Building upon recently characterized approaches to delineate all major immature hematopoietic compartments, we identified specific alterations in the composition of HSPC compartments in MDS with excess blasts and showed the aberrant expression of several markers including aldehyde dehydrogenase (ALDH), C-type lectin-like molecule-1 (CLL-1, also known as CLEC12A), CD13/CD33, CD44 and CD47 in a differentiation-stage specific manner. Here, CLEC12A is linked to myelodysplastic syndrome.