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Tables
- Table 1.
NCI-60 cell lines
Cell line Tumor type 786-0 renal cell carcinoma A498 renal cell carcinoma A549 lung carcinoma ACHN renal cell carcinoma BT-549 breast carcinoma CAKI-1 renal cell carcinoma CCRF-CEM acute lymphoblastic leukaemia COLO205 colorectal carcinoma DU-145 prostate carcinoma EKVX lung adenocarcinoma HCC-2998 colorectal carcinoma HCT-116 colorectal carcinoma HCT-15 colorectal carcinoma HL-60 acute myeloid leukaemia HOP62 lung adenocarcinoma HOP-92 lung large cell carcinoma HS578T breast carcinoma HT29 colorectal carcinoma IGROV1 ovarian carcinoma K-562 chronic myeloid leukaemia KM12 colorectal carcinoma LOXIMVI melanoma M14 melanoma MALME-3M melanoma MCF7 breast carcinoma MDA-MB-231 breast carcinoma MDA-MB-435 melanoma (see text) MOLT-4 acute lymphoblastic leukaemia NCI/ADR-RES ovarian carcinoma (see text) NCI-H226 lung squamous cell carcinoma NCI-H23 lung adenocarcinoma NCI-H322M lung bronchoalveolar carcinoma NCI-H460 lung large cell carcinoma NCI-H522 lung adenocarcinoma OVCAR3 ovarian carcinoma OVCAR-4 ovarian carcinoma OVCAR-5 ovarian carcinoma OVCAR-8 ovarian carcinoma PC-3 prostate carcinoma RPMI-8226 myeloma RXF393 renal cell carcinoma SF-268 glioma SF-295 glioma SF-539 glioma SK-MEL-2 melanoma SK-MEL-28 melanoma SK-MEL-5 melanoma SK-OV-3 ovarian carcinoma SN12C renal cell carcinoma SNB19 glioma (see text) SNB-75 glioma SR non Hodgkin lymphoma SW620 colorectal carcinoma T47D breast carcinoma TK-10 renal cell carcinoma U251 glioma UACC-257 melanoma UACC-62 melanoma UO-31 renal cell carcinoma - Table 2.
Cancer genes analyzed
Gene symbol Gene name National Center for Biotechnology Information gene ID Likely oncogenic mutations* APC Adenomatous polyposis coli 324 8 BRAF v-raf murine sarcoma viral oncogene homologue B1 673 10 BRCA1 Familial breast/ovarian cancer gene 1 672 0 BRCA2 Familial breast/ovarian cancer gene 2 675 0 CDKN2A Cyclin-dependent kinase inhibitor 2A, p16 1029 33 CTNNB1 Catenin (cadherin associated protein) β1 1499 1 ERBB2 v-erb-b2 erythroblastic leukemia viral oncogene homologue 2 2064 0 HRAS v-Ha-ras Harvey rat sarcoma viral oncogene homologue 3265 1 EGFR Epidermal growth factor receptor 1956 0 FLT3 fms-related tyrosine kinase 3 2322 0 KIT v-KIT Hardy-Zuckerman 4 feline sarcoma viral oncogene homologue 3815 0 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homologue 3845 11 MAP2K4 Mitogen-activated protein kinase kinase 4 6416 0 MET met proto-oncogene 4233 0 NRAS Neuroblastoma RAS viral (v-ras) oncogene homologue 4893 3 PDGFRA Platelet-derived growth factor receptor, α polypeptide 5156 0 PIK3CA Phosphoinositide-3-kinase, catalytic, α polypeptide 5290 7 PTEN Phosphatase and tensin homologue 5728 11 RB1 Retinoblastoma 1 5925 3 RET ret proto-oncogene 5979 0 SMAD4 SMAD, mothers against DPP homologue 4 (MADH4) 4089 2 STK11 Serine/threonine kinase 11/LKB1 (Peutz-Jehgers syndrome) 6794 4 TP53 Tumor protein p53 (Li-Fraumeni syndrome) 7157 41 VHL von Hippel-Lindau tumor suppressor 7428 2 ↵* Mutations seen in common ancestor lines counted once.
- Table 3.
