Re: 2 matches in block tree but no big y matches
Jason, when you open your block tree page you should see all of your distant and recent matches! You will not see them in your Big Y match list if they are? over the 30 YSNP threshold for FTDNA two testers.?
On Monday, June 17, 2024 at 07:21:43 AM UTC, jason jordan <jasonmjordan76@...> wrote:
Is this a quirk of the system if not where would this match be?
Theirs an option an $99 to download this data.??
Is their any benefit to this and where else can it be uploaded.
Jason
|
Re: 2 matches in block tree but no big y matches
Jason, when you open your block tree page you should see all of your matches! You will not see them in your Big Y match list as they are probably over the 30 YSNP threshold for FTDNA two test matches.?
On Monday, June 17, 2024 at 07:21:43 AM UTC, jason jordan <jasonmjordan76@...> wrote:
Is this a quirk of the system if not where would this match be?
Theirs an option an $99 to download this data.??
Is their any benefit to this and where else can it be uploaded.
Jason
|
Re: Family Finder haplogroups
Hi Debbie and all,
?
Thank you very much, Debbie, for your detailed answers to my previous questions, always relevant and informative in my humble opinion. I'm starting to see it a little more clearly now.
?
As for FGC57405, I think it would be more appropriate to talk about SNV (Single Nucleotide Variant), rather than SNP. In fact, to date, given the number of testers identified, we are far from reaching the minimum 1% of the population. FGC57405 appears to be an SNP/SNV detectable by the version of the GSA chips used by FTDNA to carry out its FamilyFinder tests. Indeed, since November 2023 (only 1 bigY tester identified), 29 new testers have been added to R-FGC57423 (haplogroup for which only FGC57405 seems detectable). The number of bigY testers remained invariably at 1 (no notable modification downstream either).
?
For my part, I carried out additional research on the GSA chips used, the type of detection probe present on them, their design as well as the biochemistry principles involved. These famous GSA chips use infinium HTS probes.
?
According to the Illumina documentation that I was able to consult, these infinium probes are based on the SBE principle (Single Base Extension aka Primer Extension, ).
?
There are actually two types of infinium probes?:
-
Infinium II?: appears to be the most widely present type of probe on GSA/OmniExpress chips. ??The infinium II design uses only 1 probe per locus (ie, 1 bead type for both alleles). This probe design is suitable for noncomplimentary SNPs (eg, A to C or G) and enables genotyping of most loci in most organisms (eg. Approximately 84?% of known SNPs in the human genome).?? This probe chemistry utilises a 50mer (¡Ô a total number of 50 nucleotides present in the disigned primers sequences - This can probably cause some problems if the target locus is in a highly repetitive area of ??DNA) sequence design to perfectly hybridise immediately adjacent to the locus of interest (the one of the SNP to check). In other words, each probe binds to a complementary sequence in the sample DNA, stopping one base before the locus of interest. Allele specificity is confered by a single base extension that incorporates one of four labeled nucleotides. This is a dual-hapten-colored system (I had previously naively imagined a quad-hapten-labelled system where each of the 4 nucleotides could thus be dedifferentiated by the detector, hence my confusion). When excited by a laser beam, the nucleotide label with a signal (dual-color channel approach). The Illumina scanner uses red and green lasers to excite the fluorophores and measure the fluorescence intensity signal for each bead on the array. C and G will appear in green (biotin), A and T in red (dinitrophenyl aka DNP). It does not seem possible, to my knowledge, to differentiate complementary nucleotides (A from T, C from G), with this infinium II probe.
-
Infinium I?: ??The infinium I design is required for relatively less-common A/T and C/G SNPs. It uses 2 probes per SNP to determine the relative intensity ratio of the 2 possible target alleles [for autosomal DNA] for any given locus (ie, 2 bead types, 1 for each allele).?? The main difference with the infinium II probe design is that the 50mer sequence of the probe cross/incorporate the locus of interest and stop at this base (and not one base before it). Only sample DNA sequences contening the complementary nucleotide at that specific locus can hybridise the probe. DNA sequences with another allelic variant cannot. For a bi-allelic marker (ancestral/1 variant), 2 probes are necessary, 1 to detect the presence or absence of the ancestral allele, 1 second for the variant one. With infinium I probes, only the desired variant, or its ancestral version (with Y-SNP) can be detected (we can nevertheless target tri or tetrallelic markers, but the space taken up on the GSA chip increases accordingly?: ).
?
Coming back to Z921/FGC57405 (A to C versus A to G), we are dealing with a tri-allelic system. I don't know, however, if this was deliberately taken into account on the GSA chip used by FTDNA (which should probably use 3 infinium I probes or a combination of infinium I/II probes for this same locus). Let us assume that, as it seems in the vast majority of cases, an infinium II probe has been incorporated on the GSA chip to target this specific locus. The scanner will then only be able to detect the presence of the ancestral allele A (or an A to T mutation if it exists) in red or a mutation towards one of the two noncomplementary alleles of A (C or G), in green, without really differentiating C from G. Z921 (E-M132) and FGC57405 (R-FGC57423) each appearing only once to date on the Y-haplotree, on branches that are very distinct from each other, it seems possible to me that FTDNA has designed an algorithm allowing, by including the results on the other Y chromosome loci targeted by the GSA chip, to define whether the positive tester for a C or G allele (in green) at position 11506634, is FGC57405+ or Z921+. For example, a tester that is actually FGC57405+ should also appear U106+. Conversely, a Z921+ tester should appear U106- (the possibility of no call obviously complicates the situation). Extrapolating this principle, if in the future, following the addition of one (PVs) or more bigY testers, forming a new branch (possibly unnamed with PVs) to the Y haplotree, a new SNV/SNP was identified at a position on the Y chromosome covered by an Infinium II probe, it would then seem possible to me, a priori, to imagine that FTDNA could possibly identify FF testers belonging to this new branch, with the results of the current GSA chip (everything would depend on the position in the Y haplotree, and the other SNPs tested upstream of it. In some cases, it would probably be impossible to decide between several potential branches).
