SW620, LoVo, T84, SW48, and SW1116 are some of the most widely used cell lines for colon cancer research. Often researchers have questions on selecting the most appropriate cell line(s) for particular research uses.

TumorComparer utilizes several data types (e.g., mutation, copy number, and expression) to perform a comparison of The Cancer Genome Atlas (TCGA) tumor data to experimental cell line models from the Cancer COSMIC Cell Line Project (CCLP) for several cancer types. Please refer to Sinha R et al., 2021. DOI: 10.1016/j.crmeth.2021.100039 for details on the methodology.

An analysis for colon cancer cell lines with differences between the colon cancer cell lines SW620 vs LoVo; SW620 vs T84; SW620 vs SW48; and etc.

If you use content from this page, please cite Sinha R et al., 2021. DOI: 10.1016/j.crmeth.2021.100039.

Characteristics of Colon Cancer Cell Lines

The figure shows the presence of alterations for genes (APC, TP53, KRAS, BCL2, BRAF, etc.) commonly associated with colon cancer in the cell lines: SW620, C2BBE1, SKCO1, T84, SW1116, etc. The gene list is retrieved from DisGeNET, and the alteration information is retrieved from cBioPortal for the Cancer Cell Line Encyclopedia (CCLE) dataset.

NOTE: Only a subset of colon cancer cell lines are shown to ensure a readable figure. Alterations for additional colon cancer cell lines and genes are available on cBioPortal using links on the table below.

Comparing colon cancer cell lines to tumor samples. Legend Abbreviations: mrna_hi = mRNA High; mrna_lo = mRNA Low; prot_hi = Protein High; prot_lo = Protein Low; mut_mis_put_pass = Missense Mutation (putative passenger); mut_mis_put_driv = Missense Mutation (putative driver); mut_inframe_put_pass = Inframe Mutation (putative passenger); mut_inframe_put_driv = Inframe Mutation (putative driver); mut_trun_put_pass = Truncating mutation (putative passenger); mut_trun_put_driv = Truncating mutation (putative driver); amp = Amplification; deep_del = Deep Deletion; homdel_rec = homdel_rec; amp_rec = amp_rec; sv = sv; sv_rec = sv_rec; splice = splice

Comparing colon cancer cell lines to tumor samples. Legend Abbreviations: mrna_hi = mRNA High; mrna_lo = mRNA Low; prot_hi = Protein High; prot_lo = Protein Low; mut_mis_put_pass = Missense Mutation (putative passenger); mut_mis_put_driv = Missense Mutation (putative driver); mut_inframe_put_pass = Inframe Mutation (putative passenger); mut_inframe_put_driv = Inframe Mutation (putative driver); mut_trun_put_pass = Truncating mutation (putative passenger); mut_trun_put_driv = Truncating mutation (putative driver); amp = Amplification; deep_del = Deep Deletion; homdel_rec = homdel_rec; amp_rec = amp_rec; sv = sv; sv_rec = sv_rec; splice = splice

List of Colon Cancer Cell Lines Compared to Pan-Cancer TCGA

The TumorComparer analysis examines the most variably expressed genes, as well as alteration information for cell lines and TCGA patient data using a weighted similarity approach; for details, read: Sinha R et al., 2021. DOI: 10.1016/j.crmeth.2021.100039.

More information for the colon cancer cell lines is available on cBioPortal using links on the table below.

