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Home / GenX spill, national coverage, but where is the data

GenX spill, national coverage, but where is the data

First (I have never blogged much about risk and hazard), I am not an toxicological expert nor a regulator. I have deepest respect for both, as these studies are one of the most complex ones I am aware off. It makes rocket science look dull. However, I have quite some experience in the relation chemical structure to properties and with knowledge integration, which is a prerequisite for understanding that relation. Anything I do does not say what the right course of action is. Any new piece of knowledge (or technology) has pros and cons[1]. It is science that provides the evidence to support finding the right balance. It is science I focus on.

The case
The AD national newspaper reported[2] spilling of the compound with the name GenX in the environment and reaching drinking water. This was picked up by other newspapers, like de VK[3]. The chemistry news outlet C2W[4] commented on the latter on Twitter:


Translated, the tweet reports that we do not know if the compound is dangerous. Now, to me, there are then two things: first, any spilling should not happen (I know this is controversial, as people are more than happy to repeatedly pollute the environment, just because of self-interest and/or laziness); second, what do we know about the compound? In fact, what is GenX even? It certainly won't be "generation X", though we don't actually know the hazard of that either. (We have IUPAC names[5], but just like with the ACS dis closures[6], companies like to make up cryptic names.)

But having working on predictive toxicology and data integration projects around toxicology, and for just having a chemical interest, I started out searching what we know about this compound.

Of course, I need an open notebook for my science[7], but I tend to be sloppy and mix up blog posts like this, with source code repositories, and public repositories. For new chemicals, as you could read earlier this weekend[8], Wikidata[9] is one of my favorites (see also doi:10.3897/rio.1.e7573[10]). Using the same approach as for the disclosures, I checked if Wikidata had entries for the ammonium salt and the "active" ingredient FRD-903 (fairly, chemically they are different, and so may their hazard and risk profiles). Neither existed, so I added them using Bioclipse[11] and QuickStatements[12] (a wonderful tool by Magnus Manke[13]): GenX[14] and FRD-903[15]. So, a seed of knowledge was planted.
A side topic... if you have not looked at hypothes.is[16] yet, please do. It allows you to annotate (yes, there are more tools that allow that, but I like this one), which I have done for the VK article:


I had a look around on the web for information, and there is not a lot. A Wikidata page with further identifiers then helps tracking your steps. Antony Williams[17], previous of ChemSpider fame, now working on the EPA CompTox Dashboard, added the DTX substance IDs, but the entries in the dashboard will not show up for another bit of time. For FRD-903 I found growth inhibition data in ChEMBL[18].

But Nina Jeliazkova[19] pointed me to her LRI AMBIT database[20] (poster abstract doi:10.1016/j.toxlet.2016.06.1469[21], PDF links[22]) that makes (public) data from ECHA[23] available from REACH[24] dossiers in a machine readable way (see this ECHA press release[25]), using their AMBIT software (doi:10.1186/1758-2946-3-18[26]). (BTW, this makes the legal hassle Hartung had last year even more interesting, see doi:10.1038/nature.2016.19365[27]). After creation of a free login, you can find a full (public) dossier[28] with information about the toxicology of the compound (toxicity, ecotoxicity, environmental fate, and more):


I reported this slide, as they worry seems to be about drinking water, so, oral toxicity seems appropriate (note, this is only acute toxicity). The LD50 is the median lethal dose[29], but is only measured for mouse and rat (these are models for human toxicity, but only models, as humans are just not rats; well, not literally, anyway). Also, >1 gram per kilogram body weight ("kg bw"; assumption) seems pretty high. In my naive understand, the rat may be the canary in the coal mine[30]. But let me refrain from making any conclusions. I leave that to the experts on risk management!

Experts like those from the Dutch RIVM, which wrote up this report[31]. One of the information they say is missing is that of biodistribution: "waar het zich ophoopt", or in English, where the compound accumulates.

References

  1. ^ pros and cons (en.wiktionary.org)
  2. ^ reported (www.ad.nl)
  3. ^ like de VK (www.volkskrant.nl)
  4. ^ chemistry news outlet C2W (www.c2w.nl)
  5. ^ IUPAC names (en.wikipedia.org)
  6. ^ ACS disclosures (chem-bla-ics.blogspot.nl)
  7. ^ open notebook for my science (en.wikipedia.org)
  8. ^ you could read earlier this weekend (chem-bla-ics.blogspot.nl)
  9. ^ Wikidata (wikidata.org)
  10. ^ 10.3897/rio.1.e7573 (doi.org)
  11. ^ Bioclipse (bmcbioinformatics.biomedcentral.com)
  12. ^ QuickStatements (tools.wmflabs.org)
  13. ^ Magnus Manke (orcid.org)
  14. ^ GenX (www.wikidata.org)
  15. ^ FRD-903 (www.wikidata.org)
  16. ^ hypothes.is (hypothes.is)
  17. ^ Antony Williams (tools.wmflabs.org)
  18. ^ growth inhibition data in ChEMBL (www.ebi.ac.uk)
  19. ^ Nina Jeliazkova (orcid.org)
  20. ^ LRI AMBIT database (ambitlri.ideaconsult.net)
  21. ^ 10.1016/j.toxlet.2016.06.1469 (doi.org)
  22. ^ PDF links (scholar.google.nl)
  23. ^ ECHA (echa.europa.eu)
  24. ^ REACH (en.wikipedia.org)
  25. ^ this ECHA press release (echa.europa.eu)
  26. ^ 10.1186/1758-2946-3-18 (doi.org)
  27. ^ 10.1038/nature.2016.1936 5 (doi.org)
  28. ^ find a full (public) dossier (ambitlri.ideaconsult.net)
  29. ^ LD50 is the median lethal dose (en.wikipedia.org)
  30. ^ canary in the coal mine (en.wiktionary.org)
  31. ^ this report (www.rivm.nl)
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