Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing

Roman K Thomas, Elizabeth Nickerson, Jan F Simons, Pasi A Jänne, Torstein Tengs, Yuki Yuza, Levi A Garraway, Thomas LaFramboise, Jeffrey C Lee, Kinjal Shah, Keith O'Neill, Hidefumi Sasaki, Neal Lindeman, Kwok-Kin Wong, Ana M Borras, Edward J Gutmann, Konstantin H Dragnev, Ralph DeBiasi, Tzu-Hsiu Chen, Karen A Glatt, Heidi Greulich, Brian Desany, Christine K Lubeski, William Brockman, Pablo Alvarez, Stephen K Hutchison, J H Leamon, Michael T Ronan, Gregory S Turenchalk, Michael Egholm, William R Sellers, Jonathan M Rothberg & Matthew Meyerson

Supplementary Fig. 1 (pdf 80K)
Schema of experimental approach for PCR-based exon resequencing.

Supplementary Fig. 2 (pdf 40K)
Power as a function of number of reads for various concentrations of mutations in the sample.

Supplementary Fig. 3 (pdf 52K)
Serial dilution of amplicons containing a single-base substitution or a 12-bp deletion into the corresponding wild-type backgrounds, followed by high-coverage sequencing or low-level mutation detection.

Supplementary Fig. 4 (pdf 376K)
Picotiter plate sequencing of samples S0373 and S0331.

Supplementary Fig. 5 (pdf 416K)
Oncogenic transformation by patient-derived EGFR mutations and differential sensitivity of Del-4 with and without T790M mutation.

Supplementary Fig. 6 (pdf 468K)
Validation of mutations detected by picotiter plate sequencing using extensive cloning and sequencing.

Supplementary Fig. 7 (pdf 508K)
Picotiter plate sequencing of a paraffin-embedded pleural effusion sample obtained before onset of therapy from patient 12.3.

Supplementary Table 1 (pdf 12K)
Mutations detected by picotiter sequencing.

Supplementary Note (pdf 204K)

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