January 26, 2016

Next-Generation Sequencing Settling Into the Laboratory

By Jeff Briggs

ngs panel

Thanks to next-generation sequencing, it’s now easier than ever to provide comprehensive genetic analysis to guide therapeutic decisions for patients with cancer, but it’s important to use resources wisely, says Linnea Baudhuin, Ph.D. Dr. Baudhuin is an 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, Minn.

For many laboratories today, next-generation sequencing is a test they send out, but it won’t always be. With new emerging technologies and platforms becoming more user-friendly, larger hospitals and health systems will bring the testing in-house. Mayo Medical Laboratories is one of the early adopters of next-generation sequencing.

Mayo Medical Laboratories is a global reference laboratory operating within Mayo Clinic's Department of Laboratory Medicine and Pathology. Its staff collaborates with clinicians, including those at the Center for Individualized Medicine, to provide knowledge of, and access to, the latest testing and treatment guidance. It works in collaboration with and support of the many specialists at the Center for Individualized Medicine to provide expert, whole-person care to everyone who needs healing.

Dr. Baudhuin recently shared her experiences with next-generation sequencing with CAP TODAY

Dr. Linnea Baudhuin

Dr. Linnea Baudhuin

“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 next generation sequencing 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 in CAP TODAY for more information from Dr. Baudhuin and other industry experts on next-generation sequencing.

 * * *

 To stay abreast of the latest developments at Mayo Medical Laboratories, follow all the news on its excellent blog.

Tags: center for individualized medicine, Department of Laboratory Medicine and Pathology, DLMP, Dr. Linnea Baudhuin, mayo medical laboratories, MML, next generation sequencing, Uncategorized

Contact Us · Privacy Policy