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Todd Allen

whole genome sequencing

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Anyone familiar with this service or similar offerings?

 
I'm thinking about ordering the 30x WGS for $299 plus one month of analysis for $20 and downloading my 100 GB of data for future analysis through whatever low cost options pop up.
 
It looks sufficiently legit and cost worthy to me but looking for others thoughts before I pull the trigger and then learn there were better options.
Edited by Todd Allen

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I signed up with Nebula and have actually mentioned them numerous times here.

I was one of the very early customers and at the time they did not offer the whole genome product.  It is a reputable company with some great scientists on its roster.  But don't expect miracles, as most of the genome is either not studied, or largely irrelevant.  But it is a good deal and I am actually thinking of doing the whole genome thing soon.

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1 hour ago, Ron Put said:

But don't expect miracles, as most of the genome is either not studied, or largely irrelevant.

I realize we don't know how to interpret most of it now but I like the idea of having my data and being able to check it whenever I read a paper studying genes. The non-coding DNA has been called junk but is now known to have functions such as coding for RNA.  Telomeres are also part of this junk.  I expect a lot more of it will become relevant with time.

 

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I agree, which is why I first jumped on Nebula's bandwagon and will do the whole genome soon, too.  It's really the best value I've found.

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Todd, did you ever sign up with Nebula Genomics? 

I decided to upgrade to the full 30x genome deal and sent the sample a few days ago.

Also, has anyone used Genetic Genie or another interpretive service to upload raw data?  My only experience is with Promethease.
 

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Not yet.  I signed up for Nebula's spam mailings to see if there were any special offers or sales as well as with a couple other competitors.  Nebula has repeatedly made an offer for $500 off their package of 30x sequencing plus a lifetime membership for their analysis site but there has been no discount offered on just the 30x sequencing which I think is $299.  I'll likely do that by the end of the year and just go with one month of analysis at $20/month and download my data to use with whatever other analysis options I find. 

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On 9/26/2020 at 5:20 PM, Ron Put said:

Also, has anyone used Genetic Genie or another interpretive service to upload raw data?  My only experience is with Promethease.

I've used https://codegen.eu with my 23andme data.  It's free so even if it is disappointing for additional insights gained on a full genome it might still be worth trying.

Edited by Todd Allen

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In my case, two weeks after I paid $299 for the 30x full genome, I received an offer of $50 off from the 30x price :)  Ah, well....

I am not exactly sure what I'll do with the full genome data, but I have run into a number of studies mentioning segments that neither 23andme nor the partial Nebula sequencing covers, so we'll see.

I am also hoping that they still include the sequencing of oral cavity bacteria they sent me when they sequenced my sample over a year ago.

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Well I'm glad I waited.  Dante Labs has just started a Black Friday sale for $149 30X WGS and $239 for 130X/30X.

https://us.dantelabs.com/collections/advanced-dna-tests

I think I'll wait a couple more days for any other Black Friday sales but I will be surprised if any beat this offer. This year anyway.  At the rate prices have been falling this might be regular non sale pricing within another year or two.

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On Friday I ordered the 130X/30X WGS for $239 which gives results in about 8 weeks.  I'm stunned at how quickly the prices have come down.  At this price it seems an incredible bargain although I expect more accurate tests at even lower prices are coming.  I wonder how long it will take to catch on and everyone will have a copy of their full genome?  And how long it will take for it to be part of standard medical practice?

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On 11/23/2020 at 1:19 PM, Todd Allen said:

Well I'm glad I waited.  Dante Labs has just started a Black Friday sale for $149 30X WGS and $239 for 130X/30X.

Wow! That's a good price!  I am not sure what the value of 130x is over 30x though, as I thought 30x is already medical-grade, does anyone have thoughts?

I am still waiting for my 30x results from Nebula Genomics, they should coming in any day now.

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1 hour ago, Ron Put said:

I am not sure what the value of 130x is over 30x though, as I thought 30x is already medical-grade, does anyone have thoughts?

I looked for an answer to that question before ordering.  And mostly failed.  As I understand it 20x is considered good enough for looking at single nucleotide variations and the accuracy barely improves at 30x although equipment, processes and sample quality all play roles.  Higher cycle counts give better accuracy of variations involving insertions and deletions although to what degree is not clear.  I went for the 130x because on sale it was less than the $299 I had been prepared to pay for the 30x.

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2 hours ago, Todd Allen said:

Higher cycle counts give better accuracy of variations involving insertions and deletions although to what degree is not clear.  I went for the 130x because on sale it was less than the $299 I had been prepared to pay for the 30x.

Good points.

Let us know your impressions when you get your results.

What are you planning to run the data through when you get it?

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3 hours ago, Ron Put said:

What are you planning to run the data through when you get it?

I plan on starting with free options at codegen.eu, geneticgenie, enlis, etc. and probably a couple low cost options such as promethease.  I've also heard there are some open source software projects for analysis tools but I haven't gone hunting for them yet.  I'm not unwilling to spend more but I don't yet know enough about premium offerings to choose between them. 

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I've been using promethease with 23andme and nebula's old basic service. I guess I'll try promethease again when I get my 30x Nebula results, but wondering if there is a better service out there.

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I just saw that promethease no longer accepts BAM files of anything larger than the low-res files available from the likes of 23andme.

The files from the 30x Nebula Genomics are between ~50 and 100 gigs and I am assuming the x100 files from Dante would be even larger.

I found that Sequencing.com would take them and it has a bunch of free and paid apps that can parse the data and spit out various reports.  Does anyone have any experience with them?

https://nebula.org/blog/sequencing-com-review/

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On 2/17/2021 at 4:48 PM, corybroo said:

Does anyone have familiarity with  Genomelink?

I had come across them while searching for a Promethease replacement in the case of very large files.  It doesn't seem that Genomelink offers anything that you can't get from Promethease, or Selfdecode, or the myriad other similar services. It reminds me of the early days of 23andme, where they offered a large and large speculative list of health predispositions until they were banned from doing it by the FDA (which I found overly intrusive, as anyone with an IQ above their shoe size should have understood the uncertainties inherent in limited studies and the speculative nature and the real-world meaning of having 10x the chance of getting a disease that affects one in 7 million people).

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Thanks Ron.  I used LivingDNA nearly two years ago and recieved some speculations on the paths my ancestors took from Africa to Northern Europe.  My daughter used 23&me and found it to be as helpful as an astology column.  Definitely we're in the early stages of understanding the impact of specific genes (and how other genes affect each other).  

 

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