I see that I had the positions of the mismatches between the HUGO reference X and Y sequences slightly off. The mismatch points are 22 bases upstream and 32 bases downstream of the PF3514 site. Also, I looked at several I2a samples (HG00360, HG01344, and HG01197) from the 1000 Genomes project and they all show C at the site of PF3514, so I have yet to see a next-generation-sequencing sample with G at this site. On Sat, Jan 4, 2014 at 3:36 AM, G. Magoon <[email protected]> wrote: > 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 > > > > ------------------------------- > 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 >

>so I have yet to see a next-generation-sequencing sample with G at this site. Will the Big Y all be done with next-generation-sequencing? I heard that it will test for 25,000 known SNPs and sequence 10 million base pairs. Will the testing for the 25,000 known SNPs also be done with next-generation-sequencing or with a chip? Matthew Simonds > Date: Sat, 4 Jan 2014 11:52:37 -0600 > From: [email protected] > To: [email protected] > Subject: Re: [yDNAhgI] PF3514 > > I see that I had the positions of the mismatches between the HUGO > reference X and Y sequences slightly off. The mismatch points are 22 bases > upstream and 32 bases downstream of the PF3514 site. Also, I looked at > several I2a samples (HG00360, HG01344, and HG01197) from the 1000 Genomes > project and they all show C at the site of PF3514, so I have yet to see a > next-generation-sequencing sample with G at this site. > > > On Sat, Jan 4, 2014 at 3:36 AM, G. Magoon <[email protected]> wrote: > > > 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 > > > > > > > ------------------------------- > > 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