?
Of course all this remains a personal hypothesis, and it is very possible that it is in whole or in part erroneous (I may also have missed or misunderstood certain subtleties). A little over a week ago, I submitted a request to the FTDNA helpdesk. I hope soon to receive in return some elements allowing me to better understand things. I'll try to get back to you on that.
Cheers,
Ewenn
|
2 matches in block tree but no big y matches
Is this a quirk of the system if not where would this match be?
Theirs an option an $99 to download this data.??
Is their any benefit to this and where else can it be uploaded.
Jason
|
Re: Family Finder haplogroups
Hi Iain and all,
Thanks for the clarification! At least the doubling of the
current BigY database in 6 years is likely to occur. And let's
hope FTDNA manage to come up with ways to keep increasing both the
recruitment of people taking BigY tests as well as their
processing rate for the foreseeable future. Even if a doubling
every six years is impossible.
Kind regards from the Netherlands,
Jan de Veen
On 16-Jun-24 11:44, Iain via groups.io
wrote:
Hi Jan,
?
Sorry, I should have said it is expected to
double in six years, not every six years. I think, apart from
that one word, the rest of the message is correct. We don't
really have data over a long enough timespan to judge beyond
that, since I'm only basing this on the last ~3 years of data.
?
We can say that the first BigY tests were
returned about 9 years 5 months ago, so let's say 3437 days
ago. If FTDNA had been processing 47.3 tests per day over that
period, we'd have 162570 tests completed and we only have
~113,000. So the throughput at FTDNA is increasing on a
decadal timescale, but not by much, and not enough to keep the
same doubling timescale.
?
Cheers,
?
Iain.
|
Re: Family Finder haplogroups
Hi Jan, ? Sorry, I should have said it is expected to double in six years, not every six years. I think, apart from that one word, the rest of the message is correct. We don't really have data over a long enough timespan to judge beyond that, since I'm only basing this on the last ~3 years of data. ? We can say that the first BigY tests were returned about 9 years 5 months ago, so let's say 3437 days ago. If FTDNA had been processing 47.3 tests per day over that period, we'd have 162570 tests completed and we only have ~113,000. So the throughput at FTDNA is increasing on a decadal timescale, but not by much, and not enough to keep the same doubling timescale. ? Cheers, ? Iain.
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Re: Family Finder haplogroups
Hi Iain and all,
I've read this a a couple of time over, thinking I must have missed something, but but surely a constant rate of 47 processed BigY tests at FTDNA per day does not mean their number of processed BigY tests (currently 113,000) doubles every six years, but instead that the first doubling will take place in 6 years, the next one in 12 years, the one after that in 24 years, etc. Doubling every six years only occurs if their rate of processed test also doubles every six years to 94 per day, then to 188 per day, etc.? For the sake of our BigY haplogroup close matches hit-rate I'm hoping that's what you meant and is also taking place at FTDNA.
Kind regards from the Netherlands,
toggle quoted message
Show quoted text
On 14-Jun-24 12:10, Iain via groups.io wrote:
Another interesting tidbit of information comes from some statistics John T sent me. Apparently, the number of BigY tests processed by FTDNA has been a surprisingly constant 47 tests per day for the last three years. At this rate, the number of BigY tests (currently around 113,000) doubles every six years, meaning the typical person can expect to find a match closer to them than their present match after six years. Similarly, if you are in a haplogroup of two, you can expect a third member within an average of three years; a haplogroup of three will get a fourth member after an average of two years, etc. Of course, there are caveats with this, notably that it assumes all testers are randomly drawn from the population, whereas in reality they are both self-selected and encouraged by nearby matches.
Best wishes,
Iain.
--
This email has been checked for viruses by AVG antivirus software.
www.avg.com
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Re: Family Finder haplogroups
Hi folks, ? Another batch of updates was released a few days ago. This last month has added roughly 32% more testers to the haplotree, bringing the total to just over 552,000. Unfortunately, the number of testers with known European ancestries has only increased by 21%, meaning most testers likely haven't entered their earliest-known-ancestor information. ? On the plus side, the increase seems to have unduly benefitted R-M269 (39%/24% increase) and R-U106 in particular (a 42%/28% increase). ? The number of testers with results deeper than R-U106 has increased by 16080 overall and 3207 within Europe (43%/29%). Again, this has limited potential for improving our understanding of very recent haplogroups, since the FF haplogroups don't cover these, but it makes a massive improvement to our capacity to understand the distribution of larger and older haplogroups across Europe, which is vital to uncovering the early dispersal of R-U106 and where individual haplogroups ended up. ? Another interesting tidbit of information comes from some statistics John T sent me. Apparently, the number of BigY tests processed by FTDNA has been a surprisingly constant 47 tests per day for the last three years. At this rate, the number of BigY tests (currently around 113,000) doubles every six years, meaning the typical person can expect to find a match closer to them than their present match after six years. Similarly, if you are in a haplogroup of two, you can expect a third member within an average of three years; a haplogroup of three will get a fourth member after an average of two years, etc. Of course, there are caveats with this, notably that it assumes all testers are randomly drawn from the population, whereas in reality they are both self-selected and encouraged by nearby matches. ? Best wishes, ? Iain.
