Fragment Enrichment of Circulating Tumor DNA With Low-Frequency Mutations
Human blood contains cell-free DNA (cfDNA), with circulating tumor-derived DNAs (ctDNAs) widely used in cancer diagnosis and treatment. However, it is still difficult to efficiently and accurately identify and distinguish specific ctDNAs from normal cfDNA in cancer patient blood samples. In this stu...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-02-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2020.00147/full |
| _version_ | 1819227256015290368 |
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| author | Xiaojun Liu Jidong Lang Shijun Li Yuehua Wang Lihong Peng Weitao Wang Yingmin Han Cuixiao Qi Lei Song Shuangshuang Yang Kaixin Zhang Guoliang Zang Hong Pei Qingqing Lu Yonggang Peng Shuxue Xi Weiwei Wang Dawei Yuan Pingping Bing Liqian Zhou Geng Tian Geng Tian |
| author_facet | Xiaojun Liu Jidong Lang Shijun Li Yuehua Wang Lihong Peng Weitao Wang Yingmin Han Cuixiao Qi Lei Song Shuangshuang Yang Kaixin Zhang Guoliang Zang Hong Pei Qingqing Lu Yonggang Peng Shuxue Xi Weiwei Wang Dawei Yuan Pingping Bing Liqian Zhou Geng Tian Geng Tian |
| author_sort | Xiaojun Liu |
| collection | DOAJ |
| description | Human blood contains cell-free DNA (cfDNA), with circulating tumor-derived DNAs (ctDNAs) widely used in cancer diagnosis and treatment. However, it is still difficult to efficiently and accurately identify and distinguish specific ctDNAs from normal cfDNA in cancer patient blood samples. In this study, ctDNA fragment length distribution analysis showed that ctDNA fragments are frequently shorter than the normal cfDNAs, which is consistent with previous findings. Interestingly, the ctDNA fragment length was found to be partially associated with the mutant allele frequency, with a low mutant allele frequency (< ~0.6%) associated with a longer ctDNA fragment length when compared to normal cfDNAs. The findings of this study contribute to improving the detection of low-frequency tumor mutations. |
| first_indexed | 2024-12-23T10:38:29Z |
| format | Article |
| id | doaj.art-0c7de90d34fa416e9c07b2dafd9517f0 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-23T10:38:29Z |
| publishDate | 2020-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-0c7de90d34fa416e9c07b2dafd9517f02022-12-21T17:50:14ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-02-011110.3389/fgene.2020.00147515133Fragment Enrichment of Circulating Tumor DNA With Low-Frequency MutationsXiaojun Liu0Jidong Lang1Shijun Li2Yuehua Wang3Lihong Peng4Weitao Wang5Yingmin Han6Cuixiao Qi7Lei Song8Shuangshuang Yang9Kaixin Zhang10Guoliang Zang11Hong Pei12Qingqing Lu13Yonggang Peng14Shuxue Xi15Weiwei Wang16Dawei Yuan17Pingping Bing18Liqian Zhou19Geng Tian20Geng Tian21School of Computer Science, Hunan University of Technology, Zhuzhou, ChinaBioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, ChinaDepartment of Pathology, Chifeng Municipal Hospital, Chifeng, ChinaDepartment of Pathology, Chifeng Municipal Hospital, Chifeng, ChinaSchool of Computer Science, Hunan University of Technology, Zhuzhou, ChinaBioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, ChinaBioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, ChinaBioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, ChinaBioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, ChinaBioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, ChinaBioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, ChinaBioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, ChinaBioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, ChinaBioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, ChinaBioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, ChinaBioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, ChinaBioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, ChinaBioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, ChinaAcademics Working Station, Changsha Medical University, Changsha, ChinaSchool of Computer Science, Hunan University of Technology, Zhuzhou, ChinaSchool of Computer Science, Hunan University of Technology, Zhuzhou, ChinaBioinformatics Department, Geneis (Beijing) Co. Ltd., Beijing, ChinaHuman blood contains cell-free DNA (cfDNA), with circulating tumor-derived DNAs (ctDNAs) widely used in cancer diagnosis and treatment. However, it is still difficult to efficiently and accurately identify and distinguish specific ctDNAs from normal cfDNA in cancer patient blood samples. In this study, ctDNA fragment length distribution analysis showed that ctDNA fragments are frequently shorter than the normal cfDNAs, which is consistent with previous findings. Interestingly, the ctDNA fragment length was found to be partially associated with the mutant allele frequency, with a low mutant allele frequency (< ~0.6%) associated with a longer ctDNA fragment length when compared to normal cfDNAs. The findings of this study contribute to improving the detection of low-frequency tumor mutations.https://www.frontiersin.org/article/10.3389/fgene.2020.00147/fulllow-frequency tumor mutationcell-free DNAcirculating tumor-derived DNAfragment length enrichmentmutant allele frequencynext generation sequencing |
| spellingShingle | Xiaojun Liu Jidong Lang Shijun Li Yuehua Wang Lihong Peng Weitao Wang Yingmin Han Cuixiao Qi Lei Song Shuangshuang Yang Kaixin Zhang Guoliang Zang Hong Pei Qingqing Lu Yonggang Peng Shuxue Xi Weiwei Wang Dawei Yuan Pingping Bing Liqian Zhou Geng Tian Geng Tian Fragment Enrichment of Circulating Tumor DNA With Low-Frequency Mutations Frontiers in Genetics low-frequency tumor mutation cell-free DNA circulating tumor-derived DNA fragment length enrichment mutant allele frequency next generation sequencing |
| title | Fragment Enrichment of Circulating Tumor DNA With Low-Frequency Mutations |
| title_full | Fragment Enrichment of Circulating Tumor DNA With Low-Frequency Mutations |
| title_fullStr | Fragment Enrichment of Circulating Tumor DNA With Low-Frequency Mutations |
| title_full_unstemmed | Fragment Enrichment of Circulating Tumor DNA With Low-Frequency Mutations |
| title_short | Fragment Enrichment of Circulating Tumor DNA With Low-Frequency Mutations |
| title_sort | fragment enrichment of circulating tumor dna with low frequency mutations |
| topic | low-frequency tumor mutation cell-free DNA circulating tumor-derived DNA fragment length enrichment mutant allele frequency next generation sequencing |
| url | https://www.frontiersin.org/article/10.3389/fgene.2020.00147/full |
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