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Survey Finds QC Best Practices in Clinical Genomics Still Developing

NEW YORK (GenomeWeb) – Quality control best practices are still evolving in clinical genomics, according to a survey conducted by SeraCare Life Sciences, a Massachusetts-based developer of laboratory quality control products, in conjunction with GenomeWeb.

The survey queried more than 150 individuals who perform next-generation sequencing in the clinical space about the quality control metrics they use, how they manage QC data, and the time they spend troubleshooting QC issues.

"The largest problem in the state of clinical NGS testing today is the lack of standardization and this survey shows that there is room for improvement across the board," Gregory Tsongalis, director of the Laboratory for Clinical Genomics and Advanced Technology at Dartmouth Hitchcock Medical Center, said in a statement. Tsongalis is a member of SeraCare's scientific advisory board.

Most of the respondents hold management positions in the lab, and most worked in oncology, followed by inherited disease and noninvasive prenatal testing, though there was overlap between the groups.

A third of survey respondents said they relied on commercially available controls, such as ones from SeraCare, Horizon Discovery, or Acrometrix, for their positive controls. About a quarter said they use cell lines, while 16 percent use patient specimens and 12 percent use a National Institute of Standards and Technology Genome in a Bottle reference.

The numbers varied a little when broken down by application, though commercial controls were always the most commonly used type of control. Of the respondents working in oncology, 42 percent said they use commercial controls, as compared to 25 percent of respondents working in inherited disease and 29 percent of those working in noninvasive prenatal testing.

But survey respondents reported inconsistent use of these positive controls. In general, 71 percent of respondents said they use a positive control every few runs, while 21 percent said they only use them on new lots. Eight percent said they never use a positive control.

Eighty-nine percent of NIPT respondents, though, said they use a positive control every few runs, as compared to 73 percent working in oncology and 63 percent in inherited disease.

When they do use positive controls, 42 percent of respondents said they measure more than 10 biomarkers, typically ones that are clinically relevant or test critical regions of their assay.

The respondents were split on how they manage their QC data. A little more than a third said they use a custom solution, another third said they rely on Excel, and just more than a quarter use a LIMS system. On average, respondents tracked 11 QC metrics, especially library DNA quantification, depth of coverage at a variant, and quality score. Other key metrics like reagent lot, operator, or instrumentation were not always tracked.

About half of respondents said they experience a QC stop every few months. These stops, they reported, were typically due to the control not passing, quality of the library prep, or instrument malfunction. On average, the stops took between one and three days to resolve.

SeraCare said the survey results suggest that standardizing QC management could help researchers improve quality and reduce the need for troubleshooting. 

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