Next-Generation Sequencing Settling Into the Laboratory
For many laboratories today, next-generation sequencing (NGS) is a test they send out, but it won’t always be. With new emerging technologies and platforms becoming more user-friendly, more large hospitals and large health systems will bring the testing in-house. Mayo Medical Laboratories is one of the early adopters of NGS and shared its experience with CAP TODAY.
According to Linnea Baudhuin, Ph.D., associate professor of laboratory medicine and pathology at Mayo Medical School and co-director of the clinical genome sequencing and personalized genomics laboratory at Mayo Clinic in Rochester, Minnesota, NGS is easier than ever to provide comprehensive genetic analysis to guide therapeutic decisions for patients with cancer, but it’s important to use resources wisely.
“Our physicians will initially say they want a large somatic gene panel, with 500, 100, or more genes, until they get their initial results back and they have all these variants of uncertain significance [VUS],” Dr. Baudhuin says. “Then they’ll say, ‘We don’t want all these genes. We just want the four or five genes strongly associated with this type of cancer.’”
Dr. Baudhuin discussed several tips for NGS testing, including:
- The most important factor in determining how many genes to include is a strong evidence base.
- Balance marketability with high clinical utility, which can be determined through literature and databases such as Online Mendelian Inheritance in Man (OMIM) and the Human Gene Mutation Database.
- When designing the reagent (nucleic acid probes), include hundreds of genes. The laboratory will capture all the genes but analyze and report only those that were ordered.
- Include probes/primers for genes that are of potential clinical utility but did not make the cut for ultimate inclusion in the orderable test.
- Aim for a good balance between maximum gene number, multiplexing, and optimal depth of coverage.
- Don’t spend a lot of time on genes that have pseudogenes or homologous regions.
Dr. Baudhuin added, “The larger the panel, the more time-consuming to the lab. A smaller lab would be wise to develop smaller panels to save on resources yet still provide clinically meaningful results.”
Read the full article for more information from Dr. Baudhuin and other industry experts.