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Table 5 Copy number estimation results obtained on 10K Array data of sample JEKO-1

From: Bayesian DNA copy number analysis

   mBPCR       
gene region FISH CN ρ ^ 2 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGafqyWdiNbaKaadaahaaWcbeqaaiabikdaYaaaaaa@2EC4@ ρ ^ 1 2 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGafqyWdiNbaKaadaqhaaWcbaGaeGymaedabaGaeGOmaidaaaaa@2FB4@ 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
  1. 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 ρ ^ 1 2 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGafqyWdiNbaKaadaqhaaWcbaGaeGymaedabaGaeGOmaidaaaaa@2FB4@ correctly estimated the gene copy numbers, apart from CCND1 whose copy number was estimated by all methods differently from the FISH technique.