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Table 6 PTEN deletion detection

From: Target enrichment using parallel nanoliter quantitative PCR amplification

Amplicon Chip Sample name End point fluorescence Cq Mean coverage Min coverage Max coverage Coverage stdev
PTEN-4 chip1 Normal1 3409.9 19.9 766.1 66 1232 314.0
PTEN-4 chip1 Normal1 3219.8 20.1 494.6 40 800 204.5
PTEN-4 chip1 MCF7 3592.8 23.7 450.0 37 720 176.9
PTEN-4 chip1 MCF7 3204.2 23.2 520.2 42 879 216.8
PTEN-4 chip2 786-O 5000.1 22.4 732.0 57 1224 310.2
PTEN-4 chip2 HCT-15 4097.8 19.8 486.7 33 823 201.9
PTEN-4 chip2 MDA-MB-231 4508.4 19.2 386.4 29 643 159.5
PTEN-4 chip2 OVCAR-5 4188.0 19.9 282.8 19 452 107.8
PTEN-4 chip3 MOLT-4 3499.5 19.6 683.9 48 1094 272.9
PTEN-4 chip3 DU-145 4686.3 18.7 364.0 24 610 144.1
PTEN-4 chip3 SN12C 3725.0 19.0 234.9 23 388 90.1
PTEN-4 chip3 BT-549 4036.6 20.0 422.5 45 643 150.1
PTEN-4 chip4 IGROV-1 4000.3 20.0 409.0 35 626 141.1
PTEN-4 chip4 CCRF-CEM 0.0 40.0 0.4 0 2 0.7
PTEN-4 chip4 PC3 0.0 40.0 0.4 0 1 0.5
PTEN-4 chip4 HCT116 3906.9 20.1 627.4 62 1033 246.2
PTEN-4 chip5 Normal1 A 4424.1 20.2 611.7 58 984 245.1
PTEN-4 chip5 ACHN 3996.0 20.2 426.6 28 699 176.5
PTEN-4 chip5 HT-29 4239.3 20.2 256.0 26 396 90.6
PTEN-4 chip5 MCF7 4035.4 20.5 503.0 38 796 196.7
PTEN-4 chip6 Normal1 2955.7 20.5 602.4 39 1015 261.2
PTEN-4 chip6 Normal2 3482.0 20.7 378.8 33 613 145.4
PTEN-4 chip6 Normal2 3440.0 21.1 225.6 18 344 83.2
PTEN-4 chip6 RPMI-8226 3660.0 21.9 365.8 36 571 135.1
  1. Consistent lack of coverage, end point fluorescence and Cq call for the 2 samples with large homozygous deletions in the PTEN gene, spanning the whole of capture assay PTEN-4.