One proportionally increased population was a subset of microglia expressing GPNMB (Extended Data Fig. 8b), which has been identified as a marker of disease-associated microglia in transcriptomic studies of Alzheimer’s disease (AD)35,36 and was robust up to one-sixth of the original dataset size (Extended Data Fig. 8c). Here, GPNMB is linked to early-onset autosomal dominant Alzheimer disease.