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View Full Version : ISOGG STR Bias? [merged threads]



RobertoCavarelli
08-26-2013, 12:44 PM
If you look at the ISOGG Wiki page for Y DNA tests

http://www.isogg.org/wiki/Y_chromosome_DNA_test

90% of it talks about STR testing. Admittedly, 10 years ago SNP testing was in its infancy but after the efforts of projects like WTY and 1000 Genomes projects and with recent beginnings of Full Y-Genome testing, SNP testing is poised to step out of the shadows and arguably overtake STR tests in usefulness.

And yet, ISOGG, the organization which most of us have come to rely on to keep track of the Y SNP tree, seems to be stuck in the dark ages and, judging by its wiki pages, is steering people to the STR testing of FTDNA rather than the SNP tests of National Geographic & BritainsDNA.

I thought ISOGG was supposed to be company neutral. Is this correct or are they tied to one company in reality? Are their wiki administrators all SNP-hating surname project administrators by any chance? If ISOGG wanted to encourage people to take the SNP tests that are the very essence of their SNP trees, you would have thought they would make the effort and keep their own wiki pages accurate and uptodate with what is happening in the SNP world!

In addition some of the links that have been added to the ISOGG wiki are selling products of the ISOGG wiki administrators. Got a car? Then sell it on the ISOGG wiki! Integrity? Pah!

ISOGG need to pull up their socks or they run the risk of turning into a vehicle used by the unethical to sell their wares..

AJL
08-27-2013, 04:35 PM
I see you have a UK IP address. You wouldn't happen to be a shill for BritainsDNA, would you?

RobertCasey
08-27-2013, 07:02 PM
For most genetic researchers, they start with YSTRs looking for matches and getting assigned to genetic clusters. I agree that YSNP testing is making a strong move in becoming a critical test but you still need YSTRs for the last 100 to 1,000 years. ISOGG spends the bulk of their time assisting with YSNP research - but WIKIs are usually for those starting out. ISOGG's haplotree has become the industry standard and is used by anyone doing any serious YSNP research - that is true leadership. If you do not like what is going on, join and volunteer your time vs. complaining about other people who spend a lot of time on your behalf.

There is a lot of bias for FTDNA testing as they are clearly the leader in the industry. The true long term values in genetic testing are atDNA for recent connections (works up to 1800 and sometimes 1750) and YDNA testing (both YSTR and YSNP) for earlier time frames. Here many various reasons why FTDNA is the leader:

1) Their primary purpose is genetics for genealogists. 23andme's primary goal is DTC medical testing and Ancestry is selling their online genealogical databases.
2) Largest database by far for YDNA - specially YSNPs - now only major company offering YSTR tests - this shows the lack of commitment of the other companies to genetic genealogical research.
3) Works with Nat Geo that has by far the best static test for YSNPs - others just add FTDNA discovered & 1K genomes SNPs to their static tests when published.
4) Only company - other than the new Full Genomes - that offers "Walk the Y" tests for new YSNP discovery. You will never see the other companies doing this as there is no profit in it.
5) Only company that has individual YSNPs tests so we known which ones need to be added to the static SNPs tests vs. more uninteresting duplicate/unstable YSNPs.
6) By far the strongest volunteer community for projects and their staff works with volunteers.
7) Only company that has rational long term storage of DNA - in case of death or incapacity.
8) Unlike other companies (your complaint probably), they always publish their SNP discoveries vs. keeping discoveries proprietary for sales reasons.

It will be interesting to see how FTDNA reacts and cooperates with Full Genomes. FTDNA walked away from the very high testing with their 454 scanner due to the huge labor costs of analyzing each new test. Hopefully, it will be a cooperative relationship where FTDNA will quickly offer new YSNPs being discovered so they can be tracked in their database. Also, with no competition for YSTR testing, their profits will come from this market which will slow down cost reductions due to no competition.

It is not just ISOGG that is biased - but most of the volunteer community. I wish there were other serious players other the atDNA crowd (which is viable for more recent research). Maybe Full Genomes will mature for the high end of testing and provide IT support at or better than the FTDNA level. Who do you suggest that we pay more attention to vs. broad disparagement of FTDNA ? The other companies are atDNA companies - who else is there that has any size database or serious product lines ?

lgmayka
08-27-2013, 08:35 PM
And yet, ISOGG, the organization which most of us have come to rely on to keep track of the Y SNP tree, seems to be stuck in the dark ages and, judging by its wiki pages, is steering people to the STR testing of FTDNA rather than the SNP tests of National Geographic & BritainsDNA.
How-to books have to be general enough for everyone--they cannot be tailored to the few favored ethnic groups that get all of the SNP attention. Let us recall that the 1000 Genomes project, on which most recent SNP work is based, never recognized the existence of humans between the Netherlands and China, nor did it ever recognize the existence of the Balkans or the Middle East. Consequently, some haplogroups received only limited attention, and others absolutely none at all.