Mutations/variants identified in 24 cancer genes in the NCI-60
Cell line Variants identified 786-0 CDKN2A Hom c.1_150 del 150, p.? LOM; PTEN Hom c.445C>T, p.Q149X LOM; TP53 Het c.832C>G, P278A c.A560-2A>G, p.? LOM; VHL Hom c.311delG p.G105fsX55 LOM A498 CDKN2A Hom c.1_471 del 471, p.? LOM; VHL Hom c.426_429delTGAC p.G144fsX14 LOM A549 CDKN2A Hom c.1_471 del 471, p.? LOM; KRAS Hom c.34G>A, p.G12S LOM; STK11 Hom c.109C>T, p.Q37X LOM ACHN CDKN2A Hom c.1_471 del 471, p.? LOM BT-549 RB1 Hom c.265_607 del 343, p.? LOM; TP53 Hom c.747G>C, p.R249S LOM CAKI-1 CDKN2A Hom c.1_471 del 471, p.? LOM CCRF-CEM CDKN2A Hom c.1_471 del 471, p.? LOM; KRAS Het c.35G>A, p.G12D LOM; PTEN Hom c. del 80-492, p.? LOM; TP53 Het c.743G>A, p.R248Q c.524G>A, p.R175H LOM; FLT3 Het c.1879G>A p.A627T TOV COLO-205 APC Hom c.4666_4667insA p.T1556fsX3 LOM; BRAF Het c.1799T>A, p.V600E LOM; SMAD4 Hom del exon1-6 LOM; TP53 Hom c.308_333>TA, p.Y103fsX37 LOM DU145 CDKN2A Hom c.250G>T p.D84Y LOM; RB1 Hom c.2143A>T, p.K715X LOM; STK11 Hom c.532_536delAAGCC p.K178fsX86 LOM; TP53 Het c.820G>T, p.V274F LOM EKVX TP53 Hom c.609_610GG>TT, p.E204X LOM HCC2998 APC Het c.1994T>A, p.L665X c.4348C>T, R1450X LOM; RB1 Het c.409G>T, p.E137X TOV; TP53 Het c.637C>T, p.R213X TOV HCT-116 CDKN2A Het c.68_69insG p.R24fsX20 c.220delG p.E74fsX15 (p14) LOM; CTNNB1 c.133_135 del TCT, p.S45 del LOM; KRAS Het c.38G>A, p.G13D LOM; PIK3CA Het c.3140A>G, p.H1047R LOM; BRCA2 Het c.8021_8022insA p.I2675fsX6 TOV HCT-15 APC Het c.6496C>T,p.R2166X Hom c.4248delC p.I1417fsX2 LOM; KRAS Het c.38G>A, p.G13D LOM; PIK3CA Het c. 1633G>A p. E545K LOM; TP53 Het c.C1101-2A>C, p.? C722T, S241F LOM; BRCA2 Het c.3599_3600delGT p.C1200fsX1 c.5351delA p.N1784fsX7 TOV HL-60 CDKN2A Hom c.238C>T p.R80X LOM; NRAS Het c.182A>T, p.Q61L LOM; TP53 Hom deletion LOM HOP62 CDKN2A Hom c.1_471 del 471, p.? LOM; KRAS Het c.34G>T, p.G12C LOM; TP53 Hom c.G673-2A>G, p.? LOM HOP-92 CDKN2A Hom c.1_471 del 471, p.? LOM; TP53 Hom c.524G>T, p.R175L LOM Hs-578-T CDKN2A Hom c.1_471 del 471, p.? LOM; HRAS Het c.35G>A p.G12D LOM; TP53 Hom c.469G>T, p.V157F LOM HT-29 APC Het c.2557G>T p.E853X c.4666_4667insA p.T1556fsX3 LOM; BRAF Het c.1799T>A, p.V600E LOM; SMAD4 Hom c.931C>T, p.Q311X LOM; PIK3CA Het c.1345C>A p.P449T LOM; TP53 Hom c.818G>A, p.R273H LOM IGROV-1 TP53 Het c.377A>G, p.Y126C LOM; BRCA1 Het c.1961delA p.K654fsX47 TOV; SMAD4 Het c.692delG p.G231fsX10 TOV; PTEN Het c.955_958delACTT p.T319fsX1 TOV K-562 CDKN2A Hom c.1_471 del 471, p.? LOM; TP53 Hom c.406_407insC p.Q136fsX13 LOM; PDGFRA Het Exon 10 +1 G>A p.? TOV KM12 PTEN Het c.385G>T, p.G129X c.800 del A, p.K267fsX9 LOM; APC Het c.5454_5455 ins A, p.N1819fsX7 TOV; TP53 Het c.215delG, p.R72fsX51 TOV; BRCA2 Het c.5351delA p.N1784fsX7 TOV LOXIMVI BRAF Het c.1799T>A, p.V600E LOM; CDKN2A Hom c.1_471 del 471, p.? LOM M14/MDA-MB-435 BRAF Het c.1799T>A, p.V600E LOM; CDKN2A Het c.150+2 T>C p.? c. 456-+24 AGgtgaggactgatgatctgagaattt >C p.? LOM; TP53 Het c.797G>A, p.G266E LOM MALME-3M BRAF Het c.1799T>A, p.V600E LOM; CDKN2A Hom c.1_471 del 471, p.? LOM