457: A deletion that raises Alzheimer risk, a duplication that lowers it

Quenez O et al., The American Journal of Human Genetics - Rare copy-number variants were called from 22,319 exomes covering early-onset Alzheimer disease, late-onset disease and unaffected controls, then tested gene by gene for a dosage effect. One locus came back with the cleanest signal in the field: at the central 22q11.21 region, deletions appeared only in early-onset cases, including one that arose de novo, while duplications piled up in controls, with late-onset cases sitting in between. Replication in nearly 400,000 further individuals confirmed it, and overexpressing SCARF2, one of the genes in the narrowed interval, increased amyloid-beta uptake in cells - the direction the protective duplications would predict. Key terms: copy-number variants, Alzheimer disease, 22q11.21, SCARF2, gene dosage. Study Highlights:The authors called rare copy-number variants from 22,319 harmonized exomes, comprising 4,150 early-onset Alzheimer cases at 65 years or younger, 8,519 late-onset cases and 9,650 unaffected controls, and found that early-onset cases carried an excess burden of rare CNVs affecting coding genes, driven particularly by deletions in genes already implicated in the disease. Pooling short truncating variants with deletions into a single loss-of-function analysis implicated ABCA1 with an odds ratio of 5.77 and ABCA7 deletions with an odds ratio of 2.29, and raised CTSB as a new candidate at an odds ratio of 5.03. An exome-wide gene-level dosage analysis then flagged 18 genes across five loci below a 10 percent false discovery rate, of which the central 22q11.21 region stood out: deletions were restricted to early-onset cases and absent from all 9,559 controls, duplications were enriched in controls, and late-onset cases fell in between, a gradient the authors narrowed to the SCARF2-KLHL22-MED15 interval. Replication across 33,977 additional cases and 362,322 controls confirmed the association at exome-wide significance, with duplications carrying an odds ratio of 0.34 and a mega-analysis p value of 5.52 times ten to the minus seven. Transfecting SCARF2 into microglial cells significantly increased uptake of fluorescent amyloid-beta with a p value of 2.2 times ten to the minus five, while uptake of inert latex beads did not change, arguing the effect is specific rather than a general boost in cell appetite. Conclusion:The same stretch of chromosome 22 pushes Alzheimer risk in opposite directions depending on how many copies you carry: losing one raises risk, gaining one lowers it. Duplications of the central 22q11.21 region emerge as one of the strongest risk-decreasing genetic factors described so far in terms of effect size, behind only the ultra-rare Icelandic APP variant, and unlike that variant they are found across multiple ancestries. The authors are careful about what this does not mean: the deletions are extremely rare, protection is relative rather than absolute, and they show it directly by pointing to duplication carriers who developed late-onset disease anyway while carrying other risk factors. Power is the central constraint, because each genome carries hundreds of rare coding point variants but typically only one rare coding CNV, and the analysis was restricted to individuals of European ancestry. Music:Enjoy the music based on this article at the end of the episode. Article title:Exome analysis of 22,319 individuals links extremely rare copy-number variants and 22q11.21 dosage to Alzheimer risk First author:Quenez O Journal:The American Journal of Human Genetics DOI:10.1016/j.ajhg.2026.07.013 Reference:Quenez O, Schramm C, Cassinari K, Nicolas A, Groeneveld J, Huguet G, et al. Exome analysis of 22,319 individuals links extremely rare copy-number variants and 22q11.21 dosage to Alzheimer risk. The American Journal of Human Genetics. 2026;113(10):1-19. doi:10.1016/j.ajhg.2026.07.013 Li...