Sunday, 18 November 2018

A 30x whole genome sequence from Dante Laboratories for €169 (£150 or $199)


Dante Laboratories have announced a special one-off promotion for Black Friday week. They are offering a next generation sequencing whole genome sequence (WGS) test at 30x coverage for just €169 (£150 or $199). The offer will end at midnight US Pacific time on Monday 26th November. Customers will also receive their raw data and a customised report without extra cost.

30x is the standard medical-grade coverage and this is the lowest price I've ever seen for 30x WGS.

The cost of the test includes the provision of a VCF file which can be downloaded from your account. There will be an option to download the BAM file from the cloud free of charge. Alternatively the FASTQ and BAM files can be sent on a 500 gigabyte hard disk for an additional fee of €59.00 ($69).

For further details visit the Dante Labs websites in the EU and the US:

https://us.dantelabs.com (US website)

The offer is also available through the Amazon market place in the US only.

There is a link to download a sample customised report on this page on the Dante Labs website.

See also the FAQs relating to this special offer.

Dante Labs introduced whole genome sequencing to the European market for €850 in May 2017. The price subsequently dropped to €449 (£400 or $499). There was a special offer in the US on Amazon Prime Day when the WGS test was on sale for $349.

What you can do with your whole genome data?
If you have your whole genome sequenced what can you do with the data? There are currently no companies that offer a relative-matching service using WGS. If you want to use a WGS test to search for relative matches you will need to extract the relevant SNPs to create a kit suitable for upload to GEDmatch. Thomas Krahn from YSEQ has provided some free code on Github to extract a 23andMe (v3) style file from a whole genome sequence BAM file (raw data file). Make sure you check out GEDmatch's revised terms of service first.

If you are interesting in discovering new SNPs from your WGS Y-chromosome data there are various tools that allow you to work with BAM files. YFull is already able to process BAM files from Dante Labs. Full Genomes Corporation offers a whole genome sequencing interpretation service for $75 and an advanced analysis for $250. The R1b Data Warehouse submission process has already been reconfigured to accept VCF files from Dante Labs and they can process WGS BAMs submitted to http://haplogroup-r.org/submit.html, However, at the moment no one appears to be working with these files.

You can also upload your whole genome sequence to the literature retrieval service Promethease to get a range of health and trait reports.

Dante Labs WGS data can also be uploaded to Sequencing.com where you can share your data for research and purchase reports from their app store.

There are also many other sites where you can share or upload your raw data. See the list of raw DNA data  tools in the ISOGG Wiki.

Other whole genome sequencing providers
Direct-to-the-consumer whole genome sequencing is available from Thomas Krahn's company YSEQ at 15x, 30x and 50x. The 15x test currently costs $740. There is an additional fee of $600 for a 30x test and a $100 fee for Sanger sequencing confirmation if required. The YSEQ test includes genealogically relevant reports for the Y-chromosome and mitochondrial DNA. YSEQ ships worldwide.

Full Genomes Corporation also provides a range of direct-to-the-consumer whole genome sequencing services as well as Y-chromosome sequencing options but sadly they stopped selling to European Union countries in May as a result of the EU's new General Data Protection Regulation (GDPR).

Nebula Genomics announced this week that they were offering low coverage 0.4x whole genome sequencing for $99. They are testing a model using cryptography and blockchain technology which will allow consumers to sell their health data to researchers and choose which research they would like to participate in. If you want a medical grade 30x sequence you would have to hope that a company or research organisation would be sufficiently interested in your data to pay for the sequencing.

There are various American companies that sell whole genome sequencing such as Veritas Genetics and Sure Genomics but they don't sell their tests outside the US and you also need to order through a doctor.

There were rumours circulating on Twitter last week that Illumina would be announcing a $100 genome in the next few months. We might therefore see other companies trying to jump on the WGS bandwagon in the next few months or additional offers in the run-up to Christmas. However, I understand that Dante are using BGI sequencing technology and not Illumina. It will be interesting to see how the market plays out.

See also this discussion A 30x full-genome sequence for $199 (€169 £150) on the Wikitree G2G forum.

Further reading
Dante Labs and the $1000 genome by Rebekah Canada

Acknowledgements
Thanks to Thomas Krahn for the information about the BGI sequencing technology used by Dante Labs. Thanks to James Kane for the information about the R1b Data Warehouse and Sequencing.com.

8 comments:

Andreas said...

Debbie, please note that the BAM and FASTA file is only available if one selects the additional option of purchasing a hard disk. Only the VCF file is available for download included in the offer.

Also there is nothing being said about Y-DNA, not in the offer, nor in older reviews of the same DNA test.

Debbie Kennett said...

Andreas

I've enquired about the provision of BAM files via the cloud and will update the blog post when I get a response. I know people have previously tested with Dante Labs and have received Y-chromosome data.

See this thread in the R1b-U106 group:

https://groups.yahoo.com/neo/groups/R1b1c_U106-S21/conversations/topics/54025

Andreas said...

This is the answer I've got from Dante: "We deliver vcf free of charge. The same is for BAM and FASTQ but for them, we charge a small fee for the cost of the Hard Disk."

I've asked about Y-DNA but no answer so far (after all, it's a Sunday there as well)

Debbie Kennett said...

I've had confirmation from Dante that the BAM file download is free. The charge is only if you want the hard drive.

The Y-DNA data is definitely included. I've also updated the blog post to include the information that YFull and the R1b Data Warehouse are already accepting BAM files from Dante.

Mark Winz said...

A guy on the U106 thread noted that he received from Dante a lot fewer Y-DNA SNP variants in his VCF file that he expected. Another guy saw that too, and extracted quite a few more SNPs from his BAM file.

Are you aware of a service or script that will inspect Dante's BAM file and extract Y-DNA SNPs?

Mark W

Debbie Kennett said...

Hi Mark

I updated the blog post to indicate that YFull can interpret the results and extract the Y-DNA SNPs. If you're in R1b then you can upload your results to the R1b Data Warehouse.

It may be that Full Genomes Corporation can provide an interpretation service.

miqui rumba said...

I have my Dantelabs WGS snp.VCF since September (offert €399 from March last days) and 2 months waiting for hard drive (I asked BAM and FASTQ files both). Last friday I wrote Dantelabs that if BAM could be downloaded, they said me that they had not BAM downloading avaible yet. There are another clients that bought WGS kit in March like me and they have not recieve no results yet. They want to sell more than they can process. results are good for medical research but people that want profit good price for get cheap genealogical results are mistaken, they need pay aditional 3rd party service for interpret BAM or FASTQ files or learning a lot of Bioinformatics and upload complete raw data to Sequencing or usegalaxy.org to run BAM splitter or align FASTQ files with GRCh38 best human reference for haplogroup research.

Debbie Kennett said...

Miqui, Thanks for sharing your experience. I do hope you are eventually able to get your BAM file. It is often the case that you get what you pay for.