Twenty six competing teams set out to find answers for five undiagnosed patients


Tuesday, September 8, 2015


Keri Stedman

Boston Children’s Hospital


Twenty six competing teams set out to find answers for five undiagnosed patients

Boston Children’s Hospital challenge seeks to add “CLARITY” to DNA diagnostics

Boston Children’s Hospital today announced the launch of the CLARITY Undiagnosed competition. Through it, 26 registered teams from around the world are vying to interpret DNA sequences and solve the medical “mysteries” of five patients with undiagnosed conditions, setting new standards for genomic medicine.

Results will be announced at Boston Children’s Hospital’s Global Pediatric Summit + Awards (Boston Seaport Hotel, Nov. 9-10, #PedInno15) by Alan Beggs, PhD, co-organizer of CLARITY Undiagnosed and director of the hospital’s Manton Center for Orphan Disease Research, and Catherine Brownstein, MPH, PhD, director of the hospital’s Molecular Genomics Core Facility.

Genomic sequencing technology is advancing rapidly, but best practices for interpreting the information and using it to help patients have been slower to evolve. Participants in the $25,000 competition will be judged by an independent panel on their ability to provide clinically useful, actionable reports.

“There are more than 7,000 rare or ‘orphan’ diseases, so it’s quite common for a patient’s physician to have never seen a similar case,” says Beggs. “Families can go for years without a diagnosis, feeling isolation and sometimes despair. The promise of discovering the genetic basis for their condition allows patients to form communities and physicians to provide accurate prognostic predictions, genetic counseling and appropriate targeted therapies.”

The five patients were identified through the producers of a forthcoming documentary film, Undiagnosed. Independent of the CLARITY Undiagnosed Challenge, the filmmakers plan to chronicle the competing teams’ efforts with the teams’ permission. The patients and families will remain anonymous for the duration of the Challenge. Contestants have a deadline of September 21 to submit their sequencing findings and reports.

“It’s quite revealing that these top-notch teams come from a wide variety of commercial and academic groups,” says co-organizer Isaac Kohane, MD, PhD, chair of the Department of Biomedical Informatics at Harvard Medical School. “It shows the market has yet to decide where best to find robust clinical genomics expertise.”

All contestants received raw DNA sequence data in July—both whole-genome and whole-exome sequences—accompanied by de-identified clinical data from the five patients and their immediate relatives.

CLARITY (Children’s Leadership Award for the Reliable Interpretation and Transmission of Your genomic information) conducted its first challenge in 2012 with the goal of creating a framework for using genomics responsibly.

“In 2012, many of the computational methods for analyzing vast amounts of genetic sequences were just being worked out,” says Beggs, also a professor of Pediatrics at Harvard Medical School. “Today, those methods are well established, but medical genetic interpretation to determine which of the thousands of genetic variants may be disease-causing remains a hurdle, as does accurately, concisely and clearly presenting this complex information to patients and caregivers. In CLARITY Undiagnosed, we are hoping to see innovative new approaches to these problems.” 

Challenge contestants include teams from seven countries:

Bina Technologies (Redwood City, CA)

  1. Centre for Genomic Regulation (CRG) (Barcelona, Spain)
  2. Clinical Institute of Medical Genetics (Ljubljana, Slovenia)
  3. Codified Genomics, LLC (Houston, TX)
  4. Emory University School of Medicine (Atlanta, GA)
  5. Enlis Genomics (Berkeley, CA)
  6. Geisinger Health System (Danville, PA) and SimulConsult (Chestnut Hill, MA)
  7. (Austin, TX)
  8. Genomatix Software GmbH (Munich, Germany)
  9. Institute for Systems Biology (ISB) (Seattle, WA) and Inova Translational Medicine Institute (ITMI) (Falls Church, VA)
  10. intelliseq (Krakow, Poland)
  11. Invitae Corporation (San Francisco, CA)
  12. Mendelics (Sao Paulo, Brazil)
  13. Miti Medicine Inc. (Cambridge, MA)
  14. Nationwide Children’s Hospital (Columbus, OH)
  15. QIAGEN (Redwood, CA)
  16. Rare Genomics Institute (Hanover, MD)
  17. Seven Bridges Genomics (Cambridge, Massachusetts)
  18. SNPedia (Potomac, MD)
  19. SolveBio (New York, NY)
  20. Stanford University (Stanford, CA)
  21. University of Southern California (Los Angeles, CA)
  22. University of Utah (Salt Lake City, UT)
  23. Tel Aviv University (Tel Aviv, Israel), and Variantyx Ltd (Ashland, MA)
  24. Tute Genomics (Provo, Utah)
  25. WuXi NextCODE Genomics (Cambridge, MA)

Full information about the Challenge is available online at

Boston Children’s Hospital is home to the world’s largest research enterprise based at a pediatric medical center, where its discoveries have benefited both children and adults since 1869. More than 1,100 scientists, including seven members of the National Academy of Sciences, 11 members of the Institute of Medicine and 10 members of the Howard Hughes Medical Institute comprise Boston Children’s research community. Founded as a 20-bed hospital for children, Boston Children’s today is a 397-bed comprehensive center for pediatric and adolescent health care. Boston Children’s is also the pediatric teaching affiliate of Harvard Medical School. For more, visit our Answers blog and follow us on our social media channels: @BostonChildrens, @BCH_Innovation, Facebook and YouTube

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