
Open Source PCR Thermocycler - apsec112
https://openpcr.org/
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joshuamcginnis
There's also PocketPCR[0] and MiniPCR[1]. $499 for OpenPCR is still pricey imo
when you can buy a proper programmable thermocycler with heated top for less
than half on eBay, presuming it actually works.

I'm documenting my journey in self-learning genetic engineering[2][3] and in
the market for PCR and electrophoresis setup, so I'd be happy to hear what
folks recommend.

[0] [https://www.minipcr.com/](https://www.minipcr.com/)

[1] [http://gaudi.ch/PocketPCR/](http://gaudi.ch/PocketPCR/)

[2] [https://everymanbio.com/](https://everymanbio.com/)

[3]
[https://www.instagram.com/everymanbio/](https://www.instagram.com/everymanbio/)

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WrtCdEvrydy
Okay... now with my trusty PocketPCR... I shall... what does a PCR do again?

~~~
zitterbewegung
It helps you sequence a genome . On the website they give examples like
sequencing beer yeast.

~~~
vikramkr
It doesn't sequence, it amplifies DNA/RNA (through reverse transcription) and
lets you detect a particular sequence or produce more of a sequence you want
to use for downstream steps

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fastaguy88
No reverse transcription. Just amplification by extending a primer using DNA
polymerase (rtPCR -- reverse transcription PCR -- of RNA does do an initial
reverse transcriptase step.) The PCR process is also used in modern DNA
sequencing, but that is not what a PCR machine does.

And a non-qPCR machine does not detect the sequence -- it just produces enough
of it by amplification so that it can be detected using other methods.

~~~
vikramkr
No, you can use a thermocycler for reverse transcription. In fact, you need
one to do rtPCR, and I don't see why this cycler wouldn't be able to do that.

And to clarify, I didn't say the device detects a sequence. I said it lets you
detect the presence of a sequence. This isn't a biology forum, so I
deliberately didn't go into excessive detail and technicalities, just
conveying the information that one of the things you use this for is detecting
a DNA sequence (and sure, there are post processing steps like running a gel
or sending it off for sanger sequencing etc), and the other sort of thing you
can do is RT-PCR. You can also do all sorts of cloning techniques like
gibsons. And technically, neither device nor a qPCR machine let you detect a
particular sequence exactly. It just amplifies a piece of dna enclosed by the
relevant primers that you are using to amplify. I'm well aware of all these
technicalities with saying that a thermocycler does sequence detection, I left
them out on purpose. And as mentioned before, the pocketPCR, like any other
thermocycler, is absolutely capable of doing RT etc. I know the parent comment
said "what does a PCR do again?," but it's pretty clear from context and use
of the article "a" that they are asking about the pocketPCR machine's
capabilities, not about polymerase chain reaction in general. If they were,
then yes you are technically correct regarding RT.

~~~
robbiep
This is overly pedantic but you did literally say _lets you detect the
sequence_ in a context where the average reader would have parsed the sentence
as referring to the capabilities of the device.

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damip
I remember finding OpenPCR too expensive for a student project, and I ended up
designing and building a cruder/cheaper alternative for that project:
[http://2013.igem.org/Team:Paris_Saclay/PS-
PCR/detailed_descr...](http://2013.igem.org/Team:Paris_Saclay/PS-
PCR/detailed_description)

~~~
tito
Nice work! Your BOM looks similar to OpenPCR's. One fundamental advantage of
these smaller PCR machines over traditional designs was running fewer samples
(i.e. 16 vs 32+), which translates to less fabrication, less peltier devices,
and less sensing/cooling, among other things.

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purpleidea
Kind of too bad, because I guess it was mildly successful at least because
they discontinued the "open" part of, see here:
[https://www.chaibio.com/openpcr](https://www.chaibio.com/openpcr)

Their newer product that they've replaced this with is:

1) Way more expensive 2) Not open hardware 3) Remove GPLv3 license (that
requires you keep things open) and replaced it with ALv2 (which allows you to
take it proprietary)

All good things end up failing because of greed. We'd all be so much better
off if we cared about bigger goals than just short term profit.

~~~
vikramkr
That's a qPCR machine, which is an _entirely_ different beast in terms of
capability and cost than your usual thermocycler. $5000 is an _amazing_ deal
on a qPCR machine. A piece of new qPCR kit is gonna run you 30-50 thousand
dollars minimum, and I've had trouble finding good functional ones from the
big players for less than 20k used.

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vikramkr
Initiatives like OpenPCR went a long way towards opening up DIY biology to the
responsible amateur and making it easier to start a DIY bio hackerspace for a
region. Glad to see them featured on HN.

~~~
tito
Here here!

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unchocked
They're barking up the right tree here. For want of widely spread PCR testing
in February, we let COVID overrun the United States.

If you have the machines and reagents widely distributed, all you need are
pathogen specific primers to test for the pathogen du-jour. Then you can do
widespread testing and contact tracing like you're supposed to. I really hope
we get that in place before the next plague hits.

~~~
projektfu
The reagents have been the limiting ... reagent.

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mtu
For those of you who are interested in this space (open source/affordable
scientific equipment) I recommend the lab on the cheap blog[0]. They have a
lot of links to interesting websites/papers in this space.

[0] [https://www.labonthecheap.com/](https://www.labonthecheap.com/)

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kf
See
[https://news.ycombinator.com/item?id=24048775](https://news.ycombinator.com/item?id=24048775)
for many diagnostic tests LAMP is superior to PCR on all metrics

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tingletech
I remember when I was doing PCR in the 1980s we needed some really scary
centrifuges. The professor I was working for said if we didn't balance them
correctly, they could fly out of the building and knock it down.

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ampdepolymerase
I am glad that this is on the frontpage. I distinctly recall that Hacker News
does not believe in the existence of open source biomedical engineering.

[https://news.ycombinator.com/item?id=22578216](https://news.ycombinator.com/item?id=22578216)

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bgitarts
Can it be used to detect a virus from a sample of say salvia?

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mtu
You'll need to run RT-qPCR (Reverse Transcriptase Quantitative PCR) to detect
Covid-19 viral sequences.

Simple thermocyclers allow us to amplify sequences but it can't do measurement
like a Quantitative PCR machine.

~~~
sannee
I know that qPCR is preferred for diagnostics, but is it actually necessary?
As in, will the false positive/false negative rates suffer enough for standard
RT-PCR to be useless?

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virusduck
No. qPCR is, well, quantitative, so it gives more information. Additionally,
it requires less pipetting, and the data is easier to report. All of these
things make it more desirable for diagnostics.

