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.