Contribution to Alzheimer's disease risk of rare variants in TREM2, SORL1, and ABCA7 in 1779 cases and 1273 controls
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We performed whole-exome and whole-genome sequencing in 927 late-onset Alzheimer disease (LOAD) cases, 852 early-onset AD (EOAD) cases, and 1273 controls from France. We assessed the evidence for gene-based association of rare variants with AD in 6 genes for which an association with such variants was previously claimed. When aggregating protein-truncating and missense-predicted damaging variants, we found exome-wide significant association between EOAD risk and rare variants in SORL1, TREM2, and ABCA7. No exome-wide significant signal was obtained in the LOAD sample, and significance of the order of 10-6 was observed in the whole AD group for TREM2. Our study confirms previous gene-level results for TREM2, SORL1, and ABCA7 and provides a clearer insight into the classes of rare variants involved. Despite different effect sizes and varying cumulative minor allele frequencies, the rare protein-truncating and missense-predicted damaging variants in TREM2, SORL1, and ABCA7 contribute similarly to the heritability of EOAD and explain between 1.1% and 1.5% of EOAD heritability each, compared with 9.12% for APOE ε4.
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SORL1 and ABCA7 carry numerous loss-of-function variants leading to strong increases in AD risk.
“both SORL1 and ABCA7 genes—already detected by GWAS—carried numerous loss-of-function variants leading to strong increases in AD risk [9, 98, 128].”
From The new genetic landscape of Alzheimer’s disease: from amyloid cascade to genetically driven synaptic failure hypothesis? (2019) · cites this paper as [9]
Sections 3.2 and 3.3 report numerous SORL1 and ABCA7 variants, and the Discussion reports elevated odds ratios for carriers of protein-truncating or strictly damaging variants in early-onset AD. But the paper only suggests that the damaging missense variants share a loss-of-function mechanism; it does not establish that all the counted variants are loss-of-function. It also says the association may be weaker in late-onset AD, so the unqualified claim about strong increases in AD risk overstates the finding. (LLM, conf=0.86)
Experimental — accuracy not yet measuredUsing a large whole-exome-sequencing study, ten genes located in genome-wide loci were identified as having rare deleterious coding, splicing or LOF burden associations with LOAD (FDR P < 0.01), including ABCA7, TREM2, SORL1, TREML4, TAP2, PSMB8, PIP, STYX, RIN3, and KCNH6.
“we also identified ten genes located in our genome-wide loci as having rare deleterious coding, splicing or LOF burden associations with LOAD (false discovery rate (FDR) P < 0.01), including previously implicated rare-variant signals in ABCA7, TREM2, and SORL1 (refs. 14,49–55), and additional associations with TREML4 in the TREM2 locus, TAP2 and PSMB8 in the HLA-DRB1 locus, PIP in the EPHA1 locus,”
From Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing (2019) · cites this paper as [52]
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Self-citation
- Authors
- Bellenguez, C., Charbonnier, C., Grenier-Boley, B., Quenez, O., Le Guennec, K., Nicolas, G., Chauhan, G., Wallon, D., Rousseau, S., Richard, A. C., Boland, A., Bourque, G., Munter, H. M., Olaso, R., Meyer, V., Rollin-Sillaire, A., Pasquier, F., Letenneur, L., Redon, R., Dartigues, J.-F., Tzourio, C., Frebourg, T., Lathrop, M., Deleuze, J.-F., Hannequin, D., Genin, E., Amouyel, P., Debette, S., Lambert, J.-C., Campion, D., Hannequin, D., Campion, D., Wallon, D., Martinaud, O., Zarea, A., Nicolas, G., Rollin-Sillaire, A., Bombois, S., Mackowiak, M.-A., Deramecourt, V., Pasquier, F., Michon, A., Le Ber, I., Dubois, B., Godefroy, O., Etcharry-Bouyx, F., Chauviré, V., Chamard, L., Berger, E., Magnin, E., Dartigues, J.-F., Auriacombe, S., Tison, F., Sayette, V. D. L., Castan, D., Dionet, E., Sellal, F., Rouaud, O., Thauvin, C., Moreaud, O., Sauvée, M., Formaglio, M., Mollion, H., Roullet-Solignac, I., Vighetto, A., Croisile, B., Didic, M., Félician, O., Koric, L., Ceccaldi, M., Gabelle, A., Marelli, C., Labauge, P., Jonveaux, T., Vercelletto, M., Boutoleau-Bretonnière, C., Castelnovo, G., Paquet, C., Dumurgier, J., Hugon, J., De Boisgueheneuc, F., Belliard, S., Bakchine, S., Sarazin, M., Barrellon, M.-O., Laurent, B., Blanc, F., Pariente, J., & Jurici, S.
