Many genetic studies for Alzheimer's disease (AD) have been focused on the identification of common genetic variants associated with AD risk and not on other aspects of the disease, such as age at onset or rate of dementia progression. There are multiple approaches to untangling the genetic architecture of these phenotypes. We hypothesized that the genetic architecture of rate of progression is different than the risk for developing AD dementia. To test this hypothesis, we used longitudinal clinical data from ADNI and the Knight-ADRC at Washington University, and we calculated PRS (polygenic risk score) based on the IGAP study to compare the genetic architecture of AD risk and dementia progression. Dementia progression was measured by the change of Clinical Dementia Rating Sum of Boxes (CDR)-SB per year. Out of the 21 loci for AD risk, no association with the rate of dementia progression was found. The PRS rate was significantly associated with the rate of dementia progression (β= 0.146, p = 0.03). In the case of rare variants, TREM2 (β= 0.309, p = 0.02) was also associated with the rate of dementia progression. TREM2 variant carriers showed a 23% faster rate of dementia compared with non-variant carriers. In conclusion, our results indicate that the recently identified common and rare variants for AD susceptibility have a limited impact on the rate of dementia progression in AD patients.

Alzheimer disease (AD), Frontotemporal lobar degeneration (FTD), Amyotrophic lateral sclerosis (ALS) and Parkinson disease (PD) have a certain degree of clinical, pathological and molecular overlap. Previous studies indicate that causative mutations in AD and FTD/ALS genes can be found in clinical familial AD. We examined the presence of causative and low frequency coding variants in the AD, FTD, ALS and PD Mendelian genes, in over 450 families with clinical history of AD and over 11,710 sporadic cases and cognitive normal participants from North America. Known pathogenic mutations were found in 1.05% of the sporadic cases, in 0.69% of the cognitively normal participants and in 4.22% of the families. A trend towards enrichment, albeit non-significant, was observed for most AD, FTD and PD genes. Only PSEN1 and PINK1 showed consistent association with AD cases when we used ExAC as the control population. These results suggest that current study designs may contain heterogeneity and contamination of the control population, and that current statistical methods for the discovery of novel genes with real pathogenic variants in complex late onset diseases may be inadequate or underpowered to identify genes carrying pathogenic mutations.

Recent studies suggest that the missing heritability in Alzheimer disease (AD) may lie under the cumulative effect of rare variants that cause functional changes. Families enriched in AD cases are a powerful source for detecting novel variants that may confer risk towards disease. In this work we analyze a highly selected cohort of 493 multigenerational families enriched in late onset AD cases for the identification of novel variants and genes implicated on AD. We have performed whole-exome or whole-genome sequencing on 1,077 clinically diagnosed LOAD and 440 non-demented relatives. All samples were recruited by the Knight ADRC or the NIA-LOAD family study group. Variant discovery was performed following GATK's best practice followed by stringent quality control. We focused our analysis on nonsynonymous variants with a minor allele frequency <1% in the general population (ExAC). We perform genome-wide scans to examine the presence of causative and low frequency coding variants in the most common neurodegenerative diseases, as well as in novel candidate genes. Known pathogenic mutations were found in 4.42% of the families as well as an enrichment of non-synonymous variants in AD and frontotemporal lobular dementia (FTLD) genes. We have detected potential risk variants that present perfect segregation in several families of 7 members in addition to few novel candidate genes with genome-wide significance associated to disease risk. Known pathogenic and low frequency coding variants in AD, FTD and PD genes can be found in clinical AD cases; indicating that more stringent selecting criteria and genetic testing must be performed before incorporating new samples into analysis. We have identified some preliminary candidate variants and genes that would confer risk to AD; network analysis and replication are underway.

GWAS have been extremely successful in identifying novel loci associated with Alzheimer’s disease (AD), however the search has shifted to look for rare and low frequency variants that will have moderate to strong effects. Since AD has a large familial component, one efficient approach to find those rare genetic variants is to examine families with multiple affected individuals. In this work we will determine if families with LOAD are enriched on rare variants in genes known to be involved on AD, or other neurodegenerative disease (FTD, PD, PSP, ALS, among others), in the largest yet familiar late onset AD (LOAD) dataset, the Familial Alzheimer Sequencing (FASe) project. We have performed whole-exome or whole-genome sequencing on 345 families with 3-5 members each, over a total of 882 cases and 333 nondemented elderly relatives. All samples included in this analysis were recruited by the Knight-ADRC or the NIA-LOAD family study. Families in which the index individual carried a known pathogenic mutation were excluded from the study. Variant discovery was performed following GATK’s best practices. After applying stringent quality controls to variants, genotypes, and samples, we focused our attention on nonsynonymous variants with a minor allele frequency <1% to generate gene-sets to evaluate the enrichment of rare variants in cases over controls, using GSKAT and EPACTS software. We have examined over 256 genes (mendelian and from GWAS studies) known to be involved on AD or other neurodegenerative diseases. We found that 12 genes were nominally significant on the family-based gene-based analyses (G-SKAT). Interestingly, one of those 12 genes was PSEN1(GSKAT P=0.046), in which the association was mainly driven by three missense rare variants (chr14:73614747, p.Pro7Leu; rs199723282, p.Val261Gly; rs200525059, p.Val412Leu). These preliminary results suggest that new risk variants will be identified that will contribute to the understanding of the genetic architecture of Alzheimer’s disease. Analyses are still underway to identify additional variants.

