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Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

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  • Charles Moore
    My thought is this, in terms of the mutual benefit for the group. With no tools to analyze 27 million Y positions, it seems to me that the idea would boil down
    Message 1 of 27 , Dec 1, 2012
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      My thought is this, in terms of the mutual benefit for the group.

      With no tools to analyze 27 million Y positions, it seems to me that the idea would boil down to trying to match one or the other of the two Z343 1000 Genomes testers.  In addition to the fact that those two guys match at Z343 and the otherwise untestable Z13, they also each have whatever number of singleton SNPs that the 1000 Genomes results show.  So they might each have say, 20, or whatever, that the other one doesn't have.

      So, we could simply go to your raw results at those 20 or whatever positions for the one guy, and the other 20 or whatever positions for the other guy, and see if you match either of them at any of those positions.  Since they don't match one another at any of the total about 40 positions, the chance that either of them would match you, would be slim.  So, it is a shot in the dark.

      If you do match one of them, then you have a new clade below Z343 shared by at least 2 people.  However, nobody else in the group can test the SNP unless Thomas makes it testable for the benefit of the tiny number of people below Z343 who might test it.  Hmmm.

      Of course, across the entire 27 million Y positions, you will have your own 20 or whatever singleton SNPs, but those won't benefit the group, and finding them would mean matching against the ancestral reference at all 27 million positions.  Good luck with that.

      Whenever whole genome testing becomes more affordable, a matching system will have to be set up similar to FF.  After gigabytes comes terabytes, then something called petabytes.  At the conference, they showed us how many petabytes FF takes to run.  I don't know what comes after petabytes or how many of those whatevers it would take to run the entire Y matching program, or what they might charge for the matching service.  It would spit out the distant cousins that you match at all but the last 20 or whatever singleton SNPs at on your SNP line of descent.  Then you could try to email them like with FF and go from there, but it would be a person to person thing.  The SNPs  would not be individually testable by others.  We aren't going to be able to maintain a Y tree with tens of thousands of SNPs, so the group effort will diminish after the initial hoopla.  

      Whole genome testing isn't an end unto itself, and the results are almost meaningless unless there is a system to run the comparison.  Then you match someone with most of the same SNPs and you email them and compare notes about your MDKA. That is how I would envision it.

      Ray and I suggested to Thomas that we should have the chance to discover new additional .x occurrences of SNPs otherwise found elsewhere in our Geno 2.0 tests, yes?  And of course, he said YES!  Then he said, "and when you do, YOU'RE ON YOUR OWN".

      Every year for the last 6 years, there have been rumors that whole genome testing for $1,000 will be available "next year".  We're not there yet.  Thomas charges $950 to test 400,000 out of 27 million possible testable Y positions, which remains a shot in the dark, which if it discovers anything, is usually a private SNP that nobody else matches.

      I'm all for progress of course, and I love this business, but the question is really exactly what Michael asks.  Whenever we eventually are able to test entire genomes for $1,000, how will we crunch the whatever comes after petabyte data, and what will be the mutual benefit?

      OK, well I'm supposed to be the off-the-scale highly intuitive "sixth sense" person in the group.  My friends know this about me, and they know I'm a fanatical genealogist and DNA guy.  So they all make fun of me by saying "Charles sees dead people".

      OK, fine, well that is the business we are in, peering in to the past to see our ancestors, and how we got here from there.  I need to learn more about FF from Tim and CeCe.  I haven't paid much attention to it, because I haven't had the time, and I don't have any close family left to test and do the type of FF matching that enabled CeCe to explain how it was that she knew that that DNA segment on Chromosome 5 came from her 3rd-great-grandmother Louise.  But whenever I think about whole genome testing for a thousand bucks, all I can "see" is another version of Family Finder.

      I'm sure it will be a good thing for people to be able to discover who their closest SNP based Y line matches are.  That is after all, essentially what we are trying to do with the sandbox SNPs and STRs.  It is the mutual benefit to the group aspect that Michael asked about that I am unable to "see".  How will the tree branch lines of descent be maintained? Etc.  Maybe Tim, or someone else, has some thoughts about how it will work.

      But certainly the 1000 Genomes tests have had a revolutionary effect on this group, and all for the better. But I'm not holding my breath waiting for the long-time false rumor about $1,000 genome testing to finally come true.  Meanwhile, we are going to plunge ahead, regardless, because it is fun to be explorers and treasure hunters, and to see the dead people whose DNA remains inside of us, and to gain whatever impression of them we can.  Forward >>>>

      Charles


      On Nov 30, 2012, at 7:32 PM, "Michael" <mgreg24@...> wrote:

       

      I received this ( http://dna-explained.com/2012/11/30/gene-by-gene-announces-landmark-dna-dtc-full-genome-sequence/  ) today and will shortly have the financial means to take up this offer if you good people who are far more o fay than myself are interested in crunching the data or see any potential value to the group in my pursuing this route for mutual benefit.

      cheers
      michael (z343)

    • Piero Sinclair
      David Carlisle, just thought I d mention I m Z346+, and DYS 568=10. I imagine I m negative for Z343 as those Sinclairs in our Caithness/Orkney cluster that
      Message 2 of 27 , Dec 1, 2012
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        David Carlisle, just thought I'd mention I'm Z346+, and DYS 568=10. I imagine I'm negative for Z343 as those Sinclairs in our Caithness/Orkney cluster that have been tested are negative.
        Cheers
        Piero 


        On Sat, Dec 1, 2012 at 6:14 AM, David Carlisle <davidcar801@...> wrote:
         

        If a full genome costs $5,500 for 23 chomosomes, then why doesn't a full Y test cost $5,500/23, or $239?  There is the issue of differing chromosome length, but then why isn't there a separate test?

        Wow, there's room for a lot of SNPs between 27,000,000 and 59,000,000.

        Back to the question of why it's good I subscribed to Geno 2.0, and that is because there are four other Z346ers taking the test, two of them with my DYS568 = 10 STR, so there is a chance of discovering a SNP that will put me with one or the other of those two, or finding a SNP that unites the three of us and further separates us from the Z343s.


        From: Tim Janzen <tjanzen@...>
        To: R1b1c_U106-S21@yahoogroups.com
        Sent: Friday, November 30, 2012 10:54 PM
        Subject: RE: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

         
        I have been thinking about the issue of complete Y sequencing for a long time.  This issue was also discussed during the WTY session I attended where Thomas Krahn spoke at the FTDNA conference.  I also talked to Thomas about it afterward as well.  Thirty times coverage is reasonably good for the Y, but not superb.  Not many people will be able to afford complete sequencing at its current price.  The new SNPs that are found through complete Y sequencing may not be readily placed on the FTDNA Y SNP menu.  It costs Thomas about $20 or so just for the primer for each new SNP that he places on the menu.  Some SNPs are challenging to make primers for.  Thomas could get bogged down designing primers, ordering primers, and getting them on the SNP menu.  Some of the new SNPs will be redundant SNPs that won’t help us in terms of placing more branches on the Y SNP tree.  There is still no reference sequence for the region between about 27,000,000 and 59,000,000 due to the fact that the vast majority of this region is high repetitive.  This region may hold SNPs, but until it can be sequenced through long read technology, it won’t be available for us.  In summary, we definitely want to go to complete Y sequencing, but there are still financial and practical hurtles to jump along the way.  In any case, I would strongly suggest that anyone who orders complete genome sequencing to make their Y sequence available for researchers in a public database like Genbank or place the sequence in the hands of serious Y SNP researchers.
        Tim Janzen
         
        From: R1b1c_U106-S21@yahoogroups.com [mailto:R1b1c_U106-S21@yahoogroups.com] On Behalf Of David Carlisle
        Sent: Friday, November 30, 2012 8:50 PM
        To: R1b1c_U106-S21@yahoogroups.com
        Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???
         
         
        Interesting question.  If you're in Z343 you're in a small group already, and I would question the value of dividing the group further -- in order to discover what?  I have asked myself the same question about Geno 2.0.  If we had 20 people in the group that were all going to take the full genome test, then the data to be crunched would be in comparing all the Y-chromosomes.  With just one person taking the test then any new markers discovered would be private until proven otherwise.  
         

        From: Michael <mgreg24@...>
        To: R1b1c_U106-S21@yahoogroups.com
        Sent: Friday, November 30, 2012 6:32 PM
        Subject: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???
         
         
        I received this ( http://dna-explained.com/2012/11/30/gene-by-gene-announces-landmark-dna-dtc-full-genome-sequence/  ) today and will shortly have the financial means to take up this offer if you good people who are far more o fay than myself are interested in crunching the data or see any potential value to the group in my pursuing this route for mutual benefit.
         
        cheers
        michael (z343)
         



      • Brian P. Swann
        Dear Tim, All I think the take-away message for family historians in all this – is that when they read in the news media about the huge advances in DNA
        Message 3 of 27 , Dec 1, 2012
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          Dear Tim, All

           

          I think the take-away message for family historians in all this – is that when they read in the news media about the huge advances in DNA sequencing and reduction of costs, etc. – all of that does not necessarily apply automatically in our field, especially the Y-DNA sequencing field.

