Journal
GENOME BIOLOGY
Volume 18, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s13059-017-1191-5
Keywords
Cell-free DNA; Liquid biopsy; DNA methylation; Next-generation sequencing; Cancer diagnosis
Funding
- NHLBI MAPGEN [U01HL108634]
- NIH/NCI [1U01CA214182-01, 1U01CA196408-01]
- National Institutes of Health (NIH) [NHLBI MAPGEN] [U01HL108634]
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We propose a probabilistic method, CancerLocator, which exploits the diagnostic potential of cell-free DNA by determining not only the presence but also the location of tumors. CancerLocator simultaneously infers the proportions and the tissue-of-origin of tumor-derived cell-free DNA in a blood sample using genome-wide DNA methylation data. CancerLocator outperforms two established multi-class classification methods on simulations and real data, even with the low proportion of tumor-derived DNA in the cell-free DNA scenarios. CancerLocator also achieves promising results on patient plasma samples with low DNA methylation sequencing coverage.
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