Exome sequencing identifies novel AD-associated genes
Holstege H., Hulsman M., Charbonnier C., Grenier-Boley B., Quenez O., Grozeva D., van Rooij JGJ., Sims R., Ahmad S., Amin N., Norsworthy P., Dols-Icardo O., Hummerich H., Kawalia A., Amouyel P., Beecham G., Berr C., Bis J., Boland A., Bossù P., Bouwman F., Campion D., Daniele A., Dartigues J-F., Debette S., Deleuze J-F., Denning N., DeStefano A., Farrer L., Fox N., Galimberti D., Genin E., Haines J., Holmes C., Ikram A., Ikram K., Jansen I., Kraaij R., Lathrop M., Lemstra E., Lleó A., Luckcuck L., Marshall R., Martin E., Masullo C., Mayeux R., Mecocci P., Meggy A., Mol M., Morgan K., Nacmia B., Naj A., Pastor P., Pericak-Vance M., Raybould R., Redon R., Richard A-C., Riedel-Heller S., Rivadeneira F., Rousseau S., Ryan N., Saad S., Sanchez-Juan P., Schellenberg G., Scheltens P., Schott J., Seripa D., Spalleta G., Tijms B., Uitterlinden A., van der Lee S., Wagner M., Wallon D., Wang L-S., Zarea A., Reinders MJT., Clarimon J., van Swieten J., Hardy J., Ramirez A., Mead S., van der Flier W., van Duijn C., Williams J., Nicolas G., Bellenguez C., Lambert J-C.
Background With the development of next-generation sequencing technologies, it is possible to identify rare genetic variants that influence the risk of complex disorders. To date, whole exome sequencing (WES) strategies have shown that specific clusters of damaging rare variants in the TREM2, SORL1 and ABCA7 genes are associated with an increased risk of developing Alzheimer’s Disease (AD), reaching odds ratios comparable with the APOE-ε4 allele, the main common AD genetic risk factor. Here, we set out to identify additional AD-associated genes by an exome-wide investigation of the burden of rare damaging variants in the genomes of AD cases and cognitively healthy controls. Method We integrated the data from 25,982 samples from the European ADES consortium and the American ADSP consortium. We developed new techniques to homogenize and analyze these data. Carriers of pathogenic variants in genes associated with Mendelian inheritance of dementia were excluded. After quality control, we used 12,652 AD cases and 8,693 controls for analysis. Genes were analyzed using a burden analysis, including both non-synonymous and loss-of-function rare variants, the impact of which was prioritized using REVEL. Result We confirmed that carrying rare protein-damaging genetic variants in TREM2, SORL1 or ABCA7 is associated with increased AD-risk. Moreover, we found that carrying rare damaging variants in the microglial ATP8B4 gene was significantly associated with AD, and we found suggestive evidence that rare variants in ADAM10, ABCA1, ORC6, B3GNT4 and SRC genes associated with increased AD risk. High-impact variants in these genes were mostly extremely rare and enriched in AD patients with earlier ages at onset. Additionally, we identified two suggestive protective associations in CBX3 and PRSS3 . We are currently replicating these associations in independent datasets. Conclusion With our newly developed homogenization methods, we identified novel genetic determinants of AD which provide further evidence for a pivotal role of APP processing, lipid metabolism, and microglia and neuroinflammatory processes in AD pathophysiology.