           

          We all know that different chromosomes tell us different stories – and we now have four to think about [Y-DNA, mtDNA, atDNA and X-DNA].

           

          I usually say in talks I give that we are all benefitting from this sequencing revolution – which is of course true.  But it does not all automatically translate to the bottom line of utility in our particular case of Y-DNA.

           

          Y-DNA is unique amongst all the chromosomes – and has some unique sequencing challenges because the analytical methodology usually applied to the other chromosomes, its many repeat motifs, and the precision required for SNP analysis, do not make the standard rules applicable, as Tim has very elegantly described below.  Like him, I have thought about these issues over several years, having spent 20 years of my scientific life in and around bioanalytical laboratories.

           

          I just hope Oxford Nanopore Technology will give Complete Genomics a run for their money with the longer reads sequencing technology:

           

          http://www.nanoporetech.com/

           

          But I still have the feeling that it will be the precision of these new technologies that will still give us problems for what we want to do – and Oxford Nanopore are very cagy about how good their precision is, right now.  I don’t know the story with Complete Genomics – but it is one of the absolute key questions with these proposed new sequencing advances and their applicability to Y-DNA – we need very precise analytical methodology indeed.

           

          And Tim usually gets everything right – except for one trivial thing.  He always mis-spells Venter as Ventor!  Cardinal sin for any family historian!

           

          ------

           

          There is a one-day meeting of the Guild of One-Name Studies at Cheltenham in February 2013 on DNA [unfortunate timing, given WDYTYA is later in the same month, but that’s another story] – which is likely to be the best forum in the UK to gauge family historians’ perceptions over here in this general area.  Nearly all of them want it simple – and Geoff Swinfield, who is on the programme below, can easily dismiss all this stuff as irrelevant to the average, or even the not-so-average, family historian.  I have had several discussions with him over the years.

           

          Only when you get from the normal tree SNPs to the personalised SNPs per surname group will he be convinced otherwise.  And whatever analytical technology emerges from this Y-SNP analysis story – that is where it ultimately has to go, unless you are interested in the general population flows across geographical areas.  Please note the Guild want DNA simple – but I suspect Debbie will tell it the way that it is, at the end.

           

          http://www.one-name.org/Seminar_2013Feb_Cheltenham.html

           

          Brian

           

          From: R1b1c_U106-S21@yahoogroups.com [mailto:R1b1c_U106-S21@yahoogroups.com] On Behalf Of Tim Janzen
          Sent: 01 December 2012 06:52
          To: R1b1c_U106-S21@yahoogroups.com
          Subject: RE: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

           

           Dear David,

          Accurately sequencing the Y is a major challenge.  All of the FGS techniques that are popular now are using shotgun technology that involves short reads (100 to 200 BPs).  These reads overlap and are pieced together to create complete sequences for each of the chromosomes.  Generally speaking, you sequence the complete genome when you use these techniques.  Complete Genomics has plans to release its long read technology within the next year or so will reportedly allow reads up to 1000 BPs or more.  This will improve accuracy significantly.  Currently FGS technologies have about 1 error per 100,000 or so BPs.  We need higher accuracy than that for the Y.  Perhaps you will recall all of the false SNPs in Craig Ventor’s Y sequence.  He had about 5000 Y SNPs in his sequence, most of which were erroneous.  We don’t want that kind of data.  I think that Thomas is taking the right approach with the WTY where he is only using primers that he is sure give him highly accurate reads for the segments covered by the primers.  Below is the summary of Thomas’ presentation that I wrote during and shortly after the conference.  It explains some of the issues involved.  Thomas said you need to build a highly accurate reference library for the Y chromosome and apparently no one has done that for the Y yet.

          Sincerely,

          Tim Janzen

          There are 206 participants in the WTY who are in R1b.  62 are in haplogroup J.  ca 86 in haplogoup I.  A total of 963 novel Y SNPs have been found in the WTY thus far. The basic process uses two 384 well plates for WTY now with ca 400,000 BPs covered.  Previously they used smaller plates. There are some samples, particularly from Native Americans, that are older and are research samples that they don’t have good data for because the DNA isn’t all that good.

          They are thinking about doing 3 plates in the future, but plan to drop the first plate since this will allow the WTY project to more readily find new SNPs and yet keep the price lower than it would be otherwise.  What about next generation Y chromosome sequencing?  Many of the challenging sections of the Y that can’t be sequenced because it is highly repetitive.  In particular, the portion of the Y between ca 27,000,000 and 59,000,000 will be quite challenging to sequence because it is generally comprised of multiple 5 BP repeats. The next generation sequencer can sequence 10 times more DNA, but it more challenging to operate.  You have to have really high quality DNA to do next generation sequencing.

          Thomas did next gen sequencing on a haplogroup J sample and successfully sequenced about 6 million BPs.  There have been 1523 confirmed SNPs that are already on the tree that were in the haplogroup J sample.  Ca 1000 new SNPs that have been found with this sample alone.  It takes a week to work on this doing large scale Y chromosome sequencing with the 454 sequencing machine.  The sequence can cause artifacts.  A bubble on the chip caused a problem in certain region that wasn’t sequenced.  The two new MiSeq can sequence 10x as much as the 454 sequencer could do.  The two new Illumina HiSeq machines can sequence a complete genome sequence in three runs.  It is approximately 2000 x as efficient as using the primers to do WTY testing and 100 x as efficient as the 454 sequencer. You need to prepare a library and then enrich it to use the new machines.  There is also a lot of bioinformatic software that is needed to process the output from the sequencing.  Illumina has SamTools, which is a great command line tool set.  You can do comparisons between various sequences using this tool.  There is much higher coverage, but the segment lengths are only ca 200 bases.

          There are sections of the Y that closely match the X sequence.  There are regions within the X degenerate portions of the Y chromosome where there are no unique SNPs found only on the Y for 800 bases or more.  Thus, it can be very difficult to sequence portions of the Y that are X degenerate since you can’t tell whether you are sequencing the Y chromosome or the X chromosome if you are getting reads that are only 200 or so BPs in length.

          The Illumina software recently crashed as a result of doing large scale Y chromosome sequencing.  Illumina designed the assay for Thomas and he doesn’t know the background of the assays.  In all they submitted 1746 targets, comprising ca 19.9 MB of sequence and the designer generated 132, 179 probes, but 58,539 of these scores had under 0.1, which is an arbitrary cut-off for poor sequencing results.  Thomas thinks that 60,000 probes may actually be functional.  Thomas is trying to get 18 million bases of coverage on the Y chromosome.  However, the average candidate score was under .1, which is relatively poor coverage.

          From: R1b1c_U106-S21@yahoogroups.com [mailto:R1b1c_U106-S21@yahoogroups.com] On Behalf Of David Carlisle
          Sent: Friday, November 30, 2012 10:15 PM
          To: R1b1c_U106-S21@yahoogroups.com
          Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

          If a full genome costs $5,500 for 23 chomosomes, then why doesn't a full Y test cost $5,500/23, or $239?  There is the issue of differing chromosome length, but then why isn't there a separate test?

          Wow, there's room for a lot of SNPs between 27,000,000 and 59,000,000.

          Back to the question of why it's good I subscribed to Geno 2.0, and that is because there are four other Z346ers taking the test, two of them with my DYS568 = 10 STR, so there is a chance of discovering a SNP that will put me with one or the other of those two, or finding a SNP that unites the three of us and further separates us from the Z343s.

        • Brian P. Swann
          The future is rarely like the past, Charles. These problems of gigantic dataset comparisons will get resolved in the human genetics / disease front first. But
          Message 4 of 27 , Dec 1, 2012
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            The future is rarely like the past, Charles.

             

            These problems of gigantic dataset comparisons will get resolved in the human genetics / disease front first.  But it will probably mean the end of us citizen scientists doing meaningful data comparisons.

             

            At present with SNP comparisons and Sandboxes we can do this on Spreadsheets and an ISOGG Tree – but maybe with this data explosion, in the future we cannot.  And we will have lost something which some of us understood and enjoyed.  I think this is called progress – but that does not mean we necessarily enjoy it.

             

            Brian

             

            From: R1b1c_U106-S21@yahoogroups.com [mailto:R1b1c_U106-S21@yahoogroups.com] On Behalf Of Charles Moore
            Sent: 01 December 2012 09:39
            To: R1b1c_U106-S21@yahoogroups.com
            Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

             

            My thought is this, in terms of the mutual benefit for the group.

