Whole genome sequencing reveals potential targets for therapy in patients with refractory KRASmutated metastatic colorectal cancer

Shanmugam, Vijayalakshmi; Ramanathan, Ramesh K; Lavender, Nicole A; Sinari, Shripad; Chadha, Manpreet; Liang, Winnie S; Kurdoglu, Ahmet; Izatt, Tyler; Christoforides, Alexis; Benson, Hollie; Phillips, Lori; Baker, Angela; Murray, Christopher; Hostetter, Galen; Von Hoff, Daniel D; Craig, David W; Carpten, John D

doi:10.1186/1755-8794-7-36

Table 4 Correlation of genes with SNVs and amplifications and deletions

From: Whole genome sequencing reveals potential targets for therapy in patients with refractory KRASmutated metastatic colorectal cancer

Sample	Chr	Gene name	SNV location	CNV variant type	Change associated with variant	Start	End	Correlation
CLN2	8	ADAMDEC1	24312932	CNV-Loss	-1.098323504	24298000	24318700	-
	18	BCL2	59136317	CNV-Loss	-1.142019005	58946900	59136800	-
	17	C17orf39	17905985	CNV-Loss	-1.086327397	17886900	17909200	-
	13	DNAJC3	95127539	CNV-Gain	1.034261883	95159600	95201700	+
	18	DOK6	65495961	CNV-Loss	-1.080170349	65220300	65659400	-
	19	EEF2	3929160	CNV-Loss	-1.10433666	3927700	3935600	-
	13	MED4	47567121	CNV-gain	1.011225847	47549300	47562800	+
	15	MORF4L1	76965549	CNV-Loss	-1.25642835	76953100	76976400	-
	19	OR1M1	9065467	CNV-Loss	-1.185833041	9065000	9065800	-
	13	PCDH17	57105203	CNV-Gain	1.158413612	57105000	57140500	+
	8	PI15	75900191	CNV-Gain	1.077222314	75901700	75924000	+
	15	PML	72124335	CNV-Loss	-1.130706684	72074500	72122000	-
	18	PTPRM	8384547	CNV-Loss	-1.028666588	7637600	8387100	-
	19	PVRL2	50083243	CNV-Loss	-1.070323897	50042300	50073700	-
	19	SHANK1	55864301	CNV-Loss	-1.135111902	55859100	55907600	-
	18	SMAD4	46858795	CNV-Loss	-1.077097357	46827500	46855600	-
	15	THSD4	69844560	CNV-Loss	-1.12539172	69808500	69856700	-
	8	VPS13B	100723477	CNV-Gain	1.06690452	100098000	100957000	+
	19	XAB2	7594144	CNV-Loss	-1.039001256	7596500	7599800	-
	19	ZNF235	49483380	CNV-Loss	-1.210566986	49486200	49499300	-
	19	ZNF480	57510937	CNV-Loss	-1.12807401	57496100	57517900	-
	19	ZNF83	57808787	CNV-Loss	-1.330073623	57808100	57809600	-
CLN3	4	ANKRD17	74175875	CNV-Gain	1.050578956	74176700	74257700	+
	2	APOB	21086873	CNV-Gain	1.381146277	21078200	21119700	+
	1	ARID1A	26973896	CNV-Gain	1.088551435	26707600	26977900	+
	3	ATP13A5	194544518	CNV-Gain	1.074832063	194495900	194576400	+
	2	CLEC4F	70897420	CNV-Gain	1.474467603	70890000	70900800	+
	1	FNDC7	109063011	CNV-Gain	1.060116535	109071800	109085900	+
	3	GADL1	30871204	CNV-Gain	1.083837201	30750200	30822400	+
	4	GUCY1A3	156862650	CNV-Gain	1.051035883	156845700	156866700	+
	4	INPP4B	143222686	CNV-Gain	1.071823665	143169400	143560600	+
	2	IWS1	127960697	CNV-Gain	1.157172502	127955100	127999800	+
	3	KCNMB2	180028679	CNV-Gain	1.036705549	180021600	180027700	+
	12	KRAS	25289551	CNV-Gain	1.035184393	25274800	25275900	+
	2	LRP2	169845248	CNV-Gain	1.274350136	169693500	169926300	+
	3	LSG1	195872054	CNV-Gain	1.046959963	195844100	195855800	+
	1	MACF1	39573148	CNV-Gain	1.075279401	39322700	39722600	+
	3	MITF	70011193	CNV-Gain	1.055910933	70070200	70096500	+
	5	PAPD4	78951267	CNV-Gain	1.023426699	78969500	78969700	+
	2	PCBP1	70168678	CNV-Gain	1.147337373	70169200	70169400	+
	4	PDE5A	120666238	CNV-Gain	1.066043219	120655300	120742100	+
	1	PHTF1	114082912	CNV-Gain	1.075512922	114060600	114098600	+
	3	RPSA	39428561	CNV-Gain	1.099952073	39424200	39428600	+
	4	SH3BP2	2805228	CNV-Gain	1.208480128	2792500	2804000	+
	5	SLC6A19	1265596	CNV-Gain	1.142273516	1257300	1274700	+
	3	SMC4	161633513	CNV-Gain	1.02766824	161602500	161603100	+
	2	SMYD5	73305580	CNV-Gain	1.59092836	73301300	73306500	+
	1	SPOCD1	32038250	CNV-Gain	1.187067318	32029900	32040400	+
	1	ST6GALNAC3	76650550	CNV-Gain	1.08116566	76355200	76864700	+
	1	TMEM39B	32340671	CNV-Gain	1.071050645	32318800	32339600	+
	2	VPS54	63993297	CNV-Gain	1.158423232	63974100	64064600	+
	2	WDR35	20045755	CNV-Gain	1.180181947	19976800	20052800	+
	5	WWC1	167824543	CNV-Gain	1.083413977	167656200	167825900	+
CLN4	16	ABCC12	46688204	CNV-Gain	0.757287	46702800	46702800	+
	13	SPATA13	23761296	CNV-Gain	0.894588	23774800	23761296	+

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ISSN: 1755-8794

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