The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Fragment Length of Circulating Tumor DNA
Open accessAbstract
Malignant tumors shed DNA into the circulation. The transient half-life of circulating tumor DNA (ctDNA) may afford the opportunity to diagnose, monitor recurrence, and evaluate response to therapy solely through a non-invasive blood draw. However, detecting ctDNA against the normally occurring background of cell-free DNA derived from healthy cells has proven challenging, particularly in non-metastatic solid tumors. In this study, distinct differences in fragment length size between ctDNAs and normal cell-free DNA are defined. Human ctDNA in rat plasma derived from human glioblastoma multiforme stem-like cells in the rat brain and human hepatocellular carcinoma in the rat flank were found to have a shorter principal fragment length than the background rat cell-free DNA (134-144 bp vs. 167 bp, respectively). Subsequently, a similar shift in the fragment length of ctDNA in humans with melanoma and lung cancer was identified compared to healthy controls. Comparison of fragment lengths from cell-free DNA between a melanoma patient and healthy controls found that the BRAF V600E mutant allele occurred more commonly at a shorter fragment length than the fragment length of the wild-type allele (132-145 bp vs. 165 bp, respectively). Moreover, size-selecting for shorter cell-free DNA fragment lengths substantially increased the EGFR T790M mutant allele frequency in human lung cancer. These findings provide compelling evidence that experimental or bioinformatic isolation of a specific subset of fragment lengths from cell-free DNA may improve detection of ctDNA.
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Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer
Dawson, S.-J., Tsui, D. W. Y., Murtaza, M., Biggs, H., Rueda, O. M., Chin, S.-F., Dunning, M. J., Gale, D., Forshew, T., Mahler-Araujo, B., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1213261 · Cited by 2,207
Detecting ultralow-frequency mutations by Duplex Sequencing
Kennedy, S. R., Schmitt, M. W., Fox, E. J., Kohrn, B. F., Salk, J. J., Ahn, E. H., Prindle, M. J., Kuong, K. J., Shen, J.-C., Risques, R.-A., et al. (2014) · Nature Protocols · doi:10.1038/nprot.2014.170 · Cited by 503 · cited 1×
“Libraries for Illumina high throughput sequencing were prepared using the KAPA biosystems Hyper Prep Kit with 10 ng input cell-free DNA according to the manufacturer’s instructions using truncated duplex molecular barcode adapters [37].”
MethodQuantitative Detection of EGFR Mutations in Circulating Tumor DNA Derived from Lung Adenocarcinomas
Taniguchi, K., Uchida, J., Nishino, K., Kumagai, T., Okuyama, T., Okami, J., Higashiyama, M., Kodama, K., Imamura, F., & Kato, K. (2011) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-11-1712 · Cited by 315
Cited by
A view on drug resistance in cancer
Vasan, N., Baselga, J., & Hyman, D. M. (2019) · Nature · doi:10.1038/s41586-019-1730-1 · Cited by 2,770
Liquid biopsies come of age: Towards implementation of circulating tumour DNA
Wan, J. C. M., Massie, C., Garcia-Corbacho, J., Mouliere, F., Brenton, J. D., Caldas, C., Pacey, S., Baird, R., & Rosenfeld, N. (2017) · Nature Reviews Cancer · doi:10.1038/nrc.2017.7 · Cited by 2,809
Current and future perspectives of liquid biopsies in genomics-driven oncology
Heitzer, E., Haque, I. S., Roberts, C. E. S., & Speicher, M. R. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-018-0071-5 · Cited by 1,557
Genome-wide cell-free DNA fragmentation in patients with cancer
Cristiano, S., Leal, A., Phallen, J., Fiksel, J., Adleff, V., Bruhm, D. C., Jensen, S. Ø., Medina, J. E., Hruban, C., White, J. R., et al. (2019) · Nature · doi:10.1038/s41586-019-1272-6 · Cited by 1,476
Enhanced detection of circulating tumor DNA by fragment size analysis
Mouliere, F., Chandrananda, D., Piskorz, A. M., Moore, E. K., Morris, J., Ahlborn, L. B., Mair, R., Goranova, T., Marass, F., Heider, K., et al. (2018) · Science Translational Medicine · doi:10.1126/scitranslmed.aat4921 · Cited by 1,069
Metadata
- Authors
- Underhill, H. R., Kitzman, J. O., Hellwig, S., Welker, N. C., Daza, R., Baker, D. N., Gligorich, K. M., Rostomily, R. C., Bronner, M. P., & Shendure, J.
- Venue
- PLOS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2016-07-18
- Volume
- 12
- Issue
- 7
- Pages
- e1006162
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- OpenAlex
- W2479773785
- Cited by
- 671
- References
- 5
- FWCI
- 24.63
- Type
- journal article
- Language
- en
- Open access
- gold
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- CoChat. (2026). Citation check: Fragment Length of Circulating Tumor DNA. https://app.cochat.ai/papers/10.1371/journal.pgen.1006162
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- Underhill, H. R., Kitzman, J. O., Hellwig, S., Welker, N. C., Daza, R., Baker, D. N., Gligorich, K. M., Rostomily, R. C., Bronner, M. P., & Shendure, J. (2016). Fragment Length of Circulating Tumor DNA. PLOS Genetics. https://doi.org/10.1371/journal.pgen.1006162
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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