Atanas, The largest cost factor for Y chromosome tests is not the sequencing, but the enrichment procedure. With enrichment the price will never drop far below $400, so you might as well sequence with sufficient coverage. On the long run there is no future for BigY and FGCs Y tests since the WGS tests keep dropping in the price, but Y tests don't. Thomas On 01/06/2016 12:55 AM, Atanas Kumbarov via wrote: > I have exactly the same idea. If you have a tree to follow, you don't > need that many reads at a given position. But I think that it will be > better if FGC designs a Y-chromosome only test at 5x instead of WGS test > at 2x with the same price tag (around $250). The increase of depth of > coverage could be compensated by the decrease of sequenced locis (the > Y-chromosome only). > > 5x is sufficient - the 1000GP had 5x to 7x coverage and never the less > we see huge 1000GP dominated segments of the YFull tree like this one > http://yfull.com/tree/R-L657/ > > If such a test was offered, it could gain a lot of popularity. > > Best regards, > Atanas Kumbarov > > > > On 05/01/16 23:37, AJ Marsh via wrote: >> Tim, >> >> Many thanks for posting this. >> >> I have been waiting for some time to see what sort of results were coming from 2x coverage. I am a little bit encouraged by the figures from FGC. >> >> For the R-L617 project we have 20+ participants who have tested YElite or BigY. So we have a good tree starting to take shape of known SNPs below L617. >> >> If the 2x coverage test "covers" about 14,000,000 bases of Y, it might be too thinly covered to "confidently" call SNPs, as many of these bases will only be covered once. But in my case, I have a "work in progress" tree for mutations below L617, so reading the 2x coverage raw data might enable me to pick up mutations which are reported in raw data, but not reported more than once to enable FGC to call them confidently as a new SNP. >> >> My feeling is that in my case, where I have the advantage of a working SNP tree to compare to, it might be cost effective for me to extract benefit from the 2x coverage test. The area covered at least once by a 2x coverage test is more than half the area covered by YElite it seems. So if I can see matches to known L617 downstream and can call them, even at only 50% certainty, I should be able to tentatively place L617s into known branches. >> >> Several branches have 20+ known SNPS, so I only need one reliable call, or several less reliable calls of some of the 20+ branch SNPs to assign a tester to a branch, at least tentatively. Often there is already other forms of evidence pointing to a branch, so if it is corroborated to a degree by data from 2x coverage tests, it is a step forward. If in doubt, a SNP could be verified from single SNP testing. >> >> I think that I just need to have a few L617s tested on the 2x test to see how it works out in practice in my case. I feel optimistic. Although I am working on a SNP tree below L617, several haplogroup projects have similar type SNP trees building, so they might also get benefit. Cost of testing is always a challenge, so even if a 2x test is cutting corners a bit, it still might enable test to be done which otherwise might not be possible. >> >> John. >> >> Sent from my iPad >> >>> On 6/01/2016, at 9:32 am, Tim Janzen via <genealogy-dna@rootsweb.com> wrote: >>> >>> Dear Atanas, >>> Justin Loe from FullGenomes just posted the information below on >>> another list: >>> >>> "As mentioned earlier, these are our beta results for 1x coverage: >>> >>> Mapped Y coverage >>> 30x 22,856,938 >>> 10x 22,025,697 >>> 4x 17,678,170 >>> 2x 13,755,442 >>> >>> Average Callable Loci >>> 30x 14,558,001 >>> 10x 8,046,540 >>> 4x 1,050,996 >>> 2x 349,397 >>> >>> Y Elite 2.0: >>> 14,000,000 Callable Loci approximately on average" >>> >>> This helps provide clearer data for your last question than I was able to do >>> in my earlier response. It thus appears that one needs to order at least >>> the 30x whole genome sequence from FullGenomes to get the same number of >>> callable Y chromosome loci as you can get from the Y Elite 2.0 test. >>> Sincerely, >>> Tim Janzen >>> >>> >>> -----Original Message----- >>> From: genealogy-dna-bounces@rootsweb.com >>> [mailto:genealogy-dna-bounces@rootsweb.com] On Behalf Of Atanas Kumbarov via >>> Sent: Tuesday, January 5, 2016 8:59 AM >>> To: genealogy-dna@rootsweb.com >>> Subject: [DNA] Full Genomes Corporation tests >>> >>> I have several questions about their tests: >>> >>> 1. I wonder how useful 2x results can be? >>> 2. What can be done with a FGS? >>> 3. Is it possible to extract usable data for GedMatch from FGS *in an easy >>> way*? >>> 4. How well is the Y-chromosome covered? >>> >>> Best regards, >>> Atanas Kumbarov >>> >>> >>> ------------------------------- >>> To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message >> >> ------------------------------- >> To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message > > ------------------------------- > To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

I have exactly the same idea. If you have a tree to follow, you don't need that many reads at a given position. But I think that it will be better if FGC designs a Y-chromosome only test at 5x instead of WGS test at 2x with the same price tag (around $250). The increase of depth of coverage could be compensated by the decrease of sequenced locis (the Y-chromosome only). 5x is sufficient - the 1000GP had 5x to 7x coverage and never the less we see huge 1000GP dominated segments of the YFull tree like this one http://yfull.com/tree/R-L657/ If such a test was offered, it could gain a lot of popularity. Best regards, Atanas Kumbarov On 05/01/16 23:37, AJ Marsh via wrote: > Tim, > > Many thanks for posting this. > > I have been waiting for some time to see what sort of results were coming from 2x coverage. I am a little bit encouraged by the figures from FGC. > > For the R-L617 project we have 20+ participants who have tested YElite or BigY. So we have a good tree starting to take shape of known SNPs below L617. > > If the 2x coverage test "covers" about 14,000,000 bases of Y, it might be too thinly covered to "confidently" call SNPs, as many of these bases will only be covered once. But in my case, I have a "work in progress" tree for mutations below L617, so reading the 2x coverage raw data might enable me to pick up mutations which are reported in raw data, but not reported more than once to enable FGC to call them confidently as a new SNP. > > My feeling is that in my case, where I have the advantage of a working SNP tree to compare to, it might be cost effective for me to extract benefit from the 2x coverage test. The area covered at least once by a 2x coverage test is more than half the area covered by YElite it seems. So if I can see matches to known L617 downstream and can call them, even at only 50% certainty, I should be able to tentatively place L617s into known branches. > > Several branches have 20+ known SNPS, so I only need one reliable call, or several less reliable calls of some of the 20+ branch SNPs to assign a tester to a branch, at least tentatively. Often there is already other forms of evidence pointing to a branch, so if it is corroborated to a degree by data from 2x coverage tests, it is a step forward. If in doubt, a SNP could be verified from single SNP testing. > > I think that I just need to have a few L617s tested on the 2x test to see how it works out in practice in my case. I feel optimistic. Although I am working on a SNP tree below L617, several haplogroup projects have similar type SNP trees building, so they might also get benefit. Cost of testing is always a challenge, so even if a 2x test is cutting corners a bit, it still might enable test to be done which otherwise might not be possible. > > John. > > Sent from my iPad > >> On 6/01/2016, at 9:32 am, Tim Janzen via <genealogy-dna@rootsweb.com> wrote: >> >> Dear Atanas, >> Justin Loe from FullGenomes just posted the information below on >> another list: >> >> "As mentioned earlier, these are our beta results for 1x coverage: >> >> Mapped Y coverage >> 30x 22,856,938 >> 10x 22,025,697 >> 4x 17,678,170 >> 2x 13,755,442 >> >> Average Callable Loci >> 30x 14,558,001 >> 10x 8,046,540 >> 4x 1,050,996 >> 2x 349,397 >> >> Y Elite 2.0: >> 14,000,000 Callable Loci approximately on average" >> >> This helps provide clearer data for your last question than I was able to do >> in my earlier response. It thus appears that one needs to order at least >> the 30x whole genome sequence from FullGenomes to get the same number of >> callable Y chromosome loci as you can get from the Y Elite 2.0 test. >> Sincerely, >> Tim Janzen >> >> >> -----Original Message----- >> From: genealogy-dna-bounces@rootsweb.com >> [mailto:genealogy-dna-bounces@rootsweb.com] On Behalf Of Atanas Kumbarov via >> Sent: Tuesday, January 5, 2016 8:59 AM >> To: genealogy-dna@rootsweb.com >> Subject: [DNA] Full Genomes Corporation tests >> >> I have several questions about their tests: >> >> 1. I wonder how useful 2x results can be? >> 2. What can be done with a FGS? >> 3. Is it possible to extract usable data for GedMatch from FGS *in an easy >> way*? >> 4. How well is the Y-chromosome covered? >> >> Best regards, >> Atanas Kumbarov >> >> >> ------------------------------- >> To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message > > ------------------------------- > To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