             

            With no tools to analyze 27 million Y positions, it seems to me that the idea would boil down to trying to match one or the other of the two Z343 1000 Genomes testers.  In addition to the fact that those two guys match at Z343 and the otherwise untestable Z13, they also each have whatever number of singleton SNPs that the 1000 Genomes results show.  So they might each have say, 20, or whatever, that the other one doesn't have.

             

            So, we could simply go to your raw results at those 20 or whatever positions for the one guy, and the other 20 or whatever positions for the other guy, and see if you match either of them at any of those positions.  Since they don't match one another at any of the total about 40 positions, the chance that either of them would match you, would be slim.  So, it is a shot in the dark.

             

            If you do match one of them, then you have a new clade below Z343 shared by at least 2 people.  However, nobody else in the group can test the SNP unless Thomas makes it testable for the benefit of the tiny number of people below Z343 who might test it.  Hmmm.

             

            Of course, across the entire 27 million Y positions, you will have your own 20 or whatever singleton SNPs, but those won't benefit the group, and finding them would mean matching against the ancestral reference at all 27 million positions.  Good luck with that.

             

            Whenever whole genome testing becomes more affordable, a matching system will have to be set up similar to FF.  After gigabytes comes terabytes, then something called petabytes.  At the conference, they showed us how many petabytes FF takes to run.  I don't know what comes after petabytes or how many of those whatevers it would take to run the entire Y matching program, or what they might charge for the matching service.  It would spit out the distant cousins that you match at all but the last 20 or whatever singleton SNPs at on your SNP line of descent.  Then you could try to email them like with FF and go from there, but it would be a person to person thing.  The SNPs would not be individually testable by others.  We aren't going to be able to maintain a Y tree with tens of thousands of SNPs, so the group effort will diminish after the initial hoopla.  

             

            Whole genome testing isn't an end unto itself, and the results are almost meaningless unless there is a system to run the comparison.  Then you match someone with most of the same SNPs and you email them and compare notes about your MDKA. That is how I would envision it.

             

            Ray and I suggested to Thomas that we should have the chance to discover new additional .x occurrences of SNPs otherwise found elsewhere in our Geno 2.0 tests, yes?  And of course, he said YES!  Then he said, "and when you do, YOU'RE ON YOUR OWN".

             

            Every year for the last 6 years, there have been rumors that whole genome testing for $1,000 will be available "next year".  We're not there yet.  Thomas charges $950 to test 400,000 out of 27 million possible testable Y positions, which remains a shot in the dark, which if it discovers anything, is usually a private SNP that nobody else matches.

             

            I'm all for progress of course, and I love this business, but the question is really exactly what Michael asks.  Whenever we eventually are able to test entire genomes for $1,000, how will we crunch the whatever comes after petabyte data, and what will be the mutual benefit?

             

            OK, well I'm supposed to be the off-the-scale highly intuitive "sixth sense" person in the group.  My friends know this about me, and they know I'm a fanatical genealogist and DNA guy.  So they all make fun of me by saying "Charles sees dead people".

             

            OK, fine, well that is the business we are in, peering in to the past to see our ancestors, and how we got here from there.  I need to learn more about FF from Tim and CeCe.  I haven't paid much attention to it, because I haven't had the time, and I don't have any close family left to test and do the type of FF matching that enabled CeCe to explain how it was that she knew that that DNA segment on Chromosome 5 came from her 3rd-great-grandmother Louise.  But whenever I think about whole genome testing for a thousand bucks, all I can "see" is another version of Family Finder.

             

            I'm sure it will be a good thing for people to be able to discover who their closest SNP based Y line matches are.  That is after all, essentially what we are trying to do with the sandbox SNPs and STRs.  It is the mutual benefit to the group aspect that Michael asked about that I am unable to "see".  How will the tree branch lines of descent be maintained? Etc.  Maybe Tim, or someone else, has some thoughts about how it will work.

             

            But certainly the 1000 Genomes tests have had a revolutionary effect on this group, and all for the better. But I'm not holding my breath waiting for the long-time false rumor about $1,000 genome testing to finally come true.  Meanwhile, we are going to plunge ahead, regardless, because it is fun to be explorers and treasure hunters, and to see the dead people whose DNA remains inside of us, and to gain whatever impression of them we can.  Forward >>>>


            Charles

             


            On Nov 30, 2012, at 7:32 PM, "Michael" <mgreg24@...> wrote:

             

            I received this ( http://dna-explained.com/2012/11/30/gene-by-gene-announces-landmark-dna-dtc-full-genome-sequence/  ) today and will shortly have the financial means to take up this offer if you good people who are far more o fay than myself are interested in crunching the data or see any potential value to the group in my pursuing this route for mutual benefit.

             

            cheers

            michael (z343)

          • Charles Moore
            I think that hits the proverbial be careful what we wish for nail on the head. Meanwhile, I think those who upgrade to 111 and test Geno 2.0, or if they are
            Message 5 of 27 , Dec 1, 2012
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              I think that hits the proverbial be careful what we wish for nail on the head.

              Meanwhile, I think those who upgrade to 111 and test Geno 2.0, or if they are apparently close to their terminal SNP, finish the job with individual SNP testing, will be better off.  Certainly in the short run over the next several years, and possibly in the long run.  Leadership matters.  The early bird gets the worm, etc.  But it is expensive, and people do have different objectives with all of this.

              I imagine that Tim may have a better idea of the future process whenever $1,000 genome testing gets here maybe a few years down the road.  But I honestly think that waiting is not a good strategy, and while we are waiting, we should be about our business....

              Charles


              On Dec 1, 2012, at 9:10 AM, "Brian P. Swann" <bps@...> wrote:

               

              The future is rarely like the past, Charles.

               

              These problems of gigantic dataset comparisons will get resolved in the human genetics / disease front first.  But it will probably mean the end of us citizen scientists doing meaningful data comparisons.

               

              At present with SNP comparisons and Sandboxes we can do this on Spreadsheets and an ISOGG Tree – but maybe with this data explosion, in the future we cannot.  And we will have lost something which some of us understood and enjoyed.  I think this is called progress – but that does not mean we necessarily enjoy it.

               

              Brian

               

            • rob sinclair
              Welcome to the 346+ club Piero, where we all sit and wait To: R1b1c_U106-S21@yahoogroups.com From: pierosinclair@gmail.com Date: Sat, 1 Dec 2012 09:45:20 +0000
              Message 6 of 27 , Dec 1, 2012
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                Welcome to the 346+ club Piero, where we all sit and wait 
                 

                To: R1b1c_U106-S21@yahoogroups.com
                From: pierosinclair@...
                Date: Sat, 1 Dec 2012 09:45:20 +0000
                Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                 
                David Carlisle, just thought I'd mention I'm Z346+, and DYS 568=10. I imagine I'm negative for Z343 as those Sinclairs in our Caithness/Orkney cluster that have been tested are negative.
                Cheers
                Piero 


                On Sat, Dec 1, 2012 at 6:14 AM, David Carlisle <davidcar801@...> wrote:
                 


                If a full genome costs $5,500 for 23 chomosomes, then why doesn't a full Y test cost $5,500/23, or $239?  There is the issue of differing chromosome length, but then why isn't there a separate test?

                Wow, there's room for a lot of SNPs between 27,000,000 and 59,000,000.

                Back to the question of why it's good I subscribed to Geno 2.0, and that is because there are four other Z346ers taking the test, two of them with my DYS568 = 10 STR, so there is a chance of discovering a SNP that will put me with one or the other of those two, or finding a SNP that unites the three of us and further separates us from the Z343s.


                From: Tim Janzen <tjanzen@...>
                To: R1b1c_U106-S21@yahoogroups.com
                Sent: Friday, November 30, 2012 10:54 PM
                Subject: RE: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                 
                I have been thinking about the issue of complete Y sequencing for a long time.  This issue was also discussed during the WTY session I attended where Thomas Krahn spoke at the FTDNA conference.  I also talked to Thomas about it afterward as well.  Thirty times coverage is reasonably good for the Y, but not superb.  Not many people will be able to afford complete sequencing at its current price.  The new SNPs that are found through complete Y sequencing may not be readily placed on the FTDNA Y SNP menu.  It costs Thomas about $20 or so just for the primer for each new SNP that he places on the menu.  Some SNPs are challenging to make primers for.  Thomas could get bogged down designing primers, ordering primers, and getting them on the SNP menu.  Some of the new SNPs will be redundant SNPs that won’t help us in terms of placing more branches on the Y SNP tree.  There is still no reference sequence for the region between about 27,000,000 and 59,000,000 due to the fact that the vast majority of this region is high repetitive.  This region may hold SNPs, but until it can be sequenced through long read technology, it won’t be available for us.  In summary, we definitely want to go to complete Y sequencing, but there are still financial and practical hurtles to jump along the way.  In any case, I would strongly suggest that anyone who orders complete genome sequencing to make their Y sequence available for researchers in a public database like Genbank or place the sequence in the hands of serious Y SNP researchers.
                Tim Janzen
                 
                From: R1b1c_U106-S21@yahoogroups.com [mailto:R1b1c_U106-S21@yahoogroups.com] On Behalf Of David Carlisle
                Sent: Friday, November 30, 2012 8:50 PM
                To: R1b1c_U106-S21@yahoogroups.com
                Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???
                 
