Opiniomics

bioinformatics, genomes, biology etc. "I don't mean to sound angry and cynical, but I am, so that's how it comes across"

Bioinformatics error responsible for retraction in Science

Update: sorry, my mistake, the paper has not been retracted, an Erratum has been issued

If you follow the same kind of feeds and blogs that I do, you can’t have missed the recent retraction in Science that was due to a simple bioinformatics error.  Others have covered this in way more detail, but the essential points are that the authors sequenced an ancient genome from an individual they called “Mota”, and compared that genome to a bunch of other human genomic datasets to put it in context – except when they compared to a reference panel of SNPs, a necessary conversion script wasn’t run, which meant that a huge number of SNPs that Mota shared with Europeans were dropped, making Mota appear less European than he actually was.

The thing that strikes me most about this story is that this could have been so easily avoided.

There are a few things I tell my post-docs and students over and over.  One of them, perhaps the most important one, is to check your work.  A second and related point is that if you get wonderful results, or unusual and striking results, they are probably wrong and you should check your work.  We tried to encapsulate some of this advice in our paper – So you want to be a computational biologist?  Honestly, I know it’s boring, but double- and triple- checking your work is so important.   Whatever you find, at the very least just take a few data points and check again to make sure you get the same result.

In the above example, what I personally would have done, is to write a script to make sure that the “255,922 SNPs out of 256,540” were genuinely missing from the samtools output.  This may sound daunting but it really isn’t – possibly 10 or 20 lines of Python or Perl could have saved the day.

I do wonder if this was a case of a lonely bioinformatician – I genuinely don’t know who did what on the paper, but so frequently errors creep in when wet and dry lab scientists communicate in every-so-slightly different languages.

Whatever the issue – the take home is this: please, for the love of everything that is good in the world, CHECK YOUR RESULTS!

3 Comments

  1. I don’t see that paper as retracted. There’s been an Erratum made, but that’s it.

    Although, I agree it probably should be as the title is no longer valid or correct.

  2. Sure, check your results. But more importantly, CHECK YOUR RESULTS WITH SOMEONE ELSE

  3. This blog post is more ironic than anything Alanis Morissette could think of 😉

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