I had not heard or thought about this concept properly, before I heard it from Thomas in a separate email about a week ago. I guess with the right tools it should enable cross-matches onto the X-Chromosome to be ruled out, but I start to get out of my depth here. Everything, long term, is going WGS - regulation permitting. I guess we would still only want the Y-DNA data out of that? At least with WGS you know there is nowhere else left to go in future! Brian -----Original Message----- From: genealogy-dna-bounces@rootsweb.com [mailto:genealogy-dna-bounces@rootsweb.com] On Behalf Of Thomas Krahn via Sent: 06 January 2016 00:07 To: genealogy-dna@rootsweb.com Subject: Re: [DNA] Full Genomes Corporation Tests Atanas The largest cost factor for Y chromosome tests is not the sequencing, but the enrichment procedure. With enrichment the price will never drop far below $400, so you might as well sequence with sufficient coverage. On the long run there is no future for Big Y and FGCs Y tests since the WGS tests keep dropping in the price, but Y tests don't. Thomas

Good observations AJ. In the link I gave above to my Wiki NGS page the so far known stats seem to confirm your feeling also to me ;-) We have two 2x just ordered to see what they can provide. Wang, Wei et al 2011 <http://dx.doi.org/10.1038/srep00055> analysis suggests 3x is considerably better then 2x (the biggest coverage increase) when looking at low-coverage NGS. So I would like to see how much this could apply to the NGS lab used by FGC. Mind that you can upgrade later the FGC WGS tests to higher coverage. Justin is regularly posting in http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=130677&viewfull=1#post130677 Also I find the WGS very interesting for men who have not done mt or autosomal testing so far. On Tue, Jan 5, 2016 at 11:37 PM, AJ Marsh via <genealogy-dna@rootsweb.com> wrote: > Tim, > > Many thanks for posting this. > > I have been waiting for some time to see what sort of results were coming > from 2x coverage. I am a little bit encouraged by the figures from FGC. > > For the R-L617 project we have 20+ participants who have tested YElite or > BigY. So we have a good tree starting to take shape of known SNPs below > L617. > > If the 2x coverage test "covers" about 14,000,000 bases of Y, it might be > too thinly covered to "confidently" call SNPs, as many of these bases will > only be covered once. But in my case, I have a "work in progress" tree for > mutations below L617, so reading the 2x coverage raw data might enable me > to pick up mutations which are reported in raw data, but not reported more > than once to enable FGC to call them confidently as a new SNP. > > My feeling is that in my case, where I have the advantage of a working SNP > tree to compare to, it might be cost effective for me to extract benefit > from the 2x coverage test. The area covered at least once by a 2x coverage > test is more than half the area covered by YElite it seems. So if I can > see matches to known L617 downstream and can call them, even at only 50% > certainty, I should be able to tentatively place L617s into known branches. > > Several branches have 20+ known SNPS, so I only need one reliable call, or > several less reliable calls of some of the 20+ branch SNPs to assign a > tester to a branch, at least tentatively. Often there is already other > forms of evidence pointing to a branch, so if it is corroborated to a > degree by data from 2x coverage tests, it is a step forward. If in doubt, > a SNP could be verified from single SNP testing. > > I think that I just need to have a few L617s tested on the 2x test to see > how it works out in practice in my case. I feel optimistic. Although I am > working on a SNP tree below L617, several haplogroup projects have similar > type SNP trees building, so they might also get benefit. Cost of testing > is always a challenge, so even if a 2x test is cutting corners a bit, it > still might enable test to be done which otherwise might not be possible. > > John. > > Sent from my iPad > > > On 6/01/2016, at 9:32 am, Tim Janzen via <genealogy-dna@rootsweb.com> > wrote: > > > > Dear Atanas, > > Justin Loe from FullGenomes just posted the information below on > > another list: > > > > "As mentioned earlier, these are our beta results for 1x coverage: > > > > Mapped Y coverage > > 30x 22,856,938 > > 10x 22,025,697 > > 4x 17,678,170 > > 2x 13,755,442 > > > > Average Callable Loci > > 30x 14,558,001 > > 10x 8,046,540 > > 4x 1,050,996 > > 2x 349,397 > > > > Y Elite 2.0: > > 14,000,000 Callable Loci approximately on average" > > > > This helps provide clearer data for your last question than I was able > to do > > in my earlier response. It thus appears that one needs to order at least > > the 30x whole genome sequence from FullGenomes to get the same number of > > callable Y chromosome loci as you can get from the Y Elite 2.0 test. > > Sincerely, > > Tim Janzen > > > > > > -----Original Message----- > > From: genealogy-dna-bounces@rootsweb.com > > [mailto:genealogy-dna-bounces@rootsweb.com] On Behalf Of Atanas > Kumbarov via > > Sent: Tuesday, January 5, 2016 8:59 AM > > To: genealogy-dna@rootsweb.com > > Subject: [DNA] Full Genomes Corporation tests > > > > I have several questions about their tests: > > > > 1. I wonder how useful 2x results can be? > > 2. What can be done with a FGS? > > 3. Is it possible to extract usable data for GedMatch from FGS *in an > easy > > way*? > > 4. How well is the Y-chromosome covered? > > > > Best regards, > > Atanas Kumbarov > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to > GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message >

Thanks Tim! That is not economically feasible for me. The 30x test is quite expensive and I am interested in the Y-chromosome only. I wish there was a scaled down version of Y Elite or Big Y at a more acceptable price. -- Best regards, Atanas Kumbarov http://dna.kumbarov.com/ On 2016-01-05 21:32, Tim Janzen via wrote: > Dear Atanas, > Justin Loe from FullGenomes just posted the information below on > another list: > > "As mentioned earlier, these are our beta results for 1x coverage: > > Mapped Y coverage > 30x 22,856,938 > 10x 22,025,697 > 4x 17,678,170 > 2x 13,755,442 > > Average Callable Loci > 30x 14,558,001 > 10x 8,046,540 > 4x 1,050,996 > 2x 349,397 > > Y Elite 2.0: > 14,000,000 Callable Loci approximately on average" > > This helps provide clearer data for your last question than I was able to do > in my earlier response. It thus appears that one needs to order at least > the 30x whole genome sequence from FullGenomes to get the same number of > callable Y chromosome loci as you can get from the Y Elite 2.0 test. > Sincerely, > Tim Janzen > > > -----Original Message----- > From: genealogy-dna-bounces@rootsweb.com > [mailto:genealogy-dna-bounces@rootsweb.com] On Behalf Of Atanas Kumbarov via > Sent: Tuesday, January 5, 2016 8:59 AM > To: genealogy-dna@rootsweb.com > Subject: [DNA] Full Genomes Corporation tests > > I have several questions about their tests: > > 1. I wonder how useful 2x results can be? > 2. What can be done with a FGS? > 3. Is it possible to extract usable data for GedMatch from FGS *in an easy > way*? > 4. How well is the Y-chromosome covered? > > Best regards, > Atanas Kumbarov > > > ------------------------------- > To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

