Format

Send to

Choose Destination
Nat Methods. 2018 Jul;15(7):531-534. doi: 10.1038/s41592-018-0036-9. Epub 2018 Jun 25.

DeTiN: overcoming tumor-in-normal contamination.

Author information

1
Broad Institute of Harvard and MIT, Cambridge, MA, USA.
2
Harvard University, Cambridge, MA, USA.
3
Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
4
Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
5
Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
6
New York Genome Center, New York, NY, USA.
7
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
8
Department of Internal Medicine, Brigham and Women's Hospital, Boston, MA, USA.
9
Department of Medicine, Harvard Medical School, Boston, MA, USA.
10
Broad Institute of Harvard and MIT, Cambridge, MA, USA. gadgetz@broadinstitute.org.
11
Department of Pathology, Harvard Medical School, Boston, MA, USA. gadgetz@broadinstitute.org.
12
Cancer Center, Massachusetts General Hospital, Boston, MA, USA. gadgetz@broadinstitute.org.
13
Department of Pathology, Massachusetts General Hospital, Boston, MA, USA. gadgetz@broadinstitute.org.

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.

PMID:
29941871
DOI:
10.1038/s41592-018-0036-9

Supplemental Content

Full text links

Icon for Nature Publishing Group
Loading ...
Support Center