Ion Torrent Platform Differences

pinecone · 11-01-2020, 12:00 PM

Hello all,

New to the forum and to the Ion Torrent platform.

From reading the literature I have noticed various different Ion Torrent sequencing machines being mentioned, but I am having a hard time understanding all the differences between them, other than throughput and chip types.

If anybody would be kind enough to explain the pros and cons of all the different machines over the years (e.g. PGM vs S5 vs S5 XL vs Genexus vs Ion Proton vs others), or could re-direct me to any papers or other sources, I would be infinitely thankful.

I look forward to becoming a part of this forum.

Bastiaan · 11-02-2020, 02:31 AM

Hi Pinecone,

The Ion PGM (0.5-5.5M reads) and Ion Proton (60-80M reads) were the first instruments released by Ion Torrent. These have been discontinued this summer (continued support until 2025). With the Ion S5 and S5XL, instrument operation was made easier because of automation of the initialization and cleaning steps. This saved a lot of hands-on time compared with the PGM and Proton. The difference between S5 and S5XL relates to the computing power. The S5XL comes with an external server for data analysis while the S5 uses the on-board computing power. In 2018, the Ion S5 was upgraded with the release of the Ion Genestudio, Ion Genestudio Plus and Ion Genestudio Prime (2-130M reads). The Ion Genestudio S5 and Genestudio S5 Plus use on-board data analysis while the Genestudio Prime comes with an external server for faster data analysis. The Genestudio Plus has more computing power as compared to the Genestudio. More details here. All of the aforementioned instruments work alongside the Ion Chef, an instrument that is used for automated templating of libraries onto Ion Sphere Particles. The Ion Chef can also be used for automated library preparation. In 2019, Ion Torrent released the Genexus (15M reads / lane, 4 lanes on a chip). This system automates all steps from DNA sample to analysis report, further reducing hands-on time. It also reduced the overall time from DNA to analysis to a single day. More details here.

Hope this helps!

KevinLam · 11-02-2020, 08:28 AM

I would have pointed you to http://seqanswers.com/forums/showthread.php?t=62920 but I think it's better to look towards the future (not sure if PGM is still being sold) and you really should just concern yourself with comparing GeneStudio and Genexus of which you can check out their product website.

The reason why they 'look similar' on the chip throughput is because the underlying design is still the same core but the GeneStudio is latest iteration.

Genexus is a game changer though promising next day reporting and flexibility to run 1/4 of the chip or lane as they call it.

You will probably get a more in-depth explanation if u leave your contact for a sales rep to contact you ...

pinecone · 11-02-2020, 09:24 AM

Quote:

Originally Posted by KevinLam

I would have pointed you to http://seqanswers.com/forums/showthread.php?t=62920 but I think it's better to look towards the future (not sure if PGM is still being sold) and you really should just concern yourself with comparing GeneStudio and Genexus of which you can check out their product website.

The reason why they 'look similar' on the chip throughput is because the underlying design is still the same core but the GeneStudio is latest iteration.

Genexus is a game changer though promising next day reporting and flexibility to run 1/4 of the chip or lane as they call it.

You will probably get a more in-depth explanation if u leave your contact for a sales rep to contact you ...

Hello Kevin,

Many thanks for your helpful input.
I had checked the thread you mention, but I didn't think it would be entirely up to date (last post in 2015).

But you have answered my question with what you've written.
Will get in touch with a sales rep for more details.
Thanks again.

pinecone · 11-02-2020, 12:48 PM

Quote:

Originally Posted by Bastiaan

Hi Pinecone,

The Ion PGM (0.5-5.5M reads) and Ion Proton (60-80M reads) were the first instruments released by Ion Torrent. These have been discontinued this summer (continued support until 2025). With the Ion S5 and S5XL, instrument operation was made easier because of automation of the initialization and cleaning steps. This saved a lot of hands-on time compared with the PGM and Proton. The difference between S5 and S5XL relates to the computing power. The S5XL comes with an external server for data analysis while the S5 uses the on-board computing power. In 2018, the Ion S5 was upgraded with the release of the Ion Genestudio, Ion Genestudio Plus and Ion Genestudio Prime (2-130M reads). The Ion Genestudio S5 and Genestudio S5 Plus use on-board data analysis while the Genestudio Prime comes with an external server for faster data analysis. The Genestudio Plus has more computing power as compared to the Genestudio. More details here. All of the aforementioned instruments work alongside the Ion Chef, an instrument that is used for automated templating of libraries onto Ion Sphere Particles. The Ion Chef can also be used for automated library preparation. In 2019, Ion Torrent released the Genexus (15M reads / lane, 4 lanes on a chip). This system automates all steps from DNA sample to analysis report, further reducing hands-on time. It also reduced the overall time from DNA to analysis to a single day. More details here.

Hope this helps!

Hi Bastiaan,

Thank you for very kindly taking the time to explain the timeline and advances in the technology. Very helpful!

