This is what Thomas had to say about PF3514: Everyone in IJ is supposed to be derived. Actually all others have an A. It seems like the region around PF3514 is very similar to ChrX:91846733..91846902. I've made a comparison here: http://genome.ucsc.edu/cgi-bin/hgc?o=91846732&g=htcUserAli&i=../trash/hgSs/hgSs_genome_49d7_4f0db0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_49d7_4f0db0.fa+ChrY:5578834..5579003&c=chrX&l=91846732&r=91846902&db=hg19&hgsid=357278251(I hope this link works for you). The X chromosome has also a "A" at this position and the probe on the Geno2 chip picks them up both. What likely happened is that his ancestors were derived for PF3514, but some X-Y recombination event has wiped that mutation out at a later time so that it shows the ancestral "A" again at this location.

Wayne, Did Thomas explicitly say that the derived value for PF3514 is G, or could it be C? My Full Genomes result clearly shows that I have C at this location. I looked at the X and Y sequences in this region and they are indeed very similar, but they do differ at points 17 bases upstream and 37 bases downstream of the PF3514 site, which must be enough for Full Genomes to separate the Y and X sequences. Full Genomes shows my X sequence to be identical to the HUGO reference, with A at the PF3514-homologous site. So Geno 2.0 was clearly in error when they reported me as AG instead of AC. Although I cannot see their raw data, Full Genomes also reports several other I1 people to have C at this position. These include another I1-Z138*, an I1-Z2541, and probably an I1-Z63. It would be interesting to hear what your Full Genomes test showed at the PF3514 site. In particular I'm wondering if Full Genomes has shown anyone to have G at the PF3514 site. I suppose it's possible that those of us who have C have had a second mutation at this site, from G to C. On Fri, Jan 3, 2014 at 7:06 PM, Wayne R. Roberts <[email protected]>wrote: > This is what Thomas had to say about PF3514: > > Everyone in IJ is supposed to be derived. Actually all others have an A. It > seems like the region around PF3514 is very similar to > ChrX:91846733..91846902. > > I've made a comparison here: > > http://genome.ucsc.edu/cgi-bin/hgc?o=91846732&g=htcUserAli&i=../trash/hgSs/hgSs_genome_49d7_4f0db0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_49d7_4f0db0.fa+ChrY:5578834..5579003&c=chrX&l=91846732&r=91846902&db=hg19&hgsid=357278251(I > hope this link works for you). > > The X chromosome has also a "A" at this position and the probe on the Geno2 > chip picks them up both. What likely happened is that his ancestors were > derived for PF3514, but some X-Y recombination event has wiped that > mutation out at a later time so that it shows the ancestral "A" again at > this location. > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

Obed, my question to Thomas was: One of our I-M223 Project members just received his Geno 2.0 results. He is from the Project's Continental 2a group CTS6433+. When his raw data is compared with that of other members he shows PF3514 with A A. All others show A G. Ybrowse has PF3514 mutation as A to G. How should I interpret his result? Is he derived and ancestral is actually G or is he ancestral (back mutation) and everyone else is derived? Thanks for any advise, Wayne. He did not indicate it should be A to C and Ybrowse has A to G. On Sat, Jan 4, 2014 at 1:10 PM, Obed W Odom <[email protected]> wrote: > Wayne, > > Did Thomas explicitly say that the derived value for PF3514 is G, or could > it be C? My Full Genomes result clearly shows that I have C at this > location. I looked at the X and Y sequences in this region and they are > indeed very similar, but they do differ at points 17 bases upstream and 37 > bases downstream of the PF3514 site, which must be enough for Full Genomes > to separate the Y and X sequences. Full Genomes shows my X sequence to be > identical to the HUGO reference, with A at the PF3514-homologous site. So > Geno 2.0 was clearly in error when they reported me as AG instead of AC. > > Although I cannot see their raw data, Full Genomes also reports several > other I1 people to have C at this position. These include another > I1-Z138*, an I1-Z2541, and probably an I1-Z63. It would be interesting to > hear what your Full Genomes test showed at the PF3514 site. In particular > I'm wondering if Full Genomes has shown anyone to have G at the PF3514 > site. I suppose it's possible that those of us who have C have had a second > mutation at this site, from G to C. > > > On Fri, Jan 3, 2014 at 7:06 PM, Wayne R. Roberts > <[email protected]>wrote: > > > This is what Thomas had to say about PF3514: > > > > Everyone in IJ is supposed to be derived. Actually all others have an A. > It > > seems like the region around PF3514 is very similar to > > ChrX:91846733..91846902. > > > > I've made a comparison here: > > > > > http://genome.ucsc.edu/cgi-bin/hgc?o=91846732&g=htcUserAli&i=../trash/hgSs/hgSs_genome_49d7_4f0db0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_49d7_4f0db0.fa+ChrY:5578834..5579003&c=chrX&l=91846732&r=91846902&db=hg19&hgsid=357278251(I > > hope this link works for you). > > > > The X chromosome has also a "A" at this position and the probe on the > Geno2 > > chip picks them up both. What likely happened is that his ancestors were > > derived for PF3514, but some X-Y recombination event has wiped that > > mutation out at a later time so that it shows the ancestral "A" again at > > this location. > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' > > without the quotes in the subject and the body of the message > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

