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Author Topic: New SNP Downstream of L21  (Read 14478 times)
Mark Jost
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« Reply #100 on: October 03, 2009, 05:35:58 PM »

In the P312 Project of those 531=12, I would bet that they have not tested for L21 and if they did they would all go L21+. Can you check if they have or not?
4131 Thomas Rice, Gloucester
59275 John Burnett, b.1794 Fettercairn, Kincardineshire
73014 Albert C. Jacobson, b. abt 1862, Norway

There were more P312* that had 531=12 a few months ago but I got some to upgrade and went L21+

The ones I was talking about I pulled from the L21- categories. I don't call someone R-P312* unless he is negative for all the established P312+ clades, including L21.

It's true 531=12 is more common in L21+ than apparently anywhere else, but it is not a slam dunk. (I wish it were!)
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Jdean
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« Reply #101 on: October 03, 2009, 06:05:48 PM »

I'm 11 as well, isn't 12 part of the Scots modal?
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rms2
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« Reply #102 on: October 03, 2009, 06:09:55 PM »

In the P312 Project of those 531=12, I would bet that they have not tested for L21 and if they did they would all go L21+. Can you check if they have or not?
4131 Thomas Rice, Gloucester
59275 John Burnett, b.1794 Fettercairn, Kincardineshire
73014 Albert C. Jacobson, b. abt 1862, Norway

You skipped Ranney, kit 93184.

Look at the categories those guys are in. They are all in R-P312* categories. I don't put people in R-P312* categories unless they are P312+ and negative for everything downstream of it.

That is why I wrote that I pulled them all from L21- categories. Just to be on the safe side I rechecked all of them just now, and they are all L21-.

The only men still untested for L21 in the R-P312 and Subclades Project are either in the "R-P312 (Need L21 Test results)" category or in "Unassigned Members".
« Last Edit: October 03, 2009, 06:14:37 PM by rms2 » Logged

rms2
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« Reply #103 on: October 03, 2009, 06:19:52 PM »

I'm 11 as well, isn't 12 part of the Scots modal?

I believe it is, but there are other parts of it that are more important, I think, like having 19-24 at YCA II.
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Mark Jost
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« Reply #104 on: October 03, 2009, 06:29:12 PM »

Dang! I was going to bet on these too.... Maybe tests are incorrect.... :)
You have the advantage of seeing all their detail that we cant. Glad your on the job.
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Jdean
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« Reply #105 on: October 03, 2009, 06:34:25 PM »

I'm 11 as well, isn't 12 part of the Scots modal?

I believe it is, but there are other parts of it that are more important, I think, like having 19-24 at YCA II.

Along with 10 at 391 and 30 at 389ii, all of which I have, after that the similarities disappear, very odd but time will tell.

As it happens I’ve noticed a 7 off match on 67 somewhere in Wales, the only one I have that is close enough for FTDNA to report, the next nearest is 12 I believe. Unfortunately he only appears in my ancestor origins page, and I can’t find him in Ysearch either, ho hum.
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NealtheRed
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« Reply #106 on: October 04, 2009, 12:17:15 AM »

The Scots cluster is found all over Scotland, right?
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rms2
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« Reply #107 on: October 04, 2009, 09:52:25 AM »

Dang! I was going to bet on these too.... Maybe tests are incorrect.... :)
You have the advantage of seeing all their detail that we cant. Glad your on the job.

