Occult Specimen Contamination in Routine Clinical Next-Generation Sequencing Testing.

Area of Science:

• Clinical diagnostics
• Genomics
• Bioinformatics

Background:

• Clinical next-generation sequencing (NGS) is increasingly used for diagnosis.
• Specimen contamination can lead to inaccurate results.
• Human-to-human specimen contamination is a potential issue in clinical NGS workflows.

Purpose of the Study:

• To quantify the prevalence of human-to-human specimen contamination in clinical NGS data.
• To assess the rate of clinically significant DNA contamination (>5%).

Main Methods:

• Haplotype analysis was employed to detect specimen admixture.
• Short tandem repeat (STR) analysis was used for orthogonal validation.
• Analysis of 296 consecutive clinical NGS cases.

Main Results:

• Nine cases (3%) exhibited at least 5% DNA admixture.
• Three of these were known bone marrow transplant chimeras.
• Six cases represented contamination, strongly correlated with DNA yield.

Conclusions:

• Human-to-human specimen contamination occurs in clinical NGS testing.
• Detection tools are crucial for clinical bioinformatics pipelines, especially with decreasing input DNA and lower variant frequency reporting.
• This study provides an estimate of contamination rates in clinical NGS.