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Re: Family Finder haplogroups
Thanks Martin. I hadn¡¯t registered that Brad¡¯s site also showed the date when the SNP was identified. ? I don¡¯t know either what the difference is between centronomic and centromeric. ? Debbie ? ?
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From: [email protected] <[email protected]> On Behalf Of Martin Abrams via groups.io
Sent: Thursday, June 13, 2024 2:03 AM
To: [email protected]
Subject: Re: [R1b-U106] Family Finder haplogroups? On Tue, Jun 11, 2024 at 02:10 PM, Debbie wrote: I don¡¯t think there¡¯s an easy way to check when a Y-SNP was discovered.
Notes from Genetic Homeland
FGC57405
Full Genomes Corp 2016
Position ? 11506634? ?
Located on centronomic region.
Not sure what the difference is between centronomic and centromeric.? It is located on the right side of the Y centromere. _._,_._,_
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Re: Family Finder haplogroups
On Tue, Jun 11, 2024 at 02:10 PM, Debbie wrote:
I don¡¯t think there¡¯s an easy way to check when a Y-SNP was discovered.
?
?
Notes from Genetic Homeland FGC57405 Full Genomes Corp 2016
Position ? 11506634? ?
Located on centronomic region.
Not sure what the difference is between centronomic and centromeric.? It is located on the right side of the Y centromere.
|
Re: Family Finder haplogroups
Hi Ewenn ? I¡¯ll do my best to answer your questions though I am by no means an expert on the technicalities of microarrays. ? A SNP is a single nucleotide polymorphism. It is a simple change to a nucleotide (also known as a base) such as an A changing to a G. It does not designate the position in the genome. It is simply the name given to the mutation that occurs at that specific position. Some positions in the genome have a higher mutation rate so you sometimes get SNPs which occur in different haplogroups. These are known as parallel mutations. The same SNP name would be used but the name would have a .1, .2 etc included after the SNP name to denote the fact that it occurred in a different part of the tree. To classify as a SNP it is supposed to occur in at least 1% of the population. In order to identify a SNP you therefore need to test lots of people in the population so that you are able to ascertain that a minority of people have, for example, a T at a particular position in the genome whereas the rest of the population have a G. ? FGC57405 would only be included on a SNP chip if this SNP was (1) known at the time the chip was launched and (2) if it was included in the collection of SNPs chosen for inclusion on the chip. Companies do have the ability to include a limited number of custom SNPs on the chip in addition to the fixed selection of SNPs provided by the company but they obviously can¡¯t include everything. It¡¯s only since the launch of next generation sequencing tests that we¡¯ve been able to discover tens of thousands of new SNPs. ? The rsID is simply the reference number for the position on the genome where the SNP has occurred. There are rsIDs for each chromosome. ? As far as I can make out Z291 and FGC57423 are on two completely different parts of the R1b tree so they would have different rsIDs. Here are the ancestral SNP paths: ? R-M207>M173>M343>L754>L761>L389>P297>M269>L23>L51>P310>L151>P312>Z46516>ZZ11>U152>L2>Z258>Z367>L20>Z291 ? R-M207>M173>M343>L754>L761>L389>P297>M269>L23>L51>P310>L151>U106>Z2265>S19589>FGC57430>FGC57423 ? Single SNPs aren¡¯t normally used in isolation to provide a haplogroup assignment. You need to have the full SNP list. Even if there was a no call at one position in the SNP chain, you would still be able to provide the haplogroup assignment because of all the other SNPs in the SNP progression list. ? Some companies allow you to download your raw data so that you can get the full rsID list and your result for each position whereas other companies (eg Living DNA) simply provide you with a SNP list. ? Affymetrix and Illumina are the names of the two main companies that manufacture microarrays. The SNPs which appear on the microarray are selected by the companies to give a good balance of SNPs spread out across the genome. The two companies will, therefore, have a different selection of SNPs on their microarrays. The Y-SNPs are selected for their phylogenetic relevance. Some SNPs don¡¯t perform well on microarrays so this is something that is also taken into consideration. Each microarray will include a fixed number of SNPs and. by definition. these SNPs have to have been discovered in order to be included on the chip. ? There is no problem with calling Ts. Microarrays are perfectly capable of calling all four DNA letters (As, Cs, Ts and Gs) with a high level of accuracy. For example the call rate is 99.5% for the GSA v3. See: ?
? If FGC57405 is not included on any of the chips it¡¯s probably not because of any difficulties in calling the SNP but because it occurs at a position in the genome that did not feature in the research that was available at the time and it was therefore still waiting to be discovered. Alternatively, if it was known at the time, it may be that for one reason or another it did not make the shortlist of SNPs that were included on the chip. ? I don¡¯t think there¡¯s an easy way to check when a Y-SNP was discovered. You can, however, do a manual check on the earlier versions of the ISOGG Y-SNP tree: ?
? That might give you an idea of when FGC57405 was first discovered. ? This page on the Illumina website provides information about the technology of microarrays: ?
? Best wishes ? Debbie ? ?