I am not taking part in round two but for those who are, following is a joker: Target SNP Available at YSEQ Y:14710648 (A/C) A7751 Y:19406232 (A/G) Z6297 Y:22181512 (C/G) Z32749 Y17712 CTS2840 Many of the V-series SNPs definitions are not available in YBrowse. And by the way Thomas, there still are unnamed SNPs in YBrowse: ChrY point snp 14724064 14724064 . + . ChrY point snp 8823895 8823895 . + . ChrY point snp 16455403 16455403 . + . ChrY point snp 22478402 22478402 . + . ChrY point snp 23156203 23156203 . + . ChrY point snp 18680627 18680627 . + . ChrY point snp 17491148 17491148 . + . ChrY point snp 21106558 21106558 . + . ChrY point snp 21429550 21429550 . + . Atanas Kumbarov On 05/01/16 19:11, Thomas Krahn via wrote: > FIRST RESULTS > > It seems like the R1b ht35 experts have made very good predictions, > however the final outcome is still open. > Here are the primary results as we have scored them today: > > Sample 3064 3804 > PF6332 failed C+ > PF6333 T+ T+ > Y7782 A+ A+ > Y7771 T+ T+ > V1684 G- failed > SK2076 G- G- > V3181 failed C- > V69 failed C- > Y18462 T- T- > Y18459 A- A- > PF6368 G- G- > Z30246 C- C- > L388 G- G- > M18 del- del- > U152 C- C- > > Unfortunately a few results failed at the first attempt. 3804 / V1684 > was likely a clogged capillary and the sample quality of 3064 is > generally a little bit lower. > I don't think we need to re-run PF6332 since it's implicit positive. > However V3181,V69 and V1684 are still interesting and we'll try to solve > them in a second sequencing attempt. > > To get your orientation I recommend to look at the following two trees: > > R1b-M343 (xM269) Y-DNA tree. v 2. November 25, 2015 (Sergey Malyshev 2015): > http://www.kumbarov.com/ht35/R1b-M343xM269%20Y-DNA%20tree_02_11_25_2015.pdf > > YFull Experimental YTree v3.18 (Vladimir Urasin 2016) > http://www.yfull.com/tree/R1b/ (top section, for Y18462 and Y18459) > > At the moment Vincent Tilroe is still in the lead since he was the first > who predicted the R1b-Y7771 level. > However, as you can see there are still plenty of phylo-equivalent SNPs > at the V3181 level that could be potentially positive. > The challenge is now to identify those SNPs out of them that could be > available at YSEQ. > I suggest you look them up in http://ybrowse.org and check what SNPs are > in the proximity. Then you look up those makers with the YSEQ search box > if they are available. I will also go through this list later today, but > of course you want to be faster than the other participants of this > challenge. > > More risk friendly participants may also check on the V1169, V69 and > Y18485 branches. > > Note that you still have time to pledge for Bonnie's A00 Cameroon > project http://experiment.com/a00west until Jan 6th and participate at > this challenge. > The rules can be found here: > http://www.yseq.net/R1bCameroonChallenge.html > > Good luck! > > Thomas > > > > On 01/04/2016 03:12 AM, Thomas Krahn via wrote: >> UPDATE UPDATE UPDATE UPDATE >> Thank you! We have had quite a few sponsored SNPs that we'll run >> tomorrow morning in the PCR. For simplicity we'll test the same SNPs for >> both samples now. The SNPs currently in processing are: >> V1684 >> L388 >> SK2076 >> Z30246 >> M18 >> U152 >> PF6333 >> PF6332 >> PF6292 >> Y7782 >> PF6368 >> V69 >> Y18462 >> Y18459 >> V3181 >> Y7771 >> Results are expected for Tuesday. Then you'll still have the chance to >> bet on markers further downstream from the SNPs that will (hopefully) be >> derived. Prepare yourself and do some research. If you want to win, you >> must be fast so that you're the first to pledge for a "terminal" SNP. >> Note that Wednesday is the last possibility to donate to the Cameroon >> A00 project. That's when the last entries for the challenge are accepted. >> http://experiment.com/a00west >> >> On 01/02/2016 10:46 PM, Thomas Krahn via wrote: >>> New Year Challenge: R1b in Cameroon >>> >>> Among our samples collected by Mathew on his last field trips we have >>> found the following two haplotypes: >>> >>> http://www.yseq.net/R1bCameroonChallenge.html >>> >>> Note that Y-GATA-H4 is in the NIST standard. If you want to compare them >>> to FTDNA you need to subtract 1. The haplogroup predictors clearly claim >>> 100% R1b. >>> >>> Now the question is: How did those two Y chromosomes find their way to >>> Sub-Saharan Africa? Could it be that some Europeans have left their >>> traces during colonization times? >>> >>> Well, if you're familiar with R1b in Europe, the haplotypes still look a >>> little bit strange. >>> >>> Also we keep finding R1b distribution maps that highlight an R1b >>> hot-spot in Northern Cameroon: >>> http://www.eupedia.com/europe/Haplogroup_R1b_Y-DNA.shtml >>> https://en.wikipedia.org/wiki/Haplogroup_R1b >>> >>> Wikipedia characterizes the hotspot in Northern Cameroon as R1b-V88. >>> However V88 is in a region of the Y chromosome that is 97.9% identical >>> to ChrX, so it wouldn't qualify for a stable marker according to the >>> newest ISOGG guidelines. I'd rather prefer to test stable known SNPs >>> that independently proof the association with the North African and >>> Arabic regions. >>> >>> I'd like to involve you, the R1b experts to use your knowledge and >>> experience to solve this mystery in a group effort. At the same time I'd >>> like to give the A00 Cameroon Research Project another push for donations. >>> >>> So here are the rules of the game: >>> >>> YSEQ will do free SNP tests on those 2 samples if you donate an equal >>> amount ($17.50 per SNP) to Bonnie Schrack's A00 Cameroon Research project. >>> >>> http://experiment.com/a00west >>> >>> When you make the donation, send Bonnie and myself an email >>> thomas@yseq.net, bonnieschrack@gmail.com with the marker you want to >>> sponsor and the YSEQ ID it should be tested for. The marker must be >>> available in the YSEQ catalog: >>> >>> https://www.yseq.net/ >>> >>> or at least we must have the primers in stock so that we can quickly >>> test them. Ask us for a distinct SNP if you're unsure. >>> >>> We will process the SNPs in the very next batch and release the results >>> to the public. You can keep sponsoring the next round when the results >>> come in. But note that the A00 Cameroon project deadline at >>> experiment.com is on January 6th! So there are only 5 days left to >>> submit your suggested SNP and the associated sample ID. >>> >>> The Prize: >>> >>> The researcher who submits the most downstream positive SNP first will >>> win a free Haplogroup Panel at YSEQ which he can use for a person of his >>> choice. Since there are two samples, there are two Haplogroup Panels >>> that you can win! >>> >>> Good luck and Happy New Year! >>> >>> Thomas >>> >>> > > ------------------------------- > To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message >

