The challenges of mRNAseq analysis

I'm worried about our current mRNAseq analysis strategies.

I recently posted a draft paper of ours to arXiv entitled RNA-Seq Mapping Errors When Using Incomplete Reference Transcriptomes of Vertebrates; the link is to the Haldane's Sieve discussion of the paper. Graham Coop said I should write something quick, and so I am (sort of -- I mean to write this post a few days ago, but teaching. family. etc.)

I decided to post the paper -- although we haven't submitted it yet -- because I wanted to solicit feedback and gauge where the disagreements or misunderstandings were likely to pop up. I suspect reviewers are going to have a hate-hate relationship with this paper, too, so I want to get rid of any obvious mistakes by crowdsourcing some early reviews ;).

Before I talk about the paper, let me mention a few related factoids that crossed my 'net firehose and that tie into the paper; I'll weave them into the paper discussion below.

  1. Dan Zerbino (one of the Assembly Gods?) wrote a good e-mail about how Oases can't really leverage coverage information when reconstructing transcripts on the oases-users mailing list.
  2. I read and reviewed the SASeq paper on mRNAseq quantification, which talks about how many of our transcript models are almost certainly not expressed.
  3. The lamprey genome paper came out, pointing out that the genome is probably missing ~20-30% of the germline content.
  4. A paper on evaluating mRNAseq expression analysis software hit arXiv.

OK, so what did our paper say?

The paper's genesis is this: for years I'd been explaining to collaborators that mRNAseq was unreliable on any organism without a pretty good reference transcriptome, and that constructing the reference transcriptome relied on either good mRNAseq assembly tools OR on having a good reference genome. So that was what my lab was working on doing with their data.

Since we tend to work on weird organisms like chick (which has an incomplete genome and a notoriously poor gene annotation), lamprey (see above -- missing 20-30% of its genome), and Molgulid ascidians (for which we are constructing the genome), we needed to go the de novo mRNAseq assembly route.

However, we also quickly realized that there were a few problems with de novo mRNAseq assembly and expression evaluation: lots of mRNAseq needed to be crunched in order to get good reconstruction, which was computationally intensive (see: diginorm); splice variants would confuse mapping (see: this paper); we were uncertain of how well splice variants could be assembled with or without a reference (see: this paper); and we weren't sure how to evaluate mapping tools.

When a new postdoc (Alexis Black Pyrkosz, the first author) joined the lab and wanted a fairly simple project to get started, I suggested that she evaluate the extent to which an incomplete reference transcriptome would screw things up, and perhaps try out a few different mappers. This took her about a year to work through, in addition to all of her other projects. She built a straightforward simulation system, tried it out on chick and mouse, and got some purely computational results that place (in my view) fundamental limits on what you can accomplish with certainty using current mRNAseq technology.

Incidentally, one piece of feedback she got at GLBio from a prof was (paraphrased) "I hope this isn't your real project, because it's not very interesting."

The results, in short, are:

  1. What mapper you use doesn't really matter, except to within a few percent; they all perform fine, and they all degrade fairly fast with sequencing errors.

  2. Incomplete reference transcriptomes matter, a lot. There are two entirely obvious reasons: if you have a splice variant A that is in your reference but not present in your mRNAseq, and a splice variant B that is not in your reference but is actually transcribed and in your mRNAseq, the reads for B will get mapped to the wrong transcript; and (the even more obvious one) you can't measure the expression of something that's not in your reference via mapping.

    The SASeq paper does a nice job of pointing out that there's something rather seriously wrong with current mRNAseq references, even in mouse, and they provide a way to minimize misestimation in the context of the reference.

  3. Direct splice variant reconstruction and measurement is, technically, impossible for about 30% of the transcripts in mouse. For standard paired-end sequencing, it turns out that you cannot claim that exon A and exon Z are present in the same isoform for about 30% of the isoforms.

  4. The slightly surprising conclusion that we reached from this is that mRNAseq assembly is also, generally speaking, impossible: you cannot unambiguously construct a reasonably large proportion of observed isoforms via assembly, since the information to connect the exons is not there.

    Until recently, I had held out a forlorn hope that Clever Things were being done with coverage. Then I saw Dan Zerbino's e-mail, point A, above.

And yet, judging by the Oases and Trinity publications, assembly works! What's up?

There's something a bit weird going on. Tools like Oases and Trinity can clearly construct a fair proportion of previously observed transcripts, even though the information to do so from direct observation isn't there and they can't necessarily use coverage inference reliably. My guess (see paper D, above) is that this is because biology is mostly cooperating with us by giving us one dominant isoform in many or most circumstances; this matches what Joe Pickrell et al. observed in their truly excellent noisy splicing paper. But I'd be interested in hearing alternate theories.

At this point, my friend and colleague Erich Schwarz tends to get unhappy with me and say "what would you have me do with my mRNAseq, then? Ignore it until you come up with a solution, which you claim is impossible anyway?" Good question! My answer is (a) "explore the extent to which we can place error bars or uncertainty on isoform abundance calculations", (b) "figure out where interesting isoform misestimation is likely to lie in the data sets", and (c) "look at exon-exon junctions and exon presence/absence instead of whole isoform abundance." But the tools to do this are still rather immature, I think, and people mostly ignore the issue or hope it doesn't bugger up their results. (Please correct me if I'm wrong - I'd love pointers!)

In my lab, we are starting to explore ways to determine what mis- or un-assembled isoforms there might be in a given transcriptome. We're also looking at non-reference-based ways of doing mRNAseq quantification and differential expression (technically, graph-based methods for mRNAseq). We are also deeply skeptical of many of the normalization approaches being used, largely because every time we evaluate them in the context of our actual data, our data seems to violate a number of their assumptions... Watch This Space.

Paper reactions

What's the reaction to the paper been, so far?

Well, on Twitter, I've been getting a fair bit of "ahh, a good reference genome will solve your problems!" But I think points #3 and #4 above stand. Plus, invoking solving a harder and more expensive problem to solve what you think is a simpler problem is an interesting approach :). And since we don't have good references (and won't for a while) it's not really a solution for us.

I've also been getting "this is a well known problem and not worth publishing!" from a few people. Well, OK, fair enough. I've been skimming papers with an eye to this for a while, but it's entirely possible I've missed this part of the literature. I'd love to read and cite such a paper in this one (and even rely on it to make our points, if it truly has significant overlap). Please post links in the comments, I'd really appreciate it!

It is clear that the paper needs some reshaping in light of some of the comments, and I'd like to especially thank Mick Watson for his open comments.

Concluding thoughts

If our results are right, then our current approaches to mRNAseq have some potentially serious problems, especially in the area of isoform expression analysis. Worse, these problems aren't readily addressible by doing qPCR confirmation or replicate sequencing. I'm not entirely sure what the ramifications are but it seems like a worthwhile thing that someone should point out.


p.s. Our simulations are fairly simple, BTW. We'll put the code out there soon for you to play with.

p.p.s. Likit Preeyanon, a graduate student in my lab, was one of the first people in my lab to look really critically at mRNAseq. Watch for his paper soon.

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