In contrast, everyone can make use of STRs. They are delightfully universal (well, almost).

In regard to particular vendors, do keep in mind that until fairly recently, some vendors refused to define their results in an open, industry-standard way--thereby cutting themselves out of the standards process entirely. Thank goodness, that customer-surly practice appears to have died.

I agree with the previous poster that FTDNA's real competition may soon be FullGenomes, which has reduced its price to $1250. But of course, FullGenomes has not produced any commercial results yet.

TigerMW
09-30-2013, 05:08 PM
... And yet, ISOGG, the organization which most of us have come to rely on to keep track of the Y SNP tree, seems to be stuck in the dark ages and, judging by its wiki pages, is steering people to the STR testing of FTDNA rather than the SNP tests of National Geographic & BritainsDNA.
...
You may not be aware, but the National Genographic Project outsources their Geno2 testing to FTDNA so I wouldn't really call them competitors.

That being said, I think FTDNA will have to consider the kind of stuff that FullGenomes is doing, particularly since FTDNA's WTY is not really being processed right now. My guess is that FTDNA and BritainsDNA will both have to respond. Still the expenses involved in the full genome technologies probably will always mandate some kind of mid to low priced combination packages like Geno2 or Chromo2. I don't see those going away.... of course, what do I know?

As far as ISOGG is concerned, they seem to be an admirable bunch of volunteers doing the best they can because of their passion for genetic genealogy. May God bless them!

SnowYorker
01-27-2014, 03:37 PM
The use of DNA testing to discover more about our past is not accepted by many. People's attitudes can be split into the following categories -


Complete Rejection due to Religious Beliefs
Sceptical - Have never seen any proof that SNP testing yields any knowledge of our past and have read in the papers/internet that it is all a load of rubbish
Believer - Has already taken an SNP test or would like to but can't afford it


The first group are not likely to be swayed, and the last need none, but reducing test costs would obviously increase the numbers of people testing.

But what is being done to educate sceptical people of the discoveries being made in SNP? Every few years a book is written by someone like Barry Cunliffe, but they are normally out of date as soon as they are released and, in the great scheme of things, are not read by that many people.

Is anything else being done by anyone to explain to people what is being found in the SNP world? For example, is there a website somewhere summarising the SNP findings of different Haplogroups and show-casing the best examples which have interesting geo-historical implications?

As far as I can see there is none, each Haplogroup is busy beavering away with their own results and not talking to anyone else and not helping recruiting newbies.

As far as ISOGG goes, it has become the main keeper of the SNP trees, and yet it does nothing to counter the "DNA is rubbish" school of thought. Where was ISOGG when the BBC broadcast its first ever 60 minute TV program on personal DNA Testing and the usual knocking took place by some journalists who stated that it was impossible to deduce ancient origins from modern DNA? If ISOGG wanted to counter the "DNA is Rubbish" camp they needed to release info explaining the subject of the documentary in much greater detail so that people could understand the over-simplifications needed in such a short program. If anything the little they have produced reinforces the "DNA is Rubbish" idea which is emotionally dumb to say the least! The phrase "Shooting yourself in the foot" comes to mind...

Perhaps ISOGG is little more than a social club these days, with its more materialistic members just using its website to market and sell their own mechandise??

S9 H9
01-30-2014, 09:21 AM
Why dump on ISOGG the problems of society?

That so many people living in 2014 are willingly ignorant (your group 1) or too uninterested or too lazy to do their own research (probably many in your group 2) is a function of how we humans have constructed our culture. This is hardly ISOGG's fault or responsibility, and definitely beyond their scope to fix.

Andrew Lancaster
01-30-2014, 10:21 AM
I have never heard of religious beliefs playing a big role in this particular issue, and I think you are begging the question by simply assuming that all sceptics of SNP testing are wrong. Unfortunately, a lot of SNP testing which has been sold was not very useful for any particular purpose, and therefore scepticism is not wrong, especially when the best tests are both expensive and difficult to use. This should not be simply equated with saying all SNP testing is rubbish though. Many people are taking the attitude that they expect the situation to develop.

The other big concern I have seen is about privacy issues. This has for example affected 23andMe, and it affects anyone trying to study (or look for) any large related family or ethnic group. This is still even an issue for Y STR testing in surname projects.

Regards
Andrew

RobertCasey
01-30-2014, 04:54 PM
I do have to agree with both sides. ISOGG is just a young organization of volunteers that has no dues for organized projects. It is really unfair to dump on any volunteer organization. If you perceive this organization to be too weak, it is due to lack of volunteers to do more (quick complaining and join ISOGG - moving it forward). Or join ISOGG and try to collect funds so many improvements can be made. They are doing the leading edge job for YDNA haplotree and national genetic conferences are now starting for education purposes. Since these groups are primarily funded by genealogists, I spread the blame to the National Genealogical Society which has turned GENTECH into another genealogy conference and left its roots of technologies for genealogists.

