Table 1 Comparison of oncogenic events and CNAs detected by ddPCR, CGH array or SNP array.

From: Detection of clinically relevant copy number alterations in oral cancer progression using multiplexed droplet digital PCR

Sample

Ploidy1

HD2

High-level Gains3

Correlation Coefficient (R)

ddPCR

SNP

ddPCR

SNP

ddPCR

CGH

SNP

ddPCR versus CGH

ddPCR versus SNP

CGH versus SNP

OKF4 E6E7

—

—

     

*

N/A

N/A

POE9n tert

—

—

9p

N/A

   

*

N/A

N/A

CAL27

2

1.94

3p

3p

7p

7p

7p

0.96

1.00

1.00

SCC-25

2

1.86

4q/9p

4q

11q

11q

11q

0.95

0.96

0.96

SCC-4

3

2.95

  

5p/11q

5p/11q

5p/11q

0.93

0.98

0.98

SCC-9

3

3.14

3p/9p

3p/9p

8q

 

8q

0.89

0.93

0.93

SiHa

3

2.95

3p

3p

5p/20q

 

5p/20q

0.92

0.94

0.94

HeLa

3

3.46

  

5p

5p

5p/9p

0.97

0.86

0.86

Oral 67

       

*

  

Oral 48

    

7p

7p

N/A

0.97

  

Oral 44

    

7p

7p

N/A

0.88

  

Oral 75

    

7p

7p

N/A

0.90

  

Oral 91

       

0.78

  
  1. 1Ploidy level inferred by ddPCR determined using algorithm described in Material and Methods, while inferred ploidy by SNP array is the genome average copy number reported by canSAR.
  2. 2HD detected by ddPCR or SNP array, no HD was detected by CGH array.
  3. 3High-level gains were identified as \({R}_{i/b}^{{Norm}}\) or log2 value ≥1.0 for ddPCR or CGH array respectively, and were identified as Δ copy number ≥2 for diploid cell lines or ≥3 for triploid cell lines in data from SNP arrays.
  4. * R values were not determined for cell lines or clinical samples with few or no significant CNAs.
  5. N/A SNP data not available.
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