferroni correction was used to calculate the LRT thresholds for genome-wide (p < 0.05) and suggestive (i.e., one false positive per genome scan) significance.ResultsGenomic heritabilities (0.31, 0.32 and 0.48, respectively) and genetic correlations (0.80, -0.42 and 0.19, between trait-pairs 1&2, 1&3 and 2&3) were similar to the simulated ones. RHM identified 7 QTL (4 at genome-wide and 3 at suggestive level) for Trait1; 4 (2 genome-wide and 2 suggestive) for Trait2; and 7 (6 genome-wide and 1 suggestive) for Trait3. Only one of the identified suggestive QTL was a false-positive. The position of these QTL tended to coincide with the position where the largest QTL (or several of them) were simulated. Several signals were detected for the simulated QTL with smaller effect. A combined analysis including all significant regions showed that they explain more than half of the total genetic variance of the traits. However, this might be overestimated, due to Beavis effect. All QTL affecting traits 1&2 and 2&3 had positive correlations, following the trend of the overall correlation of both trait-pairs. All but one QTL affecting traits 1&3 were negatively correlated, in agreement with the simulated situation. Moreover, RHM identified extra loci that were not found by association and linkage analysis, highlighting the improved power of this approach.ConclusionsRHM identified the largest QTL among the simulated ones, with some signals for the ones with small effect. Moreover, RHM performed better than association and linkage analysis, in terms of both power and resolution.

Project description:ObjectiveTo determine whether there is a correlation between obesity-related variants and regional brain volumes.MethodsBased on a mixed linear model (MLM), we analyzed the association between 1,498 obesity-related SNPs in the GWAS Catalog and 164 regional brain volumes from 29,420 participants (discovery cohort N = 19,997, validation cohort N = 9,423) in UK Biobank. The statistically significant brain regions in association analysis were classified into 6 major neural networks (dopamine (DA) motive system, central autonomic network (CAN), cognitive emotion regulation, visual object recognition network, auditory object recognition network, and sensorimotor system). We summarized the association between obesity-related variants (metabolically healthy obesity variants, metabolically unhealthy obesity variants, and unclassified obesity-related variants) and neural networks.ResultsFrom association analysis, we determined that 17 obesity-related SNPs were associated with 51 regional brain volumes. Several single SNPs (e.g., rs13107325-T (SLC39A8), rs1876829-C (CRHR1), and rs1538170-T (CENPW)) were associated with multiple regional brain volumes. In addition, several single brain regions (e.g., the white matter, the grey matter in the putamen, subcallosal cortex, and insular cortex) were associated with multiple obesity-related variants. The metabolically healthy obesity variants were mainly associated with the regional brain volumes in the DA motive system, sensorimotor system and cognitive emotion regulation neural networks, while metabolically unhealthy obesity variants were mainly associated with regional brain volumes in the CAN and total tissue volumes. In addition, unclassified obesity-related variants were mainly associated with auditory object recognition network and total tissue volumes. The results of MeSH (medical subject headings) enrichment analysis showed that obesity genes associated with brain structure pointed to the functional relatedness with 5-Hydroxytryptamine receptor 4 (5-HT4), growth differentiation factor 5 (GDF5), and high mobility group protein AT-hook 2 (HMGA2 protein).ConclusionIn summary, we found that obesity-related variants were associated with different brain volume measures. On the basis of the multiple SNPs, we found that metabolically healthy and unhealthy obesity-related SNPs were associated with different brain neural networks. Based on our enrichment analysis, modifications of the 5-HT4 pathway might be a promising therapeutic strategy for obesity.

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Mapping the genetic variation of regional brain volumes as explained by all common SNPs from the ADNI study.

Publications

Mapping the genetic variation of regional brain volumes as explained by all common SNPs from the ADNI study.

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