I used to volunteer for many major genealogical projects organizing many people to address a particular need - but no longer do this due to all the nay-sayers out there attempting to control how you conduct your project but unwilling to assist with the heavy lifting. Before you have the right to complain, you have to contribute as a volunteer in the area. What have you done to fix this problem - just complain that others fix it according to your viewpoint. I do have a volunteer web site for R-L21 research (100s of pages, dozens of spreadsheets), my Casey surname project and my L21 YSNP tool:

http://www.rcasey.net/DNA/Home.html

Of course, you will immediately complain that it is not as up to date as it could be or not as comprehensive - so why don't you clone this web site for your particular haplogroup or surname. It probably takes too much of your time and you expect others to volunteer to assist you and your agenda.

There are a few religious people that are against this testing as well as some privacy type advocates as well (this is more important). With YDNA, we are now getting close to identifying the vast majority of male individuals - both dead and alive for the 1,000 years (women are lucky in this respect for privacy - but have to conduct research by male proxy for genealogical research) . Exciting for genealogists but a little scary for privacy related issues. But these are a very small minority and usually are people with their own religious or other agendas. The number of skeptical people is and remains a big issue - but some serious recent progress and education is slowly turning the large ship which takes time. Go pressure NGS to offer courses in genetic analysis to match the scale of its strategic importance for genealogists. There are believers and leaders. We need more leaders but there is a lot to do and some areas take a lot of technical skills (anyone want to help me write some complex MySQL queries could really help advance research faster). With only two posts, you are really probably not a believer or leader.

Scarlet Ibis
01-30-2014, 06:53 PM
Threads merged. Please don't create multiple accounts.

Jean M
01-30-2014, 07:46 PM
Where was ISOGG when the BBC broadcast its first ever 60 minute TV program on personal DNA Testing and the usual knocking took place by some journalists

Does this refer to Meet the Izzards? There is a review here: BritainsDNA, the BBC and Eddie Izzard http://cruwys.blogspot.co.uk/2014/01/britainsdna-bbc-and-eddie-izzard.html


First of all I want to provide a little background information because to understand some of the problems it's necessary to look at the wider picture. A company by the name of BritainsDNA, who also trade under the names ScotlandsDNA, IrelandsDNA and YorkshiresDNA, have claimed the credit for doing the DNA testing for Meet the Izzards. For the last couple of years Alistair Moffat, the company's Managing Director, has been actively courting the media, and a number of national newspapers have taken the bait. The stories that have been published have been so exaggerated that BritainsDNA has earned itself an unfortunate reputation for what Private Eye has described as its "ludicrous but headline-grabbing claims". However, it is the BBC which has given Alistair Moffat the most publicity. As the former director of Scottish Television Moffat seems to have friends in high places at the BBC.

R.Rocca
01-30-2014, 08:24 PM
The use of DNA testing to discover more about our past is not accepted by many. People's attitudes can be split into the following categories -


Complete Rejection due to Religious Beliefs
Sceptical - Have never seen any proof that SNP testing yields any knowledge of our past and have read in the papers/internet that it is all a load of rubbish
Believer - Has already taken an SNP test or would like to but can't afford it


The first group are not likely to be swayed, and the last need none, but reducing test costs would obviously increase the numbers of people testing.

But what is being done to educate sceptical people of the discoveries being made in SNP? Every few years a book is written by someone like Barry Cunliffe, but they are normally out of date as soon as they are released and, in the great scheme of things, are not read by that many people.

Is anything else being done by anyone to explain to people what is being found in the SNP world? For example, is there a website somewhere summarising the SNP findings of different Haplogroups and show-casing the best examples which have interesting geo-historical implications?

As far as I can see there is none, each Haplogroup is busy beavering away with their own results and not talking to anyone else and not helping recruiting newbies.

As far as ISOGG goes, it has become the main keeper of the SNP trees, and yet it does nothing to counter the "DNA is rubbish" school of thought. Where was ISOGG when the BBC broadcast its first ever 60 minute TV program on personal DNA Testing and the usual knocking took place by some journalists who stated that it was impossible to deduce ancient origins from modern DNA? If ISOGG wanted to counter the "DNA is Rubbish" camp they needed to release info explaining the subject of the documentary in much greater detail so that people could understand the over-simplifications needed in such a short program. If anything the little they have produced reinforces the "DNA is Rubbish" idea which is emotionally dumb to say the least! The phrase "Shooting yourself in the foot" comes to mind...

Perhaps ISOGG is little more than a social club these days, with its more materialistic members just using its website to market and sell their own mechandise??

Hopefully you can provide a link to your website where you counter the "DNA is rubbish".

