Identification of genetic variants associated with skeletal muscle function deficit in childhood acute lymphoblastic leukemia survivors

Figures & data

Table 1 Cohort characteristics and distribution of study outcomes

	Category	Overall count (%)
Sex	Female	124 (51.2)
	Male	118 (48.8)
Age at PETALE investigation visit (years)	Median (range)	21.92 (9 - 41)
Age at Dx (years)	Median (range)	4.00 (0-18)
Time since end of Tx (years)	Median (range)	13.06 (4-26)
Risk level	Standard	111 (45.9)
	High	131 (54.1)
DFCI Protocol	DFCI 87-01	20 (8.3)
	DFCI 91-01	48 (19.8)
	DFCI 95-01	71 (29.3)
	DFCI 2000-01	77 (31.8)
	DFCI 2005-01	26 (10.7)
MTX Cumulative (mg/m^2)	Median (range)	6723 (1004-12999)
GC Cumulative dose (Pred. Eq. mg/m^2)	Median (range)	9025(4078-30210)
CRT	No	99 (40.9)
	Yes	143 (59.1)
BMI category at visit^a	Normal	163 (67.4)
	Overweight	46 (19.0)
	Obese	33 (13.6)
Fmax	Average Z-score (range)	-0.86 (-5.64 - 2.03)
	Z-score ≤ -1 SD	96 (39.7)
	Z-score ≤ -2 SDs	32 (13.2)
	Missing	27 (11.2)
Pmax	Average Z-score (range)	-1.45 (-7.30 - 1.36)
	Z-score ≤ -1SD	133 (55.0)
	Z-score ≤ -2 SDs	65 (26.9)
	Missing	16 (6.6)

Notes: ^a Normal ≤ 24.9 kg/m²; 25 kg/m² ≤ overweight <30 kg/m²; obese ≥ 30 kg/m².

Abbreviations: Dx, diagnosis; Tx, treatment; DFCI, Dana-Farber Cancer Institute; CRT, cranial radiation therapy; BMI, body mass index; MTX, methotrexate; GC, glucocorticoids.

Figure 1 Stratification result of association for DUOX2 rs2001616. Frequencies of AA and AG+GG genotypes (gray bars) and unaffected (black bars) individuals, as defined by Pmax Z≤−2 SD and Z>−2 SD, respectively. P-value with OR (odds radio) and 95% CI (confidence interval) is presented for each comparison. Number of patients in each genotype group is indicated in brackets with percentages. BMI; non obese: <30 kg/m², obese: ≥30 kg/m².

Figure 2 Stratification result of association for ADAMTS rs4127041. Frequencies of GG and GC+CC genotypes for affected (grey bars) and unaffected (black bars) individuals, as defined by Fmax Z≤−2 SD and Z>−2SD, respectively. P-value with OR (odds radio) and 95% CI (confidence interval) is presented for each comparison. Number of patients in each genotype group is indicated on each bar.

Table 2 Top-ranking common SNPs, genotyping data, and associated phenotypes

PHENOTYPE	GENE_SNP	COMPLICATION		MODEL	COMPLICATION		OR (95% - CI)	P VALUE
		Unaffected	Affected		Unaffected	Affected
Pmax (Z≤-2)	rs2001616DUOX2 A > G
	AA	135 (84.9%)	40 (62.5%)	AA	135 (84.9%)	40 (62.5%)	1	0.0002
	AG	20 (12.6%)	23 (35.9%)	AG + GG	24 (15.1%)	24 (37.5%)	3.4 (1.7 - 6.6)
	GG	4 (2.5%)	1 (1.6%)
Fmax (Z≤-2)	rs41270041ADAMTS4 G > C
	GG	146 (84.4%)	19 (65.5%)	GG	146 (84.4%)	19 (65.5%)	1	0.015
	GC	26 (15.0%)	10 (34.5%)	GC + CC	27 (15.6%)	10 (34.5%)	2.8 (1.2 - 6.8)
	CC	1 (0,6%)	0

Abbreviations: OR; odds ratio, CI; confidence interval.

Table 3 Regression model

Phenotype	Co-variable	B	P-value	OR (95%-CI)
Pmax (Z≤−2)	DUOX2	1.08	0.003	2.9 (1.4–6.1)
	Sex	0.87	0.009	2.4 (1.2–4.6)
	BMI at visit	0.61	0.004	1.8 (1.2–2.8)
	Risk	1.1	0.001	3.0 (1.5–5.9)

Notes: DUOX2 gene: dominant model (AG and GG vs AA). Sex: Females are compared to males; BMI: participants given normal (≤24.9 kg/m²), overweight (≥25 kg/m², <30 kg/m²), or obese status (≥30 kg/m²); risk: standard or high.

