5 ms·

The Nobel Prize tends to favor initial breakthroughs. Svante's lab sequenced the very first complete Neandertal genome, showing it was possible to reconstruct g

by dkural 4y ago

The Nobel Prize tends to favor initial breakthroughs. Svante's lab sequenced the very first complete Neandertal genome, showing it was possible to reconstruct genomes from ancient DNA, with high-throughput sequencers, and developing the necessary lab protocols and software to put it all together (with his lab). Svante was senior author on the Denisova paper as well. So, I am not surprised. There was no major advance needed for Reich to do his work further elucidating the origin and dispersion of various hominin species and ancient human populations.

dekhn 4y ago
Paabo told me (when he visited to give a talk at my institution) that the first few years of Neandertal sequencing, he was just sequencing his own genome accidentally, since he didn't have truly stringent lab technique. He was out ahead of everybody else for at least 2-3 years at the time, and could demonstrate to people trying to replicate his results that they were just using contaminated samples. Sequencing is absurdly sensitive- it can pick up a real signal from just a few individual molecules.
- hajimuz 4y ago
  Seriously? Nobody was verifying that end to end?
  - dkural 4y ago
    This reminds me of another story - BGI was sequencing the chicken genome, and for a while, a lot of people who did other sequencing projects kept receiving chicken DNA in their sequencing data files (as contamination).
  - searine 4y ago
    As it turns out, paleogenomics takes next level cleanliness, far more than anyone expected, particularly when you're trying to sequence something so close to human DNA.
  - dekhn 4y ago
    Sometimes verifying the little details can get in the way of publication velocity. It's a risk many advanced scientists take because the chance of getting caught (publishing something that is later shown to be obviously false using careful control experiments) is low, and the risk to your career of being second to publish.
- bjelkeman-again 4y ago
  Does this mean that inexpensive DNA tests you can buy online are likely to contain contaminated samples? As the person taking the sample at home hardly has stringent lab tech available?
  - dekhn 4y ago
    No, tests like that work with an abundance of DNA and so contamination is less likely. A DNA test typically works with saliva or blood which contains a ton of DNA> That DNA can then be amplified, which amplifies both the signal and the noise, but the noise is very low and can be trivially ignored after the fact. With paleogenomics, you're collecting a tiny amount of DNA, mostly degraded, from ancient samples, and so the "noise" (contamination DNA) ends up being close to or more than the signal you get from the sample. Details here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3926038/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3926038/
  - jhbadger 4y ago
    The issue with paleo DNA is that the target is much lower in concentration than potential contaminants from the lab worker. etc. This wouldn't be the case in DNA tests where the concentration of the sample would be comparatively high.
- jhbadger 4y ago
  That was a common problem in Paabo's early work. He also "sequenced an Egyptian mummy" that turned out to be himself as well.

by dkural 4y ago

dekhn 4y ago

Paabo told me (when he visited to give a talk at my institution) that the first few years of Neandertal sequencing, he was just sequencing his own genome accidentally, since he didn't have truly stringent lab technique. He was out ahead of everybody else for at least 2-3 years at the time, and could demonstrate to people trying to replicate his results that they were just using contaminated samples. Sequencing is absurdly sensitive- it can pick up a real signal from just a few individual molecules.

hajimuz 4y ago
Seriously? Nobody was verifying that end to end?
- dkural 4y ago
  This reminds me of another story - BGI was sequencing the chicken genome, and for a while, a lot of people who did other sequencing projects kept receiving chicken DNA in their sequencing data files (as contamination).
- searine 4y ago
  As it turns out, paleogenomics takes next level cleanliness, far more than anyone expected, particularly when you're trying to sequence something so close to human DNA.
- dekhn 4y ago
  Sometimes verifying the little details can get in the way of publication velocity. It's a risk many advanced scientists take because the chance of getting caught (publishing something that is later shown to be obviously false using careful control experiments) is low, and the risk to your career of being second to publish.
bjelkeman-again 4y ago
Does this mean that inexpensive DNA tests you can buy online are likely to contain contaminated samples? As the person taking the sample at home hardly has stringent lab tech available?
- dekhn 4y ago
  No, tests like that work with an abundance of DNA and so contamination is less likely. A DNA test typically works with saliva or blood which contains a ton of DNA> That DNA can then be amplified, which amplifies both the signal and the noise, but the noise is very low and can be trivially ignored after the fact. With paleogenomics, you're collecting a tiny amount of DNA, mostly degraded, from ancient samples, and so the "noise" (contamination DNA) ends up being close to or more than the signal you get from the sample. Details here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3926038/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3926038/
- jhbadger 4y ago
  The issue with paleo DNA is that the target is much lower in concentration than potential contaminants from the lab worker. etc. This wouldn't be the case in DNA tests where the concentration of the sample would be comparatively high.
jhbadger 4y ago
That was a common problem in Paabo's early work. He also "sequenced an Egyptian mummy" that turned out to be himself as well.