Case-control genome-wide association studies (GWAS) have identified loci associated with risk for Alzheimer disease (AD) but they require very large sample sizes and usually identify variants with small effect sizes. GWAS of informative endophenotypes for disease have more power to identify novel variants and provide information about biological mechanisms. Cerebrospinal fluid (CSF) levels of tau, ptau181, and amyloid beta (Aß42) have been well established as endophenotypes for AD. By analyzing data from 1,269 unrelated individuals, we previously identified risk variants for AD that were also associated with CSF levels of tau and ptau181, including a novel variant associated with AD risk. CSF levels of tau, ptau181, and Aß42 were collected from 3,189 unrelated individuals and linear regression was used to determine single nucleotide polymorphisms (SNPs) associated with these CSF proteins. We analyzed independent data sets to determine if associated SNPs were also associated with AD risk, age of symptom onset, or disease progression. We also performed pathway analyses to determine whether SNPs that were suggestive, but did not reach genome-wide significance, can provide information about the biology of AD. We found novel variants associated with ptau181 in OLFM4 (Chromosome 13, p=1.51×10-8) and CTDP1 (Chromosome 18, p=3.05×10-9) loci. In the analyses of CSF levels of Aß42 we found near genome-wide significant signals in GLIS1 (Chromosome 1, p=6.41×10-8) and SERPINB1 (Chromosome 6, p=1.31×10-7) loci. We also replicated our previous findings that variants located in APOE (Chromosome 19, p=1.17×10-31), GLIS3 (Chromosome 9, p=2.63×10-8), and SNAR-I (Chromosome 3, p=2.65×10-10) loci were associated with ptau181 levels. In the previous GWAS we found a novel variant associated with AD risk, tangle pathology, and cognitive decline. Our preliminary analyses of these novel loci for ptau181 and Aß42 levels did not indicate association with AD risk, age at symptom onset, or cognitive decline. By significantly increasing the sample size for our GWAS, we were able to identify novel loci associated with CSF levels of ptau181 and near genome-wide significant associations with Aß42 levels. We are performing additional analyses to determine potential impact of these findings in AD. We will also perform rare variant, gene-based, and additional pathway analyses.

The accumulation of the toxic Aβ peptide in Alzheimer's disease (AD) largely relies upon an efficient recycling of amyloid precursor protein (APP). Recent genetic association studies have described rare variants in SORL1 with putative pathogenic consequences in the recycling of APP. In this work, we examine the presence of rare coding variants in SORL1 in three different European American cohorts: early-onset, late-onset AD (LOAD) and familial LOAD.

Much of the heritability of late-onset Alzheimer's disease (LOAD) remains unaccounted for, despite progress from genome-wide association studies. The overall contribution of rare variants to the risk of LOAD remains to be determined and, to date, few rare variants in LOAD have been identified and functionally characterized. We hypothesized that families with multiple affected individuals are enriched for genetic risk factors. In previous studies, we performed whole-exome sequencing in 14 families with LOAD and found an enrichment of coding variants in the phospholipase D3 (PLD3) gene and Unc-5 Homolog C (UNC5C). We have generated whole exome sequencing for additional 103 families (380 individuals). Enrichment of coding exons and flanking intronic regions was performed using VCRome. This step was performed by the Genome Institute at Washington University. Captured DNA was sequenced by paired-end reads on the HiSeq 2000 sequencer (Illumina). Sequencing data and variant calling was performed with the BWA/GATK pipeline. To identify novel variants and genes associated with AD risk, we performed analyses within families (Mendelscan: http://gmt.genome.wustl.edu/packages/mendelscan/) and across families (GSKAT). We found more than 700,000 variants. Around 20% of those variants were located on coding regions. Of these 53.8% were missense and 40.8% were synonymous. We also found between 12 to 324 low frequency variants (MAF<1%) segregating with disease status within the sequencing individuals. The number of segregating variants depended on the number of sequenced samples per family. First, we tested whether the genes known to be involved on AD, showed a significant association with AD. PSEN1, 2, APOE, PLD3, SORL1, AKAP9 showed a nominal association, but none of the GWAS genes. In the G-SKAT analyses we did not found any gene that passed multiple test correction, but we found three genes with a suggestive association (p=9x10−5): PROM2, BEST1 and HIST1H1C. We have identified several new candidate genes for risk for AD, however additional studies are needed to validate their association with AD. We plan to perform additional segregation analyses in the rest of the family members, as well as deep resequencing in large datasets to validate the role of those genes in AD risk.

Introduction A recent study found a significant increase of ABCA7 loss-of-function variants in Alzheimer’s disease (AD) cases compared to controls. Some variants were located on noncoding regions, but it was demonstrated that they affect splicing. Here, we try to replicate the association between AD risk and ABCA7 loss-of-function variants at both the single-variant and gene level in a large and well-characterized European American dataset. Methods We genotyped the GWAS common variant and four rare variants previously reported for ABCA7 in 3476 European–Americans. Results We were not able to replicate the association at the single-variant level, likely due to a lower effect size on the European American population which led to limited statistical power. However, we did replicate the association at the gene level; we found a significant enrichment of ABCA7 loss-of-function variants in AD cases compared to controls ( P = 0.0388; odds ratio =1.54). We also confirmed that the association of the loss-of-function variants is independent of the previously reported genome-wide association study signal. Conclusions Although the effect size for the association of ABCA7 loss-of-function variants with AD risk is lower in our study (odds ratio = 1.54) compared to the original report (odds ratio = 2.2), the replication of the findings of the original report provides a stronger foundation for future functional applications. The data indicate that different independent signals that modify risk for complex traits may exist on the same locus. Additionally, our results suggest that replication of rare-variant studies should be performed at the gene level rather than focusing on a single variant.