Examination of candidate exonic variants for association to Alzheimer disease in the Amish.

Alzheimer disease (AD) is the most common cause of dementia. As with many complex diseases, the identified variants do not explain the total expected genetic risk that is based on heritability estimates for AD. Isolated founder populations, such as the Amish, are advantageous for genetic studies as they overcome heterogeneity limitations associated with complex population studies. We determined that Amish AD cases harbored a significantly higher burden of the known risk alleles compared to Amish cognitively normal controls, but a significantly lower burden when compared to cases from a dataset of unrelated individuals. Whole-exome sequencing of a selected subset of the overall study population was used as a screening tool to identify variants located in the regions of the genome that are most likely to contribute risk. By then genotyping the top candidate variants from the known AD genes and from linkage regions implicated previous studies in the full dataset, new associations could be confirmed. The most significant result (p = 0.0012) was for rs73938538, a synonymous variant in LAMA1 within the previously identified linkage peak on chromosome 18. However, this association is specific to the Amish and did not generalize when tested in a dataset of unrelated individuals. These results suggest that additional risk variation in the Amish remains to be identified and likely resides outside of the classical protein coding gene regions

Demographics of Amish Samples Used For Follow-up Genotyping.

<p>Percent female, age of exam and onset averages and standard deviations were calculated for the 921 samples which passed QC for follow-up genotyping.</p><p>Demographics of Amish Samples Used For Follow-up Genotyping.</p

MQLS-corrected allele frequencies and case-control association p-values for the top sequencing variants in the sequencing dataset.

<p>Chr = chromosome. MAF = minor allele frequency. Nucleotide position is based upon the UCSC hg19 human reference genome. Gene and Function annotated by SeattleSeq134.</p><p>MQLS-corrected allele frequencies and case-control association p-values for the top sequencing variants in the sequencing dataset.</p

Details of Risk Loci from Meta-Analysis Used to Calculate Total Genetic Risk Score.

<p>Alleles, MAF, and overall OR are published values. Chr = chromosome. Pos = position in bp. MAF = minor allele frequency. OR = odds ratio. Adapted from Lambert, et al, 2013 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118043#pone.0118043.ref016" target="_blank">16</a>]. Allele frequency was calculated using the 921 Amish samples and the 971 samples from the unrelated dataset that passed QC in the follow-up genotyping phase.</p><p>Details of Risk Loci from Meta-Analysis Used to Calculate Total Genetic Risk Score.</p

Flow Diagram of this Study.

<p>Individuals were selected from the full Amish dataset for whole-exome sequencing. The variants identified from these data were used to screen three classes of variants, genes that are very near or contain GWAS hits or carry early-onset mutations, genes within four candidate linkage regions implicated by previous studies and genes that harbor variants that occur uniquely in cases or in controls. The top variants from these three classes were then genotyped in the full dataset and case-control association was performed.</p

Distributions of Total Genetic Risk Scores.

<p>Total genetic risk score averages and standard deviations were calculated for the 629 Amish LOAD cases and cognitively normal controls and the 971 LOAD cases and cognitively normal controls from the unrelated case-control dataset who passed QC for the follow-up genotyping phase. n = total number of individuals. μ = average total risk score for group.</p