Primer-initiated sequence synthesis to detect and assemble structural variants

Abstract

To evaluate the performance of PrInSeS-G, we simulated pairedend reads from a 1 megabase (Mb) region of human chromosome 21 in which we introduced 500 insertions and deletions (indels) of 5 bp to 10 kb. PrInSeS-G’s performance was robust, but the false positive and false negative rates were, as we expected, affected by indel size and by the quality of the alignment profile, which itself is dependent on the read format and the overall coverage (Supplementary Fig. 1 and Supplementary Table 1). Moreover, PrInSeS-G’s performance compared favorably with that of the structural variation mapper Breakdancer3 (Supplementary Data and Supplementary Methods) with the important benefit that PrInSeS-G yielded sequence information on the variants. To evaluate the performance of PrInSeS-G on real data, we used single-ended reads from Salmonella paratyphi A AKU12601. First, we used the AKU12601 genome as reference to detect false positives. PrInSeS-G detected 74 non–single-nucleotide polymorphism (nonSNP) variants. For 54 of these, we did not obtain improved read depth after realigning the reads to the new consensus sequence, indicating that this validation approach is efficient at removing potential false positives. To estimate the true positive rate, we used the genome of a related S. paratyphi strain, ATCC9150, as reference template and found that PrInSeS-G assembled 68% of detectable variants (28 of 41; Primer-initiated sequence synthesis to detect and assemble structural variants

DOI: 10.1038/nmeth.f.308
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@article{Massouras2010PrimerinitiatedSS, title={Primer-initiated sequence synthesis to detect and assemble structural variants}, author={Andreas Massouras and Korneel Hens and Carine Gubelmann and Swapna Uplekar and Frederik Decouttere and Jacques Rougemont and Stewart T Cole and Bart Deplancke}, journal={Nature Methods}, year={2010}, volume={7}, pages={485-486} }