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Thread: YSEQ's Wish An SNP

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    YSEQ's Wish An SNP

    When trying to add new SNP's, you need the name of the SNP (which I can take from YFull?) its position on ChrY (It says hg19 on the website) and the ancestral/derived mutation bases. Is there somewhere I can find this information online?

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    If it is a SNP that has been named, you may be able to find it on ybrowse: http://ybrowse.y-chromosome.org/gb2/gbrowse/chrY/?

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     Almagest (03-12-2016)

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    Quote Originally Posted by Almagest View Post
    When trying to add new SNP's, you need the name of the SNP (which I can take from YFull?) its position on ChrY (It says hg19 on the website) and the ancestral/derived mutation bases. Is there somewhere I can find this information online?
    When I requested a new SNP that was in YFull's database but not yet in YBrowse I just copied over the information from YFull including the name, and I included a note on it's associated subclade. Not long after the Wish transaction completed, the SNP was made available for testing using the name from YFull, and was also added to YBrowse.

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     Almagest (03-12-2016)

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    Quote Originally Posted by Huntergatherer1066 View Post
    If it is a SNP that has been named, you may be able to find it on ybrowse: http://ybrowse.y-chromosome.org/gb2/gbrowse/chrY/?
    Quote Originally Posted by KSDA View Post
    When I requested a new SNP that was in YFull's database but not yet in YBrowse I just copied over the information from YFull including the name, and I included a note on it's associated subclade. Not long after the Wish transaction completed, the SNP was made available for testing using the name from YFull, and was also added to YBrowse.
    Thanks guys. I didn't know it was as simple as going on YBrowse and typing the name.

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     Jatt1 (07-25-2018)

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    Do they let you know when the SNP is now available for testing? How long of a wait usually after you wish it?

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    I have ordered "Wish a YSNP" around a dozen times. Generally, in five to ten days, they send you an email summary of which ones they have added which are ready to order (expect a 10 to 20 % drop out rate due to being located in complex areas where Sanger Sequencing has issues with and YSEQ taking a purist approach of not testing these YSNPs). But occasionally, they will have trouble with creating primers that work and may require another pass which adds another two or more weeks for the ones that have tried again. They recently made a requirement of a minimum order for Wish a YSNP - either five or ten. So have five to ten ready to go as it costs no more to get the others included. But at $1 each, it will not cost much but I have ordered over 100 date so it can add up over time.

    You will need the Hg38 position, ancestral and derived states and the label that you want them to use (they will create A labels if you do not provide Y or BY labels). The first test includes $5 for the DNA collection kit and then $18 per YSNP from then on.
    Last edited by RobertCasey; 07-25-2018 at 07:38 PM.

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    Quote Originally Posted by RobertCasey View Post
    I have ordered "Wish a YSNP" around a dozen times. Generally, in five to ten days, they send you an email summary of which ones they have added which are ready to order (expect a 10 to 20 % drop out rate due to being located in complex areas where Sanger Sequencing has issues with and YSEQ taking a purist approach of not testing these YSNPs). But occasionally, they will have trouble with creating primers that work and may require another pass which adds another two or more weeks for the ones that have tried again. They recently made a requirement of a minimum order for Wish a YSNP - either five or ten. So have five to ten ready to go as it costs no more to get the others included. But at $1 each, it will not cost much but I have ordered over 100 date so it can add up over time.

    You will need the Hg38 position, ancestral and derived states and the label that you want them to use (they will create A labels if you do not provide Y or BY labels). The first test includes $5 for the DNA collection kit and then $18 per YSNP from then on.
    I ordered two of them separately. Got a response within 24 hours for each of them. Iím very happy with the quick customer service. One of them is located in a tough spot or is too homologous so they donít recommend testing it. The other one they added so Iíll be testing it shortly.

    Can you elaborate on what you meant about being a purist with Sanger sequencing? Is that why the Isogg ytree has fewer branches? Itís harder for snps to be accepted?

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     C J Wyatt III (07-27-2018)

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    Quote Originally Posted by mwauthy View Post
    Can you elaborate on what you meant about being a purist with Sanger sequencing? Is that why the Isogg ytree has fewer branches? Itís harder for snps to be accepted?
    YSEQ (who offers individual YSNPs for testing) will reject YSNPs found in complex areas. These can be more problematic but this discards a lot of useful YSNPs. The ISOGG haplotree is separate for YSEQ's YBrowser (which is maintained by Thomas Krahn). The criteria and requirements make the ISOGG haplotree not very relevant these days (but it is still very handy for older branches). FTDNA has really improved for their haplotrees and is your best source (at least for R1b and probably HG I). