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 1801 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 the 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.

Rare genetic variation in fibronectin 1 (FN1) protects against APOEε4 in Alzheimer’s disease

“…Duplicate entries with irreconcilable phenotypes were excluded. APOE genotypes were adjudicated using state-of-the-art APOE prioritization approaches, filtering out samples where APOE genotypes lacked robustness (prioritizing APOE genotypes from sequencing data and cross-referencing APOE genotypes from high-quality imputation with those provided in study demographics through various protein-based and DNA-based methods) [ 8 ].…”

APOE Genotype and Alzheimer Disease Risk Across Age, Sex, and Population Ancestry

“…APOE genotypes were adjudicated using state-of-the-art APOE prioritization approaches, filtering out samples in which APOE genotypes lacked robustness (prioritizing APOE genotypes from sequencing data and cross-referencing APOE genotypes from high-quality imputation with those provided in study demographics through various protein-based and DNA-based methods). 17 Finally, samples were filtered to age older than 55 years, cases or controls, belonging to 1 of 3 racial and ethnic groups available (Black, Hispanic, or White), and having no first-degree relatives included in any of the data sets. Inclusion of related individuals for modeling with mixed models was not pursued given that genetic relationship matrices in the current pooled analysis design would have variable accuracy due to various genetic sources.…”

“…Through substantial advances in AD genetics, including the addition of various novel cohorts and increased efforts from the Alzheimer’s Disease Genetics Consortium and the Alzheimer’s Disease Sequencing Project to increase sample diversity, we now have access to publicly available data sets with substantially larger sample sizes for Black, Hispanic, and White individuals . Furthermore, given that these samples underwent array-based or sequencing-based genotyping, we can also perform extensive genetic and phenotypic data harmonization, evaluate effects of global population ancestry, and apply state-of-the-art quality control for more robust APOE genotyping . In parallel, other efforts in the field have led to the construction of genetic cohorts among East Asian individuals, for which summary statistics are available .…”

“… 10 , 12 , 14 , 15 , 16 Furthermore, given that these samples underwent array-based or sequencing-based genotyping, we can also perform extensive genetic and phenotypic data harmonization, evaluate effects of global population ancestry, and apply state-of-the-art quality control for more robust APOE genotyping. 17 , 18 , 19 In parallel, other efforts in the field have led to the construction of genetic cohorts among East Asian individuals, for which summary statistics are available. 20 Considering these important advances, we sought to reassess, in the largest such study to date, the association of APOE genotype with AD risk across important demographic and biologic variables that are known to interact with APOE .…”

Beyond guilty by association at scale: searching for causal variants on the basis of genome-wide summary statistics

“…We consider summary statistics from the ten overlapping studies including: 1. The genome-wide survival association study by Huang et al (2017) (14,406 [29][30][31][64][65][66][67][68][69] All studies focused on individuals with European ancestry.…”