Coming of Age: Whole Exome Sequencing

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Whole exome sequencing (WES) is an efficient way to identify genetic variants in all of an individual's genes. It does this by sequencing the functionally relevant regions of approximately 20,000 genes of the human genome.  Compared to traditional genetic testing trajectory, which tends to be more time-consuming, recent studies indicate WES can provide better results at a lower overall cost to the healthcare system. A growing number of clinicians now view this test as a more comprehensive diagnostic tool that can be used to streamline the genetic assessment of their patients.  To support this growing demand, more and more, commercial labs are adding WES tests to their test menu.1 

Along with other innovative firsts in the genetic testing industry, Ambry Genetics was the first commercial lab to offer WES.  Introduced in 2011, Ambry’s first-to-market WES test has helped multiple patients and families and now has assembled one of the biggest WES database in the industry. These archives, combined with data from other commercial labs has helped to increase the diagnostic rate of WES. Today, the diagnostic rate ranges from 25-35%2-9 and is 2-3 times more likely than traditional genetic testing trajectory to identify the underlying causes of a patient’s genetic condition.10-14   With the explosion of newly identified gene-disease discoveries, the rate of diagnosis from WES will undoubtedly continue to rise. 

Along with an improved diagnosis rate, the use of WES can also lead to significant cost savings to patients and the overall healthcare system.  Recent studies have shown that the use of WES is only 25-50% the cost of traditional genetic testing trajectory.14-16 Moreover, the use of WES as a first line test compared to standard clinical practices saves $1,000 to $7,640 per case.12,14,17  While these studies provide strong data to support the cost-effectiveness of WES, reimbursement for exome-specific tests remain low, and significant less than prenatal and hereditary cancer testing.1        

With the broader use of exome testing, there is increasing evidence supporting the increased clinical utility of this comprehensive test, compared to traditional genetic testing trajectory.  Additionally, more studies are expected to support the significant cost-savings by using clinical exome compared to traditional genetic testing trajectory. 

When Ambry launched the industry’s first WES test seven year ago, we believed it would eventually become the definitive diagnostic genetic test by helping patients find answers and lower the overall cost savings to the healthcare system.  Today, with strong clinical evidence to support its effective use and economic data to demonstrate its cost savings, we see the realization of our vision.  Despite the reimbursement hurdles, we are encouraged by the advantages exome testing brings and most importantly the positive impact it is having on patient care.



  1. “The Current Landscape of Genetic Testing  – 2018 Edition.” Concert Genetics, Apr. 2018,
  2. Farwell KD, Shahmirzadi L, El-Khechen D, et al. Genet Med. 2015;17(7):578-586.
  3. Farwell Hagman KD, Shinde DN, Mroske C, et al. Genet Med. 2016.
  4. Yang Y, Muzny DM, Reid JG, et al. N. Engl. J. Med. 2013;369(16):1502-1511.
  5. Yang Y, Muzny DM, Xia F, et al. JAMA. 2014;312(18):1870-1879.
  6. Lee H, Deignan JL, Dorrani N, et al. JAMA. 2014;312(18):1880-1887.
  7. Srivastava S, Cohen JS, Vernon H, et al. Ann Neurol. 2014;76(4):473-483.
  8. Iglesias A, Anyane-Yeboa K, Wynn J, et al. Genet Med. 2014.
  9. Retterer K, Juusola J, Cho MT, et al. Genet Med. 2016;18(7):696-704.
  10. Shashi V, McConkie-Rosell A, Rosell B, et al. Genet Med. 2013.
  11. Vissers LE, van Nimwegen KJ, Schieving JH, et al. Genet Med. 2017.
  12. Stark Z, Schofield D, Alam K, et al. Genet Med. 2017;19(8):867-874.
  13. Gomez CM, Das S. JAMA Neurol. 2014;71(10):1215-1216.
  14. Monroe GR, Frederix GW, Savelberg SM, et al. Genet Med. 2016;18(9):949-956.
  15. Dixon-Salazar TJ, Silhavy JL, Udpa N, et al. Sci. Transl. Med. 2012;4(138):138ra178.
  16. Martin HC, Kim GE, Pagnamenta AT, et al. Hum. Mol. Genet. 2014;23(12):3200-3211.
  17. Soden SE, Saunders CJ, Willig LK, et al. Sci. Transl. Med. 014;6(265):265ra168.

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