I think you did a great job spotting that tendency in L21. It is definitely something to look for that will make selecting potential L21+ candidates easier. It tilts the odds in our favor.
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Mike Walsh
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« Reply #108 on: October 04, 2009, 12:36:38 PM »

Are any of Robert Hughe's 17-14-10 / Wales modal 1 cluster in the WTY or doing an L159 test?   I just noticed a pattern holds across both this cluster and the Leinster cluster.  It may be nothing, but this loose pattern holds across these two groups and not to many other L21* guys.  They are on both sides of the Irish Sea.  Of course, maybe I'm seeing things.
I wasn't looking for a L159+ look-alike cluster to the Leinster guys, when I stumbled on this.   I have identified/listed about 40 "potential" clusters of R-L21*.  A number of these are variants of traditional modals - i.e. Scots, Wales 1, Wales 2, Wales 3, Irish TII, Irish TIII, Unknown Scots, Cluster X, Irish Sea/Leinster, etc.
I started looking for relationships among the clusters where there were "clean breaks," not a bunch of random clutter.   I noticed that DYS448<=18  and DYS449<=30 showed both Leinster/Irish Sea and the Wales 1 17-14-10 guys.
None of the other clusters that I've seen have this so it is a pretty clean break.  The only exception is a few Wales 2 Cadwgon guys have it also.
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Jdean
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« Reply #109 on: October 04, 2009, 01:21:37 PM »

The Scots cluster is found all over Scotland, right?

It's certainly very strong there, if you do a search against it's entry in Ysearch 2XD3U comparing matches over 57 markers and select for people who know there origin you get

Scotland 77
Ireland 29
England 11
Wales 0
Germany 1
Scandinavia 2

Of these only 7 don't have 12 at 531, and only one is Scottish.
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secherbernard
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« Reply #110 on: October 04, 2009, 01:23:03 PM »

I just received my WTY results, but these results seem to me
a bit esoteric.

How to know if there are new SNPs in my results?

Bernard
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YDNA: R-DF13+ L69+ DYS464X: cccc.3
mtDNA: U6a7a1
mtDNA of my father: U5a2c
YDNA of my maternal uncle: I1*
Ysearch and Mitosearch: UE9BU
Ysearch of my maternal uncle: CEC59

Jdean
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« Reply #111 on: October 04, 2009, 01:28:53 PM »

I just received my WTY results, but these results seem to me
a bit esoteric.

How to know if there are new SNPs in my results?

Bernard

well you're been reported as having a 'new' SNP L69, this is another one in the L159 area, but I've looked at your result for this and can't see any difference with anybody else’s
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rms2
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« Reply #112 on: October 04, 2009, 01:43:00 PM »

I think Dr. Krahn and Kirsten Saxe are the ones to ask about understanding WTY results.
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NealtheRed
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« Reply #113 on: October 04, 2009, 02:03:23 PM »

Bernard,

You're SRY2627, right?


Neal
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Y-DNA: R-Z255 (L159.2+) - Downing (Irish Sea)


MTDNA: HV4a1 - Centrella (Avellino, Italy)


Ysearch: 4PSCK



Jdean
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« Reply #114 on: October 04, 2009, 02:14:38 PM »

Bernard's part of the L21 WTY, he's the French participant
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secherbernard
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« Reply #115 on: October 04, 2009, 02:58:09 PM »

Thomas Krahn give me the following comment about my WTY results:

Quote
To make things clear, there was no NEW SNP found in your DNA. However
there were two things observed that distinguish you from all other R-L21
participants:

First you have a 14.3 micro-allele at DYS464 which is essentially a 1 bp
deletion SNP in one of the 4 DYS464 amplicons. We didn't sequence this
part of your DNA (we only measured the length of the segments) so we
can't tell if the SNP is inside the repeat unit or in the flanking
region. If the deletion is in the flanking region it is as good as a new
SNP and could be used as a marker for a new R-L21 branch. If it is
inside the repeat then chances are high that it is rather unstable. It
may be a good idea to do further research on your DNA and try to
sequence at least the flanking regions of your DYS464 alleles. Also note
that you have a DYS464X cccc configuration (No G-type allele!). This is
definitely a signature that lets you exclude all R-L21 with a G-type
allele from being a descendant of the first person in your male lineage
that had the cccc haplotype.

The second irregular feature is the L69+ marker which hasn't been
observed in other R-L21 persons so far. The L69/L159 polymorphism is
essentially a SNP/STR oxymoron. The base change happens right at the
intersection of a poly G homopolymer and a GT dinucleotide repeat.

