Rare variants in APP, PSEN1 and PSEN2 increase risk for AD in late-onset Alzheimer's disease families

Abstract

Pathogenic mutations in APP, PSEN1, PSEN2, MAPT and GRN have previously been linked to familial early onset forms of dementia. Mutation screening in these genes has been performed in either very small series or in single families with late onset AD (LOAD). Similarly, studies in single families have reported mutations in MAPT and GRN associated with clinical AD but no systematic screen of a large dataset has been performed to determine how frequently this occurs. We report sequence data for 439 probands from late-onset AD families with a history of four or more affected individuals. Sixty sequenced individuals (13.7%) carried a novel or pathogenic mutation. Eight pathogenic variants, (one each in APP and MAPT, two in PSEN1 and four in GRN) three of which are novel, were found in 14 samples. Thirteen additional variants, present in 23 families, did not segregate with disease, but the frequency of these variants is higher in AD cases than controls, indicating that these variants may also modify risk for disease. The frequency of rare variants in these genes in this series is significantly higher than in the 1,000 genome project (p = 5.09 × 10⁻⁵; OR = 2.21; 95%CI = 1.49-3.28) or an unselected population of 12,481 samples (p = 6.82 × 10⁻⁵; OR = 2.19; 95%CI = 1.347-3.26). Rare coding variants in APP, PSEN1 and PSEN2, increase risk for or cause late onset AD. The presence of variants in these genes in LOAD and early-onset AD demonstrates that factors other than the mutation can impact the age at onset and penetrance of at least some variants associated with AD. MAPT and GRN mutations can be found in clinical series of AD most likely due to misdiagnosis. This study clearly demonstrates that rare variants in these genes could explain an important proportion of genetic heritability of AD, which is not detected by GWAS.

Figure 1. Pedigrees for some of the sequenced families illustrating the presence of phenocopies and low penetrance mutations or the presence of presymptomatic cases.

A) Pedigree for a family with the PSEN1 A79V mutation. B) Pedigree for a family with the GRN R493X mutation. AO indicates the subject or family report of age of onset of symptoms. AE = the age of last evaluation. MCI: Mild cognitive impairment or questionable dementia by family report.+symbol indicates that the subject is positive for the indicated mutation.−symbol indicates that the subject is negative for the indicated mutation. A number inside of a diamond indicates the number of subjects with the same status. Fully shaded circles or squares indicate confirmed AD by autopsy. Three/fourths shaded symbol indicates probable AD diagnosed using NINCDS-ADRDA criteria. One/fourth shaded symbol indicates that the family reports this individual has AD.