Information About Demonstration Samples

As a proof-of-principle experiment, we applied Vanno to targeted sequencing data from 11 cancer cell lines, which can be further classified into
three different tissue types, including colon, oral and normal lung. Amplicons were amplified from the genomic DNA of 11 cancer cell lines
based on the Ion AmpliSeq Cancer Panel v2 protocol, which were subsequently sequenced by the Life Technologies Ion PGM sequencer,
on a single Ion 318 chip, targeted mutation hotspot regions of 50 oncogenes and tumor suppressor genes.



Test Run







Retrieve Demonstration Output


(Variant from different datasets are displayed in single color)


(Variants from different datasets are colored accoding to their sample group or clinical features )



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 Uniformity
1 Colon HCT116 colorectal carcinoma, Human CCL-247 HCT116 IonXpress_001 338,875 95.87% 89.70% 1,504.94 100.00% 100.00% 100.00% 23 98.78%
2 Colon HT29 Human colorectal adenocarcinoma HTB-38 HT29 IonXpress_003 461,651 96.72% 90.51% 2,052.76 100.00% 100.00% 100.00% 18 99.10%
3 Colon LoVo Colon, colorectal adenocarcinoma; metastatic site: left supraclavicular region, human CCL-229 LOVO IonXpress_006 394,552 95.39% 89.24% 1,745.56 100.00% 100.00% 100.00% 22 98.25%
9 Colon SW48 Human colon adenocarcinoma CCL-231 SW48 IonXpress_009 748,418 96.52% 89.29% 3,402.62 100.00% 100.00% 100.00% 14 99.59%
10 Colon SW480 Human colon adenocarcinoma CCL-228 SW480 IonXpress_010 605,697 97.79% 90.50% 2,775.17 100.00% 99.65% 99.65% 20 97.82%
5 Oral OC3 Oral squamous cell carcinoma Ref.1 OC3 IonXpress_007 490,228 95.63% 90.27% 2,149.46 98.84% 98.84% 98.84% 18 98.82%
6 Oral OECM1 Oral squamous cell carcinoma, derived from a Taiwanese patient Ref.2 OECM1 IonXpress_008 468,325 95.33% 90.08% 2,042.21 100.00% 100.00% 100.00% 16 99.01%
7 Oral SCC25 Tongue, squamous cell carcinoma CRL-1624 SCC25 IonXpress_004 357,331 97.17% 90.99% 1,609.86 98.84% 98.84% 98.84% 17 98.01%
8 Oral SCC4 Tongue, squamous cell carcinoma CRL-1628 SCC4 IonXpress_005 456,218 96.57% 90.47% 2,054.57 100.00% 100.00% 100.00% 15 98.79%
4 Normal MRC-5 Human normal lung CCL-75 MRC5 IonXpress_012 448,787 97.43% 90.39% 2,060.54 100.00% 100.00% 100.00% 13 100.00%
11 Normal Wi-38 Lung, normal, fibroblast, human CCL-171 WI38 IonXpress_002 450,575 96.45% 90.48% 2,023.66 100.00% 100.00% 100.00% 16 99.99%

References
Ref.1    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.2    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.