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Salkin
12-29-2014, 07:52 PM
If one already has a sample being processed for Y Elite, how much gain would there be in ordering other NGS Y testing, i.e. Big Y? I'm sure it could be interesting comparing the two results, but I'm not sure I'd want to spend that much further just to satisfy idle curiosity. :)

I have encountered a few who have results from both, so I know it's been done. If you've done it, was the result worth it, and if so, why in particular?

GailT
12-30-2014, 04:18 AM
I tested the Full Genomes Elite Y and Big Y for the same sample: 50 Private SNPs in the Elite Y compared to 26 in BigY. 25 of the BigY SNPs were also found in the FullY test. There was one BigY SNP that was a low reliability postive (2 stars) in the FullY. There were also 10 SNPs that were low reliability positive in both the FullY and BigY (from 1 to 3 stars) so perhaps some of these are also private SNPs.

If you are part of a surname project and have close matches who also tested both, it might have some additional value. But it might be better to test the Full Y twice to see how two samples with better coverage compare. Has anyone done that experiment?

VinceT
12-30-2014, 04:39 AM
I see no real advantage in testing BigY after testing Y-Elite. From my R-FGC396 analysis so far, all SNPs found in BigY are also detectable in Y-Elite, with the possible exception of some existing in the centromere or pseudo-autosomal regions.

On the other hand, my guess would be that FGC's WGS test likely wouldn't find much in terms of new SNPs than that of Y-Elite (~4%? chance of novel variant discovery based on breadth of coverage increase from Y-Elite to WGS); but more likely that with the longer read lengths leading to better mapping for WGS data, many variants found but not previously tagged due to quality or reliability issues stand a good chance of providing better scores.

asquecco
11-19-2016, 07:26 PM
Hi,
Just to add my personal experience on this topic.
I tried to compare my FTDNA BIGY results (FTDNA Screeen "Novel Variants") with my FGC Y Elite 2.1 results (file 7XV8B.variantCompare.20140314.named.tab).
Here is what I found.

BIGY => KIT# 72367 (R-S22778) = YFull KIT# YF01733 (R-Y16860)
FGC Y Elite 2.1 => KIT# 7XV8B (R-S20782) = YFull KIT# YF07634 (Still in process)

BIGY lists 40 Novel Variants SNPS: 30 High and 10 Medium Confidence
10 BIGY Medium Confidence Novel Variants:
=> 4 are not reported in my FGC results
Position: 13447311
Position: 18982587
Position: 18982595
Position: 22301589

=> 6 are reported (derived) in my FGC result:
==> 2 are also derived in other L2 FGC results (FGC ** Confidence)
Position: 13686963
Position: 28793052

==> 1 is also derived in other S8183 FGC results (FGC ** Confidence)
Position: 28818135

==> 3 are derived only in my FGC results (FGC ** Confidence, Downstream S8183)
Position: 9147185
Position: 9147186
Position: 9147187

30 BIGY High Confidence Novel Variants:
=> 5 are not reported in my FGC results
Position: 13448404
Position: 13687807
Position: 13687826
Position: 13687977
Position: 13689668

=> 25 are reported (derived) in my FGC result:
==> 3 are derived in other L2 FGC results (FGC ** Confidence)
Position: 13142443
Position: 13142458
Position: 22288897

==> 1 is derived in other S8183 FGC results (FGC ** Confidence)
Position: 9321336

==> 21 are derived only in my FGC results
Position: 13677199 (Reported by FGC as Shared SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 14010118 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 14836005 (Reported by FGC as Shared SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 16698090 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 18742506 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 18742779 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 18956738 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 19319655 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 19346957 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 20835036 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 21872623 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 22471737 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 23510102 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 6959295 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 7273475 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 8335267 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 8402925 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 8585310 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 9170638 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 9500598 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)
Position: 9790413 (Reported by FGC as Private SNP, FGC <blank> Confidence, Dowstream S8183)

In a future post I'll try to do the opposite comparison, starting from my FGC results.
Just to score 10 posts and to be able to reply to some PMs I received in the meantime ;)
Adriano

asquecco
11-20-2016, 05:52 PM
Hi,
just a couple of remarks about my previous post.
1) Considering my 5 BIGY High Confidence Novel Variants not reported in my FGC results, I checked their Y-Chr positions with the "YFull Browse raw data function" for both my YFull results, KIT# YF01733 (FTDNA BIGY) and KIT# YF07634 (FGC Y Elite).
Here is what I found:

Position: 13448404 Reference Value: C
BIGY # reads 105: 84T 21C => MY SAMPLE VALUE: T (DERIVED)
Y Elite # reads 84: 2A 11T 71C => MY SAMPLE VALUE: C (NOT DERIVED)

Position: 13687807 Reference Value: T
BIGY # reads 2535: 71A 57T 1C 2404G => MY SAMPLE VALUE: G (DERIVED)
Y Elite # reads 40: 19T 21G => MY SAMPLE VALUE: G or T

Position: 13687826 Reference Value: A
BIGY # reads 2865: 61A 2T 2802G => MY SAMPLE VALUE: G (DERIVED)
Y Elite # reads 48: 15A 33G => MY SAMPLE VALUE: A or G

Position: 13687977 Reference Value: T
BIGY # reads 1229: 1A 78T 1148G => MY SAMPLE VALUE: G (DERIVED)
Y Elite # reads 38: 19T 1C 18G => MY SAMPLE VALUE: G or T

Position: 13689668 Reference Value: C
BIGY # reads 4594: 764C 3779G 2DEL 1CA 48CG => MY SAMPLE VALUE: G (DERIVED)
Y Elite # reads 64: 16C 48G => MY SAMPLE VALUE: C or G

So, about these 5 SNPs, it seems the BIGY results are stronger than Y Elite.

