APOE and Huntington disease: PDYN showed the highest individual discriminatory ability for distinguishing late HD from early/mid HD individuals (Supplementary Table 4, AUC = 0.84, 95% CI: 0.61–1.00, P = 0.021), whereas we identified five unique combinations of five CSF proteins that perfectly classified individuals with late HD and early/mid HD, including combination 5A: CNR1, PPP1R1B, BDNF, APOE and IGHG1 (Fig. 3E, AUC = 1).