In order to identify risk loci significantly different between cases and controls that might contain genetic lesions responsible for AD, empirical p-values for consensus homozygous regions were determined in both cases and controls groups. One consensus ROH in chromosome 8 was found to be significantly overrepresented in cases when compared to controls after correction for multiple testing. This region contains seven genes, three of which have previously been studied in relation to AD ().
gene product, beta-3-adrenergic receptor, is one of three beta-adrenergic receptor subtypes. The product is located mainly in adipose tissue and is involved in the regulation of adipocyte lipolysis, thermogenesis and oxygen consumption [26
]. There is evidence that a disturbance in the insulin signal transduction pathway may be a central and early pathophysiologic event in sporadic AD [27
]. Patients with diabetes and insulin resistance have an increased risk of impaired cognition or dementia [28
]. Hamilton et al performed a two stage association study to investigate the role of insulin signaling genes in the risk of developing AD showing one SNP in ADRB3
(rs4998) was studied and found to be associated with AD in ApoE4 negative samples [23
The steroidogenic acute regulatory protein (StAR), coded by the STAR
gene, plays a key role in the acute regulation of steroid hormone synthesis by enhancing the conversion of cholesterol into pregnenolone [29
]. To test the hypothesis that hormones of the hypothalamic-pituitary-gonadal axis have a role in AD pathogenesis, K.M. Webber et al studied the expression levels of StAR in AD and control brains. The authors found an increase of this protein in AD hippocampal neurons as well as other non-neuronal cells compared to aged matched controls. These results, together with the finding that StAR is present in the same brain regions as the luteinizing hormone (LH) receptors, suggest that steroidogenic pathways regulated by LH may play a role in AD [24
gene encodes one member of a family of translation repressor proteins, which interacts with eukaryotic translation initiation factor 4E (eIF4E). This is a limiting component of the multi-subunit complex that recruits 40S ribosomal subunits to the 5′ end of mRNAs. Interaction of this protein with eIF4E inhibits the complex assembly and represses translation. The 4E-BP1protein is phosphorylated in response to several signals, including insulin signaling and together with several other components of the translational machinery is regulated through signaling events that require the mammalian target of rapamycin (mTOR) [30
]. Neurofibrillary tangles, composed mainly of hyperphosphorylated tau protein, is one of the neuropathological hallmarks of AD. Tau mRNA levels have been shown not to be altered in sporadic AD brains. Nevertheless, Li X, et al studied the possibility that tau mRNAs in AD brains could be abnormally regulated by investigating the levels of various translation control elements including 4E-BP1, in the brains of AD and controls subjects. Together with increased levels of p-mTOR, they found increased levels of phosphorylated 4E-BP1 in AD and a positive significant correlation with total tau and phosphorylated tau [25
Genetic variation in one or more of these genes may account for the development of different phenotypes related to LOAD and it is possible that this form of genetic heterogeneity coexists with the multifactorial, common-disease/common-variant mode of inheritance that is generally studied in whole-genome association [21
From a methodological perspective, using ROHs to identify possible candidate loci for small effects size or rare recessive variants in unrelated individuals may be useful. This method uses relatively few statistical tests compared to conventional genome-wide association studies to probabilistically model recessive genome-wide associations with disease, increasing power to some degree. The method itself likely trades specificity of results for sensitivity, by seeking to identify large regions of homozygosity harboring as-of-yet unknown recessive disease components. In particular, homozygosity mapping is limited by fine mapping within the risk ROH not being feasible in the discovery population. To identify a more focused risk region in replication of a homozygosity mapping finding, a population of a different ethnic background or an admixed population would have to be studied, as boundaries of the ROHs would likely be different from the discovery cohort. The summary measures of genome-wide extended homozygosity may also prove useful in quantifying distant consanguinity in a single unrelated population, for which Fst calculations may not be applicable to gauge genetic distance from a founder group.
Using public whole genome SNP analysis data on late onset Alzheimer’s disease and neurologically normal controls we identified an average of 52.1 homozygous runs larger than 1 Mb containing more than 50 consecutive SNPs in 1387 samples. In order to determine if Alzheimer’s disease populations are more consanguineous than healthy controls we statistically compared the total number of homozygous runs, average length of homozygous runs and total length of genome contained in runs of homozygosity between cases and controls. For this analysis we used a stringent method, assuming that the presence of large tracts of contiguous homozygous SNPs represent a direct association with increased levels of relatively recent consanguinity [17
]. Only homozygous runs with sizes over 1 Mb were included in the analysis in order to rule out the effect of copy number variation, which could confound results if smaller minimum run sizes were used. Our borderline significant results suggest that the AD cases in this study may be characterized by a higher degree of extended homozygosity than the control group, although this generalization would need to be tested in a larger sample size.
As the individual ages were not available to the public, it was not possible to establish a relation between age and homozygosity. Still, our group has recently reported the first genetic proof that younger individuals present less homozygosity than older ones, presumably due to populations increased mobility in the last generations. Linear predictive models of homozygosity and current age, showed that younger individuals have smaller percentage of their genome contained in homozygous runs; which are significantly shorter in length (Nalls et al unpublished data). Similar results would be expected for the present populations.
The E4 allele of APOE
has been the only genetic risk factor consistently associated with familial and sporadic forms of AD [12
]. In the present study no association between homozygosity at the APOE gene and AD was found. This is explained by the size of the statistical window used (1Mb), as the methodology used was designed to pick up variants with recently created ROHs that have not been broken up by recombination. High recombination rates in this genomic region in the European American population, prevent detection of any signal at the APOE gene using homozygosity mapping [31
In summary, we conclude that extended runs of homozygosity are common in out bred populations and present statistical data that show specific large tracts of homozygosity are a risk factor for Alzheimer’s disease. The present results, together with the previously reported cases of consanguineous families with AD [8
] and the speculation that recessive genes for AD are responsible for the high AD prevalence in the Wadi Ara [33
], demonstrate that particular regions of homozygosity have a significant role in AD genetics. It is possible that future sequencing and additional follow-up analyses will allow the identification of small-effect size recessive risk variant(s) within the described ROHs.