PDA

View Full Version : DANTE lab troubles



pauleug
04-19-2019, 04:45 AM
I got back the results of my Dante lab Whole GenomeZ (130X exome + 30X the rest+mtDNA) and it is not satisfactory.

Dante labs advertised "GENOME EXPLORER A simple tool to explore all the variants in your DNA" but have not actually provided the tool. On their website they promise "FASTQ, BAM, VCF files available for download free of charge" but it is a lie. They only provide vcf files for download. To get FASTQ and BAM files I had to pay extra $72 for Dante to send the files on a hard drive. I requested the FASTQ and BAM files two weeks ago, but Dante still have not shipped the drive.

Further, it seems to me, that they screwed up the structural variants calling. The structural variants .vcf file they provided has 113,000 (!) structural variants, that is insertions, inversions, translocations and large deletions while their number should be under 10,000.

Finally, their customer service has not responded to my emails. Anyone having similar experience?

pauleug
04-19-2019, 05:22 AM
Here is a pearl. DANTE CEO Andrea Riposati blames a customer who waited for a year without getting any results - "you make baseless accusations". Not a word of apology. Also note that the guy got his results only after the CEO noticed his internet posting. See down the page in comments https://gasstationwithoutpumps.wordpress.com/2019/02/17/full-genome-sequencing-pricing/

FGC Corp
04-19-2019, 05:48 AM
Here is a pearl. DANTE CEO Andrea Riposati blames a customer who waited for a year without getting any results - "you make baseless accusations". Not a word of apology. Also note that the guy got his results only after the CEO noticed his internet posting. See down the page in comments https://gasstationwithoutpumps.wordpress.com/2019/02/17/full-genome-sequencing-pricing/

I am not a fan of Andrea either. Of course, Dante Labs is a competitor, but for a variety of reasons a number of us have doubts about that company.

Also: we can provide variant analysis of the Dante WGS bam.

MacUalraig
04-19-2019, 06:00 AM
There is a dedicated thread for Dante under Commercial/Other

https://anthrogenica.com/showthread.php?12075-Dante-Labs-(WGS)

This is a section for Full Genomes Inc. rather than genome sequencing in general.

(NB I'm a customer of both so staying out of the arguments).

Donwulff
04-19-2019, 08:49 AM
I looked at that post, in the comments the CEO wrote "Your case is a case where we made a mistake" which is actually a more meaningful apology than using the word apology. He probably writes "you make baseless accusations" because the author of the article flat out claimed that Dante Labs is a scam; indeed the author since then changed his opinion & post to say "I am cautiously optimistic that Dante Labs is not a scam". It's certainly true that all DTC sequencing companies seem to have room for improvement, from my experience with four of them grossly missing their promised delivery targets or just not making one in the first place is par for the course for all of them.

This is indeed a group for Full Genomes Corporation, but just pointing out that even the person whose blog was linked has since then backed down from their accusations. Also the main Dante Labs thread has 637 posts now, it's impossible to find anything of relevance on that thread and same things get talked over and over again, so I propose that people create a new thread in the Other category https://anthrogenica.com/forumdisplay.php?140-Other if they have a specific topic.

FGC Corp
04-19-2019, 03:54 PM
I looked at that post, in the comments the CEO wrote "Your case is a case where we made a mistake" which is actually a more meaningful apology than using the word apology. He probably writes "you make baseless accusations" because the author of the article flat out claimed that Dante Labs is a scam; indeed the author since then changed his opinion & post to say "I am cautiously optimistic that Dante Labs is not a scam".

Since this thread is in our forum, I'll make a comment. The concerns that I've seen go beyond delivery time and relate to a mass offering that includes health reports. According to US FDA regulations, that's not permitted as a DTC test. So, either the FDA is ignoring the issue or they have a double standard. 23andme's offering was shut down because of far fewer reports.

If a company offers health reports, then under US law they can incur liability. 23andme was sued for that reason and had to settle a class action lawsuit. It took 5 years for the FDA to shutdown 23andme's health reports. It took 4 years before they were sued.

Recently, the FDA shut down a health test by the Northern Virginia Inova system. Inova was using doctors to offer the test. FDA's standards are high. We shall see whether they enforce the regulations or not.

The FDA buys tests using "undercover" customers. They do that to determine how companies are processing their data and preparing reports.

We'll see what happens, but the FDA may take a couple years to make their move.

It is also worth pointing out that the issues I've raised here are common knowledge among specialists in FDA regulations and enforcement.

bjp
04-19-2019, 04:54 PM
Also: we can provide variant analysis of the Dante WGS bam.

I'll vouch for the quality of FGC's third party analysis of bam data, I was thoroughly pleased with what they returned based on my Veritas bam nearly three years ago. They were also very interested and communicative when some odd things popped up in my results.

