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Evaluation of next generation sequencing platforms for population targeted sequencing studies

Olivier Harismendy1, Pauline C Ng2, Robert L Strausberg2, Xiaoyun Wang1, Timothy B Stockwell2, Karen Y Beeson2, Nicholas J Schork1, Sarah S Murray1, Eric J Topol1, Samuel Levy2* and Kelly A Frazer1*

Author Affiliations

1 Scripps Genomic Medicine - Scripps Translational Science Institute - The Scripps Research Institute, N. Torrey Pines Court, La Jolla, CA 92037, USA

2 The J Craig Venter Institute, Medical Center Drive, Rockville, MD 20850, USA

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Genome Biology 2009, 10:R32  doi:10.1186/gb-2009-10-3-r32

Published: 27 March 2009

Additional files

Additional data file 1:

Supplemental Table 1: result of the NGS pipeline analysis. Supplemental Table 2: coverage information of all the samples in each NGS. Supplemental Table 3: coverage variability between amplicons. Supplemental Table 4: coverage variability between different repeat elements. Supplemental Table 5: amount of sequence with no or low coverage. Supplemental Table 6: list of regions with no or low coverage for each NGS. Supplemental Table 7: analysis of the allelic imbalance amplification of the LR-PCR amplicons. Supplemental Table 8: result of the comparison between sequencing and genotyping on Illumina Hap550. Supplemental Table 9: loci with discrepant calls between genotyping and sequencing. Supplemental Table 10: genotype calls comparison between ABI Sanger and each NGS. Supplemental Table 11: quality metrics of the comparison of the genotype calls between ABI Sanger and NGS technologies. Supplemental Table 12: all the loci with discordant genotype calls between ABI Sanger and NGS Technologies. Supplemental Table 13: all indel loci identified by ABI Sanger and their calls in Roche 454. Supplemental Table 14: all indels identified by Roche 454 and missed by ABI Sanger. Supplemental Table 15: all the primers and oligonucleotides used in the study.

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Additional data file 2:

Additional information to the methods used and calculations performed for this study.

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Additional data file 3:

Supplemental Figure 1: coverage distribution as a function of GC content for the 3 NGS. Supplemental Figure 2: distribution of alternate allele read frequency obtained for each NGS. Supplemental Figure 3: Sanger Traces of eight loci found to have discrepant calls between Sanger and NGS.

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