Table 1.
Cell Lines Containing Larger-Scale Genomic Alterations, Homozygous Deletions, and Genomic Amplification, Together With Their Chromosomal Locations, Flanking SNPs, and Size of Region
|
|
|
|
Copy number |
|
|
|
||
|---|---|---|---|---|---|---|---|---|
| Cell line |
Genomic alteration |
Chromosomal position |
p501 |
PCR |
Flanking SNPs |
Size (Mb) |
Status |
|
| NCI-H1395 | Amplification | 1q21.3 | 14 | 11.6 | TSC0602316-TSC0902438 | 4.7 | Known | |
| HCC38 | Homozygous deletion | 3p12.2 | 0 | 0 | TSC0041186-TSC0261189 | 2.7 | Known | |
| COR-L96-CAR | Amplification | 5p13.1 | 19 | — | TSC0260201-TSC0066115 | 2.5 | Known | |
| NCI-H209 | Homozygous deletion | 5q14.3 | 0 | 0 | TSC0052315-TSC0061600 | 1.0 | Novel | |
| HCC1395 | Homozygous deletion | 6q16.3 | 0 | 0 | TSC0553269-TSC0152381 | 2.1 | Novel | |
| HCC1395 | Homozygous deletion | 6q16.3 | 0 | 0 | TSC0833631-TSC0050825 | 3.7 | Novel | |
| NCI-H2171 | Amplification | 8q12.2 | 11 | 85.8 | TSC0272325-TSC0681497 | 3.2 | Known | |
| HCC1395 | Homozygous deletion | 8q11.21 | 0 | 0 | TSC0048903-TSC0065447 | 1.6 | Novel | |
| Cor-L96-CAR | Amplification | 8q24.21 | 27 | 74 | TSC0719292-TSC0741747 | 1.9 | Known | |
| NCI-H2171 | Amplification | 8q24.21 | 15 | 31 | TSC0719292-TSC0741747 | 1.9 | Known | |
| BB132-MEL | Homozygous deletion | 9p23 | 0 | 0 | TSC0823256-TSC0048714 | 2.2 | Known | |
| HCC38 | Homozygous deletion | 9p21.3 | 0 | 0 | TSC0827951-TSC0544304 | 10.2 | Known | |
| LB1047-RCC | Homozygous deletion | 9p21.3 | 0 | 0 | TSC0055892-TSC0049516 | 2.3 | Known | |
| NCI-H2126 | Homozygous deletion | 9p21.3 | 0 | 0 | TSC0056694-TSC0602274 | 2.2 | Known | |
| HCC1395 | Homozygous deletion | 11p13 | 0 | 0 | TSC0741958-TSC0345031 | 0.6 | Known | |
| NCI-H2171 | Amplification | 11p13 | 5 | 8.6 | TSC0055572-TSC0059555 | 1.0 | Known | |
| NCI-H2171 | Amplification | 11q14.1 | 7 | 27.6 | TSC0050602-TSC1007318 | 1.2 | Known | |
| 1542T-P41A | Amplification | 11q22.3 | 9 | 20 | TSC0050600-TSC0308740 | 16.1 | Known | |
| 1156-Q-E | Amplification | 12p | 9 | — | TSC0046300-TSC0585919 | 36.6 | Known | |
| NCI-H2171 | Amplification | 12p11.23 | 9 | 7.6 | TSC0081620-TSC0055751 | 5.5 | Known | |
| 833-KE | Amplification | 12p13.31 | 6 | 6.6 | TSC0052512-TSC0083456 | 25.5 | Known | |
| NCI-H2171 | Amplification | 12p13.31 | 10 | 9.2 | TSC0556975-TSC0056780 | 2.7 | Known | |
| NCI-H2171 | Amplification | 14q11.2 | 7 | 22.6 | TSC1031933-TSC0549368 | 1.6 | Novel | |
| I82
|
Amplification
|
20q13.13
|
7
|
7
|
TSC0615769-TSC0543744
|
7
|
Known
|
|
-
The copy number estimation from both the p501 array and confirmation data is included (— indicates no data); homozygous deletions were confirmed by PCR of SNPs from the affected region, whereas amplifications were confirmed by qPCR using TaqMan dual-labelled probes. The status of the amplifications and homozygous deletions is (Novel) not previously reported in the literature or (Known) previously identified.
