Obed, my samples went to UCLA and unfortunately UCLA results were not satisfactory. I have sent new samples off to Full Genomes so will have to wait longer for results. Do you know what result Adam Waalkes received for PF3514? Ken, Aaron and I have all his results data but I'm not so sure how to read the raw data files. On Sat, Jan 4, 2014 at 4:12 PM, Obed W Odom <[email protected]> wrote: > 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 > > > > ------------------------------- > 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 >

Hi Wayne, You should be able to find results for PF3514 in the genotyping ("gtype") report. Nice analysis, Obed! Greg On Jan 4, 2014 3:50 AM, "Wayne R. Roberts" <[email protected]> wrote: > Obed, my samples went to UCLA and unfortunately UCLA results were not > satisfactory. I have sent new samples off to Full Genomes so will have to > wait longer for results. > > Do you know what result Adam Waalkes received for PF3514? Ken, Aaron and I > have all his results data but I'm not so sure how to read the raw data > files. > > > On Sat, Jan 4, 2014 at 4:12 PM, Obed W Odom <[email protected]> wrote: > > > 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 > > > > > > > ------------------------------- > > 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 >