All: I have the Big Y, a Full Genomes WGS at 3X, and the imputed VCF from my V3 23andMe results at DNA.Land. Who can compare the Y DNA results in all three files? I'd like to have it compared to another R1a with similar result files. After seeing the numbers in the post by Justin quoted by Tim, I will be increasing the coverage of the WGS file from Full Genomes. Steven On Tue, Jan 5, 2016 at 7:07 PM, Thomas Krahn via <genealogy-dna@rootsweb.com > wrote: > Atanas, > > The largest cost factor for Y chromosome tests is not the sequencing, > but the enrichment procedure. > With enrichment the price will never drop far below $400, so you might > as well sequence with sufficient coverage. > > On the long run there is no future for BigY and FGCs Y tests since the > WGS tests keep dropping in the price, but Y tests don't. > > Thomas > > > On 01/06/2016 12:55 AM, Atanas Kumbarov via wrote: > > I have exactly the same idea. If you have a tree to follow, you don't > > need that many reads at a given position. But I think that it will be > > better if FGC designs a Y-chromosome only test at 5x instead of WGS test > > at 2x with the same price tag (around $250). The increase of depth of > > coverage could be compensated by the decrease of sequenced locis (the > > Y-chromosome only). > > > > 5x is sufficient - the 1000GP had 5x to 7x coverage and never the less > > we see huge 1000GP dominated segments of the YFull tree like this one > > http://yfull.com/tree/R-L657/ > > > > If such a test was offered, it could gain a lot of popularity. > > > > Best regards, > > Atanas Kumbarov > > > > > > > > On 05/01/16 23:37, AJ Marsh via wrote: > >> Tim, > >> > >> Many thanks for posting this. > >> > >> I have been waiting for some time to see what sort of results were > coming from 2x coverage. I am a little bit encouraged by the figures from > FGC. > >> > >> For the R-L617 project we have 20+ participants who have tested YElite > or BigY. So we have a good tree starting to take shape of known SNPs below > L617. > >> > >> If the 2x coverage test "covers" about 14,000,000 bases of Y, it might > be too thinly covered to "confidently" call SNPs, as many of these bases > will only be covered once. But in my case, I have a "work in progress" > tree for mutations below L617, so reading the 2x coverage raw data might > enable me to pick up mutations which are reported in raw data, but not > reported more than once to enable FGC to call them confidently as a new SNP. > >> > >> My feeling is that in my case, where I have the advantage of a working > SNP tree to compare to, it might be cost effective for me to extract > benefit from the 2x coverage test. The area covered at least once by a 2x > coverage test is more than half the area covered by YElite it seems. So if > I can see matches to known L617 downstream and can call them, even at only > 50% certainty, I should be able to tentatively place L617s into known > branches. > >> > >> Several branches have 20+ known SNPS, so I only need one reliable call, > or several less reliable calls of some of the 20+ branch SNPs to assign a > tester to a branch, at least tentatively. Often there is already other > forms of evidence pointing to a branch, so if it is corroborated to a > degree by data from 2x coverage tests, it is a step forward. If in doubt, > a SNP could be verified from single SNP testing. > >> > >> I think that I just need to have a few L617s tested on the 2x test to > see how it works out in practice in my case. I feel optimistic. Although > I am working on a SNP tree below L617, several haplogroup projects have > similar type SNP trees building, so they might also get benefit. Cost of > testing is always a challenge, so even if a 2x test is cutting corners a > bit, it still might enable test to be done which otherwise might not be > possible. > >> > >> John. > >> > >> Sent from my iPad > >> > >>> On 6/01/2016, at 9:32 am, Tim Janzen via <genealogy-dna@rootsweb.com> > wrote: > >>> > >>> Dear Atanas, > >>> Justin Loe from FullGenomes just posted the information below on > >>> another list: > >>> > >>> "As mentioned earlier, these are our beta results for 1x coverage: > >>> > >>> Mapped Y coverage > >>> 30x 22,856,938 > >>> 10x 22,025,697 > >>> 4x 17,678,170 > >>> 2x 13,755,442 > >>> > >>> Average Callable Loci > >>> 30x 14,558,001 > >>> 10x 8,046,540 > >>> 4x 1,050,996 > >>> 2x 349,397 > >>> > >>> Y Elite 2.0: > >>> 14,000,000 Callable Loci approximately on average" > >>> > >>> This helps provide clearer data for your last question than I was able > to do > >>> in my earlier response. It thus appears that one needs to order at > least > >>> the 30x whole genome sequence from FullGenomes to get the same number > of > >>> callable Y chromosome loci as you can get from the Y Elite 2.0 test. > >>> Sincerely, > >>> Tim Janzen > >>> > >>> > >>> -----Original Message----- > >>> From: genealogy-dna-bounces@rootsweb.com > >>> [mailto:genealogy-dna-bounces@rootsweb.com] On Behalf Of Atanas > Kumbarov via > >>> Sent: Tuesday, January 5, 2016 8:59 AM > >>> To: genealogy-dna@rootsweb.com > >>> Subject: [DNA] Full Genomes Corporation tests > >>> > >>> I have several questions about their tests: > >>> > >>> 1. I wonder how useful 2x results can be? > >>> 2. What can be done with a FGS? > >>> 3. Is it possible to extract usable data for GedMatch from FGS *in an > easy > >>> way*? > >>> 4. How well is the Y-chromosome covered? > >>> > >>> Best regards, > >>> Atanas Kumbarov > >>> > >>> > >>> ------------------------------- > >>> To unsubscribe from the list, please send an email to > GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message > >> > >> ------------------------------- > >> To unsubscribe from the list, please send an email to > GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to > GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message > -- Steven C. Perkins SCPerkins@gmail.com http://stevencperkins.com/ Indigenous Peoples' Rights http://intelligent-internet.info/law/ipr2.html Indigenous & Ethnic Minority Legal News http://iemlnews.blogspot.com/ Online Journal of Genetics and Genealogy http://jgg-online.blogspot.com/ S.C. Perkins' Genealogy Page http://stevencperkins.com/genealogy.html S.C. Perkins' Genealogy Blog http://scpgen.blogspot.com/

