To determine whether distinctive Hh pathway gene expression patterns predict CML progression, we utilized RNA-seq to compare expression levels of 41 a priori selected Hh pathway genes [19-21,45,46] in chronic phase (CP, n = 8), blast crisis (BC, n = 9), normal cord blood (CB, n = 3) and normal peripheral blood (NPB, n = 3) FACS-purified CD34+CD38+Lin− progenitors (Additional file 1: Table S1 and S2). Here, CD38 is linked to chronic myelogenous leukemia, BCR-ABL1 positive.