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Control Charting Genomic Data.

Jing Xu1, Eric Crossley2, Jennifer Wagenfuehr2

  • 1Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX.

The Journal of Applied Laboratory Medicine
|December 15, 2020
PubMed
Summary
This summary is machine-generated.

Control charting effectively monitors clinical genomic next-generation sequencing (NGS) assay performance. This quality assurance method ensures reliable genomic testing by tracking sequencing coverage and identifying variations.

Keywords:
Levey-JenningsNA12878control chartepilepsygenomic

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Area of Science:

  • Genomics
  • Clinical Laboratory Science
  • Quality Assurance

Background:

  • Traditional clinical laboratory testing utilizes control charting for quality assurance.
  • Genomic tests, specifically next-generation sequencing (NGS) assays, are not routinely managed using control charting.
  • This study investigates the application of control charting for monitoring clinical NGS assay performance.

Purpose of the Study:

  • To evaluate the utility of control charting for quality assurance in clinical genomic testing.
  • To assess the impact of reagent lot changes on sequencing coverage in genomic regions.
  • To determine the correlation between control material and clinical sample performance.

Main Methods:

  • Retrospective analysis of 3 years of control material (NA12878) data from clinical genomic epilepsy testing.
  • Utilization of Levey-Jennings plots to visualize sequencing coverage depth in targeted genomic regions.
  • Correlation analysis of coverage depth changes with capture probe reagent lot changes and clinical sample data.

Main Results:

  • Lot changes in capture probe reagents significantly altered average and minimum sequencing coverage in numerous genomic regions.
  • Sensitivity to lot-to-lot variation differed between average and minimum coverage metrics.
  • Levey-Jennings plots effectively visualized coverage differences across reagent lots, with moderate correlation (r² = 0.45) between control material and clinical samples.

Conclusions:

  • Genomic control charting is a viable and routine method for clinical laboratories.
  • It enables effective monitoring of assay performance and ensures the quality of genomic testing.
  • Implementation of control charting enhances the reliability of clinical genomic data.