Gas station without pumps

2018 March 28

Personal genome sequencing

Filed under: Uncategorized — gasstationwithoutpumps @ 12:41
Tags: ,

I have just ordered whole-genome sequencing (WGS) for myself from Dante Labs, as I suggested I would do in Direct-to-consumer genome sequencing.

Dante Labs has the cheapest WGS service I could find at $499.  They say that they ship the data in 3 forms: FASTQ, BAM , and gVCF.  The FASTQ format is basically the raw read information from the sequencing machine, BAM is the alignment of the reads to a reference genome, and gVCF is a variant-call file based on the alignment of the reads to the genome.

Many other sequencing services charge extra for sending you the data, as they want to hang onto it and charge ridiculously large amounts to run little software genetic tests on it.  You can get essentially all the standard tests run on the data by Promethease for about $10.  The Promethease analysis is limited to what is in the SNPedia database, which is a fairly large database of published information about genomic variation, with pointers to the original literature.

I’m interested in finding out what my inherited bradycardia (resting heartbeat lower than 60bpm) stems from. The inheritance of this condition has not been studied much as it has little medical consequence by itself (an increased need for pacemakers in old age, perhaps).  Most bradycardia is caused by heart damage and old age, so that is what gets studied.

I found a good open-access survey article on the subject,

Inherited bradyarrhythmia: A diverse genetic background
Taisuke Ishikawa, DVM, PhD, Yukiomi Tsuji, MD, PhD, Naomasa Makita, MD, PhD
Journal of Arrhythmia 32 (2016) 352–358

in which 16 genes are linked with bradycardia (though often with serious other conditions, which our family does not have).  SNPedia only mentions bradycardia 8 times (talking about only 3 genes), and there is no overlap between SNPedia’s entries and the genes in the survey article, so it is clear that SNPedia is not going to be very useful here.

I believe that Dante Labs uses SNPeff to do its annotation, a free tool that seems to be even older and less up to date than Promethease’s use of SNPedia.  But I don’t think that any of the commercial services will be any better for the analysis I’m interested in, as it is quite likely that my family has an idiosyncratic mutation that has not been published.

I’ve communicated with Dante Labs, and they say that the $500 produce is for 30X sequencing with BGI sequencers (not Illumina).  I was worried that the price was too low to be real, as even wholesale sequencing for large numbers of genomes is $600 each from BGI, but a couple of people in Europe that I communicated with were pretty sure that Dante Labs was a reputable lab, and one said that he’d run 10 genome samples through them.  I was reassured enough to risk the $500 on testing my own genome, but I’ll wait until that data comes back before testing anyone else in the family.

I expect that it will take 3 or 4 months before I have any data from them, as they are not paying for quick turnaround from the sequencing labs, and even quick turnaround would be a couple of weeks with the low-cost sequencing methods.

5 Comments »

  1. The promethease looks like a great resource. We’ve thought about sequencing genomes in our family but I didn’t know where to start. This brings me one step closer.

    Comment by RFon — 2018 March 29 @ 11:57 | Reply

  2. Actually, all 16 genes in the 2016 paper you cite are in SNPedia, and there are literally hundreds of SNPs from them. Searching by gene name is far better than text searching using a term like brachycardia, because the gene name is specific, whereas a given medical term may not been used (for example, some publications discussing brachycardia and other conditions may use terms like cardiac arrhythmia, bradyrhythmia, etc, at least in the title of the paper).

    There are certainly plenty of brachycardia-associated genotypes in SNPedia that could be more extensively curated, though, and if you’d be interested in doing a bit of research to help out feel free to contact us any time.

    Comment by Greg Lennon — 2018 March 30 @ 10:13 | Reply

    • Thanks.

      I must have been doing searches wrong in SNPedia then, because I tried each of the gene names given in article and didn’t get anything. There was no text for the genes and no mention of what conditions they were involved in.

      Trying again now, I see that I get a list of variants that requires clicking through to find out what the variant is and whether it has any known significance (the “max magnitude” and “summary” columns of the table seem to be contentless, at least for SCN5A—this seems to be an automatically populated table using metadata that has not been entered).

      Once I know what variants I have, I can probably go directly to the variants, so the uninformativeness of the gene-wide summary may not be such a big deal, but if I have an idiosyncratic variant, it would be good to have a gene-wide summary of what conditions other variants of the gene are known to be related to. If there is good metadata on the individual variants, it shouldn’t be too difficult to construct an automatically generated summary for the gene.

      Comment by gasstationwithoutpumps — 2018 March 30 @ 12:04 | Reply

    • I wonder whether SNPedia could use NLM’s MESH headings https://www.nlm.nih.gov/mesh/ to provide better searching for medical conditions. NLM does provide an API to access the MESH trees, as well as downloads of the trees.

      Pubmed has MESH terms associated with journal articles, but I don’t know whether any of the SNP databases have MESH terms associated with the variants. It would be useful for improving subject-based searches, just as MESH terms are for article databases.

      Comment by gasstationwithoutpumps — 2018 March 30 @ 12:14 | Reply

  3. […] I sent in my spit kit (formally “ORAgene⋅Dx For collection of human DNA”) to Dante Labs for whole-genome sequencing (WGS) for myself yesterday, as the next step after ordering the sequencing as mentioned in Personal genome sequencing. […]

    Pingback by Spit kit sent | Gas station without pumps — 2018 April 13 @ 09:22 | Reply


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