Clinical-grade whole-genome sequencing and 3′ transcriptome analysis of colorectal cancer patients

Table 2 List of potentially oncogenic structural variants in the cohort (DEL deletion, BND breakend translocation, INV inversion, DUP duplication)

Gene	Consequence	Chromosome	Position	Ref	Alt
GNAM11	GNA11 i > HNRNPM i >	chr19	3109401	Intron	DEL
NRG1	NRG1 i > L3HYPDH i >	chr8	32154965	Intron	BND
SMAD4	MRO i < SMAD4 i <	chr18	51065790	Intron	INV
PTPRK	MAN1A1 i > PTPRK i >	chr6	128452884	Intron	DUP
IDH1	VRK2 i < IDH1 i <	chr2	208257287	Intron	INV
IDH1	IDH1 e < PTH2R i <	chr2	208242100	Exon	INV
CDK6	CDK14 i > CDK6 e >	chr7	92612231	Exon	INV
CDK6	CDK14 i > CDK6 e >	chr7	92612048	Exon	INV
SRGAP3	LMCD1-AS1 i < SRGAP3 i <	chr3	9168820	Intron	DEL
NGR1	LDAH i > NGR1 i >	chr8	32654703	Intron	BND
NRG1	LDAH i < NGR1 i <	chr8	32654498	Intron	BND
KAT6B	RBMS3 i > KAT6B e >	chr10	75031261	Exon	BND
FAM46C	MAN1A2 i > FAM46C i >	chr1	117619648	Intron	DEL
SMAD4	CTIF i < SMAD4 i <	chr18	51062229	Intron	DUP
RARA	RARA i < TTC25 i <	chr17	40354212	Intron	DUP
NRG1	NRG1 i < UNC5D I <	chr8	32192673	Intron	DUP
CDK12	FBX047 i < CDK12 i <	chr17	39521585	Intron	INV
CDK12	PLXDC1 i > CDK12 i >	chr17	39465725	Intron	INV
ERBB2	ERBB2 e > HAP1 e >	chr17	39727989	Exon	INV
ZNF521	MCHR2-AS1 i < ZNF521 i <	chr18	25327550	Intron	BND
PPP6C	SCAI i < PPP6C i <	chr9	125174,977	Intron	DEL
EML4	EML4 i > MTA3 i >	chr2	42,284332	Intron	DEL
BRD4	BRD4 i < AKAP8 e <	chr19	15332325	Intron	DEL
KMT2C	KMT2C i <TPTEP1 i <	chr7	1522434118	Intron	BND
CCDC6	TMEM212-AS1 i < CCDC6 e <	chr10	59788825	Exon	BND
CCDC6	TMEM212-AS1 i > CCDC6 e >	chr10	59906506	Exon	BND
BRAF	DLG1 i > BRAF e >	chr7	140794385	Exon	BND
GPHN	GPHN i > FAM71D i >	chr14	66721301	Intron	DEL
ELL	RFX2 i < ELL i <	chr19	18478021	Intron	DEL

ISSN: 1756-994X