Friday, 2 September 2011

Next generation sequencing acronyms

The list at the bottom is occasionally edited to include new methods.

There is an ever increasing number of next generation sequencing acronyms (see the link to a table at the bottom of this post), other than the commonly used ChIP-Seq and RNA-Seq most have been used only once in the article where the acronym was first used. I suspect authors are trying to come up with something as catchy as "ChIP-Seq" in the ope that their paper will be cited more frequently. A search through PubMed suggests otherwise.

My list contains just over 30 acronyms presented in papers, posters or meetings over the past few years. A search for these in PubMed brings up almost 850 papers. RNA-Seq (including mRNA-Seq or RNASeq) account for 48%, ChIP-Seq has 47%, ClIP-Seq (including RIP-Seq and HITS-ClIP) has 2%, about 1% of papers are versions of methylation sequencing.

The 2007 ChIP-Seq paper "Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing" in Nat Methods started this sequencing acronym name game. However this has been played out before with other technologies.

I am certain I will have missed a few out so feel free to comment and I'll upadte the tabel with this information in it. I'd also like to ask authors and editors to strongly consider adding any more to this list unless there is a strongly compelling reason.

Here's my list: ALEXA-Seq, Apopto-Seq, AutoMeDip-Seq, Bind-n-Seq, Bisulfite-Seq, ChIA-PET, ChIP-Seq,  ChiRP-seq, ClIP-Seq, CNV-Seq, Degradome-seq, DGE-Seq, DNA-Seq, DNase-Seq, dRNA-Seq, F-Seq, FAIRE-seq, FRT-Seq, HITS-CLIP, Immune-Seq, indel-Seq, MBD-Seq, MeDIP-Seq, MethylCap-Seq, microRNA-Seq, mRNA-Seq, NA-Seq, NET-Seq, NOMe-seq, NSR-Seq, PAS-Seq, Peak-Seq, PhIP-Seq, Protein-seq, ReChIP-Seq, RIP-Seq, RIT-seq, RNA-Seq, RNASeq, rSW-Seq, SAGE-Seq, Seq-Array, Sono-Seq, Sort-seq, Tn-Seq.

Others added by you:  (now all moved to the list above)
One comment suggested I should have labeled the post as "Sequencing abbreviations". Having now taken the time to look at what the difference is between an acronym and an abbreviation, I think there is a bit of both here so I'll leave it for now.


Here's the data... 

14 comments:

  1. NET-seq, nascent transcript sequencing

    http://www.nature.com/nature/journal/v469/n7330/full/nature09652.html

    dRNA-seq, differential RNA-seq

    http://www.nature.com/nature/journal/v464/n7286/abs/nature08756.html

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  2. Immune-Seq
    PhIP-Seq (Phage immunoprecipitation sequencing)

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  3. Many of these abbreviations are not acronyms. An acronym is an abbreviation pronounced like a word (e.g. AIDS, laser). If you pronounce at least some of the letters individually (e.g. RNA-Seq), it's not an acronym. "Acronym" sounds more sophisticated than "abbreviation", but it's most often used incorrectly.

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  4. Actually, ChIP-Seq was first mentioned by Barbara Wold in a lecture at Marcos Island. Though our Science paper came out a week or two after the Snyder paper, our group should be credited with the acronym.

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  5. Degradome-seq or "PARE" (without a -seq):
    http://en.wikipedia.org/wiki/Degradome_sequencing
    Method: http://www.nature.com/nprot/journal/v4/n3/full/nprot.2009.8.html
    And recently used here:
    http://www.sciencedirect.com/science/article/pii/S0092867411007677

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  6. Seq-Array This is sequencing followed by microarray with design based on the sequencing results.

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  7. http://hmg.oxfordjournals.org/content/early/2011/08/24/hmg.ddr356.abstract - NOMe-seq

    http://en.wikipedia.org/wiki/ChIA-PET - ChIA-PET

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  8. Excellent! Congratulations :)
    You can add FragSeq, to investigate the "structurome": http://www.nature.com/nmeth/journal/v7/n12/abs/nmeth.1529.html

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  9. We use a method similar to Tn-seq called TraDIS (Transposon Directed Insertion-site Sequencing, PMID 19826075). Others have called comparable methods HITS (High-throughput Insertion Tracking by deep Sequencing; PMID 21431773) and INSeq (insertion-sequencing; PMID 19748469). The methods are all similar, but ours is the only one that is bigger on the inside (http://en.wikipedia.org/wiki/TARDIS).

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  10. Here's a biophysics application of NGS: Sort-Seq

    "Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence." http://www.ncbi.nlm.nih.gov/pubmed/20439748

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  11. And here comes: ProteinSeq !

    Darmanis S, Nong RY, Vänelid J, Siegbahn A, Ericsson O, et al. (2011) ProteinSeq: High-Performance Proteomic Analyses by Proximity Ligation and Next Generation Sequencing. PLoS ONE 6(9): e25583. doi:10.1371/journal.pone.0025583

    http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0025583

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  12. And now
    ChIRP-seq=Chromatin isolation by RNA purification followed by deep sequencing

    See:
    Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions.
    Mol Cell. 2011 Sep 29.
    Chu C, Qu K, Zhong FL, Artandi SE, Chang HY.
    PMID: 21963238

    http://www.cell.com/molecular-cell/abstract/S1097-2765%2811%2900680-0

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  13. Two more: Shape-Seq and BS-Seq

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