
DNA sequencing progress has stagnated - dbcooper
https://twitter.com/erlichya/status/1156195896067088394
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tuvan
Why would sequencing follow Moore's law when it isn't really related to
computing? Sequencing technology is limited by our knowledge of chemistry,
physics, and mechanical engineering to apply the concepts. None of which is
doubling every 2 years.

There are 3rd gen sequencing techs that provide much longer reads than
previous tech like Illumina but they also get much higher rate of erroneous
reads.

Another point is current sequencing tech is enough for tasks that were just
unfeasible to do couple of years ago. Such as HiC (Extracting 3D structure of
chromosomes with sequencing) or more recent applications like DNA Microscopy,
where you can construct a very high resolution visual image of a cell just by
using sequencing.

Our usage of genomic data isn't really limited by sequencing tech since DNA is
such a complex structure that we don't even fully understand the data we
currently have.

~~~
virusduck
This is exactly right. The Moore's law slide is a cute comparison that has
been used to try and demonstrate that sequencing volume has outpaced our
computational ability in one context or another. Variously, it is used as
commentary on computers' ability to keep up, our need for better storage , our
lack of trained professionals, and so on.

Dollars/Mb is not a super-meaningful statistic anyway. If you include
quality/value (either as raw base confidence or the value of that base in the
context of longer read lengths), the Dollar/Base/Value number has likely kept
falling. It's just hard to quantify the "Value" as a number.

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dekhn
As somebody who has worked in genomics for decades, I don't really see
progress in DNA sequencing as being motivated by extrinsic factors. Put
another way, there really isn't enough scientific discovery being driven by
new sequence data to justify the spending. Many articles have been written
claiming that sequencing is going to revolutionize medicine. It's been a very
useful research tool, and _some_ genomics has been very valuable medically,
but it doesn't live up to the hype.

~~~
nknealk
To add to this, I worked in melanoma genomics for 2 years. Off the top of my
head I cannot think of a single cancer drug on the market who's target was
discovered through NGS.

It was great as a research tool. But I have yet to see it improve patient
outcomes

~~~
avani
It's not quite _discovering_ a target from NGS, but lots of existing cancer
drugs are targeted based on genotyping tumours. Breast cancer is the classic
one, where, say, if you can quickly determine if your sample is Her2+ your
treatment plan drastically changes. Now, getting enough cancer cells in your
tumour sample to reliably genotype at that stage is a separate hard problem.

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lacker
The key problem is that DNA sequencing for individuals is not useful (yet) for
that individual. Right now DNA sequencing is useful for scientific research
and for industrial research. But the current price is basically fine for that;
it isn't anywhere near the main component of the cost of research.

If there were a reason to get the DNA of each American sequenced, the price
would go down drastically. Like if there was any real medical usefulness of
having your DNA sequenced. But right now there isn't.

It's kind of like the Apple I era of personal computing. It's finally cheap
enough that individuals can get this technology themselves. There just isn't
really a great reason to, besides interested hobbyists.

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throwaway07Ju19
23andme will let you download a zip file of your sequence data. But if I
recall the data had only about 4 million nucleotides. So I assumed that I need
to get their "baseline" human full genome somewhere and my file is just the
difference.

But the above assumption can't be correct given that it still costs $1000 for
a full sequence according the the parent article. Can anyone clarify ?

~~~
ben1040
23andMe ran a microarray analysis, which probes your genome at a specific set
of locations.

If you want to know how your genome differs versus what's called the
"reference genome," then you'd need a whole-genome sequence. That process
shards up your genome, sequences it, aligns the pieces back to the human
reference, and then calculates a "consensus" that represents the software's
best guess as to how your genome relates to the reference.

Then they could provide you with a diff of the consensus with respect to the
reference, which would probably be distributed to you in a VCF file (variant
call format).

This process is the one that costs more money versus 23andMe's $99.

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roenxi
Moore's Law in context is doubling every 2 years? This isn't general news;
you'd need to be very clued in to understanding what the problem is. Doubling
every 2 years is not the natural state of things. That sort of growth rate is
hard to maintain even from truly trivial starting points (my favorite example
is the wheat & chessboard parable [0]).

The news is processes that don't stagnate fairly quickly after getting past
the low hanging fruit of research and development. Processors have maintained
an exponential growth rate for ~50 years and that has completely
revolutionised every aspect of society and realistically probably our
relationship with the world at large. We don't expect things to do that, and
although it is taking a lot longer than everyone expected at some point the
transistor doubling will have to end.

[0]
[https://en.wikipedia.org/wiki/Wheat_and_chessboard_problem](https://en.wikipedia.org/wiki/Wheat_and_chessboard_problem)

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phkahler
In order for the public to really want their genes sequenced,there will have
to be privacy in place. Nobody should have access to the data. Just deliver it
and provide analysis tools. Even then, it something you only need to do once.
Demand won't get higher than that, so demand isn't really going to be a big
price driver.

~~~
Despegar
Yep. I refuse to have my DNA sequenced by any of these direct to consumer
businesses that think they're going to be the next platforms and start making
money on the back end.

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waiquoo
Maybe divert resources DNA synthesis? Sequencing is very cheap per base,
especially compared to a few years ago

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folli
This doesn't take the increase of read lengths into account, which also is of
value, not only pure read depth.

~~~
mbreese
It does... the graph is price per megabase, not per read.

(or at least, it's supposed to)

But, I don't think the plot is all that accurate anymore though... given the
cost/GB and raw capacity of the newer Novaseq's, the cost per individual
experiment is just as much a function of how multiplexed the machine can run.

~~~
sp332
Read length improves read quality, especially for sequences with lots of
repetition.
[https://news.ycombinator.com/item?id=15534325](https://news.ycombinator.com/item?id=15534325)

~~~
mbreese
Mappable sequence isn't what is being measured here... it's just $/Mbase

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dbcooper
Quality may have improved though.

