Nature Comment : The case for locus-specific databases

There’s an interesting comment available in Nature today (EDIT: it came out last month, though I only found it today.) Unfortunately, it’s by subscription only, but let me save you the hassle of downloading it, if you don’t already have a subscription.  It’s not what I thought it was.

The entire piece fails to make the case for locus-specific databases, but instead conflates locus-specific with “high-resolution”, and then proceeds to tell us why we need high resolution data.  The argument can roughly be summarized as:

  • Omim and databases like it are great, but don’t list all known variations
  • Next-gen sequencing gives us the ability to see genome in high resolution
  • You can only get high-resolution data by managing data in a locus-specific manner
  • Therefore, we should support locus-specific databases

Unfortunately, point number three is actually wrong.  It’s just that our public databases haven’t yet transitioned to the high resolution format.  (ie, we have an internal database that stores data in a genome-wide manner at high resolution…  the data is, alas, not public.)

Thus, on that premise, I don’t think we should be supporting locus specific databases specifically –  indeed, I would say that the support they need is to become amalgamated in to a single genome-wide database at high resolution.

You wouldn’t expect major gains in understanding of car mechanics if you, by analogy, insisted that all parts should be studied independently at high resolution.  Sure you might improve your understanding of each part, and how it works alone, but the real gains come from understanding the whole system.  You might not actually need certain parts, and sometimes you need to understand how two parts work together.  It’s only by studying the whole system that you begin to see the big picture.

IMHO, Locus-specific databases are blinders that we adopt in the name of needing higher resolution, which is more of a comment on the current state of biology.  In fact, the argument can really be made that we don’t need locus-specific databases, we need better bioinformatics!

2 thoughts on “Nature Comment : The case for locus-specific databases

  1. Follow the money — for whom does the author of the piece consult?

    Better bioinformatics is hard work — tough to sell. “Locus specific database” is something you can put in a grant or sell to a university. Ch-ching!

    • It’s a good theory, but I’m not convinced. This seems more like two researchers who are focused on the biology and are completely missing the bioinformatics aspect of the field, despite doing next-gen work.
      There is some information on the authors on the web, but I don’t see much that would lead me to think that this will be a profitable article. Perhaps I’m just naive about how academic funding works, tho.

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