In the case of L69+ the poly G is shortened from 6 to 4 bases and the
dinucleotid repeat gains one unit.
In the case of L159+ the poly G is elongated from 6 to 8 bases and the
dinucleotid repeat looses one unit.

This alignment of sequences may make this clearer:

AAACTGGGGGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCG (L69+)
AAACTGGGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCG (HUGO and most others)
AAACTGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCG (L159+)
L69......^
L159.......^
(note that the GT repeat count may vary and is disregarded for the
L96/L159 status)

The L69/L159 polymorphism is certainly not a UEP because it has been
observed in various other haplogroups and we are certainly at the very
beginning of understanding its mechanism and phylogenetic relevance. We
have to be careful because it can "mutate" back  like a regular STR.
However with caution it may be a good help to sort out genealogies and
haplotype clusters. Only further testing will answer the question how
useful this polymorphism may be and what mutation frequency we can expect.

Bernard
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YDNA: R-DF13+ L69+ DYS464X: cccc.3
mtDNA: U6a7a1
mtDNA of my father: U5a2c
YDNA of my maternal uncle: I1*
Ysearch and Mitosearch: UE9BU
Ysearch of my maternal uncle: CEC59

rms2
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« Reply #116 on: October 04, 2009, 03:42:50 PM »

Bernard,

You're SRY2627, right?


Neal

Bernard was one of our first French R-L21s.
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rms2
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« Reply #117 on: October 04, 2009, 03:44:39 PM »

Thomas Krahn give me the following comment about my WTY results:

Quote
To make things clear, there was no NEW SNP found in your DNA. However
there were two things observed that distinguish you from all other R-L21
participants:

First you have a 14.3 micro-allele at DYS464 which is essentially a 1 bp
deletion SNP in one of the 4 DYS464 amplicons. We didn't sequence this
part of your DNA (we only measured the length of the segments) so we
can't tell if the SNP is inside the repeat unit or in the flanking
region. If the deletion is in the flanking region it is as good as a new
SNP and could be used as a marker for a new R-L21 branch. If it is
inside the repeat then chances are high that it is rather unstable. It
may be a good idea to do further research on your DNA and try to
sequence at least the flanking regions of your DYS464 alleles. Also note
that you have a DYS464X cccc configuration (No G-type allele!). This is
definitely a signature that lets you exclude all R-L21 with a G-type
allele from being a descendant of the first person in your male lineage
that had the cccc haplotype.

The second irregular feature is the L69+ marker which hasn't been
observed in other R-L21 persons so far. The L69/L159 polymorphism is
essentially a SNP/STR oxymoron. The base change happens right at the
intersection of a poly G homopolymer and a GT dinucleotide repeat.

In the case of L69+ the poly G is shortened from 6 to 4 bases and the
dinucleotid repeat gains one unit.
In the case of L159+ the poly G is elongated from 6 to 8 bases and the
dinucleotid repeat looses one unit.

This alignment of sequences may make this clearer:

AAACTGGGGGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCG (L69+)
AAACTGGGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCG (HUGO and most others)
AAACTGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCG (L159+)
L69......^
L159.......^
(note that the GT repeat count may vary and is disregarded for the
L96/L159 status)

The L69/L159 polymorphism is certainly not a UEP because it has been
observed in various other haplogroups and we are certainly at the very
beginning of understanding its mechanism and phylogenetic relevance. We
have to be careful because it can "mutate" back  like a regular STR.
However with caution it may be a good help to sort out genealogies and
haplotype clusters. Only further testing will answer the question how
useful this polymorphism may be and what mutation frequency we can expect.

Bernard[/size]

Some of that I don't really understand, but the stuff about 464 certainly sounds interesting and promising.

I guess we should all have our 464 tested for the c/g pattern. I have never done that yet.
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NealtheRed
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« Reply #118 on: October 04, 2009, 05:39:02 PM »

Bernard,

You're SRY2627, right?


