We conducted a large-scale study of rare CNVs in AD. Overall, there was no excess of CNVs in cases compared with controls, which is what has been observed in the other smaller genome-wide studies of CNVs in AD published so far (16
). When the CNVs were divided into four size ranges and type (deletions and duplications), there was a significant excess of deletions >1 Mb in cases, but this finding did not remain significant after multiple testing.
This is in contrast with the findings of CNV studies of neurodevelopmental disorders. For example, the ISC (20
) identified a significant excess of rare CNVs >100 kb in cases with schizophrenia (case–control ratio = 1.15) and this excess was more pronounced for deletions >500 kb (case–control ratio = 1.67). Williams et al
) also found a significant excess of CNVs >500 kb in cases with attention deficit/hyperactivity disorder (ADHD) (case–control ratio = 2.09). We observed an excess of deletions >100 kb in controls, but this was not significant after correction for multiple testing. This is a similar finding to that of Swaminathan et al
. in their recent genome-wide study of CNVs in AD, where they observed a trend towards a reduced rate of both deletions and duplications in their AD cases (18
). However, much higher CNV rates overall were observed in that study (CNVs per person = 9.3) as they did not filter the data for rare CNVs >100 kb when carrying out this analysis.
We investigated potentially interesting loci in which previous AD CNV studies identified an excess of CNVs in AD cases (16
). Although we observed an excess of CNVs in our cases in the 15q11.2 region identified by Ghani et al
), this excess did not reach significance in our study. The rate of CNVs in this region in their AD cases of Caribbean Hispanic origin is five times what we have observed in our cases. This difference may be due to population differences in CNV rates at this locus. We identified CNVs in four other loci which had been highlighted in the two studies by Swaminathan et al
), but we observed a higher rate of CNVs in our controls than in our cases. This discrepancy may be due to the small control sample sizes of the previous two studies (combined n
= 339). This present study consists of nearly four times as many controls and so has greater power to detect more CNVs in these regions.
We investigated if any known AD risk genes were intersected by CNVs. APP
was overlapped by a duplication identified in an individual with early-onset AD, but no CNVs overlapped this gene in controls. This duplication was independently identified and validated in this same sample by another group that specifically focused on the APP
). A number of previous studies have also identified duplications at the APP
locus in early-onset AD cases (15
). We also identified duplications of CR1
in two individuals with late-onset AD. One of these duplications overlaps the low-copy repeat-associated CNV in CR1
. This is particularly interesting as Brouwers et al
. have shown that duplication of this intragenic CNV in the CR1-S isoform of the gene increases risk for AD, possibly by increasing the number of C3b/C4b-binding sites (34
Our pathway analysis did not show a significant enrichment of any biological pathways after correction for multiple testing. However, we have shown that a number of pathways were found to be enriched in both the SNP data and in deletions, more so than would be expected by chance. This suggests that some biological mechanisms for AD susceptibility may act through both SNPs and CNVs (specifically, deletions). The signifcant pathways include lipid/cholesterol homoeostatsis, as well as cell signalling. Cholesterol homoeostatsis is of particular interest with AD as a number of AD risk genes are thought to be involved in lipid metabolism; APOE
are involved in the formation and transport of lipoprotein particles, both systematically and in the brain (1
) and ABCA7
is involved in the release of cholesterol and phopholipids from cells to lipoprotein particles (35
may also have roles in the internalization and transport of lipids through receptor-mediated endocytosis (1
We observed a low rate of very large (>1 Mb) deletions in our elderly control population compared with younger control sets used in the CNV studies conducted by the ISC (20
) and Grozeva et al
). Although different arrays were used in each of these analyses, deletions >1 Mb in size are the most reliable to call, allowing for fairly confident comparisons between studies. This raises the question of whether healthy elderly individuals have a reduced rate of large deletions, in other words, do deletions >1 Mb cause other general health problems that reduce life expectancy? This finding needs to be replicated in additional samples of elderly individuals before conclusions can be drawn.
In summary, we did not find a global excess of rare and large CNVs in AD cases and we did not replicate findings for an excess of CNVs in loci highlighted by previous AD CNV studies. Furthermore, we did not find an excess of CNVs overlapping AD candidate genes in cases, but did identify duplications overlapping APP and CR1 which may be pathogenic. We have also shown potential biological overlap between the involvement of SNPs and CNVs in AD susceptibility, centred on lipid/cholesterol metabolism. We also find a reduced rate of large, rare deletions in our elderly controls than has been observed in other control sets, raising the possibility that this class of CNVs not only increase the rate of various neurodevelopmental disorders, but might also reduce life expectancy in general. Thus, in contrast to diseases such as schizophrenia, autism and ADHD, CNVs do not appear to make a significant contribution to the development of AD.