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From: [email protected] <[email protected]> On Behalf Of Ewenn via groups.io
Sent: Monday, June 3, 2024 2:11 PM
To: [email protected]
Subject: Re: [R1b-U106] Family Finder haplogroups? Hi Debbie, Thank you for these detailed and very informative explanations. In summary, there appears to be extremely little chance that new Y chromosome positions will be covered by the Omniexpress chips. We will therefore have to make do. I must admit that I remain a little confused with the definitions of SNPs and RSID. Maybe that¡¯s where my incomprehension comes from. I'm also not very familiar with microarray chip-based analysis techniques (I just understood that Affymetrix and Illumina chip-based analyzes are slightly different). In my mind, a SNP designates both the position in the genome (locus) and the nucleotide (base). In short, to return to my previous example, Z921 and FGC57405 are two different SNPs (two different mutations of the same ancestral base A), located at the same position of the Y chromosome. Is that correct? Since the A to T mutation has never (it seems) been listed, and therefore taken into account for the GSA chip, it would in fact be undetectable by said microarray chip? Finally, if FGC57405 is detected, it is because this A to G mutation was known during the development of the GSA chip, and these developers voluntarily and specially chose to look for it (and not just A/C which corresponds to Z921) ? To summarize, the GSA chip can detect the presence of bases A, G or C at position 11,506,634 of the Y chromosome, but will never be able to detect T (if this mutation exists in someone)... If someone could take a little time to shed some light on these points which must seem very basic to more than one of you, I would be very grateful (I am probably not the only one to experience a little confusion).
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Re: Evidence for dynastic succession among early Celtic elites in Central Europe
I saw this for the first time yesterday too (thanks Brad). Supplementary tables show the Y-DNA haplogroups in the first sheet, columns AA and AB. There's one R-Z347 in there from our group, a few R-P312s and some other fairly typical European haplogroups (mostly Gs, an I and and a J). ? - Iain.
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Evidence for dynastic succession among early Celtic elites in Central Europe
I have not seen this before and thought it might be of interest:
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Re: Family Finder haplogroups
Hello John,
Thank you for this additional information. It is therefore likely that this last tester was added in the last few weeks.
Kind regards,
Ewenn
Hello Ewin
Rob has not yet updated his SNP tracker this month, so as late as May 13th we can see that FTDNA had only 1 kit (the England one) at that date.?
Kind regards John
On Wednesday, 5 June 2024 at 07:10:43 pm ACST, Ewenn < gwenng008@...> wrote:
[Edited Message Follows]
Hi,
?
I tried to find a haplogroup that could possibly match the answer I got from FTDNA?in December 2023:
°Ú¡±Õ The short answer is yes, in very rare instances we have found SNPs that have been previously seen in only one other tester in the database. These situations have allowed us to form new branches.
?
Among the potential candidates, I found one that I find quite interesting, and that I would like to share: R-S10807.
?
As of June 5, 2024 (version 4818 of Y-DNA_HaploTree of June 3, 2024), R-S10807 is a terminal haplogroup, consisting of the single SNP S10807, located downstream of R-U106 in the haplotree, immediately downstream of R-Z301 (TMRCA of R-Z301 ~2500 BCE), and made up to date of only 2 testers, only 1 of which is a bigY whose EKA would have its origins in England (this tester is also in the R-U106 group, but locates its EKA in the state of Ohio in the USA). The second tester being of unknown origin.
?
S10807:
-
position: 8 036 213,
-
ancestral: G,
-
derived: A,
-
region: p11.2.
To my knowledge, position 8 036 213 of the Y chromosome is covered by the GSA chip used by FTDNA. S10807 (A to G mutation) is currently the only SNP identified by Ybrowse at this position of the Y chromosome. Still according to data from Ybrowse.org, S10807 was discovered in 2014 by Jim Wilson in an R1b-DF21 individual (a priori currently R-L720 or downstream of it).
?
The Y-DNA Haplotree currently lists (version 4818) 3 haplogroups containing S10807:
-
E-BY200986, block of 6 SNPs
-
R-S10807, 1 single SNP (R-U106>R-Z2265>R-BY30097>R-FFT8>R-Z381>R-Z301>R-S10807)
-
R-L720, block of 37 SNPs
?
For its part, Yfull lists 5 haplogroups associated with S10807:
After going back in time, using the small data I still have, it turns out that FTDNA was already aware of this branch of the Y tree before November 29, 2022 (version 2936 of the Y-DNA Haplotree ). At this time, only one tester was associated with it (the only bigY tester identified to date). In the version published on November 18, 2023, Discover still only included one kit for R-S10807. As well as version 4267 of the Y-DNA Haplotree from November 10, 2023. Ditto for version 4564 from February 26, 2024.
?
In deduction, it seems quite likely to me that an Family Finder tester (FF), probably not having provided an origin for his EKA, was added to this terminal haplogroup between February 26 and the beginning of June. Of course these deductions are only mine, and in this matter I regularly make mistakes! As to why FTDNA had already created a R-S10807 branch in its Y Tree before December 2022, when its public databases only seemed to have one positive tester, this remains a certain mystery to me.
?
If anyone has some observations contradicting my deductions (which may obviously turn out to be inaccurate), or new elements to add on R-S10807, I would be grateful.
Cheers,
Ewenn
|
Re: Family Finder haplogroups
Hello Ewin
Rob has not yet updated his SNP tracker this month, so as late as May 13th we can see that FTDNA had only 1 kit (the England one) at that date.?
Kind regards John
On Wednesday, 5 June 2024 at 07:10:43 pm ACST, Ewenn <gwenng008@...> wrote:
[Edited Message Follows]
Hi,
?
I tried to find a haplogroup that could possibly match the answer I got from FTDNA?in December 2023:
°Ú¡±Õ The short answer is yes, in very rare instances we have found SNPs that have been previously seen in only one other tester in the database. These situations have allowed us to form new branches.
?
Among the potential candidates, I found one that I find quite interesting, and that I would like to share: R-S10807.
?
As of June 5, 2024 (version 4818 of Y-DNA_HaploTree of June 3, 2024), R-S10807 is a terminal haplogroup, consisting of the single SNP S10807, located downstream of R-U106 in the haplotree, immediately downstream of R-Z301 (TMRCA of R-Z301 ~2500 BCE), and made up to date of only 2 testers, only 1 of which is a bigY whose EKA would have its origins in England (this tester is also in the R-U106 group, but locates its EKA in the state of Ohio in the USA). The second tester being of unknown origin.
