* YSEQ jumps into the DTC WGS market with WGS400

Randy Harr - Tue 16 of Feb, 2021 16:50 EST

Long an innovator in the genetic genealogy market, Thomas Krahn of YSEQ has developed a new entry that is going to (likely again) shake the market up. And finally put closure to the adoption by everyone of WGS technology as the first choice to be applied to genetic genealogy. Something we have been seeing and preparing for over the last few years.

YSEQ.net's NGS Tests Product Page (16 Feb 2021)

YSEQ has long been a player in the market since formed when Thomas and Astrid Krahn left FamilyTreeDNA back in 2012 or so. They started in the business with DNA Fingerprint which was acquired by FamilyTreeDNA in 2006. For 6 years they innvoated at FTDNA concluding with the release of the BigY test based on NGS technology — the first for the genetic genealogy industry and which took yDNA SNP testing into the forefront of modern scientific discovery. YSEQ has long offered WGS testing. Just at a price point expected of a European vendor. Not the Direct-to-Consumer (DTC) of under $500 that we have defined here. Often close with $700, but not below $500. In fact, look at the screen capture shown here. They offered a 45 gbases test (that is 15x) for more than Nebula or Dante offer a 30x one.

Then, today, on the day of the 20th anniversary of the first publication of a human genome reference model, they come out with their WGS400 product for $399. Combined with all the best-in-class analysis they offer in the yDNA field, and support for mtDNA and Autosomal extraction and analysis, they now become a better solution than anything available on the genetic genealogy market. Without a doubt.

YSEQ.net's yFull analysis

Why so bullish on being best available? Not only do they tend to offer the "cadillac" of services and tests with a solid reputation of over-delivering. But the big waited break-through in current WGS technology (especially as it relates to yDNA testing), has been how to get longer read lengths to better read those longer STR values. We could go on explaining why this is important but instead point you to a nice web page developed by Thomas and buried in his sample data location: https://genomes.yseq.net/WGS/400SE/STR_examples/. Read it carefully to see what this longer read length will assist with. And then their WGS Product Page for actual comparisons and results. With the yFull chart shown there for yDNA STR extraction, they jump far into the lead of the pack for having successful yDNA STR extraction.

We had been hearing rumors of them working on this technology for years. And according to Thomas, this is an in-house development of proprietary technology. Hopefully with a strong enough backing to navigate any potential patent issues that so many face when going up against the now behemoth Illumina. But he has been a proven innovator through the years so we have little doubt. What is very interesting is this goes in the face of the typical market prowess I promote. That it takes a while for the costly, can-afford-it, medical market uses to filter down to affordable, cost-effective use in genetic genealogy. Here we have the technology being developed for genetic genealogy with likely wider use coming in the medical community later.

Like we did for the second player entrant to the market (Nebula Genomics) this time last year, here is a chart to compare the now three different company offerings. We will update as more information is made available. Please also realize this is just one of many offerings from YSEQ; not just in the WGS space. This is only focused on YSEQs WGS400 product and not their other WGS offerings that still exceed $500. If testing for medical, likely still best to stick with Nebula for their 30x mapped guaranteed deliverable. If genetic genealogy and testing a male where longer STRs are important on the yDNA, then YSEQs new WGS400 is the way to go.

Feature	YSEQ	Nebula	Dante	Notes
Read Length	350-400 SE	100 PE¹	150 PE	150 paired-end is the best offered for short-read, paired-end, massively parallel sequencing. YSEQ is single-end read. We are measuring 350 in their yDNA sample files but yFull and yDNA-warehouse show 400; which we read on their full WGS file.
Avg Read Depth	15x+	30x mapped	30x RAW (maybe)	Dante only now guarantees 90 RAW gigabases of sequencing independent of what mapping rate may occur. Sometimes as low as 20% making it ~6x mapped! This is a 45 gbase product from YSEQ. Which is usually sufficient for genetic genealogy but does not meet clinical lab standards for medical uses.
Quality	45+ gbases mapped	90+ gbases mapped	90 gbases	Dante has been a sore point for many in that mappings of results have been as low as 20%. Thus making the deliverable useless. They blame any low mapping on customer contamination. A clinical lab must deliver 30x / 90 gbases mapped.
Equipment	MGI DNBSEQ-G400 (in SE mode)	MGI DNBSEQ-T7	Illumina NovaSeq 6000	Dante originally started with the BGI Hong Long lab as did FGC; but both with older sequencers only doing 100 bp read length when Illumina had 120.
Price	$399	$299+	$150-$700	Dante's price depends on sales; usually flash sale in November. Nebula charges $299. But you are required to order a subscription which will be charged when results are delivered. Minimum is one month at $19 which you can cancel after 29 days.
Subscription	None	Required (minimum $20 for one month)	Offered	Nebula requires a subscription to purchase the product; but allows cancellation within the first month; billed $20 and starts once the results are received. YSEQ has no health and wellness reports nor subscription. The others require a subscription to get report updates (mostly medical analysis reports). Dante does not require a subscription to get reports; you purchase the reports individually. Nebula does not provide access to reports without a subscription. You can buy a lifetime subscription for $200 from Nebula at the time of the order
Reports	none	(medical)	(medical)	Both are focused on offering medical reports and interpretation. See above for access and update costs with subscriptions. Dante reports are mostly a-la-carte.
Reports	(see below)	(genealogy)	(genealogy)	This is YSEQ forte and focus. They do not offer an autosomal match database (yet) but have strong ties to yFull and offer an 23andMe API microarray file output. Others have no direct focus here but 3rd party (free) tools are available for transfer results to other sites.
File Delivery	FASTQ, BAM, VCF, uSD	FASTQ, CRAM, VCF (online 90 days)	FASTQ, BAM, VCF (online 90 days)	Data files are generally available initially without any subscription or additional cost CRAM is another form of a BAM. But Dante and Nebula take the large files offline after 90 days. Dante requires a subscription and weeks to get access back. Nebula just a button click and 48 hours to restore. The VCF is/are always available. YSEQ will send your files on a microSD card through the post. Otherwise, to date, available on their server (other two use AWS). YSEQ provides many additional post processing files like mtDNA FASTA, Y-only BAM, 23andMe API microarray file, and various forms of not typical VCF files. See 400SE 16672 for an example.
BAM ref model	hg38 hg19/rCRS on request	hs38	hs37d5 hs38 on request	Not a big deal either way as you need both and one can be easily converted to the other.
Delivery Time	2-6 weeks?	8-10 weeks	4-52 weeks	Both have issues delivering in a timely fashion (likely, typically). Nebula's kits purely because they are going to a processing center, then a Hong Kong lab for sequencing, then data back to the USA for bioinformatics. Dante kits in USA go to Utah first, then Italy. Both count the test processing time as starting from once received in the actual laboratory. Which can be 0 to 6 weeks after receipt depending on the initial facility that receives the kit. YSEQ is based on their other WGS offerings.
Sample Kit	Swab	Swab	Spit	Like for MyHeritage and FTDNA, Nebula uses the scrape / swab collection. Samples based on cheek cells. Dante uses the more typical spit tube that relies on white blood cells in the saliva. Spit is more difficult to obtain and unreliable from older adults and young children. YSEQ is known for their dry swab collection — fewer issues of contamination that way.
Market Coverage	Worldwide	Worldwide; Only USA Free return ship	Worlwide; Longer USA return ship	Nebula was using Gene by Gene Ltd (FTDNAs parent) to ship and receive kits. They are located in Houston, TX and only offer free return shipping within the USA. But do ship out worldwide. Dante ships with DHL from Italy to anywhere in the world and offers free return shipping. So more knowledge of custom handling by DHL. For Dante, this is except USA generally; which are shipped from its partner Spectrum in Utah, an Ancestry spinoff. So Dante is free return shipping worldwide (to Italy or Utah; respectively) with Nebula free return shipping only in the USA. Note: a few countries customs units restrict the spit/swab kits across their borders. Australia and New Zealand seem to be constant problems in this regard.
Genetic Genealogy	In-house, yFull	FTDNA (announced)	yFull (announced, never delivered on)	Dante announced a yFull partnership in Fall 2018 but nothing ever came of it. (yFull says they finished their end). Nebula and FTDNA announced a planned partnership for 2H20. Nebula has since confirmed their side is complete and access to all FTDNA databases / match lists / trees is planned "for a small fee". Still awaiting FTDNA to turn on the Nebula interface as of Jan 2021.
Resellers	None	Sequencing.com, Genomes.io	None	Simply listing resellers of their lab services that are also under $500. The resellers may charge more or have more, less or different reports and analysis services.
Lab	In-house	Hong Kong (BGI) (CLIA certified)	In-house (as of 2020), Hong Kong (BGI) in 2018-19	Nebula used to use FTDNA's parent Gene-by-Gene in Houston, TX for shipping sample kits and receiving them back for initial processing before going to Hong Kong. Now they use AKESOgen, Inc. in Georgia. Dante has a kit delivery and collection service with Ancestry subsidiary Spectrum Solutions in Draper, Utah for USA customers and xxx in Germany for much of the EU now. But it seems to come and go as to whether the service is used or they handle it directly from Italy.
Location	Berlin, Germany	Boston, USA	L'Aquila, Italy

¹As of June 2021, Nebula has started delivering 100 base-pair read length sequencing. This calls into question other details of their delivery like the sequencing equipment it is being performed on as well. They had been reliably delivering 150 base-pair reads for the first 1.5 years.
²As of Dec 2019, it was announced that Tempus has acquired AKEsoGen. As of Jan 2021, it was announced that MyDNA of Australia has acquired Gene by Gene Ltd (parent to FamilyTreeDNA aka FTDNA). As of Aug 2021, it was announced that ProPhase Labs has acquired Nebula Genomics.

Some other items to note. YSEQ offers to send your files via a microSD card. We have long considered this as the way to go. 256 GB microSD cards are under $15 these days and can easily be put in a 1st class letter not requiring any custom declaration or tracking. For those that have trouble downloading data, this is a game changer if reliably delivered. Which, from this company, they have a strong track record of customer service in the industry.

It is not clear yet of the real advantage of single-end over paired-end. You often see paired-end written as 2x150 because you really are getting 300 base-pair read segments, on average. So the 400 SE may only be a 25% advantage. But then it is hard to say how often the aligner has problems with the paired-end reads in the all important long STR areas when it does not span the repetitive area.

WGS test companies, in general, are not providing match databases. YSEQ is a genetic genealogy focused company though. And either provides these services or links to those providing it. More importantly, they are innovating through in-house development and collaboration on many new tools. Just never focused on microarray to date. Either the original CE testing services or the newer WGS. But we expect stronger support of microarray style matching services going forward.

Information is deemed accurate at the time of publication. Minor updates or corrections may occur after that point if notified of errors or new information becomes available. Other long-time WGS providers in the genetic genealogy community but not dipping under the DTC $500 price barrier mentioned here are Full Genomes Corp, and previously YSEQ. Others that were but no longer offering are Veritas (a sister spin-off from Harvard to Nebula).

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