Pharmacogenomics of in vitro response of the NCI-60 cancer cell line panel to Indian natural products

Sankaran, Hari; Negi, Simarjeet; McShane, Lisa M.; Zhao, Yingdong; Krushkal, Julia

doi:10.1186/s12885-022-09580-7

BMC Cancer

Table 3 Association of functionally important variants and likely oncogenic variants with response to Indian natural products

From: Pharmacogenomics of in vitro response of the NCI-60 cancer cell line panel to Indian natural products

NSC number	Gene	Variant	p-value	t-statistic	# of cell lines with variant	# of cell lines without variant	Mean logGI50 with variant	Mean logGI50 without variant	Prevalence in 1000 Genomes	SNP Type	OncoKB level	OncoKB annotation	FDR adjusted p-value	INP name
112166	MET	T992I	0.0000368	-4.782802	3	47	-5.806500	-5.703000	0.01	Missense	NA	Likely Oncogenic	0.0027367	Cucurbitacin K
112167	MET	T992I	0.0006802	-3.743424	3	47	-6.801167	-6.709511	0.01	Missense	NA	Likely Oncogenic	0.0243927	Elatericin B
308606	BRAF	V600E	0.0000006	-6.134195	9	41	-7.159667	-6.693878	0.00	Missense	1	Oncogenic	0.0000742	Cucurbitacin D
328426	KDR	C482R	0.0019152	-3.308867	3	56	-8.222667	-7.909268	0.01	Missense	NA	Likely Oncogenic	0.0414968	Phyllanthoside
643160	MET	T992I	0.0001938	4.076171	3	44	-4.000000	-4.145977	0.01	Missense	NA	Likely Oncogenic	0.0089764	3-Bromo-4-dimethylamino-alpha-benzoyl cinnamonitrite
710351	KDR	C482R	0.0017855	3.286695	3	55	-4.000000	-4.137891	0.01	Missense	NA	Likely Oncogenic	0.0406327	Achilleol A
710351	MET	T992I	0.0017855	3.286695	3	55	-4.000000	-4.137891	0.01	Missense	NA	Likely Oncogenic	0.0406327	Achilleol A
717335	MET	T992I	0.0000616	-4.338376	3	55	-7.993333	-7.741146	0.01	Missense	NA	Likely Oncogenic	0.0042724	Tylophorin
717335	KNSTRN	A40E	0.0017579	-3.300053	7	51	-7.954286	-7.726725	0.06	Missense	NA	Likely Oncogenic	0.0406327	Tylophorin
731920	KNSTRN	A40E	0.0007237	-3.790673	7	42	-4.671286	-4.511429	0.06	Missense	NA	Likely Oncogenic	0.0250871	Calendulaglycoside B-6'-O-butyl ester
731921	KDR	C482R	0.0014349	-3.902824	3	48	-5.905667	-5.644375	0.01	Missense	NA	Likely Oncogenic	0.0406327	Calendulaglycoside D2
731922	KDR	C482R	0.0017287	-3.535183	3	47	-5.191333	-5.088383	0.01	Missense	NA	Likely Oncogenic	0.0406327	Calendulaglycoside D-6'-O-methyl ester
731922	KNSTRN	A40E	0.0010801	-3.482230	7	43	-5.183857	-5.080023	0.06	Missense	NA	Likely Oncogenic	0.0351046	Calendulaglycoside D-6'-O-methyl ester

NSC INP NSC number, Gene Gene name, Variant Sequence variant, p-value original p-value (prior to adjustment for multiple testing) from the Student’s t-test comparing the mean logGI50 values in those cell lines that had each variant to those that were not reported to have the variant, t-statistic value from the Student’s t-test comparing the mean logGI50 values in those cell lines that had each variant to those that were not reported to have the variant, # of cell lines with variant Number of NCI-60 cell lines which had that variant according to information from CellMiner, # of cell lines without variant number of NCI-60 cell lines which were not reported to have that variant according to data from CellMiner, Mean logGI50 with variant Average logGI50 value in NCI-60 cell lines that had the variant, Mean logGI50 without variant average logGI50 value in NCI-60 cell lines not reported to have the variant, Prevalence in 1000 Genomes Frequency of the variant in the 1000 Genomes dataset, according to CellMiner, OncoKB level Highest level of evidence for the variant across tissues according to the OncoKB annotation; OncoKB annotation, OncoKB classification as oncogenic or likely oncogenic, FDR adjusted p-value, p-value (adjusted for multiple testing) from the Student’s t-test comparing the mean logGI50 values in those cell lines that had each variant to those that were not reported to have the variant; INP name, name of the Indian natural product

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ISSN: 1471-2407

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