Marcela Astete · 01-16-2021, 11:49 AM

Hi, it is possible that the ion chef could contaminate other experiments in a quant study. the two machines are in the same room

can you help me

r.rosati · 01-18-2021, 12:34 PM

Oi Marcela!
I suppose the quantstudio plates are brought in the post-PCR room already sealed, right? Then the Ion Chef shouldn't be contaminating them.
On the other side, if somebody is preparing NGS libraries in a pre-PCR room, then it is possible that the libraries could be contaminating the plates, I suppose...

Marcela Astete · 01-19-2021, 04:17 AM

Thank you very much for answering.
The QuantStudio plates are brought in the post-PCR room already sealed. In this same post-pcr room, where the QuantStudio are located, the libraries are made with the ion chef. We believe that amplicons are formed the moment the library is finished and we open the ion chef. It is possible that this thought is correct, added to the bad laboratory practices of some people who do not use protection and who supposedly transport the amplicons to other rooms.

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11-01-2020, 12:00 PM	#1
pinecone Junior Member Location: uk Join Date: Nov 2020 Posts: 4	Ion Torrent Platform Differences Hello all, New to the forum and to the Ion Torrent platform. From reading the literature I have noticed various different Ion Torrent sequencing machines being mentioned, but I am having a hard time understanding all the differences between them, other than throughput and chip types. If anybody would be kind enough to explain the pros and cons of all the different machines over the years (e.g. PGM vs S5 vs S5 XL vs Genexus vs Ion Proton vs others), or could re-direct me to any papers or other sources, I would be infinitely thankful. I look forward to becoming a part of this forum.

11-02-2020, 08:28 AM	#3
KevinLam Senior Member Location: SEA Join Date: Nov 2009 Posts: 203	I would have pointed you to http://seqanswers.com/forums/showthread.php?t=62920 but I think it's better to look towards the future (not sure if PGM is still being sold) and you really should just concern yourself with comparing GeneStudio and Genexus of which you can check out their product website. The reason why they 'look similar' on the chip throughput is because the underlying design is still the same core but the GeneStudio is latest iteration. Genexus is a game changer though promising next day reporting and flexibility to run 1/4 of the chip or lane as they call it. You will probably get a more in-depth explanation if u leave your contact for a sales rep to contact you ... __________________ http://kevin-gattaca.blogspot.com/

01-16-2021, 11:49 AM	#6
Marcela Astete Junior Member Location: Bahia, Brazil Join Date: May 2014 Posts: 4	Hi, it is possible that the ion chef could contaminate other experiments in a quant study. the two machines are in the same room can you help me Last edited by Marcela Astete; 01-16-2021 at 11:57 AM.

11-02-2020, 02:31 AM	#2
Bastiaan Junior Member Location: Netherlands Join Date: Jul 2019 Posts: 3	Hi Pinecone, The Ion PGM (0.5-5.5M reads) and Ion Proton (60-80M reads) were the first instruments released by Ion Torrent. These have been discontinued this summer (continued support until 2025). With the Ion S5 and S5XL, instrument operation was made easier because of automation of the initialization and cleaning steps. This saved a lot of hands-on time compared with the PGM and Proton. The difference between S5 and S5XL relates to the computing power. The S5XL comes with an external server for data analysis while the S5 uses the on-board computing power. In 2018, the Ion S5 was upgraded with the release of the Ion Genestudio, Ion Genestudio Plus and Ion Genestudio Prime (2-130M reads). The Ion Genestudio S5 and Genestudio S5 Plus use on-board data analysis while the Genestudio Prime comes with an external server for faster data analysis. The Genestudio Plus has more computing power as compared to the Genestudio. More details here. All of the aforementioned instruments work alongside the Ion Chef, an instrument that is used for automated templating of libraries onto Ion Sphere Particles. The Ion Chef can also be used for automated library preparation. In 2019, Ion Torrent released the Genexus (15M reads / lane, 4 lanes on a chip). This system automates all steps from DNA sample to analysis report, further reducing hands-on time. It also reduced the overall time from DNA to analysis to a single day. More details here. Hope this helps!

01-18-2021, 12:34 PM	#7
r.rosati Member Location: Brazil Join Date: Aug 2015 Posts: 94	Oi Marcela! I suppose the quantstudio plates are brought in the post-PCR room already sealed, right? Then the Ion Chef shouldn't be contaminating them. On the other side, if somebody is preparing NGS libraries in a pre-PCR room, then it is possible that the libraries could be contaminating the plates, I suppose...

01-19-2021, 04:17 AM	#8
Marcela Astete Junior Member Location: Bahia, Brazil Join Date: May 2014 Posts: 4	Thank you very much for answering. The QuantStudio plates are brought in the post-PCR room already sealed. In this same post-pcr room, where the QuantStudio are located, the libraries are made with the ion chef. We believe that amplicons are formed the moment the library is finished and we open the ion chef. It is possible that this thought is correct, added to the bad laboratory practices of some people who do not use protection and who supposedly transport the amplicons to other rooms.