Dante Labs (WGS)

[ntk]

Did anyone else watch the webinar with Andrea Riposati just now (8am PST)? He acknowledged several customer issues (delays, raw data, etc). Did anyone feel like their issue was not even mentioned, or poorly addressed?

Also, thanks to MacUalraig for the heads up, I would have missed it otherwise.

I didn't, since they didn't notify customers (at least not me), I wasn't hitting F5 in this thread that day, and they haven't posted audio.

It's a joke: "the truth behind the delays in 2018", as if this was a 2018 problem and not ongoing. My kit ordered mid-February 2019 and returned that same month has now been in "Sequencing started" with no results for 22 days.

Feb 16, 2019: Ordered kit ($299)
Feb 18, 2019: Shipping notification
Feb 25, 2019: Kit received by Dante/logistics partner in Draper UT
Mar 26, 2019: Message support to ask why kit messenger still says "Waiting Confirmation from Dante Labs".
Apr 13, 2019: Response from Dante: "I can confirm that your sample has been received in our labs. We are currently running the DNA extraction ..."
Jun 28, 2019: Dante switches to new kit manager, status is still "QC Completed"
Sep 2, 2019: Dante: "84% of all our samples received by the end of July have been sequenced ... We plan to finish the entire backlog of samples by mid-October." I email to clarify about my kit status: same-day response: "Your sample is also being sequenced as with all our samples."
Oct 3, 2019: Kit manager still shows "QC Completed." Ask for status, same-day response: "I have checked your kit and it is still being sequenced within your [sic] lab." Asked how this is possible. Same-day response: "We are in the process of releasing data to all our customers."
Oct 13, 2019: "We are now sequencing more than 300 samples per week ... We have not completed our backlog yet, but we are getting closer every day."
Oct 19, 2019: Kit status updated to "Sequencing Started"

still nothing.

And is Dante Labs now offering the same 30x WGS for $199 again with "8 week turnaround time"? Why yes they are. Do you believe it?

[pmokeefe]

Is the webinar still available anywhere, missed it myself and nobody reporting what they actually said.

Dante Labs Webinar on November 9th, 2019
https://www.youtube.com/watch?v=sgLwwsYinRA

[ntk]

Well, a few hours after my last post, I got a notification that my VCF and FASTA files are now available (looks like no BAM yet). Will be reviewing these.

So here is my timeline to results:

Feb 16, 2019: Ordered kit ($299)
Feb 18, 2019: Shipping notification
Feb 25, 2019: Kit received by Dante/logistics partner in Draper UT
Mar 26, 2019: Message support to ask why kit messenger still says "Waiting Confirmation from Dante Labs".
Apr 13, 2019: Response from Dante: "I can confirm that your sample has been received in our labs. We are currently running the DNA extraction ..."
Jun 28, 2019: Dante switches to new kit manager, status is still "QC Completed"
Sep 2, 2019: Dante: "84% of all our samples received by the end of July have been sequenced ... We plan to finish the entire backlog of samples by mid-October." I email to clarify about my kit status: same-day response: "Your sample is also being sequenced as with all our samples."
Oct 3, 2019: Kit manager still shows "QC Completed." Ask for status, same-day response: "I have checked your kit and it is still being sequenced within your [sic] lab." Asked how this is possible. Same-day response: "We are in the process of releasing data to all our customers."
Oct 13, 2019: "We are now sequencing more than 300 samples per week ... We have not completed our backlog yet, but we are getting closer every day."
Oct 19, 2019: Kit status updated to "Sequencing Started"
Nov 11, 2019: VCF and FASTA received

[pmokeefe]

My Trustpilot review of Dante Labs
I have ordered 9 test kits from Dante Labs so far. I have complete results for the first 3 kits, including all the raw data. All the results I received were very satisfactory. Customer support for the earlier kits was satisfactory as well. Because of that positive experience, I ordered four more kits on the Black Friday sale of 2018. It's now almost 11 months later and I have no results from those. When I contacted customer support about the 2018 Black Friday kits I received perfunctory, uninformative replies. I gave up trying to contact customer support. The last kit I ordered was for their Long Read test in the spring of 2019. I have received partial results for that test, but the results appear to be for a short-read test, not a long read test! The long read test was more expensive, but I appear to have received the results of a less expensive test. I'm waiting to see if I receive the full results before trying to contact Dante Labs about it. Dante Labs recently claims to have a new laboratory and new procedures that will address the sorts of issues I have experienced. I just ordered a new kit to test that. I feel rather foolish doing so, throwing good money after bad! But it is for my elderly father who is in very poor health. His was also one of the 2018 Black Friday kits with no results. I hope Dante Labs has actually improved its service, if they do I will write another, much better review and order many more kits. Wish me luck!

