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Thirty teams compete to interpret three families’ genomes

Monday, August 20, 2012

In a contest led by Boston Children’s Hospital, 30 teams from around the world are vying to interpret the DNA sequences of three children with rare conditions whose cause remains a mystery—with the goal of establishing “best practices” for interpreting genomic data.

Participants in the competition, known as the CLARITY challenge, range from small biotech startups to the National Institutes of Health, representing the U.S., Canada, China, India, Israel, Italy, Germany, The Netherlands, Singapore, Slovenia, Spain, Switzerland and Sweden.

Results of the challenge will be announced in November at the American Society of Human Genetics annual meeting in San Francisco by the contest’s organizers—David Margulies, MD, executive director of The Gene Partnership at Boston Children’s, Isaac Kohane, MD, PhD, director of the hospital’s informatics program, and Alan Beggs, PhD, director of the Manton Center for Orphan Disease Research at the hospital.

The goals of CLARITY (Children’s Leadership Award for the Reliable Interpretation and Transmission of Your genomic information) are to address technical and bioinformatics questions in analyzing DNA sequence results, bring standardization to the analysis of genetic variants and generate a comprehensive, actionable report that can guide decision-making by doctors, genetic counselors and patients. Contestants have a deadline of September 30 to submit their findings and reports.

“The last major barrier to widespread clinical use of DNA sequencing is the creation of accurate, understandable interpretations of sequence findings for doctors and patients,” said Margulies, also affiliated with the Center for Biomedical Informatics, Harvard Medical School. “The goal of this contest is to define norms, standards and models for reporting findings from exomes and genomes. We are excited about the number and quality of participants, and we look forward to seeing their entries.”

All contestants have been given raw DNA sequence data (both whole-genome and whole-exome sequences) and de-identified clinical data from three children and their immediate relatives identified by The Manton Center for Orphan Disease Research at Boston Children’s.

Of the three children, two have a neuromuscular disorder and the third a cardiovascular disorder. While all three are believed to have a genetic cause for their disorder, they have come up negative on all known genetic tests.

“Traditional genetic tests examine our genes one by one, requiring doctors to have a good idea ahead of time which of our roughly 20,000 genes is the likely cause,” said Beggs, also a professor of pediatrics at Harvard Medical School. “The beauty of whole-genome sequencing is that it provides results for virtually all of our genes at once. The challenge for our contestants is to pick out that one disease-causing mutation from the vast numbers of genetic differences that make each of us unique.”

Contest sponsors Life Technologies and Complete Genomics generated the genome sequences being used in the challenge. Boston Children’s will award a prize of $25,000 to the winning research team, which will be selected by a panel of judges according to pre-specified criteria.

“We wanted researchers at small institutions and startups, anywhere in the world, to be able to compete with the ‘big boys’ of genomics and in so doing find better solutions,” said Kohane, who co-directs the Center for Biomedical Informatics at Harvard Medical School. “This contest gives everyone a level playing field on which to innovate.”

Challenge contestants include:

1. BGI (Shenzhen, China)

2. Brigham and Women’s Hospital, Division of Genetics (Boston, Mass.)

3. British Columbia Cancer Agency (Vancouver, Canada)

4. Children’s Hospital of Eastern Ontario (Ottawa, Canada)

5. Clinical Institute of Medical Genetics (Ljubljana, Slovenia)

6. Genedata AG (Basel, Switzerland)

7. Genomatix (Munich, Germany), CeGaT (Tübingen, Germany), Institute of Pathology, University Hospital of Bonn (Bonn, Germany)

8. Genome Institute of Singapore Agency for Science, Technology and Research (A*STAR) (Biopolis, Singapore)

9. HudsonAlpha Institute for Biotechnology (Huntsville, Ala.)

10. Institute for Systems Biology (Seattle, Wash.)

11. IRCCS Casa Sollievo della Sofferenza (San Giovanni Rotondo, Foggia, Italy)

12. National Institutes of Health (Bethesda, Md.)

13. NextBio (Santa Clara, Calif.)

14. Omicia, Inc. (Emeryville, Calif.)

15. Pearlgen (Chapel Hill, N.C.)

16. Radboud University Nijmegen Medical Center (Nijmegen, The Netherlands)

17. Sanofi  (Cambridge, Mass.)

18. Science For Life Laboratory (SciLifeLab), Karolinska Institute (Solna, Sweden)

19. Scripps Genomic Medicine, Scripps Translational Science Institute (San Diego, Calif.)

20. Seven Bridges Genomics (Cambridge, Mass.)

21. SimulConsult/Geisinger (Chestnut Hill, Mass. / Danville, Penn.)

22. SNPedia (Potomac, Md).

23. Strand Life Sciences (Bangalore, India)

24. Tel Aviv University (Israel)

25. The Medical College of Wisconsin (Milwaukee, Wis.)

26. The Research Institute at Nationwide Children’s Hospital (Columbus, Ohio)

27. The University of Texas Health Science Center at Houston, The Brown Foundation Institute of Molecular Medicine (Houston, Texas)

28. Universidad de Cantabria (Santander, Spain)

29. University of Iowa (Iowa City, Iowa)

30. Yale School of Public Health, Division of Biostatistics (New Haven, Conn.)

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