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1	Challenges at the APOE locus: a robust quality control approach for accurate APOE genotyping. Alzheimers Res Ther 2022;14:22. [PMID: 35120553 PMCID: PMC8815198 DOI: 10.1186/s13195-022-00962-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/12/2022] [Indexed: 04/22/2023] Abstract BACKGROUND Genetic variants within the APOE locus may modulate Alzheimer's disease (AD) risk independently or in conjunction with APOE2/3/4 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 APOE2/3/4 genotype quality. Here, we present a novel APOE2/3/4 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 APOE4/4 carriers. Additional supporting analyses were performed in APOE3/4 and 3/3 strata. Outcomes were compared under two different APOE2/3/4 filtering approaches. RESULTS Using more conventional APOE2/3/4 filtering criteria (approach 1), we showed that, when in-phase with APOE4, rs439401 was variably associated with protective effects on AD case-control status. However, when applying a novel filter that increases the certainty of the APOE2/3/4 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 APOE2/3/4. Collapse Key Words Alzheimer’s disease (AD) Apolipoprotein E (APOE) Genetics Haplotypes Novel approaches rs439401 Collapse MESH Headings Alzheimer Disease/genetics Apolipoprotein E4/genetics Apolipoproteins E/genetics Genetic Predisposition to Disease/genetics Genotype Humans Middle Aged Quality Control Collapse Grants R01 AG054076 NIA NIH HHS P30 AG013854 NIA NIH HHS P30 AG053760 NIA NIH HHS HHSN268201100012C NHLBI NIH HHS P50 MH060451 NIMH NIH HHS P30 AG066444 NIA NIH HHS RC2 HL102419 NHLBI NIH HHS HHSN268201100009I NHLBI NIH HHS P30 AG062428 NIA NIH HHS R01 AG018016 NIA NIH HHS R01 AG060747 NIA NIH HHS R01 AG022374 NIA NIH HHS P50 AG023501 NIA NIH HHS U01 AG046152 NIA NIH HHS P30 AG010124 NIA NIH HHS U01 HG006375 NHGRI NIH HHS U01 HL096812 NHLBI NIH HHS R01 NS017950 NINDS NIH HHS RC2 AG036528 NIA NIH HHS P30 AG028377 NIA NIH HHS U54 HG003067 NHGRI NIH HHS P50 AG005142 NIA NIH HHS HHSN268201100010C NHLBI NIH HHS R01 AG035137 NIA NIH HHS R01 AG009029 NIA NIH HHS P50 AG005131 NIA NIH HHS R01 NS069719 NINDS NIH HHS R01 AG015928 NIA NIH HHS P01 NS026630 NINDS NIH HHS P50 AG005128 NIA NIH HHS P30 AG010133 NIA NIH HHS U24 AG021886 NIA NIH HHS R01 AG031581 NIA NIH HHS R01 AG009956 NIA NIH HHS HHSN268201100008C NHLBI NIH HHS U01 HL080295 NHLBI NIH HHS HHSN268201500001C NHLBI NIH HHS P50 AG016574 NIA NIH HHS P50 AG005146 NIA NIH HHS HHSN268201100005G NHLBI NIH HHS U01 AG049507 NIA NIH HHS U01 HL096917 NHLBI NIH HHS HHSN268201100008I NHLBI NIH HHS U01 AG052411 NIA NIH HHS RC2 AG036650 NIA NIH HHS R01 AG019085 NIA NIH HHS U01 AG032984 NIA NIH HHS U01 HG008657 NHGRI NIH HHS U01 HL130114 NHLBI NIH HHS HHSN268201100007C NHLBI NIH HHS R01 AG013616 NIA NIH HHS P30 AG062421 NIA NIH HHS R01 AG030146 NIA NIH HHS HHSN268200800007C NHLBI NIH HHS U01 AG024904 NIA NIH HHS NU38 CK000480 CDC HHS P30 AG035982 NIA NIH HHS P50 AG008702 NIA NIH HHS UL1 RR029893 NCRR NIH HHS HHSN268201100011I NHLBI NIH HHS HHSN268201100011C NHLBI NIH HHS RF1 AG054074 NIA NIH HHS U01 AG016976 NIA NIH HHS P50 NS039764 NINDS NIH HHS P01 AG003991 NIA NIH HHS P30 AG008051 NIA NIH HHS P50 AG005681 NIA NIH HHS RC2 AG036502 NIA NIH HHS P01 AG026276 NIA NIH HHS R01 AG017917 NIA NIH HHS RC2 HG005605 NHGRI NIH HHS P50 AG047270 NIA NIH HHS R56 AG051876 NIA NIH HHS P30 AG062429 NIA NIH HHS U01 HL096902 