Table 1

Results of next generation gene sequencing before imatinib treatment. PRKG2-PDGFRA translocation with 33.6% variant allele frequency and breakpoints at exon 10 of PRKG2 and exon 12 of PDGFRA.

A. Annotated variants TRANSLOCATION:
GeneA	GeneB		cnt_ReadA		cnt_ReadB		Total_read	ChrA	ChrB		Read.posA			Read.posB		Direction
PDGFRA	PRKG2		154		129		283	chr4:55141064	chr4:82065407		NM_006206_Exon(12/23)_Frame(0,1)			NM_006259_Exon(10/19)_Frame(2,2)		PRKG2→PDGFRA
B. Known variants SNV:
Gene	RefseqID	Exon		DNAchange		AAchange		Func		ChrPos	Read depth	VAF	COSMIC		dbSNP
MKI67	NM_002417	exon14		c.9670C>T		p.R3224W		nonsynonmous SNV		chr10:129899557	1746	42.55%	COSM916078		rs754802357
MCU2	NM_002457	exon30		c.5356A>C		p.K1786Q		nonsynonmous SNV		chr11:1093537	697	8.03%	COSM4145288		rs80200693
LRRK2	NM_198578	exon11		c.1256C>T		p.A419V		nonsynonmous SNV		chr12:40646786	1020	44.41%	COSM147473		rs34594498
BCL7A	NM_020993	exon4		c.359A>C		p.N120T		nonsynonmous SNV		chr12:122481879	724	46.55%	COSM5880386		rs34821485
WDR90	NM_145294	exon16		c.1804C>T		p.R602W		nonsynonmous SNV		chr16:705658	758	44.2%	COSM3273238		rs201699835
PALB2	NM_024675	exon4		c.925A>G		p.I309V		nonsynonmous SNV		chr16:23646942	1710	45.5%	COSM3957351		rs3809683
ZNF24	NM_006965	exon3		c.427C>T		p.L143F		nonsynonmous SNV		chr18:32919934	1054	43.93%	COSM5854150		rs148053646
INDEL:
Gene	RefseqID	Exon		DNAchange		AAchange		Func		ChrPos	Read depth	VAF	COSMIC		dbSNP
MSH6	NM_000179	exon10		c.4065_4066insTTGA		p.T1355fs		frameshift insertion		chr2:48033981	764	40.45%	COSM3186044		NA
C. Novel Variants SNV:
Gene	RefseqID	Exon		DNAchange		AAchange		Func		ChrPos	Read depth	VAF	COSMIC		dbSNP
SDHC	NM_003001	exon2		c.25G>A		p.V9I		nonsynonmous SNV		chr1:161293408	689	55.15%			rs774768866
ALK	NM_004304	exon18		c.3035C>T		p.T1012M		nonsynonmous SNV		chr2:29449820	1332	46.1%			rs35073634
ERBB4	NM_005235	exon24		c.2935C>G		p.R979G		nonsynonmous SNV		chr2:212286761	1177	45.2%			rs574197848
BARD1	NM_000465	exon4		c.722C>G		p.S241C		nonsynonmous SNV		chr2:215645876	2397	46.06%			rs3738885
HIST1H2BJ	NM_021058	exon1		c.215A>G		p.E72G		nonsynonmous SNV		chr6:27100315	1660	47.89%			NA
KDM4C	NM_015061	exon18		c.2447G>A		p.R816Q		nonsynonmous SNV		chr9:7103707	1055	44.36%			rs180710573
ABL1	NM_007313	exon10		c.1601T>C		p.V534A		nonsynonmous SNV		chr9:133755917	559	40.97%			rs776483252
NUP98	NM_016320	exon11		c.1192A>G		p.S398G		nonsynonmous SNV		chr11:3774621	937	46.42%			rs144302699
PTPRO	NM_030667	exon17		c.2648A>T		p.Y895F		nonsynonmous SNV		chr12:15713183	1553	49.45%			rs759525747
FANCA	NM_000135	exon42		c.4232C>T		p.P1411L		nonsynonmous SNV		chr16:89805318	1230	45.61%			rs201494304
GTSE1	NM_016426	exon9		c.1688G>C		p.R563T		nonsynonmous SNV		chr22:46722515	1135	47.84%			rs760482340
PCLO	NM_033026	exon2		c.1561C>G		p.P521A		nonsynonmous SNV		chr7:82784396	618	14.24%			NA

Blood Res 2022;57:69~74 https://doi.org/10.5045/br.2022.2021138