                 
                Interesting question.  If you're in Z343 you're in a small group already, and I would question the value of dividing the group further -- in order to discover what?  I have asked myself the same question about Geno 2.0.  If we had 20 people in the group that were all going to take the full genome test, then the data to be crunched would be in comparing all the Y-chromosomes.  With just one person taking the test then any new markers discovered would be private until proven otherwise.  
                 

                From: Michael <mgreg24@...>
                To: R1b1c_U106-S21@yahoogroups.com
                Sent: Friday, November 30, 2012 6:32 PM
                Subject: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???
                 
                 
                I received this ( http://dna-explained.com/2012/11/30/gene-by-gene-announces-landmark-dna-dtc-full-genome-sequence/  ) today and will shortly have the financial means to take up this offer if you good people who are far more o fay than myself are interested in crunching the data or see any potential value to the group in my pursuing this route for mutual benefit.
                 
                cheers
                michael (z343)
                 





              • Piero Sinclair
                Thanks Rob Cheers Piero ... Thanks Rob Cheers Piero On Sat, Dec 1, 2012 at 5:56 PM, rob sinclair wrote:   Welcome to the 346+ club
                Message 7 of 27 , Dec 1, 2012
                • 0 Attachment
                  Thanks Rob
                  Cheers
                  Piero


                  On Sat, Dec 1, 2012 at 5:56 PM, rob sinclair <rjsinc@...> wrote:
                   

                  Welcome to the 346+ club Piero, where we all sit and wait 
                   

                  To: R1b1c_U106-S21@yahoogroups.com
                  From: pierosinclair@...
                  Date: Sat, 1 Dec 2012 09:45:20 +0000

                  Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                   
                  David Carlisle, just thought I'd mention I'm Z346+, and DYS 568=10. I imagine I'm negative for Z343 as those Sinclairs in our Caithness/Orkney cluster that have been tested are negative.
                  Cheers
                  Piero 


                  On Sat, Dec 1, 2012 at 6:14 AM, David Carlisle <davidcar801@...> wrote:
                   


                  If a full genome costs $5,500 for 23 chomosomes, then why doesn't a full Y test cost $5,500/23, or $239?  There is the issue of differing chromosome length, but then why isn't there a separate test?

                  Wow, there's room for a lot of SNPs between 27,000,000 and 59,000,000.

                  Back to the question of why it's good I subscribed to Geno 2.0, and that is because there are four other Z346ers taking the test, two of them with my DYS568 = 10 STR, so there is a chance of discovering a SNP that will put me with one or the other of those two, or finding a SNP that unites the three of us and further separates us from the Z343s.


                  From: Tim Janzen <tjanzen@...>
                  To: R1b1c_U106-S21@yahoogroups.com
                  Sent: Friday, November 30, 2012 10:54 PM
                  Subject: RE: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                   
                  I have been thinking about the issue of complete Y sequencing for a long time.  This issue was also discussed during the WTY session I attended where Thomas Krahn spoke at the FTDNA conference.  I also talked to Thomas about it afterward as well.  Thirty times coverage is reasonably good for the Y, but not superb.  Not many people will be able to afford complete sequencing at its current price.  The new SNPs that are found through complete Y sequencing may not be readily placed on the FTDNA Y SNP menu.  It costs Thomas about $20 or so just for the primer for each new SNP that he places on the menu.  Some SNPs are challenging to make primers for.  Thomas could get bogged down designing primers, ordering primers, and getting them on the SNP menu.  Some of the new SNPs will be redundant SNPs that won’t help us in terms of placing more branches on the Y SNP tree.  There is still no reference sequence for the region between about 27,000,000 and 59,000,000 due to the fact that the vast majority of this region is high repetitive.  This region may hold SNPs, but until it can be sequenced through long read technology, it won’t be available for us.  In summary, we definitely want to go to complete Y sequencing, but there are still financial and practical hurtles to jump along the way.  In any case, I would strongly suggest that anyone who orders complete genome sequencing to make their Y sequence available for researchers in a public database like Genbank or place the sequence in the hands of serious Y SNP researchers.
                  Tim Janzen
                   
                  From: R1b1c_U106-S21@yahoogroups.com [mailto:R1b1c_U106-S21@yahoogroups.com] On Behalf Of David Carlisle
                  Sent: Friday, November 30, 2012 8:50 PM
                  To: R1b1c_U106-S21@yahoogroups.com
                  Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???
                   
                   
                  Interesting question.  If you're in Z343 you're in a small group already, and I would question the value of dividing the group further -- in order to discover what?  I have asked myself the same question about Geno 2.0.  If we had 20 people in the group that were all going to take the full genome test, then the data to be crunched would be in comparing all the Y-chromosomes.  With just one person taking the test then any new markers discovered would be private until proven otherwise.  
                   

                  From: Michael <mgreg24@...>
                  To: R1b1c_U106-S21@yahoogroups.com
                  Sent: Friday, November 30, 2012 6:32 PM
                  Subject: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???
                   
                   
                  I received this ( http://dna-explained.com/2012/11/30/gene-by-gene-announces-landmark-dna-dtc-full-genome-sequence/  ) today and will shortly have the financial means to take up this offer if you good people who are far more o fay than myself are interested in crunching the data or see any potential value to the group in my pursuing this route for mutual benefit.
                   
                  cheers
                  michael (z343)
                   






                • David Carlisle
                  Hopefully we ll get some results that apply to our little group.   ________________________________ From: Piero Sinclair To:
                  Message 8 of 27 , Dec 1, 2012
                  • 0 Attachment
                    Hopefully we'll get some results that apply to our little group.  


                    From: Piero Sinclair <pierosinclair@...>
                    To: R1b1c_U106-S21@yahoogroups.com
                    Sent: Saturday, December 1, 2012 11:47 AM
                    Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                     
                    Thanks Rob
                    Cheers
                    Piero


                    On Sat, Dec 1, 2012 at 5:56 PM, rob sinclair <rjsinc@...> wrote:
                     
                    Welcome to the 346+ club Piero, where we all sit and wait 
                     

                    To: R1b1c_U106-S21@yahoogroups.com
                    From: pierosinclair@...
                    Date: Sat, 1 Dec 2012 09:45:20 +0000

                    Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                     
                    David Carlisle, just thought I'd mention I'm Z346+, and DYS 568=10. I imagine I'm negative for Z343 as those Sinclairs in our Caithness/Orkney cluster that have been tested are negative.
                    Cheers
                    Piero 





                  • rob sinclair
                    Yes let s hope so, I personally opted out on the Geno testing but I thank those who tested and wish you all good luck with the results if any. Sent from my
                    Message 9 of 27 , Dec 1, 2012
                    • 0 Attachment
                      Yes let's hope so, I personally opted out on the Geno testing but I thank those who tested and wish you all good luck with the results if any. 

                      Sent from my iPhone

                      On Dec 1, 2012, at 11:40 AM, "David Carlisle" <davidcar801@...> wrote:

                       

                      Hopefully we'll get some results that apply to our little group.  


