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September 25th, 2017

Study evaluates effectiveness of deep genomic profiling in clinical setting

By Colette Gallagher

Genomic profiling is used today for patients with advanced cancers to help develop new ways to diagnose and treat their disease and offer an individualized treatment plan. While gene panel testing is relatively commonplace, there are many barriers to using new and more sophisticated DNA technologies.

According to Mitesh Borad, M.D., an oncologist at the Mayo Clinic campus in Arizona, there are two key obstacles to applying advanced DNA testing to cancers.

First, this type of approach is cost prohibitive for many patients. Insurance coverage is inconsistent for whole exomes, RNA sequencing and structural genomic assays and some patients may have to pay out-of-pocket.

Second,  it takes a large multi-disciplinary team (bioinfomaticians, lab scientists, oncologists) typically found only at large academic cancer centers.

Mitesh Borad, M.D.

To better understand these obstacles, Dr. Borad and a team of researchers pursued a genomic deep dive using clinical grade testing to better understand the impact.

The study, in Nature Scientific Reports, represents one of the earliest published efforts to date of Clinical Laboratory Improvement Amendments (CLIA)-enabled integrated deep genomic profiling for the identification of therapeutic targets in patients with advanced cancer.

The researchers pursued three objectives:

  1. Determine how much time it takes to complete integrated whole exome/long insert whole genome/transcriptome sequencing.
  2. Estimate how much time it takes to report results of therapeutically relevant drug targets derived from integrated whole exome/long-insert whole genome/whole transcriptome sequencing, along with CLIA validation.
  3. Determine process of drug access.

As a result of the study, researchers determined integrated genomic profiling in a CLIA enabled workflow was successfully demonstrated in a consistent fashion in patients with complex disease diagnosis.

“It is anticipated that with development of faster sequencing, better informatics tools and automation and drop in costs (e.g. recent announcement of potential for a $100 genome) that this will become more broadly applicable and the work presented in the study along with other complementary efforts in the field will lay a groundwork for future activities,” says Dr. Borad.

The study also provides a contextual framework to incorporate other genomic analyses into the workflow as therapeutics using these approaches enter the clinic and their role in therapeutic response prediction is better defined.

This study was supported by: NIH/NCI 1DP2CA195764, and the Mayo Clinic Center for Individualized Medicine. Dr. Borad has been involved in implementation of genome wide assays into molecular profiling efforts in early phase studies since 2007.

Register to attend Individualizing Medicine 2017 and learn more about pharmacogenomics 

Join us to learn more about bringing precision medicine into practice at Individualizing Medicine 2017: Advancing Care Through Genomics.

The Mayo Clinic Center for Individualized Medicine is hosting the sixth annual genomics conference October 9–10, in Rochester, Minnesota.

Explore all conference offerings:

Mayo Clinic Center for Individualized Medicine is hosting the conference with support from the Jackson Family Foundation.

Tags: #cancer treatment, #CIMCon17, #Dr. Mitesh Borad, #genetic profiling, #Individualizing Medicine 2017, #long-insert whole genome, #Nature scientific Reports, #targeted therapies, #whole transcriptome sequencing, Advanced Cancer, center for individualized medicine, mayo clinic, Precision Medicine, whole exome sequencing

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