FIRST RESULTS It seems like the R1b ht35 experts have made very good predictions, however the final outcome is still open. Here are the primary results as we have scored them today: Sample 3064 3804 PF6332 failed C+ PF6333 T+ T+ Y7782 A+ A+ Y7771 T+ T+ V1684 G- failed SK2076 G- G- V3181 failed C- V69 failed C- Y18462 T- T- Y18459 A- A- PF6368 G- G- Z30246 C- C- L388 G- G- M18 del- del- U152 C- C- Unfortunately a few results failed at the first attempt. 3804 / V1684 was likely a clogged capillary and the sample quality of 3064 is generally a little bit lower. I don't think we need to re-run PF6332 since it's implicit positive. However V3181,V69 and V1684 are still interesting and we'll try to solve them in a second sequencing attempt. To get your orientation I recommend to look at the following two trees: R1b-M343 (xM269) Y-DNA tree. v 2. November 25, 2015 (Sergey Malyshev 2015): http://www.kumbarov.com/ht35/R1b-M343xM269%20Y-DNA%20tree_02_11_25_2015.pdf YFull Experimental YTree v3.18 (Vladimir Urasin 2016) http://www.yfull.com/tree/R1b/ (top section, for Y18462 and Y18459) At the moment Vincent Tilroe is still in the lead since he was the first who predicted the R1b-Y7771 level. However, as you can see there are still plenty of phylo-equivalent SNPs at the V3181 level that could be potentially positive. The challenge is now to identify those SNPs out of them that could be available at YSEQ. I suggest you look them up in http://ybrowse.org and check what SNPs are in the proximity. Then you look up those makers with the YSEQ search box if they are available. I will also go through this list later today, but of course you want to be faster than the other participants of this challenge. More risk friendly participants may also check on the V1169, V69 and Y18485 branches. Note that you still have time to pledge for Bonnie's A00 Cameroon project http://experiment.com/a00west until Jan 6th and participate at this challenge. The rules can be found here: http://www.yseq.net/R1bCameroonChallenge.html Good luck! Thomas On 01/04/2016 03:12 AM, Thomas Krahn via wrote: > UPDATE UPDATE UPDATE UPDATE > Thank you! We have had quite a few sponsored SNPs that we'll run > tomorrow morning in the PCR. For simplicity we'll test the same SNPs for > both samples now. The SNPs currently in processing are: > V1684 > L388 > SK2076 > Z30246 > M18 > U152 > PF6333 > PF6332 > PF6292 > Y7782 > PF6368 > V69 > Y18462 > Y18459 > V3181 > Y7771 > Results are expected for Tuesday. Then you'll still have the chance to > bet on markers further downstream from the SNPs that will (hopefully) be > derived. Prepare yourself and do some research. If you want to win, you > must be fast so that you're the first to pledge for a "terminal" SNP. > Note that Wednesday is the last possibility to donate to the Cameroon > A00 project. That's when the last entries for the challenge are accepted. > http://experiment.com/a00west > > On 01/02/2016 10:46 PM, Thomas Krahn via wrote: >> New Year Challenge: R1b in Cameroon >> >> Among our samples collected by Mathew on his last field trips we have >> found the following two haplotypes: >> >> http://www.yseq.net/R1bCameroonChallenge.html >> >> Note that Y-GATA-H4 is in the NIST standard. If you want to compare them >> to FTDNA you need to subtract 1. The haplogroup predictors clearly claim >> 100% R1b. >> >> Now the question is: How did those two Y chromosomes find their way to >> Sub-Saharan Africa? Could it be that some Europeans have left their >> traces during colonization times? >> >> Well, if you're familiar with R1b in Europe, the haplotypes still look a >> little bit strange. >> >> Also we keep finding R1b distribution maps that highlight an R1b >> hot-spot in Northern Cameroon: >> http://www.eupedia.com/europe/Haplogroup_R1b_Y-DNA.shtml >> https://en.wikipedia.org/wiki/Haplogroup_R1b >> >> Wikipedia characterizes the hotspot in Northern Cameroon as R1b-V88. >> However V88 is in a region of the Y chromosome that is 97.9% identical >> to ChrX, so it wouldn't qualify for a stable marker according to the >> newest ISOGG guidelines. I'd rather prefer to test stable known SNPs >> that independently proof the association with the North African and >> Arabic regions. >> >> I'd like to involve you, the R1b experts to use your knowledge and >> experience to solve this mystery in a group effort. At the same time I'd >> like to give the A00 Cameroon Research Project another push for donations. >> >> So here are the rules of the game: >> >> YSEQ will do free SNP tests on those 2 samples if you donate an equal >> amount ($17.50 per SNP) to Bonnie Schrack's A00 Cameroon Research project. >> >> http://experiment.com/a00west >> >> When you make the donation, send Bonnie and myself an email >> thomas@yseq.net, bonnieschrack@gmail.com with the marker you want to >> sponsor and the YSEQ ID it should be tested for. The marker must be >> available in the YSEQ catalog: >> >> https://www.yseq.net/ >> >> or at least we must have the primers in stock so that we can quickly >> test them. Ask us for a distinct SNP if you're unsure. >> >> We will process the SNPs in the very next batch and release the results >> to the public. You can keep sponsoring the next round when the results >> come in. But note that the A00 Cameroon project deadline at >> experiment.com is on January 6th! So there are only 5 days left to >> submit your suggested SNP and the associated sample ID. >> >> The Prize: >> >> The researcher who submits the most downstream positive SNP first will >> win a free Haplogroup Panel at YSEQ which he can use for a person of his >> choice. Since there are two samples, there are two Haplogroup Panels >> that you can win! >> >> Good luck and Happy New Year! >> >> Thomas >> >>

I just visited the FGC website and noticed that they offer some new tests: Whole Genome Sequencing 2x $280 Whole Genome Sequencing 4x $395 Whole Genome Sequencing 10x $725 Whole Genome Sequencing 15x $895 Whole Genome Sequencing 20x $1,200 Whole Genome Sequencing 30x $1,650 Ultimate 100x Whole Genome $5,350 Y Elite 2.0 Sequencing $775 I have several questions about their tests: 1. I wonder how useful 2x results can be? 2. What can be done with a FGS? 3. Is it possible to extract usable data for GedMatch from FGS *in an easy way*? 4. How well is the Y-chromosome covered? It will definitely make a lot of sense if they offered a test with the same width of coverage as the Y Elite but at a lesser depth. For example 10x would be twice as good as 1000 GP and if the price can be reduced to something like $250, it would make sense, especially if you run a private DNA project with many tests and limited funding. -- Best regards, Atanas Kumbarov http://dna.kumbarov.com/

List This new paper is a free download at: http://www.biorxiv.org/content/biorxiv/early/2015/12/23/035105.full.pdf "A protein truncating R179X variant in RNF186 confers protection against ulcerative colitis" Manuel A Rivas, et al. I cannot say this is the easiest paper to read (as it appears to have been written by committee !), but the paper discusses the relevance of Loss-of-Function SNPs (LoF). Is this relevant ? Well yes, as 23andMe has included 1,000s of this type of SNP in its specially commisioned V4 chip. However, this paper deals with rs36095412 which is NOT on the 23andMe chip. As for the paper itself, the researchers have shown (to their surprise) that the protein 'truncated' by the mutated SNP is expressed; and the people with the uncommon homozygous-recessive inheritance do not appear to have any particular problems. But whether one should accept that the truncated protein protects against inflammatory bowel disease to a significant degree would seem a little uncertain. Overall, this is an interesting and informative paper, not perhaps because of its findings, but more in its explanation of why 23andMe appears to be getting considerable funding from the pharmaceutical industry. And how each LoF SNP will have to be studied one-by-one. Ian ---------------------------------------------- Abstract We conducted a search for protein truncating variants conferring protection against inflammatory bowel disease exploiting knowledge of common variants associated with the same disease. We found that a protein truncating variant (rs36095412, p.R179X, genotyped in 11,148 ulcerative colitis patients and 295,446 controls, MAF = up to 0.78%) in RNF186, a single-exon ring finger E3 ligase with strong colonic expression, protects against ulcerative colitis (overall P = 6.89×10-7, odds ratio (OR) = 0.30). We further demonstrate that the truncated protein is expressed, suggesting the protective mechanism may reside in the loss of an interaction or function via mislocalization or loss of an essential protein element.