2) Checking with the YFull tool "Group: R-U152 => Y-Chr browser" these 5 SNPs (Y-Chr positions: 13448404, 13687807, 13687826, 13687977, 13689668), I see my BIGY values (T,G,G,G,G) are quite common in my R-U152 Group, so I would say that today, they are not so "Novel Variants" as reported by FTDNA.
Regards,
Adriano

A Norfolk L-M20
11-20-2016, 05:54 PM
I tested Big Y, then submitted the raw file for analysis by both Full Genomes Corp and YFull. My FTDNA project manager used their analysis to pull out some additional SNPs.

asquecco
11-22-2016, 07:20 PM
Hi,
again about comparing my FTDNA BIGY results (FTDNA Screeen "Novel Variants") with my FGC Y Elite 2.1 results (file 7XV8B.variantCompare.20140314.named.tab).

FGC KIT# 7XV8B (R-S20782) = YFull KIT# YF07634 (R-Y16860)
FTDNA KIT# 72367 (R-S22778) = YFull KIT# YF01733 (R-Y16860)

In the file 7XV8B.variantCompare.20140314.named.tab I started with the "Shared SNPs" section.
I considered only SNPs with "Reliability warning level" equal to <blank> or "*" (ie: Highest Confidence)
Then I considered only my positive SNPs that are not positive in any of the other 5 FGC S8183+ results (also reported in this "Shared SNPs" Section as "Neighborhood" of my YDNA S8183 subclade).
In this way I found 5 "Shared SNPs" downstream of S8183 positive only in my FGC results:
===> 2 are also reported in my BIGY results (High Confidence):
Position: 13677199 Named Variant: Z14583+
Position: 14836005 Named Variant: FGC57666+

===> 1 is listed in my BIGY BAM file but it does not appear in the FTDNA Screeen "Novel Variants":
Position: 26354560 Named Variant: FGC57667

===> 2 are not reported in my BIGY results (BIGY No Call/Ambiguous):
Position: 13826137 Named Variant: FGC57665+
Position: 3606704 Named Variant: FGC57668+

Then I checked my "Private SNPs" section with the same logic applied above.
In this way I found 55 "Private SNPs" downstream of S8183 positive only in my FGC results:
===> 19 are also reported in my BIGY results (High Confidence):
Position: 6959295 Named Variant: FGC57677+
Position: 7273475 Named Variant: FGC57678+
Position: 8335267 Named Variant: FGC57679+
Position: 8402925 Named Variant: Y5383+
Position: 8585310 Named Variant: FGC57680+
Position: 9170638 Named Variant: Y17178+
Position: 9500598 Named Variant: FGC57681+
Position: 9790413 Named Variant: FGC57682+
Position: 14010118 Named Variant: FGC6057+
Position: 16698090 Named Variant: FGC57690+
Position: 18742506 Named Variant: FGC57693+
Position: 18742779 Named Variant: FGC57694+
Position: 18956738 Named Variant: FGC57695+
Position: 19319655 Named Variant: FGC57697+
Position: 19346957 Named Variant: FGC57698+
Position: 20835036 Named Variant: FGC57700+
Position: 21872623 Named Variant: FGC57702+
Position: 22471737 Named Variant: Z39225+
Position: 23510102 Named Variant: FGC57704+

===> 12 are listed in my BIGY BAM file but they do not appear in the FTDNA Screeen "Novel Variants":
Position: 8425530 Named Variant: Y17176+
Position: 7542491 Named Variant: Y17177+
Position: 8735689 Named Variant: Y16860+
Position: 9401804 Named Variant: Y16861+
Position: 17354634 Named Variant: Y16862+
Position: 14892862 Named Variant: Y17179+
Position: 16350552 Named Variant: Y17180+
Position: 19282874 Named Variant: Y17181+
Position: 16052904 Named Variant: FGC57688+
Position: 22443865 Named Variant: FGC57703+
Position: 27872826 Named Variant: FGC57706+
Position: 21260728 Named Variant: S22778+

===> 24 are not reported in my BIGY results (BIGY No Call/Ambiguous):
Position: 3688041 Named Variant: FGC57669+
Position: 4839877 Named Variant: FGC57670+; site of F14229 (also Z25900)
Position: 4849146 Named Variant: FGC57671+
Position: 5248673 Named Variant: FGC57672+
Position: 5259221 Named Variant: FGC57673+
Position: 5306551 Named Variant: FGC57674+
Position: 5612443 Named Variant: FGC57675+
Position: 6045191 Named Variant: FGC57676+
Position: 13134120 Named Variant: FGC57683+
Position: 13241312 Named Variant: FGC57684+
Position: 13964731 Named Variant: FGC57685+
Position: 14191241 Named Variant: FGC57686+
Position: 14267866 Named Variant: FGC57687+
Position: 16425921 Named Variant: FGC57689+
Position: 18421659 Named Variant: FGC57691+
Position: 18462774 Named Variant: FGC57692+
Position: 19252857 Named Variant: FGC57696+
Position: 19417436 Named Variant: FGC57699+
Position: 21381973 Named Variant: FGC57701+; site of F14783
Position: 25157336 Named Variant: FGC57705+
Position: 28555333 Named Variant: FGC57707+
Position: 22651334 Named Variant: M4208+
Position: 15394958 Named Variant: FGC24135+
Position: 18188853 Named Variant: S20782+

Regards,
Adriano