Table 2.

Single nucleotide variants (SNVs) detected by whole exome sequencing (WES) and targeted deep sequencing (TDS) in diagnosis/pre-treatment samples and in the last available FU sample.

UPN	Gene	Chr	Transcript	Type of Alteration	Variant	Aminoacid Change	VAF (%)
							WES DX/PRE	TDS DX/PRE	TDS FU
P1	CUX1	7	NM_001202543	Stopgain SNV	c.3019C>T	p.Arg1007 *	3
	SETBP1	18	NM_015559	Non-synonymous SNV	c.2612T>C	p.Ile871Thr	15	14	17
	MAP7D2	X	NM_001168465	Non-synonymous SNV	c.116A>G	p.Asn39Ser	24
	TENM1	X	NM_014253	Non-synonymous SNV	c.3857G>T	p.Cys1286Phe	27
	LRTOMT	11	NM_001145310	Non-synonymous SNV	c.671G>A	p.Arg224His	34
	CCDC168	13	NM_001146197	Non-synonymous SNV	c.122A>C	p.Gln41Pro	34
	TP53	17	NM_001126115	Non-synonymous SNV	c.448C>T	p.Arg150Trp	39	38	42
	NUP93	16	NM_001242795	Non-synonymous SNV	c.473C>A	p.Ala158Asp	40
	UNC79	14	NM_020818	Non-synonymous SNV	c.7055T>A	p.Val2352Glu	44
P2	LRRC45	17	NM_144999	Non-synonymous SNV	c.1670A>G	p.Glu557Gly	7
	CRIPAK	4	NM_175918	Non-synonymous SNV	c.25A>C	p.Asn9His	7
	CACHD1	1	NM_020925	Non-synonymous SNV	c.1161G>T	p.Arg387Ser	9
	IL21R	16	NM_181078	Non-synonymous SNV	c.179A>G	p.Asp60Gly	27
	SF3B1	2	NM_012433	Non-synonymous SNV	c.2098A>G	p.Lys700Glu	40	39	43
	YLPM1	14	NM_019589	Stopgain SNV	c.4087C>T	p.Arg1363 *	46
P3	CGNL1	15	NM_001252335	Non-synonymous SNV	c.3481C>A	p.Arg1161Ser	7
	IBSP	4	NM_004967	Non-synonymous SNV	c.231G>T	p.Glu77Asp	8
	SLC22A12	11	NM_144585	Non-synonymous SNV	c.232C>T	p.Pro78Ser	14
	TRIM24	7	NM_015905	Non-synonymous SNV	c.263A>G	p.Tyr88Cys	14
	SETD2	3	NM_014159	Non-synonymous SNV	c.6197A>G	p.Asp2066Gly	21
	FAT1	4	NM_005245	Non-synonymous SNV	c.1507G>A	p.Ala503Thr	23
	TCHH	1	NM_007113	Non-synonymous SNV	c.3770A>G	p.Gln1257Arg	28
	PPM1D	17	NM_003620	Stopgain SNV	c.1434C>A	p.Cys478 *	29
	SS18L1	20	XM_005260390	Non-synonymous SNV	c.604A>G	p.Ser202Gly	29
P4	TP53	17	NM_001276761	Non-synonymous SNV	c.283T>C	p.Phe95Leu	ND	ND	7
	SCUBE1	22	NM_173050	Non-synonymous SNV	c.1700C>T	p.Ala567Val	8
	BMP7	20	NM_001719	Non-synonymous SNV	c.908G>A	p.Arg303His	14
	NUP85	17	NM_024844	Non-synonymous SNV	c.877G>C	p.Ala293Pro	17
	DNMT3B	20	NM_006892	Splicing variant	c.1906-1G>T	NA	21

SNVs in bold were selected for single cell analysis. Abbreviations: Chr: chromosome; DX: diagnosis; FU: follow-up; ND: not detected; PRE: pre-treatment; SNV: single nucleotide variant; TDS: targeted deep sequencing; UPN: unique patient number; VAF: variant allele frequency; WES: whole exome sequencing. * is to indicate that a stop codon is introduced.