Dear John, If you get additional relatives on the paternal line of descent to test even at 2x the shared SNPs downstream from L617 become more valuable and more likely to be true SNPs than SNPs found only in one person's 2x results. A reasonable strategy might be to test two 1st, 2nd, or 3rd cousins who share the same surname at 2x and then test additional L617+ males who have different surnames as well. Sincerely, Tim -----Original Message----- From: AJ Marsh [mailto:ajmarshnz@gmail.com] Sent: Tuesday, January 5, 2016 2:38 PM To: Tim Janzen; genealogy-dna@rootsweb.com Subject: Re: [DNA] Full Genomes Corporation tests Tim, Many thanks for posting this. I have been waiting for some time to see what sort of results were coming from 2x coverage. I am a little bit encouraged by the figures from FGC. For the R-L617 project we have 20+ participants who have tested YElite or BigY. So we have a good tree starting to take shape of known SNPs below L617. If the 2x coverage test "covers" about 14,000,000 bases of Y, it might be too thinly covered to "confidently" call SNPs, as many of these bases will only be covered once. But in my case, I have a "work in progress" tree for mutations below L617, so reading the 2x coverage raw data might enable me to pick up mutations which are reported in raw data, but not reported more than once to enable FGC to call them confidently as a new SNP. My feeling is that in my case, where I have the advantage of a working SNP tree to compare to, it might be cost effective for me to extract benefit from the 2x coverage test. The area covered at least once by a 2x coverage test is more than half the area covered by YElite it seems. So if I can see matches to known L617 downstream and can call them, even at only 50% certainty, I should be able to tentatively place L617s into known branches. Several branches have 20+ known SNPS, so I only need one reliable call, or several less reliable calls of some of the 20+ branch SNPs to assign a tester to a branch, at least tentatively. Often there is already other forms of evidence pointing to a branch, so if it is corroborated to a degree by data from 2x coverage tests, it is a step forward. If in doubt, a SNP could be verified from single SNP testing. I think that I just need to have a few L617s tested on the 2x test to see how it works out in practice in my case. I feel optimistic. Although I am working on a SNP tree below L617, several haplogroup projects have similar type SNP trees building, so they might also get benefit. Cost of testing is always a challenge, so even if a 2x test is cutting corners a bit, it still might enable test to be done which otherwise might not be possible. John.

Dear Atanas, Justin Loe from FullGenomes just posted the information below on another list: "As mentioned earlier, these are our beta results for 1x coverage: Mapped Y coverage 30x 22,856,938 10x 22,025,697 4x 17,678,170 2x 13,755,442 Average Callable Loci 30x 14,558,001 10x 8,046,540 4x 1,050,996 2x 349,397 Y Elite 2.0: 14,000,000 Callable Loci approximately on average" This helps provide clearer data for your last question than I was able to do in my earlier response. It thus appears that one needs to order at least the 30x whole genome sequence from FullGenomes to get the same number of callable Y chromosome loci as you can get from the Y Elite 2.0 test. Sincerely, Tim Janzen -----Original Message----- From: genealogy-dna-bounces@rootsweb.com [mailto:genealogy-dna-bounces@rootsweb.com] On Behalf Of Atanas Kumbarov via Sent: Tuesday, January 5, 2016 8:59 AM To: genealogy-dna@rootsweb.com Subject: [DNA] Full Genomes Corporation tests I have several questions about their tests: 1. I wonder how useful 2x results can be? 2. What can be done with a FGS? 3. Is it possible to extract usable data for GedMatch from FGS *in an easy way*? 4. How well is the Y-chromosome covered? Best regards, Atanas Kumbarov

I would think that if two relatives both took a FGS, that it just *might* possibly find new changes that the other tests overlook. I thought that the existing atDNA tests look at just the frequently changing spots. But what if you and a relative share a rare change? -----Original Message----- From: Atanas Kumbarov via <genealogy-dna@rootsweb.com> To: genealogy-dna <genealogy-dna@rootsweb.com> Sent: Tue, Jan 5, 2016 8:59 am Subject: [DNA] Full Genomes Corporation tests I just visited the FGC website and noticed that they offer some new tests: Whole Genome Sequencing 2x $280 Whole Genome Sequencing 4x $395 Whole Genome Sequencing 10x $725 Whole Genome Sequencing 15x $895 Whole Genome Sequencing 20x $1,200 Whole Genome Sequencing 30x $1,650 Ultimate 100x Whole Genome $5,350 Y Elite 2.0 Sequencing $775 I have several questions about their tests: 1. I wonder how useful 2x results can be? 2. What can be done with a FGS? 3. Is it possible to extract usable data for GedMatch from FGS *in an easy way*? 4. How well is the Y-chromosome covered? It will definitely make a lot of sense if they offered a test with the same width of coverage as the Y Elite but at a lesser depth. For example 10x would be twice as good as 1000 GP and if the price can be reduced to something like $250, it would make sense, especially if you run a private DNA project with many tests and limited funding. -- Best regards, Atanas Kumbarov http://dna.kumbarov.com/ ------------------------------- To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

Dear Atanas, I think you raise some good questions. The way I have always thought about whole genome sequencing is that it will complement the current data we are getting from SNP arrays such as the Illumina Omni Express chip. I see whole genome sequencing discovering autosomal variants (SNPs, indels, etc.) that provide additional insight from both a genealogical and/or an anthropological perspective above and beyond what can be learned from phased haplotypes from SNP arrays. I think that we are a ways from using new autosomal variants found in whole genome sequencing data in a meaningful way genealogically and/or an anthropologically. We need a means to readily cluster everyone who has a specific autosomal variant as found during whole genome sequencing. A search could then be undertaken for shared genealogical connections or shared ancestral locations or populations. All of this will need to be done in the context of a large genetic database in which phased autosomal haplotypes are linked to specific ancestors in an integrated worldwide family tree. The accuracy of the results is also highly important. The advantage of doing 20x or higher sequencing is that you can be much more certain about the accuracy of the sequence data than you can with 2x data. I haven't generated a specific SNP panel dataset such as the data found on the Illumina Omni Express chip from whole genome sequencing data before, but I am sure it can be done by people who are experienced at working with whole genome sequencing data. I believe that the coverage on the Y with Full Genomes' whole genome sequencing is the same coverage that you get with the Y Elite 2.0 test. Someone from Full Genomes should be able to verify that. I would like to point out that even Full Genomes' Ultimate 100x Whole Genome is not the Holy Grail in whole genome sequencing because the data is unphased. What we are still waiting for is a company to generate phased whole genome sequencing data with an extremely high level of accuracy. I know that companies are working on this, but so far it has been challenging for the companies to do. Sincerely, Tim Janzen -----Original Message----- From: genealogy-dna-bounces@rootsweb.com [mailto:genealogy-dna-bounces@rootsweb.com] On Behalf Of Atanas Kumbarov via Sent: Tuesday, January 5, 2016 8:59 AM To: genealogy-dna@rootsweb.com Subject: [DNA] Full Genomes Corporation tests I have several questions about their tests: 1. I wonder how useful 2x results can be? 2. What can be done with a FGS? 3. Is it possible to extract usable data for GedMatch from FGS *in an easy way*? 4. How well is the Y-chromosome covered? Best regards, Atanas Kumbarov

