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Where’s the truth? Thoughts from the GIAB Conference

Author: Spiral ⋅ Categories: Industry Trends, News from Spiral ⋅ Modified on: Sep. 9, 2014

Sitting in the auditorium at NIST, fortified by my 75-cent tea from their café, and waiting for the GIAB conference to start, I couldn’t help but wonder whether the clock on the wall was linked to the atomic clock.  Before accurate, portable, timekeepers, how did people arrange meetings?  The benefit of accurate timekeeping is virtually invisible in our modern world.  Standardization is sometimes crucial to move to the next stage of development. This was the case for container shipping, for property rights in postwar Japan, for the development of the typewriter, bed sizes, door frame sizes, automobile operation, light bulb fixtures, and more. 

Next generation sequencing, by the nature of the data produced, is susceptible to uncertainty in interpretation. Having a set of known variants in one individual is important to be able to compare different methods of analysis, whether sequencing chemistry or bioinformatics. We often use the GIAB set with customers to compare our method with other methods. We are happy to work with the consortium to develop a validated set of high confidence structural variants for NA12878.

The trend at this meeting was certainly toward getting a truth set for structural variants in NA12878, as well as developing truth sets for other ancestral lines from the Personal Genomes Project. Certainly, a truth set for a real tumor/ normal sample is not far off. 

We appreciate the hospitality.

http://www.slideshare.net/GenomeInABottle/aug2014-spiral-genetics-anchored-assembly

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