                      From: Piero Sinclair <pierosinclair@...>
                      To: R1b1c_U106-S21@yahoogroups.com
                      Sent: Saturday, December 1, 2012 11:47 AM
                      Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                       
                      Thanks Rob
                      Cheers
                      Piero


                      On Sat, Dec 1, 2012 at 5:56 PM, rob sinclair <rjsinc@...> wrote:
                       
                      Welcome to the 346+ club Piero, where we all sit and wait 
                       

                      To: R1b1c_U106-S21@yahoogroups.com
                      From: pierosinclair@...
                      Date: Sat, 1 Dec 2012 09:45:20 +0000

                      Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                       
                      David Carlisle, just thought I'd mention I'm Z346+, and DYS 568=10. I imagine I'm negative for Z343 as those Sinclairs in our Caithness/Orkney cluster that have been tested are negative.
                      Cheers
                      Piero 





                    • Tim Janzen
                      Dear Charles, Brian, and others, Thanks for your comments earlier today. I will try to spell Craig Venter’s name correctly from now on. In any case, I
                      Message 10 of 27 , Dec 1, 2012
                      • 0 Attachment

                        Dear Charles, Brian, and others,

                                        Thanks for your comments earlier today.  I will try to spell Craig Venter’s name correctly from now on.  In any case, I think it is important to have a frank discussion about how we will be handling large volumes of Y sequence data as a genetic genealogy community as it starts flowing out of sequencing machines over the next several years.  I see the raw sequence data being held in large databases such as GenBank and the sequences being analyzed using chromosome browsers such as Thomas Krahn’s Y browser and other similar popular browsers such as the UCSC chromosome browser http://genome.ucsc.edu/.  We are going to need to keep track of each of these sequences by haplogroup and subclade so that each of the sequences can be compared to each other, much like how Adriano Squecco organizes the 23andMe Y SNP data.  We will want to generate Y SNP lists relative to the Human Reference Sequence for each person whose Y chromosome is sequenced.  These lists will need to be carefully analyzed and the reported SNPs will need to be vetted to determine which are truly valid SNPs and which are simply misreads.  In many cases it will be difficult to determine which SNPs are rare private SNPs found only in a particular family line and which are misreads.  It will be helpful to sequence the Y chromosomes of closely related males with the same surname (first or 2nd degree relatives) to help fine tune the list of truly valid SNPs.  Doing this doubles the cost of testing, but leads to a much cleaner list of SNPs to work with.  We will want to work with Thomas Krahn to develop primers for as many SNPs as feasible since wider testing of many of these SNPs will be advantageous to many people.  I am a strong supporter of the WTY project, but I think in the near future once the price of complete Y sequencing comes down it will be better for people to do complete Y sequencing of pairs of two closely related males from as many subclades as possible in an effort to pinpoint all of the SNPs that are downstream from the terminal SNP in any particular subclade than to simply keep doing WTY testing if only 400,000 BPs are included in the WTY.

                                        I don’t really see any obvious correlation between Y chromosome testing and autosomal testing such as the Family Finder database.  I think that Y chromosome sequence data will not be analyzed in the same way we analyze autosomal data.  However, once we have extremely highly accurate Y sequence data (a maximum of 0-2 errors per Y sequence) then a matching system similar to FTDNA’s matches for full mtDNA sequences could eventually be developed.

                                        The nanopore sequencing technologies certainly look promising and may finally give us the opportunity to sequence sections of the Y such as the 27,000,000 to 57,000,000 position section that we haven’t been able to sequence up to this point in time.  No matter what sequencing system finally wins out, the key will be that we need to have accuracy rates in the range of one or less errors per 10 million to 100 million base pairs.  We aren’t there yet.  In any case, we are living in an exciting time for Y chromosome SNP research.

                        Sincerely,

                        Tim Janzen

                         

                        From: R1b1c_U106-S21@yahoogroups.com [mailto:R1b1c_U106-S21@yahoogroups.com] On Behalf Of Charles Moore
                        Sent: Saturday, December 01, 2012 1:39 AM
                        To: R1b1c_U106-S21@yahoogroups.com
                        Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                         

                        Whenever whole genome testing becomes more affordable, a matching system will have to be set up similar to FF.  After gigabytes comes terabytes, then something called petabytes.  At the conference, they showed us how many petabytes FF takes to run.  I don't know what comes after petabytes or how many of those whatevers it would take to run the entire Y matching program, or what they might charge for the matching service.  It would spit out the distant cousins that you match at all but the last 20 or whatever singleton SNPs at on your SNP line of descent.  Then you could try to email them like with FF and go from there, but it would be a person to person thing.  The SNPs  would not be individually testable by others.  We aren't going to be able to maintain a Y tree with tens of thousands of SNPs, so the group effort will diminish after the initial hoopla.  

                         

                        Whole genome testing isn't an end unto itself, and the results are almost meaningless unless there is a system to run the comparison.  Then you match someone with most of the same SNPs and you email them and compare notes about your MDKA. That is how I would envision it.

                         

                        Every year for the last 6 years, there have been rumors that whole genome testing for $1,000 will be available "next year".  We're not there yet.  Thomas charges $950 to test 400,000 out of 27 million possible testable Y positions, which remains a shot in the dark, which if it discovers anything, is usually a private SNP that nobody else matches.

                         

                        I'm all for progress of course, and I love this business, but the question is really exactly what Michael asks.  Whenever we eventually are able to test entire genomes for $1,000, how will we crunch the whatever comes after petabyte data, and what will be the mutual benefit?

                         

                        OK, fine, well that is the business we are in, peering in to the past to see our ancestors, and how we got here from there.  I need to learn more about FF from Tim and CeCe.  I haven't paid much attention to it, because I haven't had the time, and I don't have any close family left to test and do the type of FF matching that enabled CeCe to explain how it was that she knew that that DNA segment on Chromosome 5 came from her 3rd-great-grandmother Louise.  But whenever I think about whole genome testing for a thousand bucks, all I can "see" is another version of Family Finder.

                         

                        I'm sure it will be a good thing for people to be able to discover who their closest SNP based Y line matches are.  That is after all, essentially what we are trying to do with the sandbox SNPs and STRs.  It is the mutual benefit to the group aspect that Michael asked about that I am unable to "see".  How will the tree branch lines of descent be maintained? Etc.  Maybe Tim, or someone else, has some thoughts about how it will work.


                        Charles

                      • Charles Moore
                        Thanks very much, Tim. I had a feeling you would make the whole thing sound more promising, and you have succeeded. Charles ... Thanks very much, Tim. I had a
                        Message 11 of 27 , Dec 1, 2012
                        • 0 Attachment
                          Thanks very much, Tim.  I had a feeling you would make the whole thing sound more promising, and you have succeeded.

                          Charles


                          On Dec 1, 2012, at 2:47 PM, "Tim Janzen" <tjanzen@...> wrote:

                           

                          Dear Charles, Brian, and others,

                                          Thanks for your comments earlier today.  I will try to spell Craig Venter’s name correctly from now on.  In any case, I think it is important to have a frank discussion about how we will be handling large volumes of Y sequence data as a genetic genealogy community as it starts flowing out of sequencing machines over the next several years.  I see the raw sequence data being held in large databases such as GenBank and the sequences being analyzed using chromosome browsers such as Thomas Krahn’s Y browser and other similar popular browsers such as the UCSC chromosome browser http://genome.ucsc.edu/.  We are going to need to keep track of each of these sequences by haplogroup and subclade so that each of the sequences can be compared to each other, much like how Adriano Squecco organizes the 23andMe Y SNP data.  We will want to generate Y SNP lists relative to the Human Reference Sequence for each person whose Y chromosome is sequenced.  These lists will need to be carefully analyzed and the reported SNPs will need to be vetted to determine which are truly valid SNPs and which are simply misreads.  In many cases it will be difficult to determine which SNPs are rare private SNPs found only in a particular family line and which are misreads.  It will be helpful to sequence the Y chromosomes of closely related males with the same surname (first or 2nd degree relatives) to help fine tune the list of truly valid SNPs.  Doing this doubles the cost of testing, but leads to a much cleaner list of SNPs to work with.  We will want to work with Thomas Krahn to develop primers for as many SNPs as feasible since wider testing of many of these SNPs will be advantageous to many people.  I am a strong supporter of the WTY project, but I think in the near future once the price of complete Y sequencing comes down it will be better for people to do complete Y sequencing of pairs of two closely related males from as many subclades as possible in an effort to pinpoint all of the SNPs that are downstream from the terminal SNP in any particular subclade than to simply keep doing WTY testing if only 400,000 BPs are included in the WTY.

                                          I don’t really see any obvious correlation between Y chromosome testing and autosomal testing such as the Family Finder database.  I think that Y chromosome sequence data will not be analyzed in the same way we analyze autosomal data.  However, once we have extremely highly accurate Y sequence data (a maximum of 0-2 errors per Y sequence) then a matching system similar to FTDNA’s matches for full mtDNA sequences could eventually be developed.

                                          The nanopore sequencing technologies certainly look promising and may finally give us the opportunity to sequence sections of the Y such as the 27,000,000 to 57,000,000 position section that we haven’t been able to sequence up to this point in time.  No matter what sequencing system finally wins out, the key will be that we need to have accuracy rates in the range of one or less errors per 10 million to 100 million base pairs.  We aren’t there yet.  In any case, we are living in an exciting time for Y chromosome SNP research.

