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

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

Belloy, Michael E. (författare): Stanford Univ, Dept Neurol & Neurol Sci, Greicius Lab, 290 Jane Stanford Way, Stanford, CA 94304 USA.

Eger, Sarah J. (författare): Stanford Univ, Dept Neurol & Neurol Sci, Greicius Lab, 290 Jane Stanford Way, Stanford, CA 94304 USA.

Le Guen, Yann (författare): Stanford Univ, Dept Neurol & Neurol Sci, Greicius Lab, 290 Jane Stanford Way, Stanford, CA 94304 USA.

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Damotte, Vincent (författare): Univ Lille, Inst Pasteur Lille, U1167 RID AGE Facteurs Risque & Determinants Mol, INSERM,CHU Lille, Lille, France.

Ahmad, Shahzad (författare): ErasmusMC, Dept Epidemiol, Rotterdam, Netherlands.;Leiden Univ, Leiden Acad Ctr Drug Res, Div Syst Biomed & Pharmacol, Leiden, Netherlands.

Ikram, M. Arfan (författare): ErasmusMC, Dept Epidemiol, Rotterdam, Netherlands.

Ramirez, Alfredo (författare): Univ Cologne, Fac Med, Dept Psychiat & Psychotherapy, Div Neurogenet & Mol Psychiat, Cologne, Germany.;Univ Cologne, Univ Hosp Cologne, Cologne, Germany.;Univ Hosp Bonn, Med Fac, Dept Neurodegenerat Dis & Geriatr Psychiat, Bonn, Germany.;Dept Psychiat, San Antonio, TX USA.;Glenn Biggs Inst Alzheimers & Neurodegenerat Dis, San Antonio, TX USA.;German Ctr Neurodegenerat Dis DZNE, Bonn, Germany.;Univ Cologne, Cluster Excellence Cellular Stress Responses Agin, Cologne, Germany.

Tsolaki, Anthoula C. (författare): Aristotle Univ Thessaloniki, AHEPA Hosp, Dept Neurol 1, Athens, Greece.

Rossi, Giacomina (författare): Fdn IRCCS Ist Neurol Carlo Besta, Unit Neurol 5 & Neuropathol, Milan, Italy.

Jansen, Iris E. (författare): Vrije Univ Amsterdam, Alzheimer Ctr Amsterdam, Dept Neurol, Amsterdam UMC,Amsterdam Neurosci, Amsterdam, Netherlands.;Vrije Univ, Ctr Neurogen & Cognit Res, Amsterdam Neurosci, Dept Complex Trait Genet, Amsterdam, Netherlands.

de Rojas, Itziar (författare): Univ Int Catalunya, Res Ctr, ACE Alzheimer Ctr Barcelona, Barcelona, Spain.;Univ Int Catalunya, Memory Clin, ACE Alzheimer Ctr Barcelona, Barcelona, Spain.;Inst Salud Carlos III, Networking Res Ctr Neurodegenerat Dis CIBERNED, Madrid, Spain.

Parveen, Kayenat (författare): Univ Cologne, Fac Med, Dept Psychiat & Psychotherapy, Div Neurogenet & Mol Psychiat, Cologne, Germany.;Univ Cologne, Univ Hosp Cologne, Cologne, Germany.;Univ Hosp Bonn, Med Fac, Dept Neurodegenerat Dis & Geriatr Psychiat, Bonn, Germany.

Sleegers, Kristel (författare): VIB, Ctr Mol Neurol, Complex Genet Alzheimers Dis Grp, Antwerp, Belgium.;Univ Antwerp, Dept Biomed Sci, Antwerp, Belgium.

Ingelsson, Martin (författare): Uppsala universitet,Geriatrik

Hiltunen, Mikko (författare): Univ Eastern Finland, Inst Biomed, Yliopistonranta 1E, Kuopio 70211, Finland.

Amin, Najaf (författare): ErasmusMC, Dept Epidemiol, Rotterdam, Netherlands.;Univ Oxford, Nuffield Dept Populat Hlth, Oxford, England.

Andreassen, Ole (författare): Oslo Univ Hosp, NORMENT Ctr, Div Mental Hlth & Addict, Oslo, Norway.;Univ Oslo, Inst Clin Med, Oslo, Norway.

Sánchez-Juan, Pascual (författare): Natl Inst Hlth Carlos III, Network Ctr Biomed Res Neurodegenerat Dis, CIBERNED, Madrid, Spain.;Univ Cantabria, Neurol Serv, Marques de Valdecilla Univ Hosp, Santander, Spain.;IDIVAL, Santander, Spain.

Kehoe, Patrick (författare): Univ Bristol, Bristol Med Sch, Translat Hlth Sci, Bristol, Avon, England.

Amouyel, Philippe (författare): Univ Lille, Inst Pasteur Lille, U1167 RID AGE Facteurs Risque & Determinants Mol, INSERM,CHU Lille, Lille, France.

Sims, Rebecca (författare): Cardiff Univ, Sch Med, Div Psychol Med & Clin Neurosci, Cardiff, S Glam, Wales.

Frikke-Schmidt, Ruth (författare): Copenhagen Univ Hosp, Dept Clin Biochem, Rigshosp, Copenhagen, Denmark.;Univ Copenhagen, Dept Clin Med, Copenhagen, Denmark.

van der Flier, Wiesje M. (författare): Vrije Univ Amsterdam, Alzheimer Ctr Amsterdam, Dept Neurol, Amsterdam UMC,Amsterdam Neurosci, Amsterdam, Netherlands.

Lambert, Jean-Charles (författare): Univ Lille, Inst Pasteur Lille, U1167 RID AGE Facteurs Risque & Determinants Mol, INSERM,CHU Lille, Lille, France.

He, Zihuai (författare): Stanford Univ, Dept Neurol & Neurol Sci, Greicius Lab, 290 Jane Stanford Way, Stanford, CA 94304 USA.;Stanford Univ, Dept Med, Quantitat Sci Unit, Stanford, CA 94304 USA.

Han, Summer S. (författare): Stanford Univ, Dept Med, Quantitat Sci Unit, Stanford, CA 94304 USA.;Stanford Univ, Dept Neurosurg, Stanford, CA 94304 USA.

Napolioni, Valerio (författare): Univ Camerino, Sch Biosci & Vet Med, I-62032 Camerino, Italy.

Greicius, Michael D. (författare): Stanford Univ, Dept Neurol & Neurol Sci, Greicius Lab, 290 Jane Stanford Way, Stanford, CA 94304 USA.

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Stanford Univ, Dept Neurol & Neurol Sci, Greicius Lab, 290 Jane Stanford Way, Stanford, CA 94304 USA Univ Lille, Inst Pasteur Lille, U1167 RID AGE Facteurs Risque & Determinants Mol, INSERM,CHU Lille, Lille, France. (creator_code:org_t)

2022-02-04
2022
Engelska.
Ingår i: Alzheimer's Research & Therapy. - : Springer Nature. - 1758-9193. ; 14:1

Relaterad länk:: https://doi.org/10.1...; visa fler...; https://uu.diva-port... (primary) (Raw object); https://alzres.biome...; https://urn.kb.se/re...; https://doi.org/10.1...; visa färre...

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

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