?
S10807:
-
position: 8 036 213,
-
ancestral: G,
-
derived: A,
-
region: p11.2.
To my knowledge, position 8 036 213 of the Y chromosome is covered by the GSA chip used by FTDNA. S10807 (A to G mutation) is currently the only SNP identified by Ybrowse at this position of the Y chromosome. Still according to data from Ybrowse.org, S10807 was discovered in 2014 by Jim Wilson in an R1b-DF21 individual (a priori currently R-L720 or downstream of it).
?
The Y-DNA Haplotree currently lists (version 4818) 3 haplogroups containing S10807:
-
E-BY200986, block of 6 SNPs
-
R-S10807, 1 single SNP (R-U106>R-Z2265>R-BY30097>R-FFT8>R-Z381>R-Z301>R-S10807)
-
R-L720, block of 37 SNPs
?
For its part, Yfull lists 5 haplogroups associated with S10807:
After going back in time, using the small data I still have, it turns out that FTDNA was already aware of this branch of the Y tree before November 29, 2022 (version 2936 of the Y-DNA Haplotree ). At this time, only one tester was associated with it (the only bigY tester identified to date). In the version published on November 18, 2023, Discover still only included one kit for R-S10807. As well as version 4267 of the Y-DNA Haplotree from November 10, 2023. Ditto for version 4564 from February 26, 2024.
?
In deduction, it seems quite likely to me that an Family Finder tester (FF), probably not having provided an origin for his EKA, was added to this terminal haplogroup between February 26 and the beginning of June. Of course these deductions are only mine, and in this matter I regularly make mistakes! As to why FTDNA had already created a R-S10807 branch in its Y Tree before December 2022, when its public databases only seemed to have one positive tester, this remains a certain mystery to me.
?
If anyone has some observations contradicting my deductions (which may obviously turn out to be inaccurate), or new elements to add on R-S10807, I would be grateful.
Cheers,
Ewenn
|
Re: Family Finder haplogroups
Hi,
?
I tried to find a haplogroup that could possibly match the answer I got from FTDNA?in December 2023:
°Ú¡±Õ The short answer is yes, in very rare instances we have found SNPs that have been previously seen in only one other tester in the database. These situations have allowed us to form new branches.
?
Among the potential candidates, I found one that I find quite interesting, and that I would like to share: R-S10807.
?
As of June 5, 2024 (version 4818 of Y-DNA_HaploTree of June 3, 2024), R-S10807 is a terminal haplogroup, consisting of the single SNP S10807, located downstream of R-U106 in the haplotree, immediately downstream of R-Z301 (TMRCA of R-Z301 ~2500 BCE), and made up to date of only 2 testers, only 1 of which is a bigY whose EKA would have its origins in England (this tester is also in the R-U106 group, but locates its EKA in the state of Ohio in the USA). The second tester being of unknown origin.
?
S10807:
-
position: 8 036 213,
-
ancestral: G,
-
derived: A,
-
region: p11.2.
To my knowledge, position 8 036 213 of the Y chromosome is covered by the GSA chip used by FTDNA. S10807 (A to G mutation) is currently the only SNP identified by Ybrowse at this position of the Y chromosome. Still according to data from Ybrowse.org, S10807 was discovered in 2014 by Jim Wilson in an R1b-DF21 individual (a priori currently R-L720 or downstream of it).
?
The Y-DNA Haplotree currently lists (version 4818) 3 haplogroups containing S10807:
-
E-BY200986, block of 6 SNPs
-
R-S10807, 1 single SNP (R-U106>R-Z2265>R-BY30097>R-FFT8>R-Z381>R-Z301>R-S10807)
-
R-L720, block of 37 SNPs
?
For its part, Yfull lists 5 haplogroups associated with S10807:
After going back in time, using the small data I still have, it turns out that FTDNA was already aware of this branch of the Y tree before November 29, 2022 (version 2936 of the Y-DNA Haplotree ). At this time, only one tester was associated with it (the only bigY tester identified to date). In the version published on November 18, 2023, Discover still only included one kit for R-S10807. As well as version 4267 of the Y-DNA Haplotree from November 10, 2023. Ditto for version 4564 from February 26, 2024.
?
In deduction, it seems quite likely to me that an Family Finder tester (FF), probably not having provided an origin for his EKA, was added to this terminal haplogroup between February 26 and the beginning of June. Of course these deductions are only mine, and in this matter I regularly make mistakes! As to why FTDNA had already created a R-S10807 branch in its Y Tree before December 2022, when its public databases only seemed to have one positive tester, this remains a certain mystery to me.
?
If anyone has some observations contradicting my deductions (which may obviously turn out to be inaccurate), or new elements to add on R-S10807, I would be grateful.
Cheers,
Ewenn
|
Re: Family Finder haplogroups
I did some research to try to understand a little better the analysis methodology used with these Infinium Global Screening Array (GSA) chips.
An illustration seems to me to summarize the situation well:
"In this genotyping system, A and T nucleotides were labeled in one color, and C and G were in another. The polymorphisms A>T and G>C could not be detected."
In my example FGC57405/Z921, mutation A to G versus A to C, the GSA chip should therefore not be able to differentiate the two mutations. I therefore assume (but I am probably wrong) that it is only in association with the other SNPs detected that FTDNA manages to assign a haplogroup. For exemple, a U106+ tester with a mutation detected at position 11,506,634 should only be A to G because it is to date the only one known downstream of R-U106.
