Spotlight on Children’s Health℠ Dallas Sequencing support for the smallest patients
The wealth of critical data generated through next-generation sequencing (NGS) helps providers understand both inherited and somatic illness, include rare diseases, congenital disorders and multiple types of cancers. Diagnosis of inherited diseases is often carried out during pediatric care. Sunquest Mitogen™ Genetics, a support tool that aids in NGS analysis with functionality to conduct variant filtration, annotation, classification and interpretation.
For this blog post, we’ll share a Q&A we recently conducted with Eric Crossley, advanced diagnostics assay development specialist at Children’s Health℠, to learn more about how the site’s clinical genomics lab – the advanced diagnostics lab – has improved operations, and thereby care, through use of the tool.
Sunquest: Great to speak with you, Eric. Can you give us an overview of the advanced diagnostics lab in terms of the type of testing you do and when you started working with Sunquest?
Eric: Thanks for having me, and sure. Our lab handles all clinical genomics testing for the Children’s Health, the eighth largest pediatric healthcare provider in the nation and the leading pediatric healthcare system in North Texas. Currently, we offer thirteen different multi-gene sequencing panels (in addition to our single gene testing) to help us diagnose inherited disease. Twelve of the thirteen panels cover different sets of disease states – for example, one panel is for epilepsy. Our thirteenth and latest multi-gene sequencing panel is a medical exome panel, which rather than being disease-specific, analyzes the entire portion of the human genome responsible for all clinically relevant phenotypic expression. Our first multi-gene sequencing panel was developed in 2014.
Sunquest: Why were you looking for NGS analysis support software? What capabilities were important to you?
Eric: As I mentioned, our first multi-gene sequencing panel was created in 2014 and then by the end of 2016 we had all twelve disease-state panels created. The exome panel was developed in 2018. However, none of our NGS analysis workflows had been significantly updated since 2014. We began looking for a support solution in 2017 because we knew there had been lots of improvements in knowledge, evidence, and interpretation, but trying to update our processes ourselves and then maintain them would have been a nearly impossible task, in terms of time and accuracy. We now use a system that is cloud-based, which allows us to easily update references and use current evidence, and we’ve reduced the number of vendors we work with from seven to three. Most importantly, we are assessing clinical implications now with current information in a more streamlined, user-friendly fashion and we became much more confident in our interpretations.
Sunquest: Great to hear about the reduction in vendors! Are there any other operational or clinical improvements you can share?
Eric: Operationally, we’ve seen reductions in labor/billable time per sample. We’ve also seen a reduction in the number of variants needing review. Anytime you can increase speed with fewer resources, you’re improving the care pathway. These types of improvements have clinical translations. Also, as we rolled our variant database over we uncovered many data entry errors which have now been corrected for future clinical interpretations. Using this tool has been incredibly helpful in our bi-annual clinical variant review – what before was a very manual process is now streamlined and less prone to error because of the software. Some numbers I can share include:
• Our processing time per sample went from 1.5-8.5 hours per sample to 45 minutes-2 hours per sample. Reductions were seen across all levels of review, from lab tech to genetic counselor to medical director.
• Across a set of six different patient samples, the average number of variants needing review went from 67 to just 14. One of these samples went from 33 variants to 5 – an 85 percent reduction. Across our whole sample set, the average number of variants per sample went from 10 to 2 – an 80 percent reduction. The variants no longer needing review were in fact benign or likely benign, which allow us to focus our time and attention on the variants most in need of interpretation.
Sunquest: Wow. That is incredible. Well done on all of Children’s Health’s efforts to streamline your genetic analysis approach and deliver outstanding care.
Eric: It’s been great to see. Thank you
About the author
Director of Product Marketing, Precision Medicine
Having worked exclusively in health technology organizations for more than fifteen years, Kiran is passionate about innovations in patient care.