Thanks, Wayne. Are you still waiting for your Full Genomes results? If so, please let us know your result at the site of PF3514 when you receive them. On Fri, Jan 3, 2014 at 9:32 PM, Wayne R. Roberts <[email protected]>wrote: > Obed, my question to Thomas was: > > One of our I-M223 Project members just received his Geno 2.0 results. He is > from the Project's Continental 2a group CTS6433+. When his raw data is > compared with that of other members he shows PF3514 with A A. All others > show A G. Ybrowse has PF3514 mutation as A to G. How should I interpret his > result? Is he derived and ancestral is actually G or is he ancestral (back > mutation) and everyone else is derived? Thanks for any advise, Wayne. > > He did not indicate it should be A to C and Ybrowse has A to G. > > > On Sat, Jan 4, 2014 at 1:10 PM, Obed W Odom <[email protected]> wrote: > > > Wayne, > > > > Did Thomas explicitly say that the derived value for PF3514 is G, or > could > > it be C? My Full Genomes result clearly shows that I have C at this > > location. I looked at the X and Y sequences in this region and they are > > indeed very similar, but they do differ at points 17 bases upstream and > 37 > > bases downstream of the PF3514 site, which must be enough for Full > Genomes > > to separate the Y and X sequences. Full Genomes shows my X sequence to be > > identical to the HUGO reference, with A at the PF3514-homologous site. So > > Geno 2.0 was clearly in error when they reported me as AG instead of AC. > > > > Although I cannot see their raw data, Full Genomes also reports several > > other I1 people to have C at this position. These include another > > I1-Z138*, an I1-Z2541, and probably an I1-Z63. It would be interesting to > > hear what your Full Genomes test showed at the PF3514 site. In particular > > I'm wondering if Full Genomes has shown anyone to have G at the PF3514 > > site. I suppose it's possible that those of us who have C have had a > second > > mutation at this site, from G to C. > > > > > > On Fri, Jan 3, 2014 at 7:06 PM, Wayne R. Roberts > > <[email protected]>wrote: > > > > > This is what Thomas had to say about PF3514: > > > > > > Everyone in IJ is supposed to be derived. Actually all others have an > A. > > It > > > seems like the region around PF3514 is very similar to > > > ChrX:91846733..91846902. > > > > > > I've made a comparison here: > > > > > > > > > http://genome.ucsc.edu/cgi-bin/hgc?o=91846732&g=htcUserAli&i=../trash/hgSs/hgSs_genome_49d7_4f0db0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_49d7_4f0db0.fa+ChrY:5578834..5579003&c=chrX&l=91846732&r=91846902&db=hg19&hgsid=357278251(I > > > hope this link works for you). > > > > > > The X chromosome has also a "A" at this position and the probe on the > > Geno2 > > > chip picks them up both. What likely happened is that his ancestors > were > > > derived for PF3514, but some X-Y recombination event has wiped that > > > mutation out at a later time so that it shows the ancestral "A" again > at > > > this location. > > > > > > ------------------------------- > > > To unsubscribe from the list, please send an email to > > > [email protected] with the word 'unsubscribe' > > > without the quotes in the subject and the body of the message > > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' > > without the quotes in the subject and the body of the message > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >