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Recommendations for patient derived xenografts (PDX) samples?

freekfreek Member
edited September 2018 in Ask the GATK team

Dear fellow bioinformaticians,

I have a large amount of PDX sample to analyze (RNAseq and DNAseq), this means that I need to separate reads that originated from the host genome from reads originating form the xenograft. There are various tools out there but I was wondering if there is GATK approved way to do this? Or if there is not, any high quality recommendations are very much appreciated.

Highest regards,

Freek.

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Answers

  • freekfreek Member
    edited September 2018

    To answer my own question, I found this paper very nice: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4414-y, it lists 3 methods, ICRG, Xenome and Disambiguate. Xenome has a bug which prevents the program from finishing and does not seem to be maintained anymore. ICRG is nice but I want to use STAR and it is unclear to me how to construct a merged GTF file matching the merged fasta reference genomes. Disambiguate is more computationally intensive than ICRG but it worked well on 2 BAM files with the same reads mapped to two different reference genomes. I ended up going with Disambiguate.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @freek
    Hi Freek,

    Thanks for posting your solution. I don't think our team is working with PDX samples, but I will forward this on to them. Hopefully your post will help others in similar situations.

    -Sheila

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