Ewenn
Hi Debbie,
Thank you for these detailed and very informative explanations. In summary, there appears to be extremely little chance that new Y chromosome positions will be covered by the Omniexpress chips. We will therefore have to make do.
I must admit that I remain a little confused with the definitions of SNPs and RSID. Maybe that¡¯s where my incomprehension comes from. I'm also not very familiar with microarray chip-based analysis techniques (I just understood that Affymetrix and Illumina chip-based analyzes are slightly different).
In my mind, a SNP designates both the position in the genome (locus) and the nucleotide (base). In short, to return to my previous example, Z921 and FGC57405 are two different SNPs (two different mutations of the same ancestral base A), located at the same position of the Y chromosome. Is that correct? Since the A to T mutation has never (it seems) been listed, and therefore taken into account for the GSA chip, it would in fact be undetectable by said microarray chip? Finally, if FGC57405 is detected, it is because this A to G mutation was known during the development of the GSA chip, and these developers voluntarily and specially chose to look for it (and not just A/C which corresponds to Z921) ? To summarize, the GSA chip can detect the presence of bases A, G or C at position 11,506,634 of the Y chromosome, but will never be able to detect T (if this mutation exists in someone)...
If someone could take a little time to shed some light on these points which must seem very basic to more than one of you, I would be very grateful (I am probably not the only one to experience a little confusion).
Cheers,
Ewenn
Ewenn ? FTDNA and MyHeritage have always used the same chips for their autosomal DNA tests. All the testing is done at the Gene by Gene labs in Texas. The only difference is that the companies process the results, the reports and the match lists separately using their own independent algorithms. Both companies originally used the Illumina OmniExpress. They changed over to the Illumina Global Screening Array in around 2019 though I¡¯m not sure of the date. ? The OmniExpress has been around in various forms since 2007 when 23andMe first launched their test. There is some information on the different versions here: ?
? Illumina allow you to add custom SNPs and 23andMe will have added additional Y-SNPs to provide better haplogroup resolution. Neither MyHeritage nor FTDNA previously provided haplogroup reports so I doubt that in the early years they would ever have added any custom Y-SNPs. The SNPs on the OmniExpress were mostly those discovered through the HapMap Project and back in those days very few Y-SNPs were known so I don¡¯t anticipate we will get very much resolution when the OmniExpress haplogroup reports start to go out. By definition, microarrays only cover known SNPs so there are no possibilities for SNP discovery. I very much doubt that there are Y-SNPs on the old OmniExpress that are not included on the GSA. However, some SNPs can¡¯t be called very accurately on microarrays so it¡¯s possible some of the early SNPs have since been dropped because of their unreliability. ? AncestryDNA use a customised version of the Illumina OmniExpress. As far as I¡¯m aware they have never changed to the GSA. According to Tim Janzen¡¯s autosomal DNA testing comparison chart in the ISOGG Wiki there are now 1691 Y-SNPs included in the AncestryDNA test. You can get a list of these SNPs if you download your raw data from Ancestry. They are labelled as chromosome 24. ?
? It may well be that the Y-SNPs reported by Ancestry are the same ones that are included on the OmniExpress chip used by FTDNA and MyHeritage. ? Best wishes ? Debbie Kennett ? ? ? Thank you very much Debbie for sharing this explanatory information with the rest of us! The question I ask myself, and which seems to remain unanswered, is whether the other chips previously used by FTDNA, like the one currently used by MyHeritage, would not be able to detect some new SNPs uncovered by the latest chip whose results we have seen appear in recent months? Small hope, probably vain in my case, of seeing newcomers appear on certain branches of the Y tree not covered until now...?It would seem interesting to me to be able to know the positions of the Y chromosome covered by the different chips (those covered by the chip currently in use at FTDNA for their autosomal tests had previously been shared in a previous post on this forum). Small subtlety to find additional information on some new FF testers added who have provided the location of their EKA: In the SNP Map tool, these new testers do not necessarily appear when searching with the matching SNP with the assigned haplogroup name. An example with R-FGC57423 covered by the current chip used for FTDNA autosomal testing. A search with FGC57423 will not yield anything new. If the search is carried out with FGC57405, which is the SNP of this haplogroup covered by the said chip (unless I am mistaken, all possible mutations of the nucleotide at this position of the Y chromosome are theoretically detectable in the process, therefore any SNP already identified at this same position is also theoretically identifiable), a geolocation of the EKAs provided by the new FF testers appears. A significant problem nevertheless exists with this tool as designed by FTDNA: if the same SNP (the same mutation at an identical position on the Y chromosome) is identified in at least two distinct haplogroups, it is sometimes possible (but not obligatory) that testers from these two haplogroups find themselves mixed in the results displayed... ? FamilyTreeDNA have advised group administrators that they have now completed the process of updating Y-DNA haplogroup assignments for everyone who tested on the current chip (the Illumina Global Screening Array). They are now working on updating haplogroups for customers tested on the old Illumina chip (the OmniExpress). ? FTDNA have also provided some useful information about the SNPs included on the chips. Here¡¯s an extract from their e-mail to group admins: ? ¡°We have received numerous requests for a count or list of the Y-DNA SNPs included on the Family Finder test chips(s). The exact number varies between chips. For example, the Ancestry v1 and v2 chips differ, and both differ from the MyHeritage chip. ? The GSA chip (the one currently used by FamilyTreeDNA) covers more than 3,250 haplotree branches (no calls for any given SNP are, of course, possible). The total number of SNPs tested is a little misleading because of several factors (validation status, tree status, duplicates, triallelics, etc.). In addition, some of the SNPs are duplicates found in multiple haplogroups and, therefore, not included in the haplotree. What's important is that as more people from rare branches test both FF and Big Y, the number of branches will expand over time.¡± ? Best wishes ? Debbie Kennett
|
Re: Family Finder haplogroups
Hi Debbie,
Thank you for these detailed and very informative explanations. In summary, there appears to be extremely little chance that new Y chromosome positions will be covered by the Omniexpress chips. We will therefore have to make do.
