Comment on "DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification"

Chip Stewart; Ignaty Leshchiner; Julian Hess; Gad Getz

doi:10.1126/science.aas9824

Comment on "DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification"

Science. 2018 Sep 28;361(6409):eaas9824. doi: 10.1126/science.aas9824.

Authors

Chip Stewart¹, Ignaty Leshchiner¹, Julian Hess¹, Gad Getz^{2

3

4}

Affiliations

¹ Broad Institute of MIT and Harvard, Cambridge, MA 02124, USA.
² Broad Institute of MIT and Harvard, Cambridge, MA 02124, USA. gadgetz@broadinstitute.org.
³ Massachusetts General Hospital Cancer Center and Department of Pathology, Boston, MA 02114, USA.
⁴ Harvard Medical School, Boston, MA 02115, USA.

Abstract

Chen et al (Reports, 17 February 2017, p. 752) highlight an important problem of sequencing artifacts caused by DNA damage at the time of sample processing. However, their manuscript contains several errors that led the authors to incorrect conclusions. Moreover, the same sequencing artifacts were previously described and mitigated in The Cancer Genome Atlas and other published sequencing projects.

Publication types

Comment

MeSH terms

Artifacts*
DNA Damage*
High-Throughput Nucleotide Sequencing
Humans
Neoplasms / genetics
Sequence Analysis, DNA

Grants and funding

U24 CA210999/CA/NCI NIH HHS/United States