FGS Services

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YDNA:
N-L1034
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H4a1*
PostPosted: Thu Apr 11, 2013 2:02 am
Mukovnikov wrote:
Svein wrote:Would it add anything to the hg N1c1 knowledge database if I took the Geno2 test? I'm N3115, "Varangian/pre-Rurikin", L550+, L1025-.

it would be better to order Y-Refine67to111 for your haplotype, imho.

or maybe Full Sequence Genome, if your finances allow it.
http://fullgenomes.com/

Is this the recommended FGS service? I have ordered a kit from them and plan to pay the invoice tomorrow. I'm wondering about other companies that charge upwards of $7000 though.
963RX: N-L1034 | H4a1*
AEYC6: I-M423 | U5b2b2
¡A la máquina!

N-Z1936 Project

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H24
PostPosted: Thu Apr 11, 2013 5:08 pm
AJRLegits wrote:
Mukovnikov wrote:
Svein wrote:Would it add anything to the hg N1c1 knowledge database if I took the Geno2 test? I'm N3115, "Varangian/pre-Rurikin", L550+, L1025-.

it would be better to order Y-Refine67to111 for your haplotype, imho.

or maybe Full Sequence Genome, if your finances allow it.
http://fullgenomes.com/

Is this the recommended FGS service? I have ordered a kit from them and plan to pay the invoice tomorrow. I'm wondering about other companies that charge upwards of $7000 though.

The $7000 range would be for the whole genome (3 billion bases), typically without much in the way of interpretation. The current offering at Full Genomes is for the Y chromosome only. However, they offer more interpretive services, including STR analysis. This is a brand new company, so we don't have reports from anyone who has tried the service. It was announced as a pilot project on Anthrogenica, and if you go ahead with this, I'd do it with the mindset of a pioneer blazing a trail for others to follow.

http://www.anthrogenica.com/showthread. ... -III-Pilot
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Posts: 77
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YDNA:
N-L1034
MtDNA:
H4a1*
PostPosted: Mon Apr 15, 2013 10:11 pm
There's just so little information on their website. I have this seemingly endless list of questions before I order from them. Coincidentally, I just got an email, and I'm even more suspicious of what's going on with this whole project now. I asked what kind of analysis they provide with the test results, and their answer was nothing more than "SNP and STR analysis." And in reference to what their quality control practices are, they said (and I quote), "QC: Very good: 50x coverage is the best available, i.e. higher coverage does not yield better quality."

Anyone else think this sounds super sketch?
963RX: N-L1034 | H4a1*
AEYC6: I-M423 | U5b2b2
¡A la máquina!

N-Z1936 Project
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Location: Edmonton, AB
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R-FGC396>L199.1
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U5a1a1h
PostPosted: Wed Apr 17, 2013 7:50 am
AJRLegits wrote:There's just so little information on their website. I have this seemingly endless list of questions before I order from them. Coincidentally, I just got an email, and I'm even more suspicious of what's going on with this whole project now. I asked what kind of analysis they provide with the test results, and their answer was nothing more than "SNP and STR analysis." And in reference to what their quality control practices are, they said (and I quote), "QC: Very good: 50x coverage is the best available, i.e. higher coverage does not yield better quality."

Anyone else think this sounds super sketch?


We shall see how things look after pilot phase II comes in. I think the PGP in comparison was doing all their sequencing runs using 30X coverage as of last year.

For comparison of sequencing depth vs SNP call rate and quality, please check out http://massgenomics.org/2011/08/a-guide ... nomes.html

STRs can only be called if their total length plus leading and tailing ends fit within the 100 base read fragment read length. This was problematic with the 1000 Gemomes Project data since those fragment lengths were limited to about 80 bases, and in many cases had 4 or less overlapping fragments. There are some STRs which simply can't be aligned with any accuracy until fragment read lengths reach 200 bases and more, but there is a significant cost penalty in order to do that. 50x coverage increases the capability of calling more STRs with more certainty, but will not necessarily compare directly with current STR reporting done by FTDNA or the former EthnoAncestry for instance.

Keep in mind that this is a start-up being organized and run by various members of the genetic genealogy community dissatisfied with conventional consumer Y-DNA test offerings, and is not (yet) backed by any particular academic institution. Academic institutions as such simply would not make a consumer product available for the consumer market at a reasonable price. Knome in particular (although not academic), does have the capability to make such an offering possible, but opted to focus their resources toward government-funded medical and pharmaceutical research interests. This is not unusual - ChrY sequencing in particular is largely being ignored by all but FTDNA, but FTDNA has their business plan seemingly compromised with a contract agreement with the Genographic Project that will be in place for several more years. FTDNA was also apparently unwilling to out-source sequencing services to a foreign company in order to keep costs down, opting to use their own more expensive in-house instrumentation, consumables, and labour. ChrY research in academia in general is at best half hearted - it doesn't have the payback that autosomal genome and exome sequencing has; most papers being published even today on ChrY research still focus on short STR haplotypes such as that provided by Y-Filer standard.

Analysis tools are still being developed and refined and are not at a marketable / presentable level yet. More data will be required to further test and develop those tools, and to make sure that the reports will be accurate. I have seen an early screenshot of one of the reports, which looks quite promising. I had found out that Leon Kull, who wrote the HIR Search website (http://hiropractic.snpology.com/22/), is heading the analysis team, and I have great confidence in his abilities.

