Information About Demonstration Samples
Amplicons amplfilied from the genomic DNA of 27 reference cell lines (25 tumor and 2 normal cell lines) based on the Ion AmpliSeq™ Cancer Panel protocol were sequenced on Ion 318 chip by using the Life Technologies Ion Personal Genome Machine (PGMTM) Sequencer.
The output files from the Ion PGM variant caller plugin can be downloaded in Excel format (test.tar.bz2 or test.tar.gz) and
in VCF format (VCF.tar.bz2 or VCF.tar.gz).



Variants from different samples were displayed in single color


Variants from different samples were colored according to their job id (group)


Information on Cell lines
ID Tissue type Cell line Description ATCC Number Sample Name Variant Caller Reports Mapped Reads Reads On-Target Bases On-Target Read Depth 1x Coverage 20x Coverage 100x Coverage Variants Detected
1 Bladder 5637 Human bladder primary carcinoma HTB-9 Bladder_5637 IonXpress_011 494,940 93.93% 86.17% 2,421.25 100.00% 99.38% 97.58% 11
2 Bladder T24 Human urinary bladder carcinoma cell line HTB-4 Bladder_T24 IonXpress_012 428,550 94.60% 85.72% 2,114.45 100.00% 99.59% 97.54% 10
3 Breast MCF-7 Human breast adenocacinoma HTB-22 Breast_MCF_7 IonXpress_001 308,306 93.03% 84.57% 1,447.70 100.00% 98.05% 96.48% 12
4 Breast MDA-MB-231 Human breast adenocacinoma, mammary gland pleural effusion HTB-26 Breast_MDA_MB_231 IonXpress_002 260,102 93.82% 85.75% 1,254.22 99.34% 98.05% 96.42% 10
5 Colon HCT116 colorectal carcinoma, Human CCL-247 Colon_HCT116 IonXpress_002 507,676 94.71% 85.88% 2,411.19 100.00% 99.59% 99.58% 16
6 Colon HT29 Human colorectal adenocarcinoma HTB-38 Colon_HT29 IonXpress_004 457,401 95.22% 86.28% 2,233.67 100.00% 99.59% 99.25% 15
7 Colon LoVo Colon, colorectal adenocarcinoma; metastatic site: left supraclavicular region, human CCL-229 Colon_Lovo_100 IonXpress_009 327,090 93.25% 85.77% 1,585.64 100.00% 99.12% 95.90% 15
8 Colon SW480 Human colon adenocarcinoma CCL-228 Colon_SW480 IonXpress_008 387,778 94.57% 86.05% 1,871.46 100.00% 99.59% 98.66% 13
9 Colon SW48 Human colon adenocarcinoma CCL-231 Colon_SW48 IonXpress_006 321,229 94.94% 86.53% 1,586.15 100.00% 99.59% 97.77% 8
10 Kidney HEK-293 Human embryonic kidney, adenovirus type 5 transformed CRL-1573 Kidney_HEK_293_new IonXpress_004 123,062 93.42% 84.23% 599.38 99.59% 98.30% 96.17% 7
11 Liver Hep3B Human hepatocellular carcinoma HB-8064 Liver_Hep3B IonXpress_005 512,594 92.94% 85.57% 2,456.51 100.00% 97.48% 96.93% 10
12 Liver HepG2 Liver, hepatocellular carcinoma, human HB-8065 Liver_HepG2 IonXpress_001 415,986 94.89% 85.87% 2,040.56 100.00% 99.59% 99.58% 8
13 Liver PLC/PRF/5 Liver, hepatoma, Alexander cells, Human CRL-8024 Liver_PLC_5 IonXpress_006 491,664 94.08% 87.16% 2,386.50 100.00% 98.72% 97.09% 10
