Mike the Mad Biologist

What Is “Deep Sequencing”?

And how is it different than genome sequencing?

So recently, I’ve been hearing people outside of the field of genomics refer to “deep sequencing.” I’m not sure what that phrase means: I would like to think that, in a philosophical sense, all of the sequencing we do is “deep” (dude). We certainly don’t set out to do shallow, stupid, and superficial projects.

If deep sequencing means the depth of coverage–the number of times, on average, a nucleotide is sequenced–depending on the project’s goals, the size of the genome, and so on, sometimes we sequence deeply, sometimes we don’t.

This sounds like a phrase invented by someone who really doesn’t know what he is talking about.

Comments

  1. #1 Epistaxis
    March 11, 2010

    Lately there have been a lot of projects to sequence a lot of genomes with low coverage (<5X) instead of one genome with high coverage (>25X), so it’s become necessary to differentiate between the two approaches.

  2. #2 Anonymous
    March 11, 2010

    Dude, Indeed. I agree, if you’re gonna do ‘deep’ sequencing, better to report on your fold coverage rather than just say ‘deep’. Better yet, just say how much coverage you’ve got, period, regardless of the depth. Now that would be deep.

  3. #3 John Danley
    March 11, 2010

    It refers to charter fishing excursions with Craig Venter.

  4. #4 JJ
    March 11, 2010

    Mike,

    We’ve been calling 7x assembly for verterbrate genomes “deep sequencing” for years. I have no idea what it means for new sequencing tech, but it will probably come to mean “sequencing that gives us coverage similar to Sanger 7x.”

    Then again, I don’t really know what I’m talking about.

  5. #5 noddin0ff
    March 12, 2010

    Deep refers to coverage that you can’t quite *fathom*. heh heh.

  6. #6 Johny
    July 29, 2010

    Deep sequencing is when you sequence many samples of certain genomic region from different individuals to determine low-frequency mutations. You need deep coverage for these, naturally.

  7. #7 Doc Wilson
    July 30, 2010

    Deep Sequencing is a new tool being used to identify the amount of RNA transcripts in specific tissues. It has contributed to a slew of new papers in the miRNA field including a recent paper in RNA by nobel prize winner Andy Fire.

  8. #8 Erol Bakkalbasi
    October 27, 2010

    Deep sequencing as I’ve heard it repeated refers to greater coverage to identify rarer variants rather than looking at sequence data that gives you the consensus of a large DNA sample.

    Maybe since you’re in the genomics field you don’t identify this as a difference, but most people who want sequences just want the consensus of some miniprep or PCR. When people use sequence to identify individual variants in a population, they refer to it as deep sequencing. This is just my experience, but other posters seem to agree.

  9. #9 Hugh Fletcher
    February 23, 2011

    This use of “deep” goes back at least as far as Tolkien (The Lord of the Rings) and Lewis Carroll (Narnia). It was a “deeper” level of magic that let Gandalph and Aslan respectively survive after death, with clear religious connotations. Deep sequencing equally adds a mythical and undefined level of superlative to Brute force and highly error prone sequencing techniques. It goes with massively parallel, avoids being quantitative, and looks impressive in adverts.

  10. #10 Mehran
    May 7, 2011

    If you don’t know about something, it’s better not to open your mouth about it!

  11. #11 Soo
    August 1, 2011

    “This sounds like a phrase invented by someone who really doesn’t know what he is talking about.”

    Seems like its you who has no clue about what you are talking about. You assume something and then ridicule it based upon your assumptions. Get the fact first then start commenting about it, Jeez!