The evolution of relapse of adult T cell acute lymphoblastic leukemia

Table 1 Summary of ALL cohorts analyzed

ALL subtype cohort name	Subtype cohort information	Source^{^}	Sequencing	Type	Num. patients
DUX4-ERG	Rearrangement and overexpression of DUX4 and transcriptional deregulation or deletion of the transcription factor gene ERG	St. Jude	WGS	B-ALL	30
Infant MLL-R	Infant patients with a fusion of the N-terminus of the MLL gene with the C-terminus of a partner gene	St. Jude	WGS	B-ALL	21
Ph positive	Patients with the “Philadelphia” chromosome present a translocation of chromosomes 9 and 22. This translocation creates the BCR-ABL fusion	St. Jude	WGS	B-ALL	11
Ph-like	Cell gene expression profile of the lymphoblasts of Ph-like ALL is similar to that of Ph positive ALL; however, they do not present BCR-ABL1 rearrangement	St. Jude	WGS	B-ALL	18
Hyperdiploid	Hyperdiploid patients are characterized by multiple chromosomal gains	St. Jude	WGS	B-ALL	40
Hypodiploid	Hypodiploid patients are characterized by chromosomal losses	St. Jude	WGS	B-ALL	22
iAMP21	Patients with intrachromosomal amplification of chromosome 21	St. Jude	WGS	B-ALL	12
T-ALL Zhang	Patients with T cell ALL from Zhang et al. [5] Nat Gen	St. Jude	WGS	T-ALL	13
T-ALL Oshima	Patients with T cell ALL from Oshima et al. [30] PNAS	Columbia University	WXS	T-ALL	31*
B-ALL Oshima	Patients with B cell ALL from Oshima et al. [30] PNAS (B cell lineage subtype unspecified)	Columbia University	WXS	B-ALL	24*
T-ALL Li^#	Patients with T cell ALL from Li et al. [37] Blood	St. Jude	WGS	T-ALL	16*
T-ALL in-house	In-house cohort	In-house	WGS	T-ALL	19*

WGS whole-genome sequencing, WXS whole-exome sequencing
*Cohorts with primary and relapsed paired samples
^#Mutations called by the authors of the original analysis; in all other cohorts, a uniform mutation calling pipeline was applied
^{^}Source: St. Jude cohorts were defined according to their ALL subtype in different publications (see the “Methods” section) except for the T-ALL pediatric cohort from Li et al. [37]

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