[MacUalraig]

Dante Labs recently claims to have a new laboratory and new procedures that will address the sorts of issues I have experienced. I just ordered a new kit to test that. I feel rather foolish doing so, throwing good money after bad!

I'm tempted too although I can't see myself switching away from YSEQ for my regular project purchases unless there is a sea change in attitude from them.

[Donwulff]

I have bit similar conundrum. Like the Black Friday sale, today's sale is again crazy good enough that it would be a steal (more affordable than many microarray tests) even if one got just the VCF and no BAM(*), and I might even test myself again for presumably 160bp reads if I couldn't talk any relatives around to it... My first sequence with them in 2017 went down without a hitch - better, in fact, than any other sequencing or microarray company I've dealt with, all who have had scheduling and sometimes quality issues.

HOWEVER, yes... it appears that for my Long Read test they intentionally returned data that fails Oxford Nanopore's standard quality control to inflate the data amount; I suspect this is intentional because other members had those reads correctly quality-filtered. This is literarally the worst possible thing you can do, since if against all advice someone was actually using these results for medical purposes, the errors could cause grievous bodily harm or even death in a way that "had to wait" or "didn't get all the data" doesn't. As it is, it undermines their credibility and good will. So far this seems like an isolated incident (of this type), but they also have not replied to my customer support request about it.

Speaking of which, I ordered their AI report for my short-read sequence just to find out what it was about couple of months ago, but the option wasn't even available in their report menu after paying for it. Their customer support replied immediately that they were on it, however... no report. If they need some specific information besides what the description on the order page says now, they should say so. Has anybody managed to get the AI report? What is it like? I also requested the personalized report because they say we can get one at the time - not even a response, though. And I tried the monthly report update subscription, but there wasn't any change at all to the reports. (Edit: Just to stress that Neurological Panel I ordered did work, received it within 24 hours. It was pretty much ClinVar dump where table formatting broke because of too long lines + Excel table of all the variants. Useful if you can't run ANNOVAR or similar.)

Common thead to the Long Read quality issues and all the reports is that none of the caveats about wet-lab work being unpredictable or having a third-party lab to blame seem to apply to these. Their price is best on the market, even if it suggests they're taking a loss to win market-share just like essentially every DNA-testing company or startup out there, and their service is great, when it works. I really want to see them succeed, however they shouldn't sell products they can't deliver (I mean, literally, not having the option in the menu...) or fail at things that should be entirely under their control like QC and reports if they hope for that market-share to amount to anything. Of course, since they must be taking a loss at that price, I'm not sure they'll REALLY miss my repeat-business, but neither am I sure I really desire a second sequence from them that badly... It's still not clear to me how large part of their customers haven't received short-read sequencing results after a long wait however; considering people are more sure to talk about negative experiences than everything going as intended, is that a large portion?

(*) And when people complain about not receiving results, can we get a clarification if they mean they received VCF but are still waiting for BAM, or if they received no VCF whatsover? Because I see all of the seemingly most vocal complainers talk about not receiving the BAM, so when people say "didn't receive data" or the like it's not clear what they mean.

[MacUalraig]

People coming from the genetic genealogy community are primed for something they can upload to YFull (if they're male!*) so like me they tend to stop the stopwatch when the BAM turns up. Possibly people who bought for medical reasons are satisfied if they get a VCF or medical report only. What is annoying is that Dante themselves seem to count the product as delivered when they put the reports up.

Right now BAMs are controversial because of what FTDNA are up to so if Dante can produce them without extra charge or delay they have a winner.

* women of course could do just an mtDNA upload to YFull if they wanted.

[tontsa]

It really sucks that FTDNA doesn't at least yet do imports of BAM/FQs as they have some populations there that won't get Y-700 or just don't upload to YFull.. so you are kinda forced in those cases to do Y-700 but for Yfull you get better coverage with 30x WGS..

[Petr]

I just received FASTQ files for one WGS 30x test ordered in February 2019. The names are:
60820188xxxxxx_SA_L001_R1_001.fastq.gz
60820188xxxxxx_SA_L001_R2_001.fastq.gz

I'm surprised that these two FASTQ files are only 25 GB each - previously, WGS 30x files from Dante were much bigger, 50 GB each.

What is the size of the FASTQ files delivered to other testers this month?

[tontsa]

If you unpack those gzips what size do you get? It's possible those 150p reads compress better especially if they have trimmed those adapter sequences away from them.