The table shows colon cancer cell lines sorted by similarity to characteristics of TCGA tumors based on expression, mutation, and copy number information. Cell Lines with higher values of โ€˜% Rank by Avg % Ranksโ€™ are considered better matches.
Cell Line % Rank by Avg % Ranks More Line Info % Rank by Mutation % Rank by Copy Number % Rank by Expression
LS123 0.99 Link 0.84 0.89 0.94
SNUC1 0.99 Link 0.94 0.79 0.98
SW626 0.99 NA 0.84 0.87 0.92
SW948 0.99 Link 0.99 0.71 0.99
HCT15 0.98 Link 0.74 0.92 0.95
SW620 0.97 Link 1.00 0.56 0.92
CL34 0.96 Link 0.50 0.95 1.00
HT115 0.96 Link 0.50 0.93 0.99
SW1417 0.96 Link 0.58 0.87 0.97
HCC56 0.95 Link 0.84 0.56 1.00
SW1116 0.95 Link 0.98 0.39 0.98
LOVO 0.94 Link 0.45 0.99 0.89
HCC2998 0.93 NA 0.34 0.98 0.99
LS1034 0.93 Link 1.00 0.31 1.00
SNU407 0.93 Link 0.42 0.95 0.96
HT55 0.92 Link 0.55 0.73 0.99
LS513 0.92 Link 0.37 0.92 1.00
KM12 0.91 Link 0.38 0.89 0.96
COLO205 0.90 Link 0.62 0.64 0.97
GP5D 0.90 NA 0.40 0.82 0.98
LS180 0.90 Link 0.32 0.89 0.99
SNU81 0.90 Link 0.44 0.79 0.98
CL40 0.89 Link 0.88 0.31 1.00
SNU1040 0.88 Link 0.30 0.92 0.95
SW48 0.88 Link 0.22 1.00 0.94
CL11 0.86 Link 0.99 0.18 0.96
RKO 0.86 Link 0.35 0.89 0.88
T84 0.86 Link 0.99 0.16 0.99
COLO678 0.85 Link 0.99 0.18 0.92
HCT116 0.82 Link 0.32 0.82 0.90
NCIH747 0.80 Link 0.98 0.10 0.94
CCK81 0.79 Link 0.34 0.66 0.97
LS411N 0.79 Link 0.35 0.64 0.99
SKCO1 0.77 Link 1.00 0.64 0.30
NCIH716 0.72 Link 0.79 0.18 0.90
C2BBE1 0.69 Link 0.59 0.26 0.93
MDST8 0.59 Link 0.46 0.66 0.51
SNUC2B 0.59 NA 0.37 0.34 0.95
SNUC5 0.54 Link 0.42 0.20 0.95
COLO320HSR 0.47 NA 1.00 0.26 0.20
SNU175 0.39 Link 0.37 0.02 0.94
CW2 0.35 Link 0.24 0.01 0.98

Cell Lines with Common Mutations Found in TCGA Colon Cancer

Alterations present in cell lines also present in at least two TCGA Pan-Cancer Atlas (COAD) samples on cBioPortal.

Alterations

CTNNB1 R582Q (TCGA Altered: 0.4%; 2 out of 526 samples)

  • CW2

CTNNB1 S45F (TCGA Altered: 0.6%; 3 out of 526 samples)

  • LS180

CTNNB1 T41A (TCGA Altered: 0.8%; 4 out of 526 samples)

  • CCK81
  • SNU407

KRAS A146T (TCGA Altered: 3%; 16 out of 526 samples)

  • LS1034
  • SNU81

KRAS G12A (TCGA Altered: 1.9%; 10 out of 526 samples)

  • SW1116

KRAS G12C (TCGA Altered: 2.9%; 15 out of 526 samples)

  • SW1463
  • SW837

KRAS G12D (TCGA Altered: 10.8%; 57 out of 526 samples)

  • CL40
  • COLO678
  • GP2D
  • LS180
  • LS513
  • SNU1033
  • SNU1197
  • SNU407
  • SNU61
  • SNUC2A

KRAS G12S (TCGA Altered: 1.5%; 8 out of 526 samples)

  • LS123

KRAS G12V (TCGA Altered: 9.3%; 49 out of 526 samples)

  • HCC56
  • RCM1
  • SKCO1
  • SW403
  • SW480
  • SW620

KRAS G13D (TCGA Altered: 7%; 37 out of 526 samples)

  • HCT116
  • HCT15
  • HRT18
  • LOVO
  • NCIH747
  • T84

KRAS Q61H (TCGA Altered: 0.8%; 4 out of 526 samples)

  • CL11

POLE P286R (TCGA Altered: 0.4%; 2 out of 526 samples)

  • SNU81

POLE V411L (TCGA Altered: 0.8%; 4 out of 526 samples)

  • HT115

TP53 G245S (TCGA Altered: 1.1%; 6 out of 526 samples)

  • LS1034
  • SNUC4

TP53 R175H (TCGA Altered: 6.1%; 32 out of 526 samples)

  • LS123
  • SNU1197
  • SNU61

TP53 R248Q (TCGA Altered: 3.4%; 18 out of 526 samples)

  • CL40
  • SW1463

TP53 R248W (TCGA Altered: 2.9%; 15 out of 526 samples)

  • COLO320
  • SNU1040
  • SNUC5
  • SW837

TP53 R273C (TCGA Altered: 2.3%; 12 out of 526 samples)

  • CL14
  • SNUC2A

TP53 R273H (TCGA Altered: 3.2%; 17 out of 526 samples)

  • HT29
  • NCIH508
  • SNUC2A
  • SW480
  • SW620

BRAF V600E (TCGA Altered: 9.1%; 48 out of 526 samples)

  • CL34
  • COLO205
  • HT29
  • LS411N
  • MDST8
  • OUMS23
  • RKO
  • SNUC5
  • SW1417

Customized Comparisons

Each project has unique questions. TumorComparer (tumorcomparer.org) facilities customized comparisons of cell line datasets to tumor samples directly from the browser.

Technical Information

This analysis was generated using TumorComparer: 0.99.25. If you use content from this page, please cite Sinha R et al., 2021. DOI: 10.1016/j.crmeth.2021.100039.