Table 5 |
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|
Copy number estimation results obtained on 10K Array data of sample JEKO-1 |
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|
mBPCR |
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|
|
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|
gene region |
FISH CN |
|
|
CBS |
CGHseg |
HMM |
GLAD |
BioHMM |
Rendersome |
|
|
|||||||||
|
BCL6 |
3/2 |
2.97 |
2.99 |
2.97 |
2.90 |
2.92 |
2.92 |
3.14 |
2.92 |
|
C-MYC |
ampl |
12.11 |
9.35 |
10.27 |
10.27 |
13.95 |
9.82 |
8.26 |
13.10/3.11 |
|
CCND1 |
2 |
4.08 |
3.77 |
4.08 |
4.08 |
3.84 |
3.79 |
3.14 |
3.50 |
|
BIRC3 |
4/5 |
4.08 |
4.29 |
4.08 |
4.08 |
3.84 |
3.79 |
3.14 |
3.50 |
|
ATM |
4 |
4.08 |
4.29 |
4.08 |
4.08 |
3.84 |
3.79 |
3.14 |
3.50/2.39 |
|
D13S319 |
4 |
3.72 |
3.59 |
3.57 |
3.72 |
3.62 |
3.58 |
3.14 |
3.43 |
|
LAMP1 |
4 |
3.41 |
3.82 |
3.41 |
3.41 |
3.62 |
2.49 |
3.14 |
3.43 |
|
TP53 |
2/3 |
2.81 |
3.00 |
2.83 |
2.50 |
3.52 |
2.93 |
3.14 |
2.93 |
|
MALT1 |
4 |
3.63 |
3.62 |
3.48 |
3.64 |
3.42 |
3.42 |
3.14 |
3.42 |
|
BCL2 |
4 |
3.63 |
3.62 |
3.48 |
3.64 |
3.42 |
3.42 |
3.14 |
3.42 |
|
|
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|
On this noisy data, BioHMM and Rendersome often estimated the gene copy number wrongly,
while this occurred only sometimes to CBS, HMM and GLAD. The method mBPCR with |
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|
Rancoita et al. BMC Bioinformatics 2009 10:10 doi:10.1186/1471-2105-10-10 |
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