Neal

Bernard was one of our first French R-L21s.

Aye.
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Y-DNA: R-Z255 (L159.2+) - Downing (Irish Sea)


MTDNA: HV4a1 - Centrella (Avellino, Italy)


Ysearch: 4PSCK



NealtheRed
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« Reply #119 on: October 04, 2009, 05:39:42 PM »

Yeah, the 464X test has been really fruitful for the Leinster cluster. It would be really interesting to have more L21 test for it.
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Ysearch: 4PSCK



Nolan Admin - Glenn Allen Nolen
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« Reply #120 on: October 04, 2009, 09:16:08 PM »

If I remember right it is part of Panel 5 of the FTDNA Advanced Orders.


Offaly - Kilkenny Clan O'Nolan: R-U152, L2-, L3-, L4-


DYS464X

N-4 - 15c-15c-17c-17c

N-30 - 15c-15c-17c-17c
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Mike Walsh
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« Reply #121 on: October 04, 2009, 09:20:13 PM »

Yeah, the 464X test has been really fruitful for the Leinster cluster. It would be really interesting to have more L21 test for it.
I wish the FTDNA reporting mechanism could list the 464x results.  It's pretty inexpensive, but I think it is more important to get to 67 markers and do a deep clade test (or deep claded extended) if you haven't already.

I'm 15c-15c-17c-17g or 3c1g.   I guess 3c1g is very common.  The 2c2g found by many if not most of the Leinster cluster is uncommon.   My understanding is that 464x mutations to 2c2g or to 4c or anything other than 3c1g is not as definitive (stable) as an SNP but more definitive (slower moving) than an STR.

I don't understand the statement that the "14.3 micro-allele at DYS464 which is essentially a 1 bp deletion SNP in one of the 4 DYS464 amplicons."  I don't see any comments like that related to a 464x test result.  Should there be or is the WTY testing the only way to know about this deletion?
« Last Edit: October 04, 2009, 09:22:59 PM by Mike » Logged

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Mark Jost
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« Reply #122 on: October 04, 2009, 09:48:32 PM »

At least your in company, mine is ccgc. I have asked FtDNA what the mutations are that get to that point. I can not find any discussion on that much detail. gggg>cccg> then I do not know what the next mutations to take me to my ccgc.
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
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« Reply #123 on: October 04, 2009, 10:09:02 PM »

Have you tried the DNA Fingerprint site?
 

http://www.dna-fingerprint.com/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=11


"Some DYS464 examples from an arbitary surname project:
(conventional results)

surname A, 1: 15-15-16-17
surname A, 2: 15-15-16-17
surname A, 3: 15-15-16-17
surname B, 1: 15-15-16-18
surname C, 1: 15-15-15-17

If all the 5 persons are R1b then they can be typed with an extended DYS464 test.

We might get the following results:

surname A, 1: 15c-15c-16g-17c
surname A, 2: 15c-15c-16g-17c
surname A, 3: 15c-15c-16c-17g
surname B, 1: 15c-15c-16g-18c
surname C, 1: 15c-15c-15g-17c

From that result we could say:

- A1 and A2 match completely
- A3 has at least a genetic distance of 2 from (A1 & A2)
- B1 has a genetic distance of 1 from (A1 & A2)
- C1 has a genetic distance of 1 from (A1 & A2)

I hope this is not too technical! Feel free to ask questions.

Thomas Krahn"
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Mark Jost
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« Reply #124 on: October 04, 2009, 10:35:06 PM »

Yes. Thanks. The document does not explain if the mutation occurs in any sequence and in what order, if any.  Since there is no additional detail, one could assume it is random in any 464 marker so I guess the question is: Does the single 'g' that most R1b's have, randomly appear at any position?

All Krahn states: "Most R1b males that we have tested show 3 C-types and 1 G-type. All other haplogroups (including R1a) show 4 G-types."
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
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