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brittney logan.
Hi,
I’m studying computational biology, and have been getting quotes from various labs for a 30X WGS of my dog.
I’ve got some questions on your Trailblazer Level sequencing:
Will I get full access access to the raw sequencing data so that I can perform my own bioinformatics analysis?
What sequencing platform will be used?
What is the expected error rate in sequencing?
Does the saliva sample provide the most accurate results? I.e. would other tissue samples such as blood lead to more accurate sequencing?
Thank you.
Hi Lyle, thank you for your interest in the Trailblazer sequencing.
1. We send your dog’s variant call file (VCF) alongside a printed booklet about their genome. We will gladly facilitate full access to raw sequencing data such as BAM files and can easily set up a data transfer that works for you.
2. We use Illumina NovaSeq with at least 30x coverage (although usually higher) through the Broad Genomics Platform in Cambridge, MA.
3. Error rate will be comparable to error rates for human 30x genomes produced using that technology. We use the standard 30x sequencing pipeline at the Broad Genomics Platform, detailed here: http://genomics.broadinstitute.org/data-sheets/DTS_WGS_12-2019.pdf
4. We typically mail two saliva swabs which we pool together. Whole blood might offer certain improvements to sequencing accuracy but saliva is sufficient. We can work with a whole blood sample, if you would prefer. The booklet we print for Trailblazer dogs does include a tree of oral microbiome diversity, which would be absent for a blood sample. If you are interested in studying the micro-organisms present in your dog’s saliva, then sequencing from saliva offers that opportunity.
Feel free to reach out for more information,
Kathleen
Hi Kathleen,
Thank you for your fast response.
I’ve been looking into different delivery options. I’m in the UK and I’m finding dry ice courier services to the US to be limited. I’ll talk to my vet next as they may already have courier agreements in place that might be usable.
Lyle
Dear Kathleen,
Sadly Cassie has now passed away so a saliva sample isn’t possible anymore. I do have a frozen blood sample though, and I’ve found a courier that says they can help.
In September I started studying for a PhD in Computational Biology at Oxford University. There may be opportunities to do the sequencing here, but it might be easier to send the sample to you, partly due to covid.
Lyle
Hi Lyle,
We are so sorry to hear of your loss, our sincerest condolences.
That is wonderful that you have a blood sample, and we can certainly use that for the Trailblazer, whole genome sequencing if interested.
Please know that there may be additional costs since blood samples, and the extraction of them, are not usually in our sequencing pipeline.
If you have any questions or concerns we would be happy to chat with you about the details at support@darwinsark.org
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