NHLBI NIH HHS P30 AG013846 NIA NIH HHS R01 MH080295 NIMH NIH HHS R01 AG026390 NIA NIH HHS R01 AG028786 NIA NIH HHS KL2 RR024151 NCRR NIH HHS N01HC55222 NHLBI NIH HHS U54 HG003273 NHGRI NIH HHS R01 AG049607 NIA NIH HHS UF1 AG047133 NIA NIH HHS U01 AG057659 NIA NIH HHS RF1 AG054023 NIA NIH HHS P50 AG005136 NIA NIH HHS P30 AG049638 NIA NIH HHS P30 AG012300 NIA NIH HHS N01HC85086 NHLBI NIH HHS R01 HL105756 NHLBI NIH HHS P30 AG062422 NIA NIH HHS R01 AG037985 NIA NIH HHS U19 AG024904 NIA NIH HHS R01 AG015473 NIA NIH HHS U01 DK066134 NIDDK NIH HHS P50 AG016573 NIA NIH HHS RF1 AG051504 NIA NIH HHS R01 AG012101 NIA NIH HHS P50 AG047266 NIA NIH HHS RF1 AG058066 NIA NIH HHS HHSN268201100006C NHLBI NIH HHS P50 AG016570 NIA NIH HHS P50 AG005134 NIA NIH HHS P30 AG008017 NIA NIH HHS R01 AG042437 NIA NIH HHS U24 AG041689 NIA NIH HHS P01 AG019724 NIA NIH HHS HHSN268201200036C NHLBI NIH HHS P30 AG010161 NIA NIH HHS R01 AG033193 NIA NIH HHS P50 AG025688 NIA NIH HHS HHSN268201100005I NHLBI NIH HHS R01 AG032990 NIA NIH HHS R37 AG015473 NIA NIH HHS U24 AG026395 NIA NIH HHS U01 NS041588 NINDS NIH HHS R01 NS080820 NINDS NIH HHS HHSN268201500001I NHLBI NIH HHS U01 AG049508 NIA NIH HHS P50 AG008012 NIA NIH HHS U01 AG052410 NIA NIH HHS R01 CA129769 NCI NIH HHS U01 HL096814 NHLBI NIH HHS P50 AG005133 NIA NIH HHS U01 AG010483 NIA NIH HHS P01 AG002219 NIA NIH HHS U01 AG006781 NIA NIH HHS R01 AG041797 NIA NIH HHS P50 AG005144 NIA NIH HHS K23 AG030944 NIA NIH HHS RC4 AG039085 NIA NIH HHS U01 AG062602 NIA NIH HHS P01 AG010491 NIA NIH HHS R01 NS029993 NINDS NIH HHS P50 AG005138 NIA NIH HHS R01 AG048927 NIA NIH HHS U01 AG052409 NIA NIH HHS R01 AG033040 NIA NIH HHS RF1 AG054052 NIA NIH HHS R01 AG021547 NIA NIH HHS R01 AG041232 NIA NIH HHS U54 HG003079 NHGRI NIH HHS R01 AG037212 NIA NIH HHS R01 AG019757 NIA NIH HHS R01 AG020688 NIA NIH HHS R01 AG022018 NIA NIH HHS U01 AG046139 NIA NIH HHS R01 AG020098 NIA NIH HHS N01HC85082 NHLBI NIH HHS R01 HL070825 NHLBI NIH HHS N01HC85083 NHLBI NIH HHS P20 MD000546 NIMHD NIH HHS R01 AG027944 NIA NIH HHS HHSN268201100005C NHLBI NIH HHS N01HC25195 NHLBI NIH HHS R01 AG017173 NIA NIH HHS R01 AG025259 NIA NIH HHS R01 AG030653 NIA NIH HHS HHSN268201100009C NHLBI NIH HHS P50 AG047366 NIA NIH HHS U01 HL096899 NHLBI NIH HHS HHSN268201100007I NHLBI NIH HHS P30 AG062715 NIA NIH HHS RF1 AG015473 NIA NIH HHS U01 AG049506 NIA NIH HHS U01 HG004610 NHGRI NIH HHS R01 AG021136 NIA NIH HHS P30 AG010129 NIA NIH HHS Wellcome Trust R01 AG011101 NIA NIH HHS P30 AG019610 NIA NIH HHS P50 AG016582 NIA NIH HHS R01 AG066206 NIA NIH HHS R01 AG041718 NIA NIH HHS R01 AG017919 NIA NIH HHS P30 AG072947 NIA NIH HHS N01HC85079 NHLBI NIH HHS R01 AG023629 NIA NIH HHS R01 AG031272 NIA NIH HHS P30 AG028383 NIA NIH HHS N01HC85080 NHLBI NIH HHS R01 AG026916 NIA NIH HHS P50 AG033514 NIA NIH HHS R01 NS059873 NINDS NIH HHS R01 AG011380 NIA NIH HHS P50 NS071674 NINDS NIH HHS R01 AG036836 NIA NIH HHS RF1 AG058267 NIA NIH HHS R01 AG015819 NIA NIH HHS N01HC85081 NHLBI NIH HHS U01 AG049505 NIA NIH HHS Collapse

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Challenges at the APOE locus: a robust quality control approach for accurate APOE genotyping. Alzheimers Res Ther 2022;14:22. [PMID: 35120553 PMCID: PMC8815198 DOI: 10.1186/s13195-022-00962-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/12/2022] [Indexed: 04/22/2023]

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.

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