Occult specimen contamination in routine clinical next-generation sequencing testing

Jennifer K. Sehn, David H. Spencer, John D. Pfeifer, Andrew J. Bredemeyer, Catherine E. Cottrell, Haley J. Abel, Eric J. Duncavage

Research output: Contribution to journalArticlepeer-review

22 Scopus citations

Abstract

Objectives: To evaluate the extent of human-to-human specimen contamination in clinical next-generation sequencing (NGS) data. Methods: Using haplotype analysis to detect specimen admixture, with orthogonal validation by short tandem repeat analysis, we determined the rate of clinically significant (>5%) DNA contamination in clinical NGS data from 296 consecutive cases. Haplotype analysis was performed using read haplotypes at common, closely spaced single-nucleotide polymorphisms in low linkage disequilibrium in the population, which were present in regions targeted by the clinical assay. Percent admixture was estimated based on frequencies of the read haplotypes at loci that showed evidence for contamination. Results: We identified nine (3%) cases with at least 5% DNA admixture. Three cases were bone marrow transplant patients known to be chimeric. Six admixed cases were incidents of contamination, and the rate of contamination was strongly correlated with DNA yield from the tissue specimen. Conclusions: Human-human specimen contamination occurs in clinical NGS testing. Tools for detecting contamination in NGS sequence data should be integrated into clinical bioinformatics pipelines, especially as laboratories trend toward using smaller amounts of input DNA and reporting lower frequency variants. This study provides one estimate of the rate of clinically significant human-human specimen contamination in clinical NGS testing.

Original languageEnglish
Pages (from-to)667-674
Number of pages8
JournalAmerican journal of clinical pathology
Volume144
Issue number4
DOIs
StatePublished - Oct 2015

Keywords

  • Cancer
  • DNA contamination
  • Health care quality assurance
  • Next-generation sequencing
  • Quality improvement
  • Specimen provenance

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