Experimental design for evaluating adult neurogenesis-associated somatic variations in the hippocampus of Alzheimer’s disease

Abstract

Alzheimer's disease, a neurodegenerative disease with a complex genetic architecture, is estimated to have a 60-70% heritability. Over the past decades, various germline variations associated with Alzheimer's risk have been revealed through genome-wide association studies, whole-exome and whole-genome sequencing analyses, and subsequent rare variants association studies. The various neuropathological features of Alzheimer's disease are known to appear first in the hippocampus. In particular, the mechanism by which the accumulation of neurofibrillary tangles originates in the hippocampus and transforms adjacent normal proteins into abnormal forms has been suggested. In addition, extensive evidence has been reported that cessation of adult neurogenesis occurring in the hippocampal dentate gyrus is associated with memory loss, the primary symptom of Alzheimer's disease. In this study, we performed experiments to accurately detect brain-specific somatic variations occurring in the dentate gyrus and proposed an optimal experimental design as follows. We devised the sample acquisition method via laser capture microdissection considering the embryology and anatomy of the dentate gyrus, and we optimized the whole-genome amplification method that enables amplification of extremely low amounts of DNA from the captured samples. In addition, we developed a method to measure somatic variation from whole-genome sequencing data and performed the identification of clonal somatic mutations through a probabilistic framework. This study laid the foundation for a follow-up study to efficiently prove the hypotheses of neurofibrillary tangle accumulation and adult neurogenesis impairment in the hippocampus in an integrated pipeline.