I must admit that I remain a little confused with the definitions of SNPs and RSID. Maybe that¡¯s where my incomprehension comes from. I'm also not very familiar with microarray chip-based analysis techniques (I just understood that Affymetrix and Illumina chip-based analyzes are slightly different).
In my mind, a SNP designates both the position in the genome (locus) and the nucleotide (base). In short, to return to my previous example, Z921 and FGC57405 are two different SNPs (two different mutations of the same ancestral base A), located at the same position of the Y chromosome. Is that correct? Since the A to T mutation has never (it seems) been listed, and therefore taken into account for the GSA chip, it would in fact be undetectable by said microarray chip? Finally, if FGC57405 is detected, it is because this A to G mutation was known during the development of the GSA chip, and these developers voluntarily and specially chose to look for it (and not just A/C which corresponds to Z921) ? To summarize, the GSA chip can detect the presence of bases A, G or C at position 11,506,634 of the Y chromosome, but will never be able to detect T (if this mutation exists in someone)...
If someone could take a little time to shed some light on these points which must seem very basic to more than one of you, I would be very grateful (I am probably not the only one to experience a little confusion).
Cheers,
Ewenn
Ewenn ? FTDNA and MyHeritage have always used the same chips for their autosomal DNA tests. All the testing is done at the Gene by Gene labs in Texas. The only difference is that the companies process the results, the reports and the match lists separately using their own independent algorithms. Both companies originally used the Illumina OmniExpress. They changed over to the Illumina Global Screening Array in around 2019 though I¡¯m not sure of the date. ? The OmniExpress has been around in various forms since 2007 when 23andMe first launched their test. There is some information on the different versions here: ?
? Illumina allow you to add custom SNPs and 23andMe will have added additional Y-SNPs to provide better haplogroup resolution. Neither MyHeritage nor FTDNA previously provided haplogroup reports so I doubt that in the early years they would ever have added any custom Y-SNPs. The SNPs on the OmniExpress were mostly those discovered through the HapMap Project and back in those days very few Y-SNPs were known so I don¡¯t anticipate we will get very much resolution when the OmniExpress haplogroup reports start to go out. By definition, microarrays only cover known SNPs so there are no possibilities for SNP discovery. I very much doubt that there are Y-SNPs on the old OmniExpress that are not included on the GSA. However, some SNPs can¡¯t be called very accurately on microarrays so it¡¯s possible some of the early SNPs have since been dropped because of their unreliability. ? AncestryDNA use a customised version of the Illumina OmniExpress. As far as I¡¯m aware they have never changed to the GSA. According to Tim Janzen¡¯s autosomal DNA testing comparison chart in the ISOGG Wiki there are now 1691 Y-SNPs included in the AncestryDNA test. You can get a list of these SNPs if you download your raw data from Ancestry. They are labelled as chromosome 24. ?
? It may well be that the Y-SNPs reported by Ancestry are the same ones that are included on the OmniExpress chip used by FTDNA and MyHeritage. ? Best wishes ? Debbie Kennett ? ? ? Thank you very much Debbie for sharing this explanatory information with the rest of us! The question I ask myself, and which seems to remain unanswered, is whether the other chips previously used by FTDNA, like the one currently used by MyHeritage, would not be able to detect some new SNPs uncovered by the latest chip whose results we have seen appear in recent months? Small hope, probably vain in my case, of seeing newcomers appear on certain branches of the Y tree not covered until now...?It would seem interesting to me to be able to know the positions of the Y chromosome covered by the different chips (those covered by the chip currently in use at FTDNA for their autosomal tests had previously been shared in a previous post on this forum). Small subtlety to find additional information on some new FF testers added who have provided the location of their EKA: In the SNP Map tool, these new testers do not necessarily appear when searching with the matching SNP with the assigned haplogroup name. An example with R-FGC57423 covered by the current chip used for FTDNA autosomal testing. A search with FGC57423 will not yield anything new. If the search is carried out with FGC57405, which is the SNP of this haplogroup covered by the said chip (unless I am mistaken, all possible mutations of the nucleotide at this position of the Y chromosome are theoretically detectable in the process, therefore any SNP already identified at this same position is also theoretically identifiable), a geolocation of the EKAs provided by the new FF testers appears. A significant problem nevertheless exists with this tool as designed by FTDNA: if the same SNP (the same mutation at an identical position on the Y chromosome) is identified in at least two distinct haplogroups, it is sometimes possible (but not obligatory) that testers from these two haplogroups find themselves mixed in the results displayed... ? FamilyTreeDNA have advised group administrators that they have now completed the process of updating Y-DNA haplogroup assignments for everyone who tested on the current chip (the Illumina Global Screening Array). They are now working on updating haplogroups for customers tested on the old Illumina chip (the OmniExpress). ? FTDNA have also provided some useful information about the SNPs included on the chips. Here¡¯s an extract from their e-mail to group admins: ? ¡°We have received numerous requests for a count or list of the Y-DNA SNPs included on the Family Finder test chips(s). The exact number varies between chips. For example, the Ancestry v1 and v2 chips differ, and both differ from the MyHeritage chip. ? The GSA chip (the one currently used by FamilyTreeDNA) covers more than 3,250 haplotree branches (no calls for any given SNP are, of course, possible). The total number of SNPs tested is a little misleading because of several factors (validation status, tree status, duplicates, triallelics, etc.). In addition, some of the SNPs are duplicates found in multiple haplogroups and, therefore, not included in the haplotree. What's important is that as more people from rare branches test both FF and Big Y, the number of branches will expand over time.¡± ? Best wishes ? Debbie Kennett
|
Re: Family Finder haplogroups
Ewenn ? FTDNA and MyHeritage have always used the same chips for their autosomal DNA tests. All the testing is done at the Gene by Gene labs in Texas. The only difference is that the companies process the results, the reports and the match lists separately using their own independent algorithms. Both companies originally used the Illumina OmniExpress. They changed over to the Illumina Global Screening Array in around 2019 though I¡¯m not sure of the date. ? The OmniExpress has been around in various forms since 2007 when 23andMe first launched their test. There is some information on the different versions here: ?