(Conflict disclaimer: I received the analysis at no cost from FGC as their pilot Veritas bam customer)

Donwulff
04-19-2019, 05:17 PM
That's the thing that has me most confused about Dante Labs strategy. I thought they were trying to get away with it being an Italian company, as the European regulators have not (yet) come out strongly against DTC genetic testing. I don't think they would, either, because in the USA health-care is a huge for-profit business with immense lobbying power. In the European single-payer system they're more like "...and they're going to pay for their own tests? Great!" Along with Europe generally being less lawsuit-happy. Of course, on the long term this will worsen health-disparity unless the tests come really affordable & easy to use and understand. All IMO, of course...

But noo, as far as I can find out, Dante Labs moved their company to New York, which is one of the most restrictive states to DTC genomic testing together with Maryland. And right on the heels of FDA issuing a "warning" to all companies about the pharmacogenetic testing, Dante Labs announced giving one free to all their customers, past and present. There's no way they can claim it's a "lab developed" test because they're using unspecified "network of labs", while 23andMe landed in hot water (on legal side) simply because they used a specific outside lab. Worse, their Italian lab is clearly not CLIA & CAP certified even though it's Oxford Nanopore certified. That said, it's all about size and visibility, there are (almost) uncountable services offering health interpretation of data, some with health interpretation of their own, so it's hard to see a double standard here, but I definitely don't understand the strategy.

It's a good time to remind that no matter the testing, the "gold standard" for clinical testing is two independent tests with different technologies. If those exist, and the results agree on the issue, I don't think it's that much of an issue whether they're DTC or even done in someone's garage somewhere. Of course, medical interpretation of sequencing results is still best left for medical professionals - and even they often don't agree, but you know, science and medicine marches on...

Dante Labs marketing is definitely making it sound like you can just buy that test & get diagnosis and whatever on basis of that. The standard boilerplate statement "Dante Labs Services are for research, informational, and educational use only. We do not provide medical advice." is hidden only deep in the Terms of Service that nobody reads, and I fear many would not buy the service if they saw that. Of course, none of that matters for people who are buying it just for genealogical or research purposes, or are aware of the limitations.

It's also interesting to note that post-FDA, the medical laboratories & professions attack on 23andMe has been squarely focused on "It's not sequencing" (Which makes no sense because sequencing is the "new" difficult to interpret test) so it will be interesting to see what the angle would be here. For FDA, it's more clear-cut though.

FGC Corp
04-19-2019, 05:20 PM
But noo, as far as I can find out, Dante Labs moved their company to New York, which is one of the most restrictive states to DTC genomic testing together with Maryland. And right on the heels of FDA issuing a "warning" to all companies about the pharmacogenetic testing, Dante Labs announced giving one free to all their customers, past and present.

It is very clear that they are violating FDA rules. The question is whether the FDA has decided to change their policy or whether they will enforce them against Dante.

Another possibility is that they never got legal opinion. Any well-informed lawyer would have told them they were breaking the rules.

I consulted our lawyer five years ago regarding the FDA rules. That's why we don't follow that model.

23andme has cause to complain to the FDA, because the FDA hasn't applied the same standards to Dante as they applied to 23andme.

FGC Corp
04-19-2019, 07:06 PM
There's another point which has been raised by a number of people. How does Dante sustain these very low prices? If they plan or reselling the data, they need to make that clear. If they are receiving a subsidy they should make that clear.

These prices are the lowest in the world for WGS, and Dante doesn't have the financials to subsidize the price. Who provides the subsidy?

Under the GDPR law, for example, the use of customer data has to be made very clear. All uses of data have to undergo an explicit and clear consent by the customer. My understanding is that the CEO lists himself as the data protection officer. If you look at his profile, his sole qualification is an MBA. That doesn't meet the GDPR standard.

Again, it may be that the EU will not enforce these requirements on Dante. However, it would be helpful if they enacted the same policies for the other companies.

Donwulff
04-19-2019, 07:56 PM
A LOT of companies are breaking FDA rules in this regard and getting away with it. Just type "genetic health test" or something in Google search. FDA appears to have shown they won't act unless health care profits are threatened, and I just do not think Dante Labs is there yet. So FDA most definitely has "double standards", but I don't think they're in benefit of Dante Labs, as such.

Separate and IMO important issue is that I think that Dante Labs should really come clear that they're not clinical/diagnostic test in the marketing *before* purchase is made. From legal perspective, 23andMe case showed that such disclaimers make no difference for FDA and ambulance-chaser lawsuits, but from ethical and customer perspective they should. For me personally it makes no difference because I'm testing with them for genealogical and research purposes, and understand the issues.

They do make that very clear in the ToS and the reports though. The DL pharmacogenetics report for example states "While this Report does not require FDA/EMA approval, we do want to point out that it has not been approved by the FDA/EMA for such use." I think that FDA showed that's wrong even before DL published that report, but DL appears to believe they do not require approval (So did 23andMe, and they did have a strong case on being lab-developed test, but FDA shot that down). I think there seems to currently be a belief that if you're only "reporting what's said in literature about a variant" you do not need FDA approval (Otherwise, libraries and journalists reporting about MTHFR or what have you would be on the line of fire). I'm not a lawyer though, so I won't even begin to try unravel that, other than to re-iterate that I don't get Dante Labs legal strategy.

