Calculating simple allele specific expression for certain variants
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15 months ago
Floris Brenk ★ 1.0k

Hi all,

I have a couple perhaps somewhat naive questions about allele specific expression and was hoping that someone could push me in the right direction.

We have a blood based RNAseq dataset and some samples have a clear pathogenic variant in them. One hypothesis is that of course if the damaging allele is more expressed then this could result in higher penetrance?

Q1: Calculating allele specific expression To tests this we called variants using this:

bcftools mpileup --threads 20 -Ou -a FORMAT/AD -a FORMAT/DP -r chrX:XXXX-XXXX -f Homo_sapiens_assembly38.fasta -b BAM_file_list.txt
-o pile_up.bcf bcftools call --threads 20 -mv -Ob pile_up.bcf -o jointcall.bcf


Then we just divided A1/A2 (using this as ratio) from the DP field of the vcf file. Is this OK to do? it feels a bit too simple but also makes sense.

Q2: If this ratio calculation is OK, we have several blood time-points and sometimes this ratio fluctuates a bit between time-points from the same individual is this due to experimental variation or biological variation?

Q3: Is it expected that most of the ASE ratio values are not 1? I kinda expected that they should be around 1 always, but seeing a lot of 1.2 ratio's and very few below 1.

Q4: In general, how stable is ASE typically across tissues? Im sure someone at GTEX must have looked at this, but cant find the paper about this. Thinking along the lines that if we see an effect in blood that must also be applicable to other tissues

Sorry if these questions are a bit too basic or naive for here, any help is appreciated!

ASE RNA-Seq allele specific expression • 369 views
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Tools & best practices for ASE can be found in this paper published in 2015. I think there are some studies that suggest that allelic imbalance favoring the deleterious allele in tumor suppressor genes could promote tumorigenesis, but I have yet to run into a paper that provides solid evidence for this.