Accuracy and speed of mutation mapping.

(a)1,000,000 sequences of 225 bp, containing the indicated number of different, randomly placed substitutions, insertions or deletions generated by the MSBAR program of th EMBOSS package [25]. The reference sequence was a part of exon 20 of the Human Epidermal Growth Factor Receptor gene (NT_033968/ENSG00000146648) exon 20, 4838312 - 4838535 bp, sequence in Supplementary Materials S1).
(b)Data collection was carried out by PCR amplicon sequencing on a Roche 454 sequencer as recommended for the 454 platform (http://454.com/applications/targeted-resequencing/index.asp). Reads containing complete sequence identifiers and longer than 80 bp were analyzed further.
(c)The samples were taken from a culture of H1975 cells carrying a a 128C>T mutation in exon 20 of the EGFR gene [26] (COSMIC [24] ID: 6240). The reference sequence was the same as in (a). 1,000,000 reads containing complete sequence identifier and longer than 80 bp were analyzed.
(d)The samples, taken from a culture of HCC827 cells carrying a 137delGGAATTAAGAGAAGCA mutation in exon 19 of the EGFR gene [27] (COSMIC ID: 6223, sequence in Supplementary Materials S1). The reference sequence was a segment of the EGFR gene(NT_033968/ENSG00000146648) exon 19, 4831698 - 4831757 bp segment, sequence in Supplementary Materials S1). 1,000,000 reads containing complete sequence identifier and longer than 80 bp were analyzed. Part of the dataset is deposited with the Supplementary Materials S1.
(e)http://bioinformatics.bc.edu/marthlab/Mosaik.