THE NCI-60 PANEL

Cell lines with an inconclusive p53 status are shown in red.

more information can be found here: Berglind et al., in press: download the manuscript

Cell line	ATCC number	DNA	Protein	ref	consensus	comment
LYMPHOMA LEUKEMIA
CCRF-CEM	CCL-119		R248Q	1018	R175H+R248Q	Two mutations in separate alleles
		c.524G>A, c.743G>A	R175H+R248Q	3
		c.524G>A, c.743G>A	R175H+R248Q	2249
HL-60	CCL-240		R248L	1018	p53 null
		null	p.M1_*394del	3000
		null	p.M1_*394del	2249
K-562	CCL-243	c.406_407insC	p.Q136fs*13	269	p.Q136fs*13	p53 RNA and protein are undetectable in this cell line
		c.406_407insC	p.Q136fs*13	2249
MOLT-4	CRL-1582	wt		3	Inconclusive	The status of MOLT-4 is highly heterogeneous in the literature. The report of a wt status could be due to the fact that only exons 5 to 8 (residues 126-306) were screened in several publications
		wt		1018
		c.331C>G	L111V	2242
		c.743G>A	R248Q	27
		c.916C>T	R306X	2249
RPMI-8226	CCL-155		R285L	1018	E285K	This mutant is temperature-sensitive
		c.853G>A	E285K	2249
		c.853G>A	E285K	98
SR	CRL-2262	wt		1018	wt
		wt		2249
NSCLC
A549	CCL-185	wt		1018	wt
		wt		16
		wt		2249
EKVX		del187-224 (exon 6)		1018	Inconclusive	Possible splicing defect. See below for more information
		c.609_610GG>TT	p.V203_E204>V	2249
HOP-62			Ins 212-225	1018		See below for more explanation
		c.673-2A>G  (splice junction)	p.?	2249
HOP-92			p.R175L	1018	R175L
		c.524G>T	p.R175L	2249
NCI-H226	CRL-5826		P309A	1018	Inconclusive
		c.473G>T	R158L	92
			wt	2249
NCI-H23	CRL-5800	c.738G>C	R246I	17	R246I
			R246I	1018
		c.738G>C	R246I	2249
NCI-H322M		c.743G>T	R248L	92	R248L
			R248L	1018
		c.743G>T	R248L	2249
NCI-H460	HTB-177	wt		1018	wt
		wt		2249
NCI-H522	CRL-5810		191delG	1018	p.P191fs*57
		c.572_572delC	p.P191fs*57	2249
		c.572_572delC	p.P191fs*58	92
COLON
COLO-205	CCL-222		G266E	1018	Inconclusive
		c.308_333>TA	p.Y103_L111>L	492
		c.308_333>TA	103del27	2249
HCC-2998			R213X	1018	R213X
		c.637C>T	R213X	2249
HCT-116	CCL-247	wt		1018	wt
		wt		2249
HCT-15	CCL-225	c.722C>T, c.1101-2A>C  (splice junction)	p.S241F, p.?	2249	Inconclusive
			P153A	1018
		c.722C>T	S241F	2251
HT-29	HTB-38	c.818G>A	R273H	492	R273H
		c.818G>A	R273H	2249
KM12			H179R	1018	Inconclusive
		c.215delG	p.R72fs*51	2249
SW620	CCL-227	c.818G>A, c.925C>T	R273H, P309S	9	R273H + P309S	SW480 and SW620 are derived from the same individual with a similar p53 alteration. The P309S mutation is not always reported
			R273H	1018
		c.818G>A, c.925C>T	R273H, P309S	2249
CENTRAL NERVOUS SYSTEN
SF268		c.818G>A	R273H	664	R273H
			R273H	1018
		c.818G>A	R273H	2249
SF295			p.R248Q	1018	R248Q
		c.743G>A	p.R248Q	2249
SF539		wt		1018	Inconclusive
		c.1024delC	p.R342fs*3	2249
SNB75			E258K	1018	E258K
		c.772G>A	E258K	2249
U251/SNB19		c.818G>A	R273H	632	R273H
			R273H	1018
		c.818G>A	R273H	2249
MELANOMA
LOXIMV1		wt		1018	wt
		wt		2249
Malme-3M	HTB-64	wt		1018	wt
		wt		2249
M14			G266E	1018	G266E
		c.797G>A	G266E	2249
SK-MEL-2	HTB-68		G245S	1018	G245S
		c.733G>A	G245S	2249
SK-MEL-28	HTB-72	c.434_435TG>GT	L145R	2249	L145R
		c.434T>G	L145R	1570
			C145V	1018
SK-MEL-5	HTB-70	wt		1018	wt
		wt		2249
UACC-257		wt		1018	wt
		wt		2249
UACC-62		wt		1018	wt
				2249
MDA-MB-435			G266E	1018	G266E	This cell line was originally reported as a breast carcinoma cell line but recent SNP analysis indicates that it is similar to the M14 melanoma cell line
		c.797G>A	G266E	2029
		c.797G>A	G266E	2249
MDA-N			G266E	1018	G266E	This cell line was originally reported as a breast carcinoma cell line but recent SNP analysis indicates that it is similar to the M14 melanoma cell line.  It is a derivative of MDA-MB-435 tranfected with a plasmid expressing erbB2
OVARY
IGROV1		wt		1018	Inconclusive
		wt		606
		c.377A>G	Y126C	2249
OVCAR-3	HTB-161	c.743G>A	R248Q	144	R248Q
			R248Q	1018
		c.743G>A	R248Q	2249
OVCAR-4		wt		1018	Inconclusive
		c.388C>G	L130V	2249
OVCAR-5			ins224	1018	Inconclusive
		wt		2249
OVCAR-8		c.376-1G>A		2249	Splicing defect	See below for more explanation
			del 126-132	1018
NCI/ADR-RES		c.376-1G>A		2249	Splicing defect	Originally named MCF-7/AdrR cells,  later re-designated NCI/ADR-RES.  Was recently found to be identical to OVCAR-8
			del 126-132	1018
			126del21	983
SK-OV-3	HTB-77		H179R	1018	Inconclusive	p53 RNA and protein are undetectable in this cell line: see below for more explanation
		c.267delC	p.S90fs*33	2249
RENAL
786-0	CRL-1932		P278A	1018	Inconclusive
		c.832C>G, c.560-2A>G  (splice junction)	p.P278A, p.?	2249
A498	HTB-44	wt		1018	wt
		wt		2249
ACHN	CRL-1611	wt		1018	wt
		wt		2249
CAKI-1	HTB-46	wt		1018	wt
		wt		2249
RXF393			R175H	1018	R175H
		c.524G>A	R175H	2249
SN12C			E336X	1018	E336X
		c.1006G>T	E336X	2249
TK10			L264R	1018	L264R
		c.791T>G	L264R	2249
U031		wt		1018	wt
		wt		2249
PROSTATE
DU-145	HTB-81		P223L	1018	P223L + V274F	See below for more explanation
		c.820G>T	V274F	2249
		c.668C>T + c.820G>T	P223L + V274F	3001
		c.668C>T + c.820G>T	P223L + V274F	59
PC-3	CRL-1435	c.414delC	p.K139fs*31	2249	p53 RNA and protein are undetectable in this cell line
			138del	1018
		c.414delC	138del	59
BREAST
BT-549	HTB-122	c.747G>C	R249S	24	R249S
			R249S	1018
		c.747G>C	R249S	2249
Hs 578T	HTB-126	c.469G>T	V157F	76	V157F
		c.469G>T	V157F	2249
			D157E	1018
MCF7	HTB-22	wt		1018	wt
		wt		249
MDA-MB-231	HTB-26	c.839G>A	R280K	24	R280K
			R280K	1018
T47D	HTB-133	c.580C>T	L194F	9	L194F
		c.580C>T	L194F	1018

