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Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine

Joanna D Holbrook12*, Joel S Parker3, Kathleen T Gallagher4, Wendy S Halsey4, Ashley M Hughes4, Victor J Weigman3, Peter F Lebowitz1 and Rakesh Kumar1

Author Affiliations

1 Cancer Research, Oncology R&D, Glaxosmithkline R&D, 1250 Collegeville Road, Collegeville, USA

2 Growth, Development and Metabolism Programme, Singapore Institute of Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), Brenner Centre for Molecular Medicine, National University of Singapore, 30 Medical Drive, 117609, Singapore

3 Expression Analysis Inc., 4324 South Alston Avenue, Durham NC27713, USA

4 MDR, Glaxosmithkline R&D, 1250 Collegeville Road, Collegeville, USA

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Journal of Translational Medicine 2011, 9:119  doi:10.1186/1479-5876-9-119

Published: 25 July 2011

Additional files

Additional file 1:

Table S1: Sample characteristics.

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Additional file 2:

Table S2: List of genes sequenced.

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Additional file 3:

Figure S1: Concordance matrices of samples based on array and sequence data.

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Addtional file 4:

Table S3: Top 200 genes with amplification at the DNA levels and concordant overexpression at the mRNA level.

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Additional file 5:

Figure S2: Array data evidencing focal amplifications. Top panels show mRNA expression data from arrays, bottom panels show log2 value for DNA abundance in genomic context as derived from SNP arrays.

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Additional file 6:

Figure S3: Comparison of genotyping calls with sequencing data. A total of 1005 common loci were mapped between the Affymetrix 6.0 SNP microarray and the targeted regions. Concordance of genotype calls between affymetrix 6.0 SNP and SAMtools with no filters applied (top left). Application of a consensus quality filters (threshold values plotted as points) improves concordance (y-axis) but reduces the total number of calls (x-axis)(top right). A similar trend is observed for the variant quality thresholds, but at different threshold values (plotted points)(middle left). Sample concordance of genotype calls is improved with consensus quality filter >= 50 and variant quality > 0 (middle right). The total number of genotype calls stratified by reference or variant genotype, and concordance (bottom left).

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Additional file 7:

Table S4: All somatic variants detected.

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Additional file 8:

Figure S4: Sanger sequencing traces. Sanger sequencing traces for variants denoted by blue boxes in Figure 3 (i.e. confirmed in Illumnia and Sanger) are provided.

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