                          Sincerely,

                          Tim Janzen

                           

                          From: R1b1c_U106-S21@yahoogroups.com [mailto:R1b1c_U106-S21@yahoogroups.com] On Behalf Of Charles Moore
                          Sent: Saturday, December 01, 2012 1:39 AM
                          To: R1b1c_U106-S21@yahoogroups.com
                          Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                           

                          Whenever whole genome testing becomes more affordable, a matching system will have to be set up similar to FF.  After gigabytes comes terabytes, then something called petabytes.  At the conference, they showed us how many petabytes FF takes to run.  I don't know what comes after petabytes or how many of those whatevers it would take to run the entire Y matching program, or what they might charge for the matching service.  It would spit out the distant cousins that you match at all but the last 20 or whatever singleton SNPs at on your SNP line of descent.  Then you could try to email them like with FF and go from there, but it would be a person to person thing.  The SNPs  would not be individually testable by others.  We aren't going to be able to maintain a Y tree with tens of thousands of SNPs, so the group effort will diminish after the initial hoopla.  

                           

                          Whole genome testing isn't an end unto itself, and the results are almost meaningless unless there is a system to run the comparison.  Then you match someone with most of the same SNPs and you email them and compare notes about your MDKA. That is how I would envision it.

                           

                          Every year for the last 6 years, there have been rumors that whole genome testing for $1,000 will be available "next year".  We're not there yet.  Thomas charges $950 to test 400,000 out of 27 million possible testable Y positions, which remains a shot in the dark, which if it discovers anything, is usually a private SNP that nobody else matches.

                           

                          I'm all for progress of course, and I love this business, but the question is really exactly what Michael asks.  Whenever we eventually are able to test entire genomes for $1,000, how will we crunch the whatever comes after petabyte data, and what will be the mutual benefit?

                           

                          OK, fine, well that is the business we are in, peering in to the past to see our ancestors, and how we got here from there.  I need to learn more about FF from Tim and CeCe.  I haven't paid much attention to it, because I haven't had the time, and I don't have any close family left to test and do the type of FF matching that enabled CeCe to explain how it was that she knew that that DNA segment on Chromosome 5 came from her 3rd-great-grandmother Louise.  But whenever I think about whole genome testing for a thousand bucks, all I can "see" is another version of Family Finder.

                           

                          I'm sure it will be a good thing for people to be able to discover who their closest SNP based Y line matches are.  That is after all, essentially what we are trying to do with the sandbox SNPs and STRs.  It is the mutual benefit to the group aspect that Michael asked about that I am unable to "see".  How will the tree branch lines of descent be maintained? Etc.  Maybe Tim, or someone else, has some thoughts about how it will work.


                          Charles

                        • Brian P. Swann
                          Dear Tim This is pretty much the way I see this area going too. It is just the error rates have to be so, so low for this to happen for real – less than 1
                          Message 12 of 27 , Dec 2, 2012
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                            Dear Tim

                             

                            This is pretty much the way I see this area going too.  It is just the error rates have to be so, so low for this to happen for real – less than 1 in 10 million – and that this is a very, very big ask in terms of precision of any analytical technique.

                             

                            Otherwise you start getting into endless discussions whether the SNP change is for real - or a measurement artefact.  I think your suggestion of doing two closely related men is a good idea, to make sure you are looking at a real SNP change.  I guess something like first cousins would be ideal.

                             

                            Whether I will be able to afford any of this – is another story.  I am always surprised as to how many of my colleagues across the pond seem to be able to afford many, many autosomal DNA tests without seemingly blinking.  My wife examines my credit card bills regularly – before exploding and reminding me that I am now retired!

                             

                            Brian

                             

                            From: R1b1c_U106-S21@yahoogroups.com [mailto:R1b1c_U106-S21@yahoogroups.com] On Behalf Of Tim Janzen
                            Sent: 01 December 2012 20:48
                            To: R1b1c_U106-S21@yahoogroups.com
                            Subject: RE: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                             

                             Dear Charles, Brian, and others,

                            Thanks for your comments earlier today.  I will try to spell Craig Venter’s name correctly from now on.  In any case, I think it is important to have a frank discussion about how we will be handling large volumes of Y sequence data as a genetic genealogy community as it starts flowing out of sequencing machines over the next several years.  I see the raw sequence data being held in large databases such as GenBank and the sequences being analyzed using chromosome browsers such as Thomas Krahn’s Y browser and other similar popular browsers such as the UCSC chromosome browser http://genome.ucsc.edu/.  We are going to need to keep track of each of these sequences by haplogroup and subclade so that each of the sequences can be compared to each other, much like how Adriano Squecco organizes the 23andMe Y SNP data.  We will want to generate Y SNP lists relative to the Human Reference Sequence for each person whose Y chromosome is sequenced.  These lists will need to be carefully analyzed and the reported SNPs will need to be vetted to determine which are truly valid SNPs and which are simply misreads.

                            In many cases it will be difficult to determine which SNPs are rare private SNPs found only in a particular family line and which are misreads.  It will be helpful to sequence the Y chromosomes of closely related males with the same surname (first or 2nd degree relatives) to help fine tune the list of truly valid SNPs.  Doing this doubles the cost of testing, but leads to a much cleaner list of SNPs to work with.  We will want to work with Thomas Krahn to develop primers for as many SNPs as feasible since wider testing of many of these SNPs will be advantageous to many people.  I am a strong supporter of the WTY project, but I think in the near future once the price of complete Y sequencing comes down it will be better for people to do complete Y sequencing of pairs of two closely related males from as many subclades as possible in an effort to pinpoint all of the SNPs that are downstream from the terminal SNP in any particular subclade than to simply keep doing WTY testing if only 400,000 BPs are included in the WTY.

                            I don’t really see any obvious correlation between Y chromosome testing and autosomal testing such as the Family Finder database.  I think that Y chromosome sequence data will not be analyzed in the same way we analyze autosomal data.  However, once we have extremely highly accurate Y sequence data (a maximum of 0-2 errors per Y sequence) then a matching system similar to FTDNA’s matches for full mtDNA sequences could eventually be developed.

                            The nanopore sequencing technologies certainly look promising and may finally give us the opportunity to sequence sections of the Y such as the 27,000,000 to 57,000,000 position section that we haven’t been able to sequence up to this point in time.  No matter what sequencing system finally wins out, the key will be that we need to have accuracy rates in the range of one or less errors per 10 million to 100 million base pairs.  We aren’t there yet.  In any case, we are living in an exciting time for Y chromosome SNP research.

                            Sincerely,

                            Tim Janzen

                            From: R1b1c_U106-S21@yahoogroups.com [mailto:R1b1c_U106-S21@yahoogroups.com] On Behalf Of Charles Moore
                            Sent: Saturday, December 01, 2012 1:39 AM
                            To: R1b1c_U106-S21@yahoogroups.com
                            Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                            Whenever whole genome testing becomes more affordable, a matching system will have to be set up similar to FF.  After gigabytes comes terabytes, then something called petabytes.  At the conference, they showed us how many petabytes FF takes to run.  I don't know what comes after petabytes or how many of those whatevers it would take to run the entire Y matching program, or what they might charge for the matching service.  It would spit out the distant cousins that you match at all but the last 20 or whatever singleton SNPs at on your SNP line of descent.  Then you could try to email them like with FF and go from there, but it would be a person to person thing.  The SNPs  would not be individually testable by others.  We aren't going to be able to maintain a Y tree with tens of thousands of SNPs, so the group effort will diminish after the initial hoopla.  

                            Whole genome testing isn't an end unto itself, and the results are almost meaningless unless there is a system to run the comparison.  Then you match someone with most of the same SNPs and you email them and compare notes about your MDKA. That is how I would envision it.

                            Every year for the last 6 years, there have been rumors that whole genome testing for $1,000 will be available "next year".  We're not there yet.  Thomas charges $950 to test 400,000 out of 27 million possible testable Y positions, which remains a shot in the dark, which if it discovers anything, is usually a private SNP that nobody else matches.

                            I'm all for progress of course, and I love this business, but the question is really exactly what Michael asks.  Whenever we eventually are able to test entire genomes for $1,000, how will we crunch the whatever comes after petabyte data, and what will be the mutual benefit?

                            OK, fine, well that is the business we are in, peering in to the past to see our ancestors, and how we got here from there.  I need to learn more about FF from Tim and CeCe.  I haven't paid much attention to it, because I haven't had the time, and I don't have any close family left to test and do the type of FF matching that enabled CeCe to explain how it was that she knew that that DNA segment on Chromosome 5 came from her 3rd-great-grandmother Louise.  But whenever I think about whole genome testing for a thousand bucks, all I can "see" is another version of Family Finder.

                            I'm sure it will be a good thing for people to be able to discover who their closest SNP based Y line matches are.  That is after all, essentially what we are trying to do with the sandbox SNPs and STRs.  It is the mutual benefit to the group aspect that Michael asked about that I am unable to "see".  How will the tree branch lines of descent be maintained? Etc.  Maybe Tim, or someone else, has some thoughts about how it will work.

