Correcting errors in PCR-derived libraries for rare allele detection by reconstructing parental and daughter strand information
Abstract Molecular barcoding methods enable high-sensitivity detection of circulating tumor DNA that is rarely present in liquid biopsy samples. Many methods involve ligation of molecular barcodes to DNA prior to hybridization capture, enabling recovery of starting molecules. Development of polymera...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-07-01
|
| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-025-08537-3 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849761700092313600 |
|---|---|
| author | Hyeonseob Lim Soyeong Jun Taehoon Kim Ji Hyun Lee Duhee Bang |
| author_facet | Hyeonseob Lim Soyeong Jun Taehoon Kim Ji Hyun Lee Duhee Bang |
| author_sort | Hyeonseob Lim |
| collection | DOAJ |
| description | Abstract Molecular barcoding methods enable high-sensitivity detection of circulating tumor DNA that is rarely present in liquid biopsy samples. Many methods involve ligation of molecular barcodes to DNA prior to hybridization capture, enabling recovery of starting molecules. Development of polymerase chain reaction (PCR)-based methods could facilitate more cost- and labor- effective detection; however, tracking molecular identity can be difficult, as new barcodes overwrite old barcodes in each cycle. Here, we present a sensitive genotyping method based on a peer-to-peer network-derived identifier for error reduction in amplicon sequencing (SPIDER-seq) and enable molecular identity tracking with PCR-derived libraries using overwritten barcodes. SPIDER-seq detected mutations at frequences as low as 0.125% after only two consecutive general PCR cycles and systematically analyzed the error pattern in the peer-to-peer network. Our method could facilitate the rapid detection of mutations associated with various cancers. |
| format | Article |
| id | doaj-art-8858435e673b4b7ab4e5425a36a68653 |
| institution | DOAJ |
| issn | 2399-3642 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj-art-8858435e673b4b7ab4e5425a36a686532025-08-20T03:05:56ZengNature PortfolioCommunications Biology2399-36422025-07-018111210.1038/s42003-025-08537-3Correcting errors in PCR-derived libraries for rare allele detection by reconstructing parental and daughter strand informationHyeonseob Lim0Soyeong Jun1Taehoon Kim2Ji Hyun Lee3Duhee Bang4Department of Chemistry, Yonsei UniversityDepartment of Chemistry, Yonsei UniversityDepartment of Chemistry, Yonsei UniversityDepartment of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee UniversityDepartment of Chemistry, Yonsei UniversityAbstract Molecular barcoding methods enable high-sensitivity detection of circulating tumor DNA that is rarely present in liquid biopsy samples. Many methods involve ligation of molecular barcodes to DNA prior to hybridization capture, enabling recovery of starting molecules. Development of polymerase chain reaction (PCR)-based methods could facilitate more cost- and labor- effective detection; however, tracking molecular identity can be difficult, as new barcodes overwrite old barcodes in each cycle. Here, we present a sensitive genotyping method based on a peer-to-peer network-derived identifier for error reduction in amplicon sequencing (SPIDER-seq) and enable molecular identity tracking with PCR-derived libraries using overwritten barcodes. SPIDER-seq detected mutations at frequences as low as 0.125% after only two consecutive general PCR cycles and systematically analyzed the error pattern in the peer-to-peer network. Our method could facilitate the rapid detection of mutations associated with various cancers.https://doi.org/10.1038/s42003-025-08537-3 |
| spellingShingle | Hyeonseob Lim Soyeong Jun Taehoon Kim Ji Hyun Lee Duhee Bang Correcting errors in PCR-derived libraries for rare allele detection by reconstructing parental and daughter strand information Communications Biology |
| title | Correcting errors in PCR-derived libraries for rare allele detection by reconstructing parental and daughter strand information |
| title_full | Correcting errors in PCR-derived libraries for rare allele detection by reconstructing parental and daughter strand information |
| title_fullStr | Correcting errors in PCR-derived libraries for rare allele detection by reconstructing parental and daughter strand information |
| title_full_unstemmed | Correcting errors in PCR-derived libraries for rare allele detection by reconstructing parental and daughter strand information |
| title_short | Correcting errors in PCR-derived libraries for rare allele detection by reconstructing parental and daughter strand information |
| title_sort | correcting errors in pcr derived libraries for rare allele detection by reconstructing parental and daughter strand information |
| url | https://doi.org/10.1038/s42003-025-08537-3 |
| work_keys_str_mv | AT hyeonseoblim correctingerrorsinpcrderivedlibrariesforrarealleledetectionbyreconstructingparentalanddaughterstrandinformation AT soyeongjun correctingerrorsinpcrderivedlibrariesforrarealleledetectionbyreconstructingparentalanddaughterstrandinformation AT taehoonkim correctingerrorsinpcrderivedlibrariesforrarealleledetectionbyreconstructingparentalanddaughterstrandinformation AT jihyunlee correctingerrorsinpcrderivedlibrariesforrarealleledetectionbyreconstructingparentalanddaughterstrandinformation AT duheebang correctingerrorsinpcrderivedlibrariesforrarealleledetectionbyreconstructingparentalanddaughterstrandinformation |