UPDATE UPDATE UPDATE UPDATE Thank you! We have had quite a few sponsored SNPs that we'll run tomorrow morning in the PCR. For simplicity we'll test the same SNPs for both samples now. The SNPs currently in processing are: V1684 L388 SK2076 Z30246 M18 U152 PF6333 PF6332 PF6292 Y7782 PF6368 V69 Y18462 Y18459 V3181 Y7771 Results are expected for Tuesday. Then you'll still have the chance to bet on markers further downstream from the SNPs that will (hopefully) be derived. Prepare yourself and do some research. If you want to win, you must be fast so that you're the first to pledge for a "terminal" SNP. Note that Wednesday is the last possibility to donate to the Cameroon A00 project. That's when the last entries for the challenge are accepted. http://experiment.com/a00west <https://l.facebook.com/l.php?u=http%3A%2F%2Fexperiment.com%2Fa00west&h=_AQG8xchr> On 01/02/2016 10:46 PM, Thomas Krahn via wrote: > New Year Challenge: R1b in Cameroon > > Among our samples collected by Mathew on his last field trips we have > found the following two haplotypes: > > http://www.yseq.net/R1bCameroonChallenge.html > > Note that Y-GATA-H4 is in the NIST standard. If you want to compare them > to FTDNA you need to subtract 1. The haplogroup predictors clearly claim > 100% R1b. > > Now the question is: How did those two Y chromosomes find their way to > Sub-Saharan Africa? Could it be that some Europeans have left their > traces during colonization times? > > Well, if you're familiar with R1b in Europe, the haplotypes still look a > little bit strange. > > Also we keep finding R1b distribution maps that highlight an R1b > hot-spot in Northern Cameroon: > http://www.eupedia.com/europe/Haplogroup_R1b_Y-DNA.shtml > https://en.wikipedia.org/wiki/Haplogroup_R1b > > Wikipedia characterizes the hotspot in Northern Cameroon as R1b-V88. > However V88 is in a region of the Y chromosome that is 97.9% identical > to ChrX, so it wouldn't qualify for a stable marker according to the > newest ISOGG guidelines. I'd rather prefer to test stable known SNPs > that independently proof the association with the North African and > Arabic regions. > > I'd like to involve you, the R1b experts to use your knowledge and > experience to solve this mystery in a group effort. At the same time I'd > like to give the A00 Cameroon Research Project another push for donations. > > So here are the rules of the game: > > YSEQ will do free SNP tests on those 2 samples if you donate an equal > amount ($17.50 per SNP) to Bonnie Schrack's A00 Cameroon Research project. > > http://experiment.com/a00west > > When you make the donation, send Bonnie and myself an email > thomas@yseq.net, bonnieschrack@gmail.com with the marker you want to > sponsor and the YSEQ ID it should be tested for. The marker must be > available in the YSEQ catalog: > > https://www.yseq.net/ > > or at least we must have the primers in stock so that we can quickly > test them. Ask us for a distinct SNP if you're unsure. > > We will process the SNPs in the very next batch and release the results > to the public. You can keep sponsoring the next round when the results > come in. But note that the A00 Cameroon project deadline at > experiment.com is on January 6th! So there are only 5 days left to > submit your suggested SNP and the associated sample ID. > > The Prize: > > The researcher who submits the most downstream positive SNP first will > win a free Haplogroup Panel at YSEQ which he can use for a person of his > choice. Since there are two samples, there are two Haplogroup Panels > that you can win! > > Good luck and Happy New Year! > > Thomas > > ------------------------------- > To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

Hi Bonnie, I am not aware of the R1b (xM269) SNPs status wrt ISOGG but I am responsible for submitting R1b-M269 (P312-, U106-) SNPs to ISOGG and I do submit all SNPs for which we have enough Sanger sequencing data. Submitting SNPs with NGS data as a proof has been problematic since I don't have the BAM files from FTDNA and FGC users and because of the tight requirements. -- Best regards, Atanas Kumbarov http://dna.kumbarov.com/ On 2016-01-03 20:54, Bonnie Schrack wrote: > Great, Atanas, thanks! Sergey's tree is impressive. Do you have any > idea why so much of it is not included in the ISOGG tree? Has anyone > tried submitting the new branches? > > I've created a transposed tree based on Sergey's which I hope will be > helpful to Thomas and others. There is some ambiguity due to the fact > that not everyone is working together. Yfull doesn't include all the > 1K Genomes samples that Sergey does, among other things. He has been > able to split the tree in some new ways, which is great! > > It should be easy for Thomas to pick a SNP for you at the V88 level, > as there look to be about 70 already recognized. > > Bonnie > > On Sun, Jan 3, 2016 at 9:42 AM, Atanas Kumbarov > <social@dna.kumbarov.com <mailto:social@dna.kumbarov.com>> wrote: > > I increased my pledge by $20. I think that sample 3064 (at least) > is R1b-V88. You can test him for any SNP on the V88 level > according to Sergey's tree: > http://www.kumbarov.com/ht35/R1b-M343xM269%20Y-DNA%20tree_02_11_25_2015.pdf > > I had a hard time determining which of these SNPs you have primers > for. > > -- > Best regards, > Atanas Kumbarov > > http://dna.kumbarov.com/ > > > > > On 2016-01-02 22:46, Thomas Krahn via wrote: > > New Year Challenge: R1b in Cameroon > > Among our samples collected by Mathew on his last field trips > we have > found the following two haplotypes: > > http://www.yseq.net/R1bCameroonChallenge.html > > Note that Y-GATA-H4 is in the NIST standard. If you want to > compare them > to FTDNA you need to subtract 1. The haplogroup predictors > clearly claim > 100% R1b. > > Now the question is: How did those two Y chromosomes find > their way to > Sub-Saharan Africa? Could it be that some Europeans have left > their > traces during colonization times? > > Well, if you're familiar with R1b in Europe, the haplotypes > still look a > little bit strange. > > Also we keep finding R1b distribution maps that highlight an R1b > hot-spot in Northern Cameroon: > http://www.eupedia.com/europe/Haplogroup_R1b_Y-DNA.shtml > https://en.wikipedia.org/wiki/Haplogroup_R1b > > Wikipedia characterizes the hotspot in Northern Cameroon as > R1b-V88. > However V88 is in a region of the Y chromosome that is 97.9% > identical > to ChrX, so it wouldn't qualify for a stable marker according > to the > newest ISOGG guidelines. I'd rather prefer to test stable > known SNPs > that independently proof the association with the North > African and > Arabic regions. > > I'd like to involve you, the R1b experts to use your knowledge and > experience to solve this mystery in a group effort. At the > same time I'd > like to give the A00 Cameroon Research Project another push > for donations. > > So here are the rules of the game: > > YSEQ will do free SNP tests on those 2 samples if you donate > an equal > amount ($17.50 per SNP) to Bonnie Schrack's A00 Cameroon > Research project. > > http://experiment.com/a00west > > When you make the donation, send Bonnie and myself an email > thomas@yseq.net <mailto:thomas@yseq.net>, > bonnieschrack@gmail.com <mailto:bonnieschrack@gmail.com> with > the marker you want to > sponsor and the YSEQ ID it should be tested for. The marker > must be > available in the YSEQ catalog: > > https://www.yseq.net/ > > or at least we must have the primers in stock so that we can > quickly > test them. Ask us for a distinct SNP if you're unsure. > > We will process the SNPs in the very next batch and release > the results > to the public. You can keep sponsoring the next round when the > results > come in. But note that the A00 Cameroon project deadline at > experiment.com <http://experiment.com> is on January 6th! So > there are only 5 days left to > submit your suggested SNP and the associated sample ID. > > The Prize: > > The researcher who submits the most downstream positive SNP > first will > win a free Haplogroup Panel at YSEQ which he can use for a > person of his > choice. Since there are two samples, there are two Haplogroup > Panels > that you can win! > > Good luck and Happy New Year! > > Thomas > ------------------------------- > To unsubscribe from the list, please send an email to > GENEALOGY-DNA-request@rootsweb.com > <mailto:GENEALOGY-DNA-request@rootsweb.com> with the word > 'unsubscribe' without the quotes in the subject and the body > of the message > > >

