GENEALOGY-DNA-L Archives

Archiver > GENEALOGY-DNA > 2011-10 > 1319385265


From: Jørgen K. Kanters <>
Subject: Re: [DNA] How should ISOGG define "private SNP" and "provisionalSNP"?
Date: Sun, 23 Oct 2011 17:54:25 +0200
References: <A6329B9FD895498A876CB51FE563B27C@PC>
In-Reply-To: <A6329B9FD895498A876CB51FE563B27C@PC>


In principle I agrees with you. However I think it is a minor problem, and
the real documented private mutation probably do not exist since most people
will not test for a private mutation. Furthermore a confirmed private
mutation is only private until other subjects are found later on with the
same private mutation. And then how related should two subjects with a SNP
be, when still conceived as a private mutation? TMCA=100 y 200y or another?

As long as ISOGG have they own but precise terminology, It is IMHO not a
problem.

Jorgen

2011/10/22 Lancaster-Boon <>

> Hello everyone
>
> I have come across a subject which seems to need some community discussion.
> I am going to present my own opinions, but I'd be very open to hear
> well-reasoned opposed positions if there are any.
>
> In some discussions I was involved in recently I have learnt that at least
> one adminstrator of ISOGG's Y phylogeny webpages, uses a definition of
> "private SNP" which seems surprising, at least to me. And he claims this is
> a decided usage within ISOGG which is unlikely to be changed. He uses this
> definition when categorizing SNPs on the phylogeny webpages. These have
> become very important to the community of genetic genealogists.
>
> The discussion came about because of a concern raised by another person
> that
> the definition being used may well make it very difficult for members of
> ISOGG (genetic genealogists) to judge what tests to invest in. And indeed,
> it appears to most discourage the testing of the SNPs which should be most
> tested.
>
> Here are some quotes from the adminstrator involved:
>
> "I believe that you misunderstand what our definition of private. Private
> merely means that we do not yet have enough data to support the position
> that a particular SNP is found in significant numbers in a known population
> or have high enough STR diversity."
>
> "The ISOGG guidelines state a SNP is classified as private until enough
> data
> has been presented to the committee that satisfy our guidelines for an
> upgrade to 'confirmed within subclade', 'provisional' or 'fully
> confirmed'."
>
> "The provisional status is for what we see as tree worthy markers. It is
> not
> a category for markers observed once and/or being researched. For such
> markers, we have the private status. It is not possible for us to add
> eleven
> SNPs to the tree as provisional subclades without strong supporting data."
>
> *"I don't have time to constantly argue what private is or what is not. You
> are risking becoming redundant. I've stated and settled my personal
> position
> and the ISOGG's definition of it."
>
> I have two concerns, which I know are shared by others:-
>
> 1. The style of responses indicates a new attitude I had never thought I
> would see in ISOGG. There are committees who decide things outside of the
> community and we should not dare to question this. It seems like a
> disconnect between ISOGG and GG. But what is ISOGG for if it sees itself as
> somehow opposed to its genetic genealogist members?
>
> 2. The definition being used seems to be as follows:
>
> *Provisional means already pretty well studied, but not yet definitively
> cross checked, and probably a significant clade defining SNP.
>
> *Private means hardly studied at all, and therefore quite often this term
> is
> being used to describe SNPs which will be found to be very significant.
>
> Indeed ISOGG's webpages, also contains a definition which can be found
> here:-
>
> http://www.isogg.org/tree/ISOGG_SNP_Requirements.html
>
> ===
> *Provisional BPs are color coded and defined as: BPs newly submitted to the
> ISOGG committee that have sufficient information to be placed in the tree
> with some certainty, but insufficient to meet all the criteria above and
> are
> awaiting evidence as described above.
>
> *Private SNPs are color coded and are defined as:
> --EITHER a BP that has been observed only once, or has been observed
> multiple times but the associated STR profiles show less than 15% of
> markers
> have diverged.
> --OR a BP for which NO specified population have been demonstrated to exist
> where the frequency is greater than 0.05% (P<0.05) and whose total male
> population exceeds 500 thousand individuals as defined geographically or
> ethnically.
> ===
>
> I guess it has slipped past me until now but this is apparently quite
> different to the definitions used by genetic genealogists, and quite
> different from what any native speaker of English would expect. I believe
> the normal common sense definition of "private SNP" is that the SNP
> actually
> been cross-checked and is NOT provisionally known about, but is actually
> known to be a relatively recent SNP that distinguishes only a very small
> group of closely related lineages.
>
> My ISOGG interlocutor has not provided much defence of this except one
> which
> was, frankly, ignorant. He said that he believes that with a few exceptions
> such as R-L21, there are hardly any SNPs which have been discovered which
> are likely to be private in the sense of being isolated to branch ends 500
> years or less. Obviously with WTY and 1000 genomes this is the opposite of
> the truth, and it means ISOGG are making an assumption which is least
> likely
> to be helpful in keeping tabs on the explosions of information which is
> coming our way. This inflexible way of working and thinking, demanding that
> reality should follow the commands of secret commitees, is not going to be
> well suited to the tasks ahead!
>
> That's why I broaden the forum of discussion, to see if there is some other
> counter argument out there! No other way of getting discussions seemed
> possible. I am posting on the GENEALOGY-DNA Rootsweb list, and on the ISOGG
> Yahoo group.
>
> One thing I am sure we expect from our organization's phylogeny pages, is
> some effort being taken to help us see which SNPs justify further testing
> and which do not. The definitions being used seem to be un-necessarily
> confusing? Even extremely misleading.
>
> PROPOSAL. Perhaps ISOGG need to define two levels of "provisional" or
> "under
> investigation" instead of wrongly using the word "private" to describe the
> least-studied provisional SNPs?
>
> I believe the word private implies that an SNP HAS BEEN STUDIED, and is no
> longer provisional.
>
> I wonder what others think?
>
> Best Regards
> Andrew
>
>
>
>
> -------------------------------
> To unsubscribe from the list, please send an email to
> with the word 'unsubscribe' without the
> quotes in the subject and the body of the message
>



--
Jørgen K. Kanters, MD
Associate Professor
Laboratory of Experimental Cardiology
Dept. of Biomedical Sciences
University of Copenhagen
Blegdamsvej 3C
DK 2200 Copenhagen N
Phone: +45 35 32 74 02
Fax: +45 35 32 74 18



This thread: