Genomics

Getting My Genome Sequencing Done (Part II)


The purpose of this exercise is to demonstrate how to get one’s genome sequenced to those without previous experience. I will build on part one of this story, in which I explained how I tried to contact several companies who might sequence my genome. In that post there was one company I did not mention on purpose, the BGI. This post is going to be mainly about my story on how I sequenced all my gene coding regions (also known as exome) with BGI’s help, for which I am very grateful. The BGI was in fact the only company that replied to me and was interested in supporting my adventures in direct-to-consumer personal genomics.

I was able to have personal contact with the BGI in June 2011, when I, and my collaborator Rafael Jimenez, presented them our plans for developing a free open source platform for self-analysis of personal genomes. This story is a key part of that enterprise in which we have already invested so much. I hope that interested readers may find some of these experiences helpful, especially if they are thinking of sequencing their genomes.

Our initial goal with the BGI was to get the sequencing of my family’s genomes for free. After several weeks of negotiation, it was clear that the best they could offer me was their cheapest deal, a personal exome sequencing for $999. This in itself was a big success for me, largely because sequencing a single genome is not profitable for a company, as I dicovered when I spoke to Complete Genomics who would only consider a minimum of 8 genomes per experiment. At current prices this would be unaffordable even with sponsorship. Second, with contact with the BGI already established, there was the possibility that my whole family might be able to have our genomes sequenced sooner rather than later.

Even though I did not have the money to be able to pay for my exome, I optimistically accepted BGI’s offer, and decided on sequencing my own exome. It was clear that whilst I would be able to send them a sample any time, they would only do the sequencing as soon they received the money. It turned out that the money arrived to Hong Kong, where BGI’s bank account is located, before the sample. In less than three days I found a generous undisclosed Spanish sponsor who agreed to pay in full the sequencing of my exome. The currency to be paid in was euros, so the final sum was 712 euros. Apart from that, I myself paid the cost of sending the sample, out of my own pocket, using DHL. The total cost for this was £45.95.

DHL Sample Shipment Receipt

Finding the right kind of DNA sample to be sent was the difficult bit. BGI initially asked for either purified DNA or a blood sample. Neither of these options were feasible for me, because here in the UK is next to impossible to extract one’s blood if it’s not for health-related purposes. Sending DNA was not an option either because I am not a wet-lab scientist and did not have easy access to DNA purification kits. Besides, for this exercise, in which I am trying to emulate an ordinary citizen with no lab access, those options would not be feasible anyway. The solution was Oragene Kits from DNA Genotek. If you are a 23andMe customer, you will know that you spit saliva into a test tube which then gets shipped to the US. Oragene kits contain a stabilizing solution that breaks down all DNA degradation enzymes naturally contained in cells. Their DNA yields from saliva are as good as from blood samples. One can send these Oragene kits at room temperature with no need to keep the sample cool with ice, as it is the case if one sends blood.

Manuel spitting in Oragene kit for DNA extraction from saliva (photo taken by Sito Torres)

I found on the DNA Genotek website that they provide 4 sample tubes for anyone to try at no cost. I sent them a request for free sample kits and the following day they called me on the phone to check what may plans were. I did not have to pay any money at all and in less than a week they had sent me enough spit tubes for me and for my parents (we hope they will be sequenced in the near future), all the way from Canada. I would like to take this chance to recommend DNA Genotek’s sample kits; they have worked really well for me.

I still had to negotiate with the BGI the shipment of saliva (instead of blood) and also the extraction of the DNA. Very kindly the sales people from the BGI agreed to try a saliva protocol for DNA extraction for free. In all respects, I am very grateful to the BGI for the impeccable service I have received. There was one last obstacle that had to be sorted before I sent my saliva sample. The Hong Kong government requires an import license for biological materials, blood and saliva included. Fortunately the sample management team at the BGI took care of this. We calculated that the sample would arrive during the first week of August (2011). The license stated the sample arrival date would be around the 1st of August. It actually reached Hong Kong slightly sooner but this did not seem to be a problem for the customs authorities.

Finally on the 6th of September I received an email from the BGI project manager who informed me that my exome was ready for download. The delivery date in fact was almost a month earlier than the one initially agreed, so from that point of view I am also grateful to the BGI. I downloaded 4 files from their ftp site taking a total of ~2.7 Giga Bytes of data, which is less than I thought. However, it still took me 4 hours to download the whole thing (even though I had a fast Internet connection). These files are in FASTQ format. Here is the first read of one of the files:

@FCD044UACXX:4:1101:1778:2233#CAGATCAT/2
CTTGGATAAAAGGAAAATTTTGAACATGGGACCCTGACTTAATGAATATTTGAATGTTNNNNNNNNNNNNNNNNNNNNNTCAAGTGTCGT
+
__aeccacgggce`ffheghhhiiiiihhhbfc_fghfhifhdhgihbghedb[egfeBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

This is the end of the series on Getting My Genome Sequencing Done. There will be a new series coming up called Getting my Genome Analysis Done.

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6 replies »

  1. Hi Manuel,
    I love reading through your post and this novel idea of family genome sequencing initiative. Any article on “Getting my Genome Analysis Done” yet ?

    Like

  2. Manuel, those sound like huge downloads! Can you somehow run this file through third-party analyses such as promethease or the dodecad project or do these files need to be reformatted? I wonder if stats program R can read something that big…?

    Like

    • Spyro,

      what I got in this case were the raw format files output from sequencers. Of course, to get the actual interesting information one has to a) align the reads provided in the raw format files against the reference genome, b) run algorithms that call for variants using the aligned read information and c) decide which of the called variants are actually worth pursuing further.

      Like

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