Direct single cancer cell to normal cell comparison . To validate and further explore this proposition , we performed single - cell RNA - sequencing ( scRNA - seq ) analysis ( 10x Genomics ) of diagnostic specimens from six infants with KMT2A - rearranged infant B - ALL , including a relapse presentation ( case 3 ) and additional day 8 specimens from responding ( case 1 ) and nonresponding ( case 2 ) patients . We compared these to four other leukemias : NUTM1 - rearranged infant B - ALL ( n = 1 ) , KMT2A - rearranged infant AML ( n = 1 ) , megakaryoblastic neonatal AML ( n = 1 ) and childhood ETV6 - RUNX1 B - ALL ( a common subtype of standard - risk childhood B - ALL ; n = 1 ) ( Supplementary Table 3 ) . From these 12 diagnostic leukemia samples , we obtained a total of 30,242 cells , including 23,286 cancer cells that we identified based on gene expression matching patient - specific diagnostic flow cytometric profiles ( Supplementary Table 4 and Extended Data Fig . 2 ) . Using a published cell - matching method based on logistic regression 12,16 , we directly compared leukemia transcriptomes with mRNA profiles of human fetal bone marrow cells to determine which normal cell type the cancer cells most closely matched . We found that KMT2A - rearranged infant B lymphoblasts overwhelmingly resembled ELP cells at diagnosis and relapse and in nonresponding disease ( Fig . 2a - c ) . By contrast , non - ELP cell signals predominated in other types of leukemia , precisely as predicted from the We assessed the differentiation state of KMT2A - rearranged infant ALL by measuring signals of human fetal bone marrow cell types across the entire spectrum of childhood leukemia in data derived from two different cohorts ( St Jude 's and TARGET ) . We then validated cell signals by single - cell mRNA sequencing for direct comparison of cancer and normal cells . b , Heatmap showing mean cell signals of human fetal bone marrow cells ( y axis ) in human leukemia bulk transcriptomes subdivided by genetic subtype ( see labels underneath , KMT2A rearrangements shown in red text ) , age ( gray circle , infant ; black circle , noninfant ) and source ( S , St Jude 's ; T , TARGET ) . Numbers next to labels refer to case load per subtype . Subtypes with only one case were excluded from analysis . baso , basophil ; CMP , common myeloid progenitor ; Eo , eosinophil ; LMPP , lymphoid - primed multipotent progenitor ; MEM progen . , ; MK , megakaryocyte ; mono . , monocyte ; MOP , monocyte progenitor ; MPP , multipotent progenitor ; Neut . , neutrophil ; NK , natural killer ; Promono . , promonocyte . c , Top : box and whisker plots showing proportional contribution of signals ( lymphomyeloid - primed progenitor , ELP and later B - cell stages combined ( i.e. , pre-/pro - B , pro - B , pre - B and naive B ) ) to the transcriptome of leukemias ( see x axis labels ) . Bottom : box and whisker plots summarizing the ratio of ELP to later B - cell stage signals . Center lines represent the median , box limits represent 25%/75 % quartiles and whiskers represent minimum/ maximum ( top ) and 1.5× interquartile range ( bottom ) . n is the number of biologically independent variables , as listed below each group of plots . Risk refers to the clinical cytogenetic risk as defined in the protocol of the current European ALL trial ' ALLTogether ' ( EudraCT 2018 - 001795 - 38 ) .