Confirming putative variants at ≤ 5% allele frequency using allele enrichment and Sanger sequencing
| dc.citation.articleNumber | 11640 | |
| dc.citation.journalTitle | Scientific Reports | |
| dc.citation.volumeNumber | 11 | |
| dc.contributor.author | Yan, Yan Helen | |
| dc.contributor.author | Chen, Sherry X. | |
| dc.contributor.author | Cheng, Lauren Y. | |
| dc.contributor.author | Rodriguez, Alyssa Y. | |
| dc.contributor.author | Tang, Rui | |
| dc.contributor.author | Cabrera, Karina | |
| dc.contributor.author | Zhang, David Yu | |
| dc.contributor.org | Systems, Synthetic, and Physical Biology | |
| dc.date.accessioned | 2021-06-17T19:01:35Z | |
| dc.date.available | 2021-06-17T19:01:35Z | |
| dc.date.issued | 2021 | |
| dc.description.abstract | Whole exome sequencing (WES) is used to identify mutations in a patient’s tumor DNA that are predictive of tumor behavior, including the likelihood of response or resistance to cancer therapy. WES has a mutation limit of detection (LoD) at variant allele frequencies (VAF) of 5%. Putative mutations called at ≤ 5% VAF are frequently due to sequencing errors, therefore reporting these subclonal mutations incurs risk of significant false positives. Here we performed ~ 1000 × WES on fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissue biopsy samples from a non-small cell lung cancer patient, and identified 226 putative mutations at between 0.5 and 5% VAF. Each variant was then tested using NuProbe NGSure, to confirm the original WES calls. NGSure utilizes Blocker Displacement Amplification to first enrich the allelic fraction of the mutation and then uses Sanger sequencing to determine mutation identity. Results showed that 52% of the 226 (117) putative variants were disconfirmed, among which 2% (5) putative variants were found to be misidentified in WES. In the 66 cancer-related variants, the disconfirmed rate was 82% (54/66). This data demonstrates Blocker Displacement Amplification allelic enrichment coupled with Sanger sequencing can be used to confirm putative mutations ≤ 5% VAF. By implementing this method, next-generation sequencing can reliably report low-level variants at a high sensitivity, without the cost of high sequencing depth. | |
| dc.identifier.citation | Yan, Yan Helen, Chen, Sherry X., Cheng, Lauren Y., et al.. "Confirming putative variants at ≤ 5% allele frequency using allele enrichment and Sanger sequencing." <i>Scientific Reports,</i> 11, (2021) Springer Nature: https://doi.org/10.1038/s41598-021-91142-1. | |
| dc.identifier.digital | s41598-021-91142-1 | |
| dc.identifier.doi | https://doi.org/10.1038/s41598-021-91142-1 | |
| dc.identifier.uri | https://hdl.handle.net/1911/110747 | |
| dc.language.iso | eng | |
| dc.publisher | Springer Nature | |
| dc.rights | This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. | |
| dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | |
| dc.title | Confirming putative variants at ≤ 5% allele frequency using allele enrichment and Sanger sequencing | |
| dc.type | Journal article | |
| dc.type.dcmi | Text | |
| dc.type.publication | publisher version |
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