MCF7 CDKN2A Hom c.1_471 del 471, p.? LOM; PIK3CA Het c.1633G>A p.E545K LOM MDA-MB-231 BRAF Het c.1391G>T, p.G464V LOM; CDKN2A Hom c.1_471 del 471, p.? LOM; KRAS Het c.38G>A p.G13D LOM; TP53 Hom c.839G>A, p.R280K LOM MOLT-4 CDKN2A Hom c.1_471 del 471, p.? LOM; NRAS Het c.34G>T p.G12C LOM; PTEN Hom c.800delA p.K267fsX9 LOM; STK11 Het c.640C>T p.Q214X TOV; TP53 Het c.916C>T, p.R306X TOV NCI-H226 CDKN2A Hom c.1_150 del 150, p.? LOM NCI-H23 KRAS Het c.34G>T, p.G12C LOM; STK11 Hom c.996G>A, p.W332X LOM; TP53 Hom c.738G>C, p.M246I LOM NCI-H322M TP53 Hom c.743G>T, p.R248L LOM NCI-H460 CDKN2A Hom del 1_457 del 457, p.? LOM; KRAS Hom c.183A>T, p.Q61H LOM; PIK3CA Het c.1633G>A p.E545K LOM; STK11 Hom c.109C>T p. Q37X LOM NCI-H522 TP53 Hom 572delC, p.P191fsX56 LOM OVCAR-3 TP53 Hom c.743G>A, p.R248Q LOM OVCAR-4 TP53 Hom c.388C>G, p.L130V LOM OVCAR-5 CDKN2A Hom c.1_471 del 471, p.? LOM; KRAS Hom c.35G>T, p.G12V LOM OVCAR-8/NCI/ADR-RES TP53 Hom c.376-1G>A, p.? LOM; ERBB2 Het c.2327G>T p.G776V TOV PC-3 PTEN Hom c.165-1026 del 862, p.? LOM; TP53 Hom c.414delC p.K139fsX31 LOM RPMI-8226 KRAS Het c.35G>C, p.G12A LOM; TP53 Hom c.853G>A, p.E285K LOM; EGFR Het c.2252C>T p.T751I TOV RXF393 CDKN2A Hom c.1_471 del 471, p.? LOM; PTEN Hom c.1_164 del 164, p.? LOM; TP53 Hom c.524G>A, p.R175H LOM SF-268 CDKN2A Hom c.1_471 del 471, p.? LOM; TP53 Hom c.818G>A, p.R273H LOM SF-295 CDKN2A Hom c.1_471 del 471, p.? LOM; PTEN Hom c.697C>T, p.R233X LOM; TP53 Hom c.743G>A, p.R248Q LOM SF539 RB1 Hom c.346_349delACTT p.T116fsX8 LOM; TP53 Hom c.1024delC p.R342fsX3 LOM; PTEN Hom c.1-1026 del 1026, p.? LOM SK-MEL-2 NRAS Hom c.182A>G, p.Q61R LOM; TP53 Het c.733G>A, p.G245S LOM SK-MEL-28 BRAF Hom c.1799T>A, p.V600E LOM; TP53 Hom c.435_436G>GT, p.L145R LOM; EGFR Hom c.2257C>T p.P753S TOV SK-MEL-5 BRAF Het c.1799T>A, p.V600E LOM; CDKN2A Hom c.1_471 del 471, p.? LOM SK-OV-3 CDKN2A Hom del 1_457 del 457, p.? LOM; PIK3CA Het c.3140A>G, p.H1047R LOM; TP53 Hom c. del267C p.S90fsX33 LOM; APC Het c.4666delA p.T1556fsX9 TOV SN12C TP53 Hom c.1006G>T, p.E336X LOM SNB-75 TP53 Hom c.772G>A, p.E258K LOM SR CDKN2A Hom c.1_471 del 471, p.? LOM SW620 KRAS Hom c.35G>T, p.G12V LOM; TP53 Hom c.818G>A, p.R273H C925T, p.P309S LOM; APC Hom c.4012C>T, p.Q1338X LOM T47D PIK3CA Het c.3140A>G, p.H1047R LOM; TP53 Hom c.580C>T, p.L194F LOM TK10 TP53 Het c.791T>G, p.L264R LOM U251/SNB-19 CDKN2A Hom c.1_471 del 471, p.? LOM; PTEN Hom c.723_724insTT p.E242fsX15 LOM; TP53 Hom c.818G>A, p.R273H LOM UACC-257 BRAF Het c.1799T>A, p.V600E LOM UACC-62 BRAF Hom c.1799T>A, p.V600E LOM; CDKN2A Hom c.1_471 del 471, p.? LOM; PTEN Hom c.741_742insA p.P248fsX5 LOM UO-31 CDKN2A Hom c.1_471 del 471, p.? LOM Abbreviations: Hom, homozygous; Het, heterozygous; del, deletion; ins, insertion; LOM, likely oncogenic mutation; TOV, tentative oncogenic variant.
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November 2006
Volume 5, Issue 11
Volume 5, Issue 11
Mutation analysis of 24 known cancer genes in the NCI-60 cell line set
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