Abstract
Background
The effect size of APOE4 varies across genetic ancestries with African (AFR) local ancestry conferring a lower risk when compared to other ancestries. Recently, we identified a strong effect of the A allele of rs10423769 (with a minor allele frequency of 0.12 in AFR and 0.003 in Europeans), which lowers the risk of AD by 71% in APOE4 carriers. rs10423769 is 2 MB from APOEe4 in a region of segmental duplications (SD) containing a cluster of pregnancy specific beta‐1 glycoprotein genes (PSGs) and a lncRNA. To gain insights into the mechanism of protection, we characterized the haplotype harboring the variant and investigated differences in methylation and structural variation (SV) between haplotypes.
Method
We used the Alzheimer’s Disease Sequencing Project (ADSP) short read sequencing database to fine map and extend the protective haplotype using Haploview 4.2. In addition, long read sequencing (LRS) with the Oxford Nanopore PromethION was performed on 16 samples of individuals carrying one or two copies of rs10423769_A. LRS was used for SV calling with Sniffles2 and differential methylation analysis using Nanomethphase.
Result
The minimum shared haplotype harboring rs10423769_A allele was ∼21kbp (chr19:43099521‐ 43120243). Though the region is rich in SDs, high quality LRS reads mapped uniquely to the region around the A allele confirming that the haplotype is unique and not duplicated elsewhere in the genome of the sequenced individuals. Moreover, the rs10423769_A haplotype harbors 23 differential CpG sites (fdr<0.05) compared to rs10423769_G, although no differential methylated region was identified. LRS revealed a 140bp insertion of repetitive MEF2 binding motifs. Initial examination demonstrated that the insertion was present in 80% of the A allele carriers.
Conclusion
We have identified an AF‐specific haplotype protective against AD risk conferred by APOE ε4. Considering the distance from APOE and the complexity of the highly SD region where the variant is located, we have identified the minimum shared haplotype from AFR origin and are investigating the potential effects of SVs and differential CpG sites. Ongoing analyses include 3D chromatin structure and LRS at higher coverage to assemble and resolve the complex genomic context of the allele.