So, as with anything, if you want something done, sometimes you have to do it yourself, or figure out how to get it done by other means. This is one of those cases. Give them time to polish things up.

I say kudos to those who are taking the initiative to get this off the ground.
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PostPosted: Sat Apr 20, 2013 11:21 am
Thanks, Vince, for supporting us.
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R-L21>DF13**
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H11a2a
PostPosted: Sun Apr 21, 2013 5:09 pm
Last year I had a conversation with someone who talked to someone at BGI, and they quoted around $750 with 10 or more, for a 5x coverage human genome. The technology appears to have come a long way in the last few years. I guess, though, what is possible at 50x isn't quite tested fully.

Is this testing through BGI?

MJost
148326 DF13** Celtic, Goidelic 111 Marker: GD1/67 & GD3/111 Watterson USA, Cook(UK/Scot Heritage) with a GD5/111, Codere(Watterson(McWalter))IOM GD8/111 and Ross Scotland GD13/111. Cluster 13*-1130-A1: 20 off-modals from L21.
Sorted slow to fast: 531=>12, 497=15, 511=11, 19=>15, 385a=12, 441=14, 552=25, 447=24, 513=11, 557=<15, 446=14, 464d=18, 456=18, 534=16, 449=31, 576=17, 710=36 and 712=>21 68-111Panel
DF13>FGC5496.
https://drive.google.com/file/d/0By9Y3j ... sp=sharing
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PostPosted: Sun Apr 21, 2013 8:11 pm
Yes it is. I believe the initial arrangement was to be through Complete Genomics, which was recently bought out by BGI. BGI does not usually do DTC sequencing AFAIK, so consequently a front-end corporation needed to be set up to take care of the front-end logistics and administration, in addition to arranging for the special requirements of limiting data to ChrY for reduced costs on volume. Of course arranging and providing for additional analysis services would be the value-added "icing" on the raw data "cake", since not everyone is a Linux expert.

Edit:
Complete Genomics approves DNA Genotek Inc. for sample transport and recovery.
http://www.completegenomics.com/news-ev ... 56865.html

BGI completes acquisition of Complete Genomics.
http://www.completegenomics.com/news-ev ... 54331.html
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Posts: 387
Joined: Wed Mar 14, 2012 4:51 pm

YDNA:
R-L21>DF13**
MtDNA:
H11a2a
PostPosted: Mon Apr 22, 2013 4:46 am
VinceT wrote:Yes it is. I believe the initial arrangement was to be through Complete Genomics, which was recently bought out by BGI. BGI does not usually do DTC sequencing AFAIK, so consequently a front-end corporation needed to be set up to take care of the front-end logistics and administration, in addition to arranging for the special requirements of limiting data to ChrY for reduced costs on volume. Of course arranging and providing for additional analysis services would be the value-added "icing" on the raw data "cake", since not everyone is a Linux expert.

Edit:
Complete Genomics approves DNA Genotek Inc. for sample transport and recovery.
http://www.completegenomics.com/news-ev ... 56865.html

BGI completes acquisition of Complete Genomics.
http://www.completegenomics.com/news-ev ... 54331.html

I am very glad you posted this info. Thanks!

Some of us DF13* guys maybe interested in the future. I hope we are kept up to date as things develop.

MJost
148326 DF13** Celtic, Goidelic 111 Marker: GD1/67 & GD3/111 Watterson USA, Cook(UK/Scot Heritage) with a GD5/111, Codere(Watterson(McWalter))IOM GD8/111 and Ross Scotland GD13/111. Cluster 13*-1130-A1: 20 off-modals from L21.
Sorted slow to fast: 531=>12, 497=15, 511=11, 19=>15, 385a=12, 441=14, 552=25, 447=24, 513=11, 557=<15, 446=14, 464d=18, 456=18, 534=16, 449=31, 576=17, 710=36 and 712=>21 68-111Panel
DF13>FGC5496.
https://drive.google.com/file/d/0By9Y3j ... sp=sharing

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K1c1e
PostPosted: Wed May 08, 2013 2:20 pm
New player on the scene: Full Genomes Corporation

http://bga101.blogspot.co.uk/2013/05/ne ... nomes.html

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Joined: Wed Mar 14, 2012 3:09 pm
PostPosted: Sun May 19, 2013 12:03 pm
AJRLegits wrote:There's just so little information on their website. I have this seemingly endless list of questions before I order from them. Coincidentally, I just got an email, and I'm even more suspicious of what's going on with this whole project now. I asked what kind of analysis they provide with the test results, and their answer was nothing more than "SNP and STR analysis." And in reference to what their quality control practices are, they said (and I quote), "QC: Very good: 50x coverage is the best available, i.e. higher coverage does not yield better quality."

Anyone else think this sounds super sketch?


We have a website in development. I can provide my raw data as an example of what we have produced. Likewise, Ray Banks has already sequenced 3 samples from the G haplogroup and analyzed the data. As an independent customer with no ties to our organization who can also speak to his experience with his results and the quality of the data he received.

Best,

Justin Loe
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