- Affiliations
- Inserm (FR)
- Université de Bordeaux (FR)
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
- McGill University and Génome Québec Innovation Centre (CA)
- Centre National de la Recherche Scientifique (FR)
- Centre Hospitalier Universitaire Amiens-Picardie (FR)
- Centre National de Recherche en Génomique Humaine (FR)
- Centre Hospitalier du Rouvray (FR)
- Centre Hospitalier Universitaire de Montpellier (FR)
- ORCID
- Bellenguez, Céline
- Charbonnier, Camille
- Quenez, Olivier
- Chauhan, Ganesh
- Boland, Anne
- Bourque, Guillaume
- Olaso, Robert
- Meyer, Vincent
- Letenneur, Luc
- Redon, Richard
- Tzourio, Christophe
- Lathrop, Mark
- Deleuze, Jean-François
- Amouyel, Philippe
- Debette, Stéphanie
- Lambert, Jean-Charles
- Bombois, Stéphanie
- Deramecourt, Vincent
- Dubois, Bruno
- Godefroy, Olivier
- Tison, François
- Sayette, Vincent de la
- Rouaud, Olivier
- Moreaud, Olivier
- Sauvée, Mathilde
- Croisile, Bernard
- Didic, Mira
- Félician, Olivier
- Koric, Lejla
- Ceccaldi, Mathieu
- Gabelle, Audrey
- Labauge, Pierre
- Jonveaux, Thérèse
- Castelnovo, Giovanni
- Paquet, Claire
- Dumurgier, Julien
- Hugon, Jacques
- Belliard, Serge
- Sarazin, Marie
- Laurent, Bernard
- Blanc, Frédéric
- Pariente, Jérémie
- Jurici, Snejana
- Venue
- Neurobiology of Aging
- Publisher
- Elsevier BV
- Published
- 2017-11
- Volume
- 59
- Pages
- 220.e1-220.e9
- ISSN
- 0197-4580 (ISSN-L)
- OpenAlex
- W2735794637
- Cited by
- 166
- References
- 56
- Citations by year
- 2026: 8 · 2025: 13 · 2024: 20 · 2023: 14 · 2022: 29 · 2021: 24 · 2020: 13 · 2019: 28 · 2018: 16
- FWCI
- 11.53
- Type
- journal article
- Language
- en
- Open access
- green
- hal.science
- Licence
- Locations
- Neurobiology of Aging (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion, cc-by)
- HAL (submittedVersion)
- Funders
- France Génomique National infrastructure
- Centre National de Génotypage
- National Foundation for Alzheimer's disease and related disorders
- Institut Pasteur de Lille
- Inserm
- FRC
- Lille Métropole Communauté Urbaine council
- French government's LABEX
- Topics
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- Alzheimer's disease, rare variants, TREM2, SORL1, ABCA7, early-onset Alzheimer's disease, late-onset Alzheimer's disease, truncating mutations, missense mutations, genetic risk, heritability, APOE ε4, gene-based association
- MeSH terms
- Whole Genome Sequencing, Adult, Aged, Aged, 80 and over, Alzheimer Disease, Female, Humans, Male, Membrane Glycoproteins, Middle Aged, Receptors, Immunologic, Genetic Variation, ATP-Binding Cassette Transporters, Genetic Predisposition to Disease, LDL-Receptor Related Proteins, Membrane Transport Proteins, Apolipoprotein E4, Genome-Wide Association Study, Young Adult, Genetic Association Studies
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