                            Charles

                          • Don Byars
                            Hi David, Back in March of this year there were three people who tested positive for SNP Z343, in April there were eight, jump to November and there were
                            Message 13 of 27 , Dec 2, 2012
                            • 0 Attachment
                              Hi David,

                              Back in March of this year there were three people who tested positive for SNP Z343, in April there were eight, jump to November and there were thirteen, and today there are fifteen, so this "small group" is growing, and with Geno 2.0, who knows.  Remember back in 2005 U106 was a relatively small group.  U106 is estimated to be about 4,000 years old, and Z343 between 1,400 and 2,000 years old, so I think Z343 still has a little room to grow before we peter out to our more recent private/family SNPs, maybe 500+ years old  (perhaps wishful thinking on my part). I'm not giving up on new SNPs being found below, and parallel, to Z346>Z343--the more tests/testers, the better.

                              It's good to see your Geno 2.0 sample is in "Isolation" on Ray's spreadsheet; a long time coming, but hopefully worth the wait.

                              Don Byars

                              --- On Fri, 11/30/12, David Carlisle <davidcar801@...> wrote:

                              From: David Carlisle <davidcar801@...>
                              Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???
                              To: "R1b1c_U106-S21@yahoogroups.com" <R1b1c_U106-S21@yahoogroups.com>
                              Date: Friday, November 30, 2012, 9:50 PM

                               

                              Interesting question.  If you're in Z343 you're in a small group already, and I would question the value of dividing the group further -- in order to discover what?  I have asked myself the same question about Geno 2.0.  If we had 20 people in the group that were all going to take the full genome test, then the data to be crunched would be in comparing all the Y-chromosomes.  With just one person taking the test then any new markers discovered would be private until proven otherwise.  


                              From: Michael <mgreg24@...>
                              To: R1b1c_U106-S21@yahoogroups.com
                              Sent: Friday, November 30, 2012 6:32 PM
                              Subject: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                               
                              I received this ( http://dna-explained.com/2012/11/30/gene-by-gene-announces-landmark-dna-dtc-full-genome-sequence/  ) today and will shortly have the financial means to take up this offer if you good people who are far more o fay than myself are interested in crunching the data or see any potential value to the group in my pursuing this route for mutual benefit.

                              cheers
                              michael (z343)


                            • David Carlisle
                              Don, The recent news makes me more confident we re going to find multiple SNPs below Z346, but if I m contemplating ordering a new test I have to ask myself if
                              Message 14 of 27 , Dec 2, 2012
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                                Don,

                                The recent news makes me more confident we're going to find multiple SNPs below Z346, but if I'm contemplating ordering a new test I have to ask myself if I'm pursuing a question about genealogy, or just feeding a SNP addiction.  If there were more testers with a wider range of backgrounds in Z346, then the more likely it is that a new test will tell me something about my possible background.  So I'm encouraged that Z346 is a growing group.

                                DC


                                From: Don Byars <snake86413@...>
                                To: R1b1c_U106-S21@yahoogroups.com
                                Sent: Sunday, December 2, 2012 2:30 PM
                                Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                                 
                                Hi David,

                                Back in March of this year there were three people who tested positive for SNP Z343, in April there were eight, jump to November and there were thirteen, and today there are fifteen, so this "small group" is growing, and with Geno 2.0, who knows.  Remember back in 2005 U106 was a relatively small group.  U106 is estimated to be about 4,000 years old, and Z343 between 1,400 and 2,000 years old, so I think Z343 still has a little room to grow before we peter out to our more recent private/family SNPs, maybe 500+ years old  (perhaps wishful thinking on my part). I'm not giving up on new SNPs being found below, and parallel, to Z346>Z343--the more tests/testers, the better.

                                It's good to see your Geno 2.0 sample is in "Isolation" on Ray's spreadsheet; a long time coming, but hopefully worth the wait.

                                Don Byars

                                --- On Fri, 11/30/12, David Carlisle <davidcar801@...> wrote:

                                From: David Carlisle <davidcar801@...>
                                Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???
                                To: "R1b1c_U106-S21@yahoogroups.com" <R1b1c_U106-S21@yahoogroups.com>
                                Date: Friday, November 30, 2012, 9:50 PM

                                 
                                Interesting question.  If you're in Z343 you're in a small group already, and I would question the value of dividing the group further -- in order to discover what?  I have asked myself the same question about Geno 2.0.  If we had 20 people in the group that were all going to take the full genome test, then the data to be crunched would be in comparing all the Y-chromosomes.  With just one person taking the test then any new markers discovered would be private until proven otherwise.  


                                From: Michael <mgreg24@...>
                                To: R1b1c_U106-S21@yahoogroups.com
                                Sent: Friday, November 30, 2012 6:32 PM
                                Subject: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                                 
                                I received this ( http://dna-explained.com/2012/11/30/gene-by-gene-announces-landmark-dna-dtc-full-genome-sequence/  ) today and will shortly have the financial means to take up this offer if you good people who are far more o fay than myself are interested in crunching the data or see any potential value to the group in my pursuing this route for mutual benefit.

                                cheers
                                michael (z343)




                              • Don Byars
                                Yeah, it s the same catch-22 situation we run into with fledgling surname projects: We need participants/haplotypes to compare to in order to attract new
                                Message 15 of 27 , Dec 2, 2012
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                                  Yeah, it's the same catch-22 situation we run into with fledgling surname projects: We need participants/haplotypes to compare to in order to attract new participants, but we need new participants in order to have participants/haplotypes to compare to.  And to make things worse, as with some surname projects, a potential tester sees a participant who has the same paternal ancestor as he has and decides that his haplotype/SNPs will be the same as this participant so why bother to test to find out something he already knows, and some project administrators know this is happening and choose to keep the surnames and most distant ancestors secret/hidden in hopes this will attract more participants wanting to find out the secret information, and this in turn makes potential participants think that the project is too secretive or is not being managed well because no surnames (or spelling variations) or most distant ancestors are shown, so why bother to join such a project, and all of of this drives a researcher crazy, and round and round we go.

                                  But it's all fun!  And I'm addicted, for sure.

                                  Don Byars

                                  --- On Sun, 12/2/12, David Carlisle <davidcar801@...> wrote:

                                  From: David Carlisle <davidcar801@...>
                                  Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???
                                  To: "R1b1c_U106-S21@yahoogroups.com" <R1b1c_U106-S21@yahoogroups.com>
                                  Date: Sunday, December 2, 2012, 3:48 PM

                                   

                                  Don,

                                  The recent news makes me more confident we're going to find multiple SNPs below Z346, but if I'm contemplating ordering a new test I have to ask myself if I'm pursuing a question about genealogy, or just feeding a SNP addiction.  If there were more testers with a wider range of backgrounds in Z346, then the more likely it is that a new test will tell me something about my possible background.  So I'm encouraged that Z346 is a growing group.

                                  DC


                                  From: Don Byars <snake86413@...>
                                  To: R1b1c_U106-S21@yahoogroups.com
                                  Sent: Sunday, December 2, 2012 2:30 PM
                                  Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                                   
                                  Hi David,

                                  Back in March of this year there were three people who tested positive for SNP Z343, in April there were eight, jump to November and there were thirteen, and today there are fifteen, so this "small group" is growing, and with Geno 2.0, who knows.  Remember back in 2005 U106 was a relatively small group.  U106 is estimated to be about 4,000 years old, and Z343 between 1,400 and 2,000 years old, so I think Z343 still has a little room to grow before we peter out to our more recent private/family SNPs, maybe 500+ years old  (perhaps wishful thinking on my part). I'm not giving up on new SNPs being found below, and parallel, to Z346>Z343--the more tests/testers, the better.

                                  It's good to see your Geno 2.0 sample is in "Isolation" on Ray's spreadsheet; a long time coming, but hopefully worth the wait.

                                  Don Byars

                                  --- On Fri, 11/30/12, David Carlisle <davidcar801@...> wrote:

                                  From: David Carlisle <davidcar801@...>
                                  Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???
                                  To: "R1b1c_U106-S21@yahoogroups.com" <R1b1c_U106-S21@yahoogroups.com>
                                  Date: Friday, November 30, 2012, 9:50 PM

                                   
                                  Interesting question.  If you're in Z343 you're in a small group already, and I would question the value of dividing the group further -- in order to discover what?  I have asked myself the same question about Geno 2.0.  If we had 20 people in the group that were all going to take the full genome test, then the data to be crunched would be in comparing all the Y-chromosomes.  With just one person taking the test then any new markers discovered would be private until proven otherwise.  


                                  From: Michael <mgreg24@...>
                                  To: R1b1c_U106-S21@yahoogroups.com
                                  Sent: Friday, November 30, 2012 6:32 PM
                                  Subject: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                                   
                                  I received this ( http://dna-explained.com/2012/11/30/gene-by-gene-announces-landmark-dna-dtc-full-genome-sequence/  ) today and will shortly have the financial means to take up this offer if you good people who are far more o fay than myself are interested in crunching the data or see any potential value to the group in my pursuing this route for mutual benefit.