In EKVX, the deletion of codon 187 to 224 detected on RNA-based analysis (ref 1018) corresponds exactly to the deletion of the entire exon 6, a strong argument for a splicing defect. Genomic analysis did not reveal a splicing defect but a tandem mutation at codons 203 and 204 in exon 6 (ref 2049). If the two cell lines analysed were really EKVX, this result suggests that a mutation at either codon 203 and/or 204 could affect p53 gene splicing

In OVCAR-8, the 126-132 deletion detected by the RNA-based assay (ref 1018) concerns the first six residues of exon 5. Genomic analysis (ref 2049) described a mutation in the acceptor site of exon 5 and a splicing defect leading to a shift of the normal donor site of exon 5 that skips 18 nucleotides (6 aa residues) in exon 5. Examination of the DNA sequence at codon 132 reveals an AG dinucleotide sequence preceded by a pyrimidine tract similar to those found in the splice donor sequence. The same situation is observed for NCI/ADR- RES that has been recently shown to be an ovarian carcinoma cell line originating from the same patient as OVCAR-8.

In HOP-62, RNA-based analysis (ref 1018) detected an insertion between codon 212-225 but no information about the insertion sequence was available. Codon 225 is at the boundary of exon 6 and intron 6 suggesting a splicing defect, as analysis at the genomic level (ref 2049) confirms the presence of a splice mutation in the acceptor signal of exon 6

In the majority of publications, the p53 status of the SK-OV-3 cell line is stated as “p53 null”. In fact, close examination of the original manuscript shows that the p53 gene in SK-OV-3 is not deleted and did not sustain any gross rearrangement but neither p53 RNA or protein are found. In these publications, no p53 mutations were found but the recent analysis performed at the Sanger Institute detected a deletion of a single nucleotide at position 267 (codon 90) (Ikediobi et al., 2006). It is therefore possible that nonsense-mediated mRNA decay (NMD) eliminates p53 aberrant mRNA. NMD has been observed in the human leukaemia cell line K562 where p53 is also inactivated via a 1 base pair insertion at nucleotide 136