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I'd argue that the discovery of Denisovans might be bigger than Neanderthal genes, but they're in the same ballpark. Modern sequencing technology has led to an

I'd argue that the discovery of Denisovans might be bigger than Neanderthal genes, but they're in the same ballpark. Modern sequencing technology has led to an explosion in discoveries about early human (and other organisms') evolution. Actually, I'd just put "rapid sequencing" right near the top of the list. When I started grad school (in 2003 if you must know), there was a feeling that it'd be very hard to get any better/faster than Sanger sequencing (and modifications of the same). Now there's a plethora of technologies that are both faster and more accurate.

new299 11y ago
> Now there's a plethora of technologies that are both faster and more accurate. Sorry to nitpick, but the inherent error rate of high throughput sequencing platforms is still higher than capillary sequencing. This is more than mitigated for by the massive throughput advantage though.
- nvusuvu 11y ago
  How fast can we sequence now? What are the error rates?
  - new299 11y ago
    About 6 Gigabases per hour, somewhere in that ballpark. Probably something like the equivalent of the human genome project (which took >10 years and 3 billion USD in the 90s) every few days. Error rates are in the region of 1 to 0.1% generally. I've never really worked directly with capillary data but understand it's error rate in early bases is limited by the amplification step. Which would be ~0.0001% (1 in 10000). That said there might be a coarse filter (based on signal intensity etc) that would identify a subpopulation of high-throughput reads which have a <0.1% error rate. But I don't believe I've seen that reported. I'd be interested in hearing from anyone who has thoughts on that though.
    - i000 11y ago
      The absolute error-rate is not really a problem if the errors are random and you have the budget to sequence enough independent fragments. Sequencing becomes tricky (both Sanger and next-gen) because of non-random recurrent artifacts associated with the sequencing method or molecular manipulations done to the DNA or RNA.
- jballanc 11y ago
  Right, thanks for clarifying that bit. An individual run still has a much higher error rate, but the ability to do exponentially more runs results in a higher accuracy per "experiment". This is not that dissimilar from the direction that other technologies have taken when facing physical measurement limits (cryo-electron tomography comes to mind, for example).
  - new299 11y ago
    Yes, though there's the added complication of time to answer however. You can turn a Sanger run around relatively quickly (I'd guess hours). High throughput runs sequence many millions of fragments of DNA in parallel very slowly. The highest throughput runs take several days to complete. This means that it's there are still (rapidly diminishing) scenarios where Sanger sequencing makes sense. Because you don't need the throughput, and you want an answer quickly.

new299 11y ago

> Now there's a plethora of technologies that are both faster and more accurate. Sorry to nitpick, but the inherent error rate of high throughput sequencing platforms is still higher than capillary sequencing. This is more than mitigated for by the massive throughput advantage though.

nvusuvu 11y ago
How fast can we sequence now? What are the error rates?
- new299 11y ago
  About 6 Gigabases per hour, somewhere in that ballpark. Probably something like the equivalent of the human genome project (which took >10 years and 3 billion USD in the 90s) every few days. Error rates are in the region of 1 to 0.1% generally. I've never really worked directly with capillary data but understand it's error rate in early bases is limited by the amplification step. Which would be ~0.0001% (1 in 10000). That said there might be a coarse filter (based on signal intensity etc) that would identify a subpopulation of high-throughput reads which have a <0.1% error rate. But I don't believe I've seen that reported. I'd be interested in hearing from anyone who has thoughts on that though.
  - i000 11y ago
    The absolute error-rate is not really a problem if the errors are random and you have the budget to sequence enough independent fragments. Sequencing becomes tricky (both Sanger and next-gen) because of non-random recurrent artifacts associated with the sequencing method or molecular manipulations done to the DNA or RNA.
jballanc 11y ago
Right, thanks for clarifying that bit. An individual run still has a much higher error rate, but the ability to do exponentially more runs results in a higher accuracy per "experiment". This is not that dissimilar from the direction that other technologies have taken when facing physical measurement limits (cryo-electron tomography comes to mind, for example).
- new299 11y ago
  Yes, though there's the added complication of time to answer however. You can turn a Sanger run around relatively quickly (I'd guess hours). High throughput runs sequence many millions of fragments of DNA in parallel very slowly. The highest throughput runs take several days to complete. This means that it's there are still (rapidly diminishing) scenarios where Sanger sequencing makes sense. Because you don't need the throughput, and you want an answer quickly.