                                  cheers
                                  michael (z343)




                                • glanyrafon01
                                  OK. Apologies for not keeping up but where can I find the list of 15 people who are Z343+. This includes me and interested to see who else is with us now :-)
                                  Message 16 of 27 , Dec 3, 2012
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                                    OK. Apologies for not keeping up but where can I find the list of 15 people who are Z343+.

                                    This includes me and interested to see who else is with us now :-)
                                    --- In R1b1c_U106-S21@yahoogroups.com, Don Byars <snake86413@...> wrote:
                                    >
                                    > Hi David,
                                    >
                                    > Back in March of this year there were three people who tested positive for SNP Z343, in April there were eight, jump to November and there were thirteen, and today there are fifteen, so this "small group" is growing, and with Geno 2.0, who knows.  Remember back in 2005 U106 was a relatively small group.  U106 is estimated to be about 4,000 years old, and Z343 between 1,400 and 2,000 years old, so I think Z343 still has a little room to grow before we peter out to our more recent private/family SNPs, maybe 500+ years old  (perhaps wishful thinking on my part). I'm not giving up on new SNPs being found below, and parallel, to Z346>Z343--the more tests/testers, the better.
                                    >
                                    > It's good to see your Geno 2.0 sample is in "Isolation" on Ray's spreadsheet; a long time coming, but hopefully worth the wait.
                                    >
                                    > Don Byars
                                    >
                                    > --- On Fri, 11/30/12, David Carlisle <davidcar801@...> wrote:
                                    >
                                    > From: David Carlisle <davidcar801@...>
                                    > Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???
                                    > To: "R1b1c_U106-S21@yahoogroups.com" <R1b1c_U106-S21@yahoogroups.com>
                                    > Date: Friday, November 30, 2012, 9:50 PM
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >  
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    > Interesting question.  If you're in Z343 you're in a small group already, and I would question the value of dividing the group further -- in order to discover what?  I have asked myself the same question about Geno 2.0.  If we had 20 people in the group that were all going to take the full genome test, then the data to be crunched would be in comparing all the Y-chromosomes.  With just one person taking the test then any new markers discovered would be private until proven otherwise.  
                                    > From: Michael <mgreg24@...>
                                    > To: R1b1c_U106-S21@yahoogroups.com
                                    > Sent: Friday, November 30, 2012 6:32 PM
                                    > Subject: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >  
                                    >
                                    >
                                    >
                                    >
                                    >
                                    >
                                    > I received this ( http://dna-explained.com/2012/11/30/gene-by-gene-announces-landmark-dna-dtc-full-genome-sequence/%c3%82%c2%a0 ) today and will shortly have the financial means to take up this offer if you good people who are far more o fay than myself are interested in crunching the data or see any potential value to the group in my pursuing this route for mutual benefit.
                                    > cheersmichael (z343)
                                    >
                                  • GTC
                                    Results are stored in the project s FTDNA pages. Scroll down to Z343+ http://www.familytreedna.com/public/U106/default.aspx?section=yresults
                                    Message 17 of 27 , Dec 3, 2012
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                                      Results are stored in the project's FTDNA pages. Scroll down to Z343+

                                      http://www.familytreedna.com/public/U106/default.aspx?section=yresults

                                      --- In R1b1c_U106-S21@yahoogroups.com, "glanyrafon01" <jdhorrell@...> wrote:
                                      >
                                      >
                                      > OK. Apologies for not keeping up but where can I find the list of 15 people who are Z343+.
                                      >
                                      > This includes me and interested to see who else is with us now :-)
                                      > --- In R1b1c_U106-S21@yahoogroups.com, Don Byars <snake86413@> wrote:
                                      > >
                                      > > Hi David,
                                      > >
                                      > > Back in March of this year there were three people who tested positive for SNP Z343, in April there were eight, jump to November and there were thirteen, and today there are fifteen, so this "small group" is growing, and with Geno 2.0, who knows.  Remember back in 2005 U106 was a relatively small group.  U106 is estimated to be about 4,000 years old, and Z343 between 1,400 and 2,000 years old, so I think Z343 still has a little room to grow before we peter out to our more recent private/family SNPs, maybe 500+ years old  (perhaps wishful thinking on my part). I'm not giving up on new SNPs being found below, and parallel, to Z346>Z343--the more tests/testers, the better.
                                      > >
                                      > > It's good to see your Geno 2.0 sample is in "Isolation" on Ray's spreadsheet; a long time coming, but hopefully worth the wait.
                                      > >
                                      > > Don Byars
                                      > >
                                      > > --- On Fri, 11/30/12, David Carlisle <davidcar801@> wrote:
                                      > >
                                      > > From: David Carlisle <davidcar801@>
                                      > > Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???
                                      > > To: "R1b1c_U106-S21@yahoogroups.com" <R1b1c_U106-S21@yahoogroups.com>
                                      > > Date: Friday, November 30, 2012, 9:50 PM
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >  
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > > Interesting question.  If you're in Z343 you're in a small group already, and I would question the value of dividing the group further -- in order to discover what?  I have asked myself the same question about Geno 2.0.  If we had 20 people in the group that were all going to take the full genome test, then the data to be crunched would be in comparing all the Y-chromosomes.  With just one person taking the test then any new markers discovered would be private until proven otherwise.  
                                      > > From: Michael <mgreg24@>
                                      > > To: R1b1c_U106-S21@yahoogroups.com
                                      > > Sent: Friday, November 30, 2012 6:32 PM
                                      > > Subject: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >  
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > >
                                      > > I received this ( http://dna-explained.com/2012/11/30/gene-by-gene-announces-landmark-dna-dtc-full-genome-sequence/%c3%82%c2%a0 ) today and will shortly have the financial means to take up this offer if you good people who are far more o fay than myself are interested in crunching the data or see any potential value to the group in my pursuing this route for mutual benefit.
                                      > > cheersmichael (z343)
                                      > >
                                      >
                                    • Piero Sinclair
                                      I m hoping U106 and the SNPs downstream are a lot more recent than that, for instance Dienekes estimates the MRCA for U106 at 2500 before present, using the
                                      Message 18 of 27 , Dec 3, 2012
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                                        I'm hoping U106 and the SNPs downstream are a lot more recent than that, for instance Dienekes estimates  the MRCA for U106 at 2500 before present, using the germline rate.  
                                        Cheers
                                        Piero


                                        On Sun, Dec 2, 2012 at 9:30 PM, Don Byars <snake86413@...> wrote:
                                         

                                        Hi David,

                                        Back in March of this year there were three people who tested positive for SNP Z343, in April there were eight, jump to November and there were thirteen, and today there are fifteen, so this "small group" is growing, and with Geno 2.0, who knows.  Remember back in 2005 U106 was a relatively small group.  U106 is estimated to be about 4,000 years old, and Z343 between 1,400 and 2,000 years old, so I think Z343 still has a little room to grow before we peter out to our more recent private/family SNPs, maybe 500+ years old  (perhaps wishful thinking on my part). I'm not giving up on new SNPs being found below, and parallel, to Z346>Z343--the more tests/testers, the better.

                                        It's good to see your Geno 2.0 sample is in "Isolation" on Ray's spreadsheet; a long time coming, but hopefully worth the wait.

                                        Don Byars

                                        --- On Fri, 11/30/12, David Carlisle <davidcar801@...> wrote:

                                        From: David Carlisle <davidcar801@...>
                                        Subject: Re: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???
                                        To: "R1b1c_U106-S21@yahoogroups.com" <R1b1c_U106-S21@yahoogroups.com>
                                        Date: Friday, November 30, 2012, 9:50 PM


                                         

                                        Interesting question.  If you're in Z343 you're in a small group already, and I would question the value of dividing the group further -- in order to discover what?  I have asked myself the same question about Geno 2.0.  If we had 20 people in the group that were all going to take the full genome test, then the data to be crunched would be in comparing all the Y-chromosomes.  With just one person taking the test then any new markers discovered would be private until proven otherwise.  


                                        From: Michael <mgreg24@...>
                                        To: R1b1c_U106-S21@yahoogroups.com
                                        Sent: Friday, November 30, 2012 6:32 PM
                                        Subject: [R1b1c_U106-S21] Geno 2.0 -vs- Gene by Gene exome test ???

                                         
                                        I received this ( http://dna-explained.com/2012/11/30/gene-by-gene-announces-landmark-dna-dtc-full-genome-sequence/  ) today and will shortly have the financial means to take up this offer if you good people who are far more o fay than myself are interested in crunching the data or see any potential value to the group in my pursuing this route for mutual benefit.

                                        cheers
                                        michael (z343)



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