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
2015 American Journal of Clinical Pathology  
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 singlenucleotide polymorphisms in low linkage
more » ... isms 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.
doi:10.1309/ajcpr88wdjjldmbn pmid:26386089 fatcat:ogu3o4un7velhlpvwvckwfdzxi