Challenges at the APOE locus: A robust quality control approach for accurate APOE genotyping

Abstract

Background: Genetic variants within the APOE locus may modulate Alzheimer′s disease (AD) risk independently or in conjunction with APOE*2/3/4 genotypes. Identifying such variants and mechanisms would importantly advance our understanding of APOE pathophysiology and provide critical guidance for AD therapies aimed at APOE. The APOE locus however remains relatively poorly understood in AD, owing to multiple challenges that include its complex linkage structure and uncertainty in APOE*2/3/4 genotype quality. Here, we present a novel APOE*2/3/4 filtering approach and showcase its relevance on AD risk association analyses for the rs439401 variant, which is located 1,801 base pairs downstream of APOE and has been associated with a potential regulatory effect on APOE. Methods: We used thirty-two AD-related cohorts, with genetic data from various high-density single-nucleotide polymorphism microarrays, whole-genome sequencing, and whole-exome sequencing. Study participants were filtered to be ages 60 and older, non-Hispanic, of European ancestry, and diagnosed as cognitively normal or AD (n=65,701). Primary analyses investigated AD risk in APOE*4/4 carriers. Additional supporting analyses were performed in APOE*3/4 and 3/3 strata. Outcomes were compared under two different APOE*2/3/4 filtering approaches Results: Using more conventional APOE*2/3/4 filtering criteria (approach 1), we showed that, when in-phase with APOE*4, rs439401 was variably associated with protective effects on AD case-control status. However, when applying a novel filter that increases certainty of the APOE*2/3/4 genotypes by applying more stringent criteria for concordance between the provided APOE genotype and imputed APOE genotype (approach 2), we observed that all significant effects were lost. Conclusions: We showed that careful consideration of APOE genotype and appropriate sample filtering were crucial to robustly interrogate the role of the APOE locus on AD risk. Our study presents a novel APOE filtering approach and provides important guidelines for research into the APOE locus, as well as for elucidating genetic interaction effects with APOE*2/3/4.

Summary statistics knockoff inference empowers identification of putative causal variants in genome-wide association studies

“…The genome-wide meta-analysis by Schwartzentruber et al 2021 46 , aggregating Kunkle et al 2019 and UK Biobank based on a proxy AD phenotype; 5. In-house genome-wide associations study of 15,209 cases and 14,452 controls aggregating 27 cohorts across 39 SNP array data sets, imputed using the TOPMed reference panels 47 ; 6-7. Two whole-exome sequencing analyses of data from The Alzheimer’s Disease Sequencing Project (ADSP) by Bis et al 2019 48 (5740 cases, 5096 controls), and Le Guen et al 2021 49 (6008 cases, 5119 controls); 8.…”