TigerMW
01-31-2014, 04:02 PM
Roberto,

I'm glad you started this topic. I very, very much agree that as it relates to the Y chromosome, SNP testing is extremely valuable and we are on a whole new wave of data that will be fantastically useful.

However, although I did not originally think of this way, I can see that Y STRs will continue to be very useful for a long time to come. I don't see STRs and SNPs as competing interests in the Y DNA testing world. To the contrary, I think they are very complementary. I'm not going to try to say one piece of data is 10% more important than another type of data or something of that ilk. The truth is all relevant data should be closely examined and used as effectively as possible.

I vehemently disagree that ISOGG is in some way biased. If you want to make accusations like you should post with a much stronger set of specific data points with some root-cause analysis of how bias caused the data points.

EDITS: Ooops, may be this thread is dead on arrival. I just noticed that a duplicitous poster has been banned. I was looking forward to a good debate on using STRs. I find it odd that I've spent a couple of years talking about important SNPs (validating through testing) are and now we are entering a period where people complain about STRs instead. My thinking has not stood still but costs and matching database sizes are always relevant to genetic genealogy. After reading the posting by Debbie K on ISOGG I have a de ja vue feeling... as in very recently. Sorry, but I may have been inspirational for this guy although I am not an ISOGG representative of any kind. ISOGG is probably a better target than me. If this is who I think it is, there is a clear personal agenda. I know because he emailed his thinking. I don't want to expose an individual to individual email, though.
BTW, I do agree with the fellow that phylogenetic tree discovery and using SNPs for genetic genealogy and population genetics needs more media coverage in general. I think the problem is we are still in its infancy.

RobertCasey
01-31-2014, 08:16 PM
I think four or five years out, there will be three YDNA tests:

1) First - everyone would order the super version of the static YSNP test (similar to Nat Geo or CROMO2). It would have 100,000+ known YSNPs - most of them private. Many of these may be assigned to
known oldest proven ancestors and even some of their descendants. This may be enough testing for many people.
2) There will also be a $200 YSTR test with 500 YSTRs. This would allow to find our ancestor's signatures, create descendant charts with known mutations and flesh out YSNPs that are not well researched to date. This could also
scan for novel YSNP mutations in YSNP rich areas as well.
3) The discovery test for those who need to find out more (geographies not currently being researched as much). This would be $400 full YDNA scan to discover new YSNPs for yet more branches of mankind
and would also include both tests 1) and 2). Or you can get your raw scan for only $100 - but good luck on understanding it.

Costs would be primarily based on IT support, databases and analysis vs. lab testing costs. In between now and this future, there will be a lot YDNA discovery and testing options to get us there. The biggest change will be
more robust tools and databases as the manual method will never get us there and lab costs will no longer be the driving factor.

TigerMW
01-31-2014, 08:35 PM
I think four or five years out, there will be three YDNA tests:
1) First - everyone would order the super version of the static YSNP test (similar to Nat Geo or CROMO2). It would have 100,000+ known YSNPs - most of them private. Many of these may be assigned to
known oldest proven ancestors and even some of their descendants. This may be enough testing for many people....

I don't know how long this will take but I think what you are prognosticating here is unfolding quickly. I think Chromo 2 has already demonstrated that you can get a lot of good things out of a targeted moderate/low cost chip based test, even if it isn't Next Generation. After a round or two of FGC and Big Y testing a Geno / Chromo type offering should be able to do a great job of targetting phylogenetically relevant SNPs. Chromo 2 targets the British Isles, but there could be a clade target, i.e. R1b1a2. That still begs that you need some nominal STR testing or something cheap to know to order the R1b1a2 package versus the J1 package, etc., etc.

I think National Genographic will always have to have a broader test, but since R1b folks have heavily invested in discovery, I think R1b SNPs have a good chance to be well represented in a jam packed low cost Geno 3, or whatever it will be. At that point I'll be cheering on Dr. Wells on while he runs all over the world. That doesn't mean I'll pay much attention to him. LOL. Am I still Cro-magnon?

GTC
01-31-2014, 09:40 PM
ISOGG need to pull up their socks or they run the risk of turning into a vehicle used by the unethical to sell their wares..

Your anti-ISOGG diatribe makes me suspect a personal agenda.

The ISOGG wiki is administered by volunteers -- thus anybody can put their hand up to become an administrator.

DMXX
01-31-2014, 09:47 PM
Everyone participating in this thread: please note the user in question has been banned by the administration for creating multiple accounts. They cannot respond to any posts directed at them.

GailT
01-31-2014, 10:05 PM
ISOGG need to pull up their socks or they run the risk of turning into a vehicle used by the unethical to sell their wares..

I checked the ISOGG consultants page and this seems to be a fair criticism, several of the "consultant" links are not actually offering any consulting services, they simply provide a list of sponsored links, so this page needs to be cleaned up.