This is the first GWA study of volumetric brain MRI and cognitive phenotypes in a community-based sample of adults with data drawn from two generations of persons within the same families. The complete results of the association and linkage analyses are available at our website http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007. This resource has the potential to detect novel susceptibility genes for brain aging, to examine the relevance within humans of promising candidate gene associations with these diseases reported in animal models, and to replicate findings observed in other cohort studies. We used several strategies to prioritize phenotype-SNP associations, but there remain other unique ways of looking at these data that we and others will continue to explore.
In our untargeted approach of ranking SNP associations by the strength of the p-value, we found several phenotype-SNP associations within biologically interesting genes (Table 2). The most exciting was a strong association between two SNPs in or adjacent to the gene SORL1 and performance on tests of abstract reasoning (rs1131497; FBAT p = 3.2 × 10-6 and rs726601; FBAT p=8.2 X 10-4). SORL1 is an apolipoprotein E receptor, binds alpha-2-macroglobulin, and is one component of a large multimeric complex, termed the retromer complex that is involved in retrograde transport of proteins from endosomes to the trans-Golgi network [43, 44]. This retromer complex appears to play a crucial role in the transportation of transmembrane proteins implicated in Alzheimer's disease, such as amyloid precursor protein (APP) and β-site APP cleaving enzyme (BACE1). SORL1 protein is underexpressed in the frontal lobes of persons with AD compared to controls and the SORL1 gene has recently been associated with the risk of developing AD in 6 population samples [45, 46]. Only 7 SNPs on or adjacent to the SORL1 gene were evaluated in the 100K Affymetrix gene chip. One of these SNPs on SORL1 that was associated with abstract reasoning (rs726601, FBAT p = 8.2 × 10-4, Table 4) was in LD (r2 > 0.8) with SNPs (rs2282649, rs1010159) strongly associated with AD in these studies [45, 46].
In unbiased analyses, we also identified 3 genes that were associated with measures of frontal or parietal brain volume and with tests of executive function and abstract reasoning. These 3 genes, ERBB4, PDLIM5 and RFX4, (FBAT ranks #11 and 12, GEE rank #9) have each been previously associated with schizophrenia or mood disorders, conditions known to be associated with smaller frontal brain volumes and poorer performance on tests of executive function, even in unaffected family members [47, 48]. ERBB4 is a neuregulin (NRG1) receptor involved in forebrain development and N-methyl-D-aspartate (NMDA) receptor function. It has been associated with schizophrenia wherein excess of the IVS 12–15C > T has been noted (odds-ratio 2.98) [49, 50]. NRG1 itself has been associated with schizophrenia in the Icelandic DeCODE population  and in other studies [52–54], with accelerated lobar atrophy , and with bipolar disorders [55, 56]. As shown in Table 4, NRG1, like ERBB4, was associated with frontal brain volume (FBV) in our sample. PDLIM5 polymorphisms have been associated with schizophrenia (rs2433320 and rs2433322) [52, 55] and bipolar disorder (rs10008257 and rs2433320) . Additionally the PDLIM5 protein is a homolog of AD7c-NTP, a neural thread protein associated with Alzheimer's disease, and is being studied as a possible CSF biomarker of AD . A final group of 3 genes, CDH4, VIPR2, CTNNB1 (GEE rank #1 and FBAT ranks #17 and 24) have been shown in animal studies to play an important role in neural tract and synaptic development [59–61]. Using linkage analyses, we were able to replicate a previous report that dyslexia was linked to a short-tandem repeat marker D18S53 on chromosome 18p11.2.
We examined pleiotropic effects by identifying SNP associations across two sets of related phenotypes. In these analyses, we uncovered a different set of genes, none of which have been related to brain volumes, cognitive function, stroke or dementia in prior population studies. However, there are biologically interesting genes related to brain volumes including PDE3A, previously related to all aspects of thrombosis , SCN8A linked to cerebellar ataxia with mental retardation , and PDE4B which has been associated with schizophrenia .
We also evaluated SNPs within some candidate genes previously reported to be associated with stroke and dementia in animal studies or in population samples, and observed that several of these SNPs were associated with MRI and cognitive endophenotypes that increase the risk of these conditions; this gene list is representative but not comprehensive. Among these genes are PDE4D and LTA4H that have been previously related to stroke in several population samples [9, 10]; NGFB, NTRK2 and NTRK3 (a neural growth factor and two receptors for neural growth factors) genes, previously associated with performance on memory tasks in animal studies [65, 66]; BACE1, PRNP and A2M, genes associated with AD in case-control or family-based association studies [36, 67, 68], VLDLR, a gene previously associated with an increased risk of dementia in the presence of vascular risk factors  and LRRK2, a gene associated with an increased risk of Parkinson's disease in population samples , but also thought to be an enabling gene for tau pathology . There has been only one prior study that directly related a gene (KIBRA) to one of the phenotypes (verbal memory) included in the current analyses. We did not have any SNPs in significant LD with the SNP (rs17070145) described in that study . We have chosen not to include details of the correlation between SNPs from the 100K and the specific SNP(s) studied within candidate genes by prior investigators since doing so would have expanded our Table 4 beyond the size and scope of this article. For example, prior associations of several of the candidate genes with related clinical disease phenotypes (for example, PDE4D with ischemic stroke, SORL1 with AD) have described allelic heterogeneity. In these studies, multiple SNPs and haplotypes within the gene were associated with the phenotype, even within Caucasian populations [73–75].