Table 4 Top-ranking rare SNPs, genotyping data, and associated phenotypes

Phenotype		Pmax^a		OR (95%-CI)	P-value
		Unaffected	Affected
Genotype	ALOX15 (rs113604586_rs11568142)
	No minor allele ≥1 minor allele	150 (100%) 0	57 (90.5%) 6 (9.5%)	-	0.001

Note: ^aAffected individuals have the Z score for Pmax ≤ −2.

Abbreviations: OR, odds ratio; CI, confidence interval is not calculated due to zero observation in one of cells.

Table S1 Top-ranking common SNPs, WES data

SNP	rs41270041	rs2001616
Gene	ADAMTS4	DUOX2
Locus	chr1: 161161284	chr15: 45404066
Genomic Location	Exon	Exon
Major allele > minor allele	G>C	A>G
MAF (%)	8.6	15.5
Role of protein connected with muscle metabolism	Degradation of aggrecan proteoglycan	Role in thyroid hormone synthesis
Associated Phenotype	Fmax (Z-score ≤ −2 SDs)	Pmax (Z-score ≤ −2 SDs)	Pmax (Z-score)
P-value	1.19×10^−4	1.02×10^−5	4.63×10^−5
Allelic Ratio	Affected:12/46	Affected: 33/83
	Unaffected:19/309	Unaffected: 24/214
Allelic OR (95%-CI)	4.24 (1.93–9.31)	3.55 (1.98–6.36)	NA

Abbreviations: MAF, minor-allele frequency; OR, Odds ratio; CI, confidence interval.

Table S2 Top-ranking rare SNPs, WES data

Gene		ALOX15
SNPs
	rs34210653	rs11568142	rs113604586
MAF (%)	1.61	0.78	0.23
Major allele > minor allele	G > A	C > G	T > C
Genomic location	Exon
Gene locus	17p13.2
Role of protein	Arachidonic acid metabolism pathway
Associated phenotype	Pmax (Z-score)
P -value	5.7x10^−6
Participants with > 1 minor allele	9 (4.05%)

Abbreviation: MAF; minor-allele frequency.

Table S3 Co-variable association with Pmax (Z-score ≤ −2)

Category	Group	Affected (%)	Unaffected (%)	P-value	OR (95%-CI)
Sex	Male	22 (20.4)	86 (79.6)	0.008	2.2 (1.2–4.1)
	Female	43 (33.9)	75 (63.6)
Risk level	Standard	17 (16.2)	88 (83.8)	0.0001	3.4 (1.8–6.4)
	High	48 (39.7)	73 (60.3)
MTX cumulative dose ^a (mg/m^2)	≤6723	40 (35.1)	74 (64.9)	0.03	0.5 (0.3–0.9)
	>6723	24 (21.8)	86 (78.2)
GC cumulative dose (pred. Eq. mg/m^2)	≤9025	23 (20.4)	90 (79.6)	0.006	2.3 (1.3–4.2)
	>9025	41 (36.9)	70 (63.1)
CRT	No	15 (16.3)	77 (83.7)	0.001	3.1 (1.6–5.9)
	Yes	50 (37.3)	84 (62.7)
BMI category at visit	Normal	31 (20.7)	119 (79.3)	0.001
	Overweight	21 (47.7)	23 (52.3)
	Obese	13 (40.6)	19 (59.4)

Note: aCumulative MTX and CS doses are recoded as below and above median.

Abbreviations: CRT, cranial radiation therapy; MTX, methotrexate; GC, glucocorticoids; BMI, body mass index.

Table S4 Association of risk groups with CRT and cumulative MTX and GC dose

	Risk			P-value
		Standard	High
CRT	No	90 (81.1%)	9 (6.9%)	1.3×10^−31
	Yes	21 (18.9%)	122 (93.1%)
MTX Cumulative^1 (mg/m^2)	≤6723	34 (30.6%)	86(66.4%)	2.6×10^−8
	>6723	77(69.4%)	43 (33.6%)
GC Cumulative (mg/m^2)	≤9025	106 (95.5%)	14 (10.9%)	4.5×10^−39
	>9025	5 (4.5%)	115 (89.1%)

Note: ¹Cumulative MTX and GC doses are recoded as above and below median.

Abbreviations: CRT, cranial radiation therapy; MTX, methotrexate; GC, glucocorticoids.