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Table 5 Mutation validation

From: Target enrichment using parallel nanoliter quantitative PCR amplification

Gene Cel line Position (prot) Position (cdna) Position (genome) QPCR amplification call RAW sequencing data Reference coverage Variant coverage
APC HT-29 p.E853* c.2557G > T 5:112173848 OK Yes 428 214
APC HCT-15 p.I1417fs*2 c.4248delC 5:112175539 OK Yes 2 963
APC HT-29 p.T1556fs*3 c.4666_4667insA 5:112175957 OK Yes 608 355
APC HCT-15 p.R2166* c.6496C > T 5:112177787 OK Yes 247 360
BRCA2 HCT-15 p.C1200fs*1 c.3599_3600delGT 13:32912089 OK Yes 165 114
BRCA2 HCT-15 p.N1784fs*7 c.5351delA 13:32913837 OK Yes 272 302
MLH1 DU-145 p.? c.117-2A > T 3:37038108 OK Yes 0 476
MLH1 IGROV-1 p.S505fs*3 c.1513delA 3:37070378 OK Yes 5 605
MLH1 CCRF-CEM p.R100* c.298C > T 3:37042536 OK Yes 354 400
MLH1 HCT116 p.S252* c.755C > A 3:37056000 OK Yes 0 30
MLH1 CCRF-CEM p.? c.790 + 1G > A 3:37056036 OK Low coverage 3 6
MSH6 IGROV-1 p.F1088fs*2 c.3261delC 2:48030647 OK Yes 65 650
MSH6 HCT-15 p.D1171fs*4 c.3511_3516 > T 2:48032121 OK No (complex?) 551 0
MSH6 HCT-15 p.L290fs*1 c.868delC 2:48025990 OK Yes 214 230
NF2 SN12C p.? c.115-1G > C 22:30032739 OK Yes 0 599
NF2 ACHN p.R57* c.169C > T 22:30032794 OK Yes 2 772
NF2 MDA-MB-231 p.E231* c.691G > T 22:30057209 OK Yes 1 817
NOTCH1 CCRF-CEM p.R1595 > PRLPHNSSFHFLR c.4783_4784ins36 9:139399362 OK Yes 96 23
NOTCH1 MOLT-4 p.P2515fs*4 c.7544_7545delCT 9:139390649 OK Yes 143 155
PTEN PC3 p.R55fs*1 c.165_1212del1048 10:89685270 Deletion No coverage 0 0
PTEN 786-O p.Q149* c.445C > T 10:89692961 OK Yes 0 910
PTEN CCRF-CEM p.? c.80_492del413 10:89653782 Deletion No coverage 0 0
PTEN MOLT-4 p.K267fs*9 c.800delA 10:89717775. OK Yes 34 1499
PTEN BT-549 p.V275fs*1 c.823delG 10:89720672 OK Yes 3 159
VHL 786-O p.G104fs*55 c.311delG 3:10183842 OK Yes 5 250
  1. Validation rates for all mutations in the NCI60 cell lines included in this publication. The number of reads on the reference and variant bases for each variant position are given in the last 2 columns.
  2. In nonsense or frameshift mutations the * symbol indicates the loss of the amino acid coding potential of the DNA sequence.