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  • last gen, next gen, third gen

    Here's a thought while I'm waiting for the cBot to finish generating my flowcell:
    When does "current generation" become "last generation", and "next generation" become "current generation", and can "third generation" become "next generation"?
    Is Sanger still "current generation"?
    Will the GA/454/Solid always be "next generation"?
    Should we stop saying "current" and "next" and start saying "first" and "second"?

  • #2
    PacBio is considered 3rd generation. However so was Helicos and look what happened to them.

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    • #3
      No offense, but I keep wondering what makes PacBio a third generation.
      It sequences by completing a strand, its massively parallelized...ok, it apparently does not use a PCR, but people have published a PCR-less protocoll for another platform in 2009...
      For what we use now, I prefer the term second generation. The downsizing and parallelization really changed the way researchers see the genome. The gap between '2nd' and '3rd' generation wont probably be that big. The next revolution probably needs to be a medical tricorder.

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      • #4
        It's funny this comes up, because I just made a huge decision to call it "Second Generation Sequencing" in my dissertation.

        "Third generation" refers to single-molecule sequencing technology, which is why PacBio qualifies. I think IonTorrent does too, as does the new tech from LifeTech.

        And yes, I've stopped calling Illumina GA/SOLiD/454 "Next Gen" and started calling them "Second Generation", especially in published works because "next gen" is simply too transient a term.
        Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
        Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
        Projects: U87MG whole genome sequence [Website] [Paper]

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        • #5
          IONT is not single molecule AFAIK.

          I am contemplating a new tagline for the site, as we clearly can't be "next-gen" forever...so I'm interested to see people's ideas.

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          • #6
            Originally posted by ECO View Post
            IONT is not single molecule AFAIK.

            I am contemplating a new tagline for the site, as we clearly can't be "next-gen" forever...so I'm interested to see people's ideas.
            Yeah, it is not single molecule. Did a little snooping after I said that.

            Does that mean it qualifies as second-gen? I'm still not so sure. Maybe "single molecule" isn't the only qualifying thing about the term, though.

            I would say that single molecule systems definitely do qualify as a new generation of technology, but sort of like how we had a pyrosequencer, a synthesis sequencer and a ligation sequencer in the second gen, multiple techs could show up in the third gen.

            It's kind of like videogame consoles, where significantly different techs (e.g. the Xbox, PS2, Gamecube last generation and the 360, PS3, Wii this generation) all get lumped into the same "generation" because they're currently competing with one another.

            ECO, I actually think you might be okay leaving "next generation" in the tag line. I mean, we are always going to be discussing the "next generation" (plus some of the last generation, probably).
            Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
            Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
            Projects: U87MG whole genome sequence [Website] [Paper]

            Comment


            • #7
              We just had a meeting with an Ion Torrent rep; I would say it straddles the line between second and third gen. It borrows heavily from the 454 chemistry which is not surprising since both technologies were developed and both companies founded by the same person, Jonathan Rothberg. With both platforms you ligate adapters to fragmented DNA and then clonally amplify on beads using an emulsion PCR. The fundamental difference between 454 and Ion Torrent is instead of linking the incorporation of a nucleotide to the apyrase cascade they directly measure the change in pH resulting from release of the H+ from the 3' end of the nascent chain.

              I would say that the fundamental aspects of second-gen sequencing are:
              - Sequencing-by-synthesis on isolated groups of clonally amplified templates.

              - All nucleotide incorporation is synchronous and occurs one nucleotide at a time.

              - Alternating phases of nucleotide incorporation and signal detection.
              The way I see third-gen:
              - Sequencing-by-synthesis of single molecules.

              - Nucleotide incorporation occurs asynchronously, in "real-time". (Lets save the debate of PacBio calling 5 nucleotides per second "real-time".)

              - Both nucleotide incorporation and signal detection occur continuously.
              The Ion Torrent technology is second-gen by the first criterion but third-gen by criteria 2 and 3.

              EDIT:
              As was pointed out down thread, nucleotide incorporation in the Ion Torrent is one base at a time, just like the 454. I don't know what I was thinking, maybe the coffee hadn't kicked in. So according to my thesis then then Ion Torrent would be a solidly in second-gen territory.
              Last edited by kmcarr; 08-04-2010, 01:01 PM. Reason: Correct really shocking mistake regarding the way Ion Torrent works.

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              • #8
                Originally posted by Michael.James.Clark View Post
                ECO, I actually think you might be okay leaving "next generation" in the tag line. I mean, we are always going to be discussing the "next generation" (plus some of the last generation, probably).
                ha ha, that's exactly what i thought too

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                • #9
                  I think we should just call all the new (non-sanger) stuff "high-throughput sequencing."

                  If you are referring to a specific brand, just name it, but in terms of data and cost I don't feel like it's as huge of a change from "2nd" to "3rd" to justify recognizing it with a new moniker.

                  My .02.

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                  • #10
                    Originally posted by ECO View Post
                    IONT is not single molecule AFAIK.

                    I am contemplating a new tagline for the site, as we clearly can't be "next-gen" forever...so I'm interested to see people's ideas.
                    I suppose we always will be the next generation sequencing community as long as everyone keeps upgrading tech, but maybe we should be the high-throughput sequencing community? I don't know, that doesn't quite give the same sort of panache.
                    I like "First Gen" for Sanger, "Second Gen" for what's out now (the "next gen") and "Third Gen" for true single molecule stuff. So, PacBio is Third, Ion is Second.

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                    • #11
                      Maybe we should take a tip from Star Trek. After Next generation comes Deep Space Nine, Voyager, and Enterprise.

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                      • #12
                        Originally posted by mgogol View Post
                        Maybe we should take a tip from Star Trek. After Next generation comes Deep Space Nine, Voyager, and Enterprise.
                        But if we stay true to the timeline then Enterprise would be casting our own gels and using radiolabeled nucleotides

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                        • #13
                          Doesn't the Ion Torrent technology rely on pulses of nucleotides just like 454? In that sense it is not "real time".

                          perhaps a better term than "real time" is "continuous data acquisition" -- this distinguishes PacBio and LifeTech/Visigen from any of the extant platforms (and Ion Torrent, if I'm correct)

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                          • #14
                            Originally posted by krobison View Post
                            Doesn't the Ion Torrent technology rely on pulses of nucleotides just like 454? In that sense it is not "real time".

                            perhaps a better term than "real time" is "continuous data acquisition" -- this distinguishes PacBio and LifeTech/Visigen from any of the extant platforms (and Ion Torrent, if I'm correct)
                            You're correct. I don't know what I was thinking of when I wrote that. I'll amend the original post.

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                            • #15
                              Originally posted by mgogol View Post
                              I think we should just call all the new (non-sanger) stuff "high-throughput sequencing."
                              Sequencing centers with massive numbers of capillary sequencer were (are?) sequencing at high-throughput also, IMO. So, I vote for sticking with 'Next-Generation'...

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