? Illumina allow you to add custom SNPs and 23andMe will have added additional Y-SNPs to provide better haplogroup resolution. Neither MyHeritage nor FTDNA previously provided haplogroup reports so I doubt that in the early years they would ever have added any custom Y-SNPs. The SNPs on the OmniExpress were mostly those discovered through the HapMap Project and back in those days very few Y-SNPs were known so I don¡¯t anticipate we will get very much resolution when the OmniExpress haplogroup reports start to go out. By definition, microarrays only cover known SNPs so there are no possibilities for SNP discovery. I very much doubt that there are Y-SNPs on the old OmniExpress that are not included on the GSA. However, some SNPs can¡¯t be called very accurately on microarrays so it¡¯s possible some of the early SNPs have since been dropped because of their unreliability. ? AncestryDNA use a customised version of the Illumina OmniExpress. As far as I¡¯m aware they have never changed to the GSA. According to Tim Janzen¡¯s autosomal DNA testing comparison chart in the ISOGG Wiki there are now 1691 Y-SNPs included in the AncestryDNA test. You can get a list of these SNPs if you download your raw data from Ancestry. They are labelled as chromosome 24. ?
? It may well be that the Y-SNPs reported by Ancestry are the same ones that are included on the OmniExpress chip used by FTDNA and MyHeritage. ? Best wishes ? Debbie Kennett ? ?
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From: [email protected] <[email protected]> On Behalf Of Ewenn via groups.io
Sent: Thursday, May 30, 2024 9:00 PM
To: [email protected]
Subject: Re: [R1b-U106] Family Finder haplogroups? Thank you very much Debbie for sharing this explanatory information with the rest of us! The question I ask myself, and which seems to remain unanswered, is whether the other chips previously used by FTDNA, like the one currently used by MyHeritage, would not be able to detect some new SNPs uncovered by the latest chip whose results we have seen appear in recent months? Small hope, probably vain in my case, of seeing newcomers appear on certain branches of the Y tree not covered until now...?It would seem interesting to me to be able to know the positions of the Y chromosome covered by the different chips (those covered by the chip currently in use at FTDNA for their autosomal tests had previously been shared in a previous post on this forum). Small subtlety to find additional information on some new FF testers added who have provided the location of their EKA: In the SNP Map tool, these new testers do not necessarily appear when searching with the matching SNP with the assigned haplogroup name. An example with R-FGC57423 covered by the current chip used for FTDNA autosomal testing. A search with FGC57423 will not yield anything new. If the search is carried out with FGC57405, which is the SNP of this haplogroup covered by the said chip (unless I am mistaken, all possible mutations of the nucleotide at this position of the Y chromosome are theoretically detectable in the process, therefore any SNP already identified at this same position is also theoretically identifiable), a geolocation of the EKAs provided by the new FF testers appears. A significant problem nevertheless exists with this tool as designed by FTDNA: if the same SNP (the same mutation at an identical position on the Y chromosome) is identified in at least two distinct haplogroups, it is sometimes possible (but not obligatory) that testers from these two haplogroups find themselves mixed in the results displayed... ? FamilyTreeDNA have advised group administrators that they have now completed the process of updating Y-DNA haplogroup assignments for everyone who tested on the current chip (the Illumina Global Screening Array). They are now working on updating haplogroups for customers tested on the old Illumina chip (the OmniExpress). ? FTDNA have also provided some useful information about the SNPs included on the chips. Here¡¯s an extract from their e-mail to group admins: ? ¡°We have received numerous requests for a count or list of the Y-DNA SNPs included on the Family Finder test chips(s). The exact number varies between chips. For example, the Ancestry v1 and v2 chips differ, and both differ from the MyHeritage chip. ? The GSA chip (the one currently used by FamilyTreeDNA) covers more than 3,250 haplotree branches (no calls for any given SNP are, of course, possible). The total number of SNPs tested is a little misleading because of several factors (validation status, tree status, duplicates, triallelics, etc.). In addition, some of the SNPs are duplicates found in multiple haplogroups and, therefore, not included in the haplotree. What's important is that as more people from rare branches test both FF and Big Y, the number of branches will expand over time.¡± ? Best wishes ? Debbie Kennett
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Re: disabled email for kits you have paid for
A person's DNA will always be theirs no matter who paid for it. This is the stance of FTDNA and a proper one in my opinion.?
I do not believe FTDNA disabled your email, but the person did most likely.?
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On Jun 2, 2024, at 4:35?AM, Priscilla Jean Tennant Skar <pjtskar@...> wrote:
?What have you others done when
You have kits you have paid for and yours was the main email that is now disabled?
I have no problem if people want to take over their kits but when I save to buy a bigY and FTDNA disables my email
with out a refund is not fair
I am not getting what I paid for??
Jean
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Ewenn
Jan de Veen