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Updated: Aug 7, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
Stratification by a polygenic risk score of common variation aids in Alzheimer's disease rare variant discovery
Oluwatosin Olayinka1,2, John J Farrell2, Congcong Zhu2
1Bioinformatics Program, Boston University, Boston, Massachusetts, USA.
Introduction:
We utilized an Alzheimer's disease (AD) polygenic risk score (PRS) to discover associations with novel rare variants (RVs).
Methods:
PRSs for European ancestry (EA) participants of the Alzheimer's Disease Sequencing Project were calculated using summary statistics from a large genome-wide association study. Participants were classified into high (n = 5738) and low (n = 5324) PRS groups based on the median PRS and on the lower and upper 35% of the PRS distribution.
Results:
Risk variants were disproportionately enriched in the low-PRS group, while protective ones were disproportionately enriched in the high-PRS group. Genome-wide significant (GWS) associations for increased AD risk were identified with RVs spanning a 3.5-Mb region on chromosome 14. GWS protective variants in ALDH9A1, BICC1, and PAN3 were identified in the upper 35% PRS group.
Conclusion:
Our findings provide unique opportunities to study RVs whose effects are opposite to the risk conferred by the genetic background.
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