Sam, I agree that full genome sequencing at birth will likely come at some stage.... sooner rather than later. What I have been wondering is how quickly will sophisticated DNA testing kill the hobby of Genealogy? Or can our hobby be killed? If our generation do our job properly, aided by future advances in computer technologies, we will end up with a tolerably complete family tree for the human race, at least for the last half millennium, leaving few mysteries for future genealogists to solve. Future generations will simply input their individual person ID into a tiny computer somehow interfaced with their body, and their past 30 generations of genealogy will spill out from some sort of world supercomputer come super net..... and somehow Ancestry will electronically get forwarded a fee. The Y line will come out complete for the past 500,000 years. If Sykes is still alive, he will have named every one of our ancestors, and the Mormons will have baptised them, every one of them. What will future genealogist have left to do? I guess a few hardy "real" genealogists will still be pawing through old records, and arguing about whether an ancestor born 800 years ago was born on a Tuesday or early Wednesday. Genealogist are a hardy breed. I expect they will reinvent a role for themselves doing something. John. Sent from my iPad > On 3/01/2016, at 4:20 pm, Sam Sloan via <genealogy-dna@rootsweb.com> wrote: > > It is inevitable that at the rate technology is advancing in this area, if > id just a question of time before everybody will know who their real > parents were, whether they want to or not. > It had been suggested that soon every child born will have a full genome > scan done at birth. The doctors will be looking for genetic defects but if > the husband had been cuckolded the doctors will know right away that he is > not the real father even if he suspects nothing. > Will this be a good thing?? > Not only that but anybody going in for any sort of routine medical checkup > will probably have a full genome scan too because the cost will be so low, > so anybody who asks will be told right away who their real parents are. > This is the future. There is no doubt this will happen. My question is how > long will it take for this brave new world to arrive. > I would say that within ten years the technology will be so advanced that > adoption searches will be obsolete. Just as nowadays the doctor will tell > you whether your coming baby will be male or female provided that you ask, > at some future date all you have to do is ask and the doctors or medical > researchers will be able to tell you who your real parents are or were. > How long will this take and will this be a good thing? > Sam Sloan > > ------------------------------- > To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

Once you have the basic family tree skeleton assembled from the basic vital records research and/or the DNA research, a good family historian puts the flesh on those bones by personal interviews, diaries, archives and newspaper research. We are the products of both our genetics and our environment (which science has shown influence and effect each other). Our personal and family realities have been influenced by war, economic cycles, natural disasters including celestial events and what would appear to be random events. In my family, the Great Depression resulted in both my mother and father being separated from their families and locating to another major city because of the difficult economic circumstances of their families. I consider the family that raised my mother from 8th grade until her marriage (1932-1940) my third set of "annexed" grandparents and part of our family. She had been babysitting for that family since she was 8 years old. [The term "annexed" was the result of the discussion by their children when in high school as how to introduce her to their friends. She wasn't formally adopted and their parents made sure my mother stayed close with and got back to her family and her family members cold visit her as well. Her "annexed" brothers and sisters were all Aunts and Uncles and their children cousins when I was growing up. Because of proximity and economics we saw more of them than our natural born grandparents, aunts, uncles and cousins. Everyone can decide the question personally but I accept both the biological reality and that of close affinity, whether legal adoption or not, based on the environmental circumstances that greatly influenced my sense of family. James Castellan Rose Valley, PA

I would agree with this, but I would add a word of warning too. Not mine, but written by Cliff Webb in his first edition of ‘My Ancestors Are Londoners, How Can I Find Out More About Them?’ I have posted this before, but it still rings true, especially in relation to Americans conducting research in British Archives. Any genealogical study needs careful planning and much reading in the home in advance, before plunging into Record Offices; where many precious hours can be wasted by inadequate preparation. I make no apology therefore for recommending the perusing (if not purchasing) of a large number of books and pamphlets [see references in book]. It is perplexing that many people, who accept that most skills and subjects cannot be learned without substantial study of written materials, expect to be able to conduct genealogical research without ever reading a text on the subject. Brian From: Karla Huebner [mailto:calypsospots@gmail.com] Sent: 03 January 2016 14:22 To: Brian Swann; genealogy-dna@rootsweb.com Subject: Re: [DNA] How long will is be before high technology puts us out of business I would suggest that although many more people have taken up genealogy in recent years due to the comparative ease of research (and for many, the chance to put together a tree without any skills or understanding of its accuracy), there will always be people who enjoy research and figuring out puzzles. Serious genealogists are that sort of person. As a university professor, I find that although most of my students regard research as a rather annoying part of gaining the BA or BFA, some are naturally inclined to enjoy it and some discover how much fun it can be and become very excited about their work. I think part of the task (for both professors and genealogists) is to convey how enjoyable and interesting (if also often frustrating) research can be. It is not for everyone, of course, but we want to awaken the interest in those who can enjoy and excel at it. In terms of genealogy, some will follow the science and others will follow the history, and some will do a bit of both. The main thing is to excite their interest and ensure that they learn the necessary skills. On Sun, Jan 3, 2016 at 7:45 AM, Brian Swann via <genealogy-dna@rootsweb.com> wrote: I will have been in this game for 50 years in 2017. So I have seen many, many people, projects and ideas come and go. And even though I know a moderate amount about DNA sequencing and analysis for family history, I am unlikely to get into genome readers or analysing my BAM files. Some people will, but I would be willing to bet those same people will not devote the time to generating the necessary datasets to analyse their own male surnames to get past where they are brick-walled. They have given up on that possibility and are getting their gratification elsewhere. Some will do it, of course, but they are the folk at the extreme end of the distribution curve. Brian

I increased my pledge by $20. I think that sample 3064 (at least) is R1b-V88. You can test him for any SNP on the V88 level according to Sergey's tree: http://www.kumbarov.com/ht35/R1b-M343xM269%20Y-DNA%20tree_02_11_25_2015.pdf I had a hard time determining which of these SNPs you have primers for. -- Best regards, Atanas Kumbarov http://dna.kumbarov.com/ On 2016-01-02 22:46, Thomas Krahn via wrote: > New Year Challenge: R1b in Cameroon > > Among our samples collected by Mathew on his last field trips we have > found the following two haplotypes: > > http://www.yseq.net/R1bCameroonChallenge.html > > Note that Y-GATA-H4 is in the NIST standard. If you want to compare them > to FTDNA you need to subtract 1. The haplogroup predictors clearly claim > 100% R1b. > > Now the question is: How did those two Y chromosomes find their way to > Sub-Saharan Africa? Could it be that some Europeans have left their > traces during colonization times? > > Well, if you're familiar with R1b in Europe, the haplotypes still look a > little bit strange. > > Also we keep finding R1b distribution maps that highlight an R1b > hot-spot in Northern Cameroon: > http://www.eupedia.com/europe/Haplogroup_R1b_Y-DNA.shtml > https://en.wikipedia.org/wiki/Haplogroup_R1b > > Wikipedia characterizes the hotspot in Northern Cameroon as R1b-V88. > However V88 is in a region of the Y chromosome that is 97.9% identical > to ChrX, so it wouldn't qualify for a stable marker according to the > newest ISOGG guidelines. I'd rather prefer to test stable known SNPs > that independently proof the association with the North African and > Arabic regions. > > I'd like to involve you, the R1b experts to use your knowledge and > experience to solve this mystery in a group effort. At the same time I'd > like to give the A00 Cameroon Research Project another push for donations. > > So here are the rules of the game: > > YSEQ will do free SNP tests on those 2 samples if you donate an equal > amount ($17.50 per SNP) to Bonnie Schrack's A00 Cameroon Research project. > > http://experiment.com/a00west > > When you make the donation, send Bonnie and myself an email > thomas@yseq.net, bonnieschrack@gmail.com with the marker you want to > sponsor and the YSEQ ID it should be tested for. The marker must be > available in the YSEQ catalog: > > https://www.yseq.net/ > > or at least we must have the primers in stock so that we can quickly > test them. Ask us for a distinct SNP if you're unsure. > > We will process the SNPs in the very next batch and release the results > to the public. You can keep sponsoring the next round when the results > come in. But note that the A00 Cameroon project deadline at > experiment.com is on January 6th! So there are only 5 days left to > submit your suggested SNP and the associated sample ID. > > The Prize: > > The researcher who submits the most downstream positive SNP first will > win a free Haplogroup Panel at YSEQ which he can use for a person of his > choice. Since there are two samples, there are two Haplogroup Panels > that you can win! > > Good luck and Happy New Year! > > Thomas > > ------------------------------- > To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message