Josue David Gonzalez Murcia and John Kauwe, Biology Department

Introduction

Alzheimer’s disease is one of the top 10 causes of death in the world and the 6th leading cause of death in the United States, with 5.5 million people diagnosed with the disease. Alzheimer’s cannot be cured, prevented or slowed. Most research with Alzheimer’s disease has been done on SNPs that have a relatively high frequency in the population this has helped facilitate researchers in finding a broad genetic pathway in the development of Alzheimer’s disease (Naj et al. 2011; Harold et al. 2009). Our research will focus on a very rare SNP, with a much lower frequency than previously has been studied. Finding rare variants that influence disease risk will help push forward research on Alzheimer’s disease and take us closer to an adequate cure or prevention. One of the most important aspects of finding this rare SNP is the ability we have to track the genetic inheritance of the SNP in families. It will help us to understand the significance of the SNP on the progression, protection, and development of Alzheimer’s disease. If there is a strong correlation between the SNP and Alzheimer’s then it can provide a greater understanding of the disease and aid researchers in finding a cure.

I will be researching the association between risk for Alzheimer’s disease and the presence of a rare genetic variant in the APP gene. Published data from our collaborators at Genentech suggest that a specific genetic variant in APP gene is considered as protective mutation in developing Alzheimer’s disease. I plan to test DNA samples from the Cache County Study on Memory Health and Aging to identify carriers of this rare variant. When we find the genetic variant in any of the Cache County DNA samples, we will then use their pedigree to check if their relatives also carry the variant. This will help us determine how much this single nucleotide polymorphism (SNP) protects to the development of Alzheimer’s disease and how it has been segregated throughout generations.

Methodology

I have access to a unique data set in the Cache County Study on Memory Health and Aging. The Cache County study was taken from Cache County, Utah in 1995. 5,092 people or around 90% of the permanent residents participated in the study. From this study we have approximately 600 DNA samples with Alzheimer’s. In addition to taking participants DNA, a pedigree was formed linking participants with their parents, siblings, children and relatives. This gives me a unique set of data to work from because I will be able to effectively track the genetic inheritance of this SNP and observe how it has segregated throughout many people in the same family.

Our samples will be drawn from the 600 DNA samples of people with Alzheimer’s disease. I will genotype the DNA samples using a specific assay designed to find the rare SNP we are researching. The genotyping will be done using a state of the art quantitative PCR (qPCR) machine that will amplify the DNA and track fluorescence sent out when custom primers and probes react in the machine. The data will be uploaded and read into the Taqman Genotyper software, where I will review it and determine the genotype for each sample. When the SNP is found, I will then genotype the DNA of closest relatives to that sample.

Results

A total of 506 AD cases and 3,838 elderly cognitive normal controls from the Cache County Study Memory in Aging were genotyped using TaqMan assay to identify the rare variant A673T. As expected, all dementia cases were homozygous for the normal A673A allele. One of the 3,838 non-demented subjects carried the A673T allele (Table). This non-demented individual was 77 year of age at last assessment had an APOE genotype of E3/E4 and had ancestor from Denmark, Ireland, Scotland, and England.

Discussion

The APP A673T variant is over-represented in Icelandic controls when compared to Icelandic AD cases. Therefore, like the APOE ε2 allele, the A673T variant appears to protect against late onset AD, defined as disease age-at-onset > 60 years. Studies on the functional consequences of the A673T substitution showed that this amino acid substitution inhibited BACE1 cleavage of APP, potentially reducing or eliminating the production of Aβ peptide from APP encoded by this allele. This allele appears to be protective provides additional genetic evidence that Aβ is a critical toxic molecule contributing to AD.

Unfortunately, after finding a non-demented A673T carried in the Cache County dataset, It was not possible to contact the carried or any relative close to the carried. Hence, analysis of segregation for the variant A673T was not possible to perform. It has been proposed to develop an Icelandic dataset using as cohort Icelandic descendent living in Spanish Fork, Utah.

Conclusion

It has been shown that the variant A673T in the APP gene has a protective effect against late- onset Alzheimer’s disease. The Cache County Study on Memory in Aging dataset provided further evidence that the variant A673T is present among Caucasian and protects against developing AD. However, we could not know how the protective variant segregates through out generations and families because the subject carrier was not contactable. Nevertheless, It is understood that the protective variant A673T has a higher frequency of expression among Icelandic population. Thus, developing an Icelandic DNA dataset using Icelandic decedents living in Spanish Fork, Utah has been proposed. If the Icelandic dataset id develop, this research can be replicated in the new dataset and proceed further with the understanding of how the variant A673T is segregated through out generation.

Table of reference of Cohort

Cohort	Cases	Control	Dementia Other	Total	% Male Cases	% Male Control	Mean Age at onset for cases (SD) Year	Mean age-atlastexam for controls (SD) years	Mean age-atsampling for controls (SD) years	Cohort type
Cache County	506 (0)	3,838 (1)	383 (0)	4727 (1)	32	42	82.4 (6.9)		79.8 (6.3)	Prospective cohort