14 Nasopharynx BM1 Nasopharyngeal carcinoma ref.1 Nasopharynx_BM1 IonXpress_016 387,177 93.98% 86.32% 1,922.95 100.00% 99.11% 96.27% 13
15 Nasopharynx C666-1 Nasopharyngeal carcinom consistently harbouring Epstein-Barr virus, undifferentiated ref.2 Nasopharynx_C666_1 IonXpress_009 424,021 93.82% 86.52% 2,137.28 100.00% 98.96% 94.94% 10
16 Nasopharynx CNE1 Epithelioid cell line derived from nasopharyngeal carcinoma ref.3 Nasopharynx_CNE1 IonXpress_010 424,200 93.75% 86.85% 2,124.43 100.00% 98.71% 94.05% 12
17 Nasopharynx HK1 Nasopharynx, well-differentiated squamous carcinomas ref.4 Nasopharynx_HK1 IonXpress_011 433,360 93.49% 87.31% 2,206.44 100.00% 98.20% 94.29% 11
18 Nasopharynx NPC-039 Nasopharyngeal carcinoma ref.5 Nasopharynx_NPC_039 IonXpress_013 429,584 93.83% 87.05% 2,138.44 100.00% 98.69% 95.13% 11
19 Nasopharynx NPC-076 Nasopharyngeal carcinoma ref.5 Nasopharynx_NPC_076 IonXpress_014 470,453 92.32% 84.94% 2,276.60 100.00% 99.58% 95.13% 11
20 Nasopharynx NPC-117 Nasopharyngeal carcinoma ref.5 Nasopharynx_NPC_117 IonXpress_015 452,920 93.98% 86.45% 2,241.46 100.00% 99.59% 96.27% 11
21 Nasopharynx NPC-TW06 Nasopharyngeal carcinoma ref.6 Nasopharynx_NPC_TW06 IonXpress_012 427,175 94.16% 87.18% 2,143.52 100.00% 98.85% 95.13% 11
22 Oral OC3 Oral squamous cell carcinoma ref.7 Oral_OC3 IonXpress_005 308,461 95.11% 86.42% 1,520.62 100.00% 98.93% 97.05% 10
23 Oral OECM1 Oral squamous cell carcinoma, derived from a Taiwanese patient ref.8 Oral_OECM1 IonXpress_007 389,746 94.72% 85.83% 1,884.93 100.00% 99.59% 98.14% 11
24 Oral SCC25 Tongue, squamous cell carcinoma CRL-1624 Oral_SCC25 IonXpress_010 562,230 93.84% 86.57% 2,761.47 99.73% 98.93% 96.48% 13
25 Oral SCC4 Tongue, squamous cell carcinoma CRL-1628 Oral_SCC4 IonXpress_009 549,716 93.54% 86.09% 2,737.23 100.00% 99.18% 96.68% 10
26 Normal MRC-5 Human normal lung CCL-75 Normal_MRC5 IonXpress_008 386,136 92.83% 85.89% 1,854.67 100.00% 99.18% 97.58% 8
27 Normal Wi-38 Lung, normal, fibroblast, human CCL-171 Normal_Wi_38 IonXpress_007 479,600 93.08% 85.91% 2,308.44 100.00% 99.17% 97.90% 9

Reference
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ref.7 S. C. Lin, C. J. Liu, C. P. Chiu, S. M. Chang, S. Y. Lu, and Y. J. Chen, 'Establishment of Oc3 Oral Carcinoma Cell Line and Identification of Nf-Kappa B Activation Responses to Areca Nut Extract', J Oral Pathol Med, 33 (2004), 79-86.
ref.8 S. H. Chiou, C. C. Yu, C. Y. Huang, S. C. Lin, C. J. Liu, T. H. Tsai, S. H. Chou, C. S. Chien, H. H. Ku, and J. F. Lo, 'Positive Correlations of Oct-4 and Nanog in Oral Cancer Stem-Like Cells and High-Grade Oral Squamous Cell Carcinoma', Clin Cancer Res, 14 (2008), 4085-95.