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Nat Methods DOI:10.1038/s41592-018-0036-9

DeTiN: overcoming tumor-in-normal contamination.

Publication TypeJournal Article
Year of Publication2018
AuthorsTaylor-Weiner, A, Stewart, C, Giordano, T, Miller, M, Rosenberg, M, Macbeth, A, Lennon, N, Rheinbay, E, Landau, D-A, Wu, CJ, Getz, G
JournalNat Methods
Volume15
Issue7
Pages531-534
Date Published2018 07
ISSN1548-7105
KeywordsComputer Simulation, High-Throughput Nucleotide Sequencing, Humans, Mutation, Neoplasms, Sequence Analysis, DNA
Abstract

Comparison of sequencing data from a tumor sample with data from a matched germline control is a key step for accurate detection of somatic mutations. Detection sensitivity for somatic variants is greatly reduced when the matched normal sample is contaminated with tumor cells. To overcome this limitation, we developed deTiN, a method that estimates the tumor-in-normal (TiN) contamination level and, in cases affected by contamination, improves sensitivity by reclassifying initially discarded variants as somatic.

DOI10.1038/s41592-018-0036-9
Pubmed

https://www.ncbi.nlm.nih.gov/pubmed/29941871?dopt=Abstract

Alternate JournalNat Methods
PubMed ID29941871
PubMed Central IDPMC6528031
Grant ListP01 CA206978 / CA / NCI NIH HHS / United States
R01 CA184922 / CA / NCI NIH HHS / United States
R01 CA182461 / CA / NCI NIH HHS / United States
T32 HG002295 / HG / NHGRI NIH HHS / United States
U24 CA143845 / CA / NCI NIH HHS / United States
U10 CA180861 / CA / NCI NIH HHS / United States