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FGC Corp
04-22-2019, 11:46 PM
We have a new price:
$395

https://www.fullgenomes.com

Peter MacDonald
05-27-2019, 12:10 AM
Great deal on the best NGS test on the market!!!

Jan_Noack
06-11-2019, 02:25 AM
I posted on a German facebook group about this test. I thought this test would provide both the YDNA and the mitochondrial results? I was challenged on this and said I'd check.

(I know FTDNA runs additional software to remove the Mito results. I thought so FTDNA could also sell that product but maybe it is because there are not sufficient coverage, although I know there are usually many mitochondria for each nucleus in a cell.)


So now I have to get this confirmed. ..ie 1) whether the Y Elite tests have mitochondrial results. is it possible to extract these oneself?

and 2) when extracted, are the mito results as detailed as a FTDNA mito test..ie the same results which could be run thru some software when extracted from the BAM to provideHVR1, HVR2 and Coding differences from the RSRS or rCRS

and 3) is this included in the latest YElite test ..ie extracted for you. (just having the mito there to be able to extract is good enough, but this is obviously better but not expected)

My comment on using FGC YElite test due to someone else recommending another lab (Dante), to be able to get the YDNA and the mito , and I suggested YElite as a reasonable alternative for both the Y and Mito, without the expense of a WGS and with more certainty about getting results in a timely manner

... but Perhaps I was wrong about the mito being available as a side product of the Y Elite. I was asked "am I sure about this?" so I said I'd check. I realise it is designed a YDNA test, just wondering about the mito.

Personally I've ordered the WGS (20X) from FGC, and am expecting results within a few weeks :), so I'll get the mito as well as his Y.(and autosomal).

MacUalraig
06-11-2019, 06:56 AM
My Y Elite chrM coverage is complete and about 50x read depth. I got a FASTA file which I uploaded to Genbank.

For comparison chrM in my YSEQ WGS has about 8000x depth coverage and also included a separate FASTA file.

They both gave me the same resolution ie complete to the latest M tree (v17).

I think the comments I saw elsewhere sounded more like they came from a certain rival's marketing department.

deadly77
06-11-2019, 07:03 AM
I posted on a German facebook group about this test. I thought this test would provide both the YDNA and the mitochondrial results? I was challenged on this and said I'd check.

(I know FTDNA runs additional software to remove the Mito results. I thought so FTDNA could also sell that product but maybe it is because there are not sufficient coverage, although I know there are usually many mitochondria for each nucleus in a cell.)


So now I have to get this confirmed. ..ie 1) whether the Y Elite tests have mitochondrial results. is it possible to extract these oneself? (just having the ability to extract the mito is enough, but this is better)

and 2) when extracted, are the mito results as detailed as a FTDNA mito test..ie the same results which could be run thru some software when extracted from the BAM to provideHVR1, HVR2 and Coding differences from the RSRS or rCRS

and 3) is this included in the latest YElite test ..ie extracted for you. (just having the mito there to be able to extract is good enough, but this is obviously better but not expected)

My comment on using FGC YElite test due to someone else recommending another lab (Dante), to be able to get the YDNA and the mito , and I suggested YElite as a reasonable alternative for both the Y and Mito, without the expense of a WGS and with more certainty about getting results in a timely manner

... but Perhaps I was wrong about the mito being available as a side product of the Y Elite. I was asked "am I sure about this?" so I said I'd check. I realise it is designed a YDNA test, just wondering about the mito.

Personally I've ordered the WGS (20X) from FGC, and am expecting results within a few weeks :), so I'll get the mito as well as his Y.(and autosomal).

The YElite test includes mitochondrial DNA results. While the YElite is designed to sequence the Y chromosome, there is some off target coverage and since there's a lot of mitochondria in each cell, the YElite will pick up that. Big Y does this too, but as you say FTDNA strip out the mt-related information out of the raw data before making it available to you.

The YElite mtDNA results include three text files - variants with respect to rCRS, variants with respect to RSRS, FASTA file. No need to extract them yourself from the BAM. You can do everything with this that you can do with FTDNA mtDNA test, except join FTDNA mtDNA projects or matching. You can upload the mtDNA data from a YElite to Genbank, MitoYDNA, James Lick's mthap site, etc. If you upload to YFull, they'll extract mtDNA from the YElite BAM and display in your results there.

As it's off target, there might be some missed reads compared to a fully sequenced mtDNA. Comparing my YElite with FTDNA's full sequence mtDNA at James Lick's mthap site, they're pretty close to identical. Both tests found 16569 markers at 16569 positions covering 100.0% of mtDNA. Reports gave identical results for haplogroup, SNP matches, mismatches and extras. So in my case, all the same. I've read from others that there are a few misread bases in their results but more than 90% is correct. Since it's bonus data rather than what the test is designed for I'd say that's not bad at all.

Main difference from a WGS in the autosomal results. There are some off target reads but since nuclear DNA less abundant in cells compared to mitochondria, don't get as much data. There's also a little bit of difference in the Y-DNA as the WGS has better horizontal coverage and will be a little better in some of the positions which can be one-read, ambiguous or no call in a YElite. And the WGS would pick up anything missed in a YElite off-target. But the YElite will get almost everything of the Y and mt DNA.

spruithean
06-11-2019, 11:08 PM
I seem to recall from Roberta Estes' blog that Big Y also provided mtDNA results via YFull. However that was discussed 5 years ago and things may have changed since then.

Jan_Noack
06-11-2019, 11:34 PM
Yes, since I have heard, 2015 FTDNA runs another program to remove the mtDNA before releasing results. I think this delayed the conversion too. Early testers got mtDNA, others didn't.

Riodhr
07-27-2019, 02:08 AM
How many SNP, STR, and mtDNA are included in the Y ELITE 2.1 test? How long does it take for the test to be completed?

FGC Corp
08-04-2019, 08:05 PM
How many SNP, STR, and mtDNA are included in the Y ELITE 2.1 test? How long does it take for the test to be completed?

Essentially, enough SNPs are discovered to find one new SNP per three generations.
FGC has discovered over 90,000 new Y SNPs from our Y Elite tests (and analyses of Big Y or whole genome data).
More information:
https://docs.google.com/file/d/0B8eigUEXUAvlMkFweDdHVzdMN2c/edit

razyn
08-04-2019, 10:15 PM
Essentially, enough SNPs are discovered to find one new SNP per three generations.
FGC has discovered over 90,000 new Y SNPs from our Y Elite tests (and analyses of Big Y or whole genome data).
More information:
https://docs.google.com/file/d/0B8eigUEXUAvlMkFweDdHVzdMN2c/edit

I was present at the I4GG conference in Maryland when Greg Magoon made this slide presentation, five years ago. It holds up very well; I suppose several things he refers to as new are now well established, but the tech possibilities (and differences among them) are well covered.

FGC Y Elite's new price is just under 1/3 of what I paid, as an early tester. But I'm not sorry that I sort of jumped in before the water warmed up. That way, earlier branching on the Y tree got defined with SNPs named from my test -- giving me a lot of male-line cousins on the tree, by now. It's fun to print out the YFull or YTree version of the known branching we've had, in the past 3600 years or so. It's a little like being a new daddy again, at age 80 -- but (happily) without the diapers, PTA, tuition bills and so on. I can, if I so choose, think of FGC15712 as our ancient surname. That is, of course, silly -- but nobody else gets to do it; so it's my very own silly.