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. 2014 Aug 18;9(8):e104417. doi: 10.1371/journal.pone.0104417

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© 2014 Klevebring et al

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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Analysis pipelines 1)–3) are displayed here with optimal base quality alignment cutoffs (BAQ) and without for pipeline 1 to display the effects of BAQ filtering. As exome sequencing is limited by the efficiency of the capture procedure, 30 whole genome sequencing was also simulated assuming 3000 variants in the genome. 1000 iterations were performed for each ctDNA fraction assuming 50 variants in the exome, starting with 10 ml of plasma (30 ng of cfDNA). The sensitivity is defined as the number of proportion of tests passing the significance threshold for each set of 1000 iterations (p<0.05, fishers' exact test, comparing the number of variant and reference reads from sample and background).

Inline graphic — Analysis pipelines 1)–3) are displayed here with optimal base quality alignment cutoffs (BAQ) and without for pipeline 1 to display the effects of BAQ filtering. As exome sequencing is limited by the efficiency of the capture procedure, 30 whole genome sequencing was also simulated assuming 3000 variants in the genome. 1000 iterations were performed for each ctDNA fraction assuming 50 variants in the exome, starting with 10 ml of plasma (30 ng of cfDNA). The sensitivity is defined as the number of proportion of tests passing the significance threshold for each set of 1000 iterations (p<0.05, fishers' exact test, comparing the number of variant and reference reads from sample and background).