Is It Feasible Look For Allele Specific Expression Of Rna-Seq Data When The Dna Sequence Is Not Known

Question

[camelbbs]

I want to ask a question about using rnaseq to detect allele.

We only have rnaseq in sample A and B, but we don't have WGS or exomeseq on that samples.

So Is that possible for us to detect allele-specific expression in sample A or B? Can we use hg19 genome reference to be a reference to filter the SNP in genome?

Thanks a lot!!!

Answer 1

[Chris Miller]

You can't detect allele-specific expression in RNA-seq unless you know the allelic status of the DNA. For example, if you see entirely As expressed at one location, does it mean that the DNA is entirely A, or does it mean that it's a het A/C with allele-specific expression?

You could, however, detect a subset of biased expression patterns. If you see 90% As and 10% Cs, you can be fairly confident that the DNA is A/C and that you're seeing biased expression of the A allele. The caveat here is that you'll miss any site that is 100% expression of one allele or the other (for the reasons outlined above).

Really, to do this type of analysis, you're going to want to have RNA and DNA sequence from the same sample.

[Sean Davis]

This is really a much better answer than mine.

[camelbbs]

Thanks so much Chris, so far we only have rnaseq data and can't have DNAseq in recent future. So if I compare allele across samples, can it be explained while there only have A in sample x, but only have C in sample y?

[Chris Miller]

Depends on your samples. If this was an extremely inbred mouse strain, then you might be able to say with some confidence that the reference strain has an AC at this position, so observing only A is likely to be due to skewed expression and not a mutation. In humans, you might also be able to look at allele frequencies from dbSNP or 1000 genomes to get an idea of how often you see A and C in the population. To be completely sure that you're seeing an RNA-level skew, though, you really need to know what the alleles are in the DNA.

[camelbbs]

Got it. Thanks a lot!

Answer 2

[Sean Davis]

Roughly, the process for calling variants in RNA-seq is going to be:

1. Align the reads using an RNA-seq aligner (gsnap, STAR, tophat2)
2. Call variants (multiple options here, also)
3. For each variant, look at the proportion of reads containing the variant

This process will likely have a high false-positive rate unless you use some heuristic filtering.

Answer 3

[Robert]

I use Partek Genomics Suite to estimate allele-specific expression from RNA-Seq data alone.

[camelbbs]

HI, I know Partek can detect allele expression across samples, but since we don't have DNA seq from that sample, how to explain our result. Maybe Chris did it above.