Minimal residual disease assessed with deep sequencing of NPM1 mutations predicts relapse after allogeneic stem cell transplant in AML

Figures & data

Table 1. Patient and disease characteristics.

Characteristic		Characteristic cont.
Age, median (range)	49 (18-66)	T cell depletion (n)
Gender (male/female) (n)	22/7	ATG	16
NPM1 mutation (n)		No ATG	13
Type A/type B/unknown	25/1/3	Donor source (n)
Cytogenetic risk stratification (n)		HLA identical sibling	10
Favorable risk	10	Matched unrelated	19
Intermediate risk	18	Stem cell source (n)
Adverse risk	1	BM/PB	5/24
Relapse before alloHCT (n)		Outcome after alloHCT (n)
No relapse	21	Relapse	8
Relapse	8	No relapse Status at last contact (n)	21
Disease status at time of alloHCT (n)
CR	20	Alive	21
CRi	9	Dead	8
Conditioning intensity (n)
Myeloablative	19
Reduced intensity	10

alloHCT: allogeneic stem cell transplantation; ATG: anti-thymoglobulin; BM: bone marrow; CR: complete remission; CRi: complete remission with incomplete recovery; HLA: human leukocyte antigen; PB: peripheral blood.

Figure 1. Outcome for AML patients with pre- and/or post-transplant deep sequencing MRD measurements. (A) Mutation load at 1-month pre-transplant (n = 25), and 3 months post-transplant (n = 27) in patients in morphological remission at the time of alloHCT; divided into patients with or without subsequent relapse. Negative MRD was set to 0. (B) Individual patient relapse-free survival in relation to pre- and/or post-transplant deep sequencing MRD status (n = 32). For patients in morphological remission with NPM1 MRD positivity and negativity 3 months after alloHCT, Kaplan–Meier curves for RFS are shown in (C) and OS in (D). Cutoff for MRD positivity with deep sequencing was VAF 0.02%, as described in Methods. *p < .05.

Table 2. Patient characteristics by MRD group before and after alloHCT, only patients in CR included.

	Before alloHCT			After alloHCT
Characteristic	MRD^+ (n = 3)	MRD^− (n = 22)		MRD^+ (n = 5)	MRD^− (n = 22)
Age, median (range)	33 (30–46)	51.5 (18–66)	NS	41 (30–50)	51.5 (18–66)	NS
Sex
Male	0	5	NS	1	6	NS
Female	3	17		4	16
Cytogenetic risk stratification
Favorable risk	1	8	NS	1	8	NS
Intermediate risk	2	13		4	13
Adverse risk	0	1		0	1
FLT3-ITD status
Positive	2	12	NS	3	12	NS
Negative	1	10		2	10
Conditioning intensity
Myeloablative	2	15	NS	4	13	NS
Reduced intensity	1	7		1	9
T cell depletion
ATG	2	10	NS	4	12	NS
No ATG	1	12		1	10
Time of transplant
First remission	2	17	NS	3	16	NS
Second remission	1	5		2	6
Degree of complete remission
CR	1	15	NS	3	15	NS
CRi	2	7		2	7

ATG: anti-thymoglobulin: CR: complete remission; CRi: complete remission with incomplete recovery; FLT3-ITD: internal tandem duplication of the fms-related tyrosine kinase 3 gene; MRD⁺: minimal residual disease positive (VAF ≥0.02%); MRD^-: minimal residual disease negative (VAF <0.02%); NS: no significant difference.

Table 3. Multivariable Cox regression for RFS and OS after alloHCT.

	After alloHCT (n = 27)
	Relapse-free survival		Overall survival
	HR (95% CI)	p value	HR (95% CI)	p value
NPM1 MRD status	44.8 (1.6–1260.6)	.025	48.7 (1.9–1253.1)	.019
Age at SCT	1.0 (0.9–1.2)	.53	1.0 (0.9–1.1)	.80
FLT3-ITD status	0.6 (0.007-53.6)	.82	0.4 (0.07–28.6)	.70
Disease status at transplant
CR2 vs CR1	28.8 (0.26–3210.9)	.16	2.0 (0.03–150.4)	.75
CR vs CRi	0.67 (0.09–5.1)	.70	3.8 (0.17–84.1)	.40
Cytogenetic risk stratification
Intermediate vs favorable	17.4 (0.20–1523.4)	.26	19.5 (0.2–1889.8)	.20
Adverse vs favorable	7.0 (0.24–198.5)	.26	179.4 (0.2–153455.3)	.13
Conditioning intensity	0.3 (0.02–3.8)	.70	0.78 (0.05-11.7)	.85

CI: confidence interval; FLT3-ITD: internal tandem duplication of the fms-related tyrosine kinase 3 gene; CR: complete remission; CRi: complete remission with incomplete recovery; PD: progressive disease.