Dante Labs selling the genetic data is red herring. Contrary to most genetic services, they do not collect any information on the customers. There are tens or hundreds of thousands of samples in existing research cohorts available to researchers, nobody is willing to pay anything for genetic data which isn't connected to any traits or other information. Even if they were able to re-identify the majority of them, you can't use samples without consent & institutional review board approval in any study, proof or application, and all conceivable "evil scientist spy" needs would be better met by clandestine sample collection. And, of course, their ToS and privacy statements make it clear they don't sell them, which we have no reason to doubt.

Their "normal" prices are slightly above break-even. BGI charges $600 off normal customers, Dante Labs $699. Oxford Nanopore calculated the price of whole genome on their device as $800 or so, Dante Labs charges $999 (Unless they raised the US price too). It's indeed possible if not likely they get bulk- and slow service discounts as well. But it's also well known they've been burning through a lot of money in the limited time discounts to establish themselves on the market, with full price expected to make bulk of the sales, like many other companies do as well.

FGC Corp
04-19-2019, 08:11 PM
Dante Labs selling the genetic data is red herring. Contrary to most genetic services, they do not collect any information on the customers.

I don't think so. There are only two ways to cover those prices (i.e. $200). A subsidy from BGI or reselling the data. Also, you can't hide from health implications from your health reports by claiming that they are not for medical purposes. 23andme did that and the FDA shut them down.


They do make that very clear in the ToS and the reports though. The DL pharmacogenetics report for example states "While this Report does not require FDA/EMA approval, we do want to point out that it has not been approved by the FDA/EMA for such use."

That doesn't protect them from FDA regulation. By admitting that it is not approved by the FDA, they acknowledge that the test violates FDA regulations. A hospital network (Inova, outside DC) had to shut down its pharmacogenetics service, even though doctors handle the service.


Contrary to most genetic services, they do not collect any information on the customers.

They collect whole genome data. That's very powerful data.


A LOT of companies are breaking FDA rules in this regard and getting away with it. Just type "genetic health test" or something in Google search.

23andme spent a lot of money complying with the FDA. If I were them, I'd ask for an investigation. I bet they have.


And, of course, their ToS and privacy statements make it clear they don't sell them, which we have no reason to doubt.

They have demonstrated a pattern of non-compliance with the FDA. As the first person mentioned in this thread they promised to provide downloads (they don't). The CEO lists himself as the data protection officer (unless that has changed). He has no qualifications for that position. The CEO doesn't help his case by his statements in response to customers. If you google him, you'll find him responding to these types of complaints all over the internet.

I think a pattern of non-compliance raises questions about their compliance on other matters.


There are tens or hundreds of thousands of samples in existing research cohorts available to researchers, nobody is willing to pay anything for genetic data which isn't connected to any traits or other information.

Data is gold for investors. They'll pay for genetic data. In particular, they will pay for the potential use of the data in the future.


For me personally it makes no difference because I'm testing with them for genealogical and research purposes, and understand the issues.

My impression is that most people are testing for genealogical purposes. The FDA isn't focused on the advanced user. Their concern is about the typical customer who isn't very knowledgeable. What happened with 23andme is that they started receiving a lot of feedback from doctors and patients who were getting confused by the 23andme reports.

The problem that Dante has in the US is that they are increasing their legal exposure with each test that they sell. If you provide health reports, you have to go through a medical order in the US. Whether or not the FDA enforces that rule in the short-term, customers can seek compensation. It could be 10 years or never. Dante takes that risk. That appears to be their decision.

FGC Corp
04-19-2019, 08:54 PM
I got back the results of my Dante lab Whole GenomeZ (130X exome + 30X the rest+mtDNA) and it is not satisfactory.

Dante labs advertised "GENOME EXPLORER A simple tool to explore all the variants in your DNA" but have not actually provided the tool. On their website they promise "FASTQ, BAM, VCF files available for download free of charge" but it is a lie. They only provide vcf files for download. To get FASTQ and BAM files I had to pay extra $72 for Dante to send the files on a hard drive. I requested the FASTQ and BAM files two weeks ago, but Dante still have not shipped the drive.

Further, it seems to me, that they screwed up the structural variants calling. The structural variants .vcf file they provided has 113,000 (!) structural variants, that is insertions, inversions, translocations and large deletions while their number should be under 10,000.

Finally, their customer service has not responded to my emails. Anyone having similar experience?

We have the capability to generate data that is compatible with all of the third party tools.

timberwolf
04-19-2019, 08:58 PM
We have the capability to generate data that is compatible with all of the third party tools.

Hi

Where is it on your site the $25 option to create an autosomal file for Gedmatch from previously uploaded files?

FGC Corp
04-19-2019, 09:00 PM
Hi

Where is it on your site the $25 option to create an autosomal file for Gedmatch from previously uploaded files?

Contact support [at] fullgenomes [dot] com.
We can handle it through paypal or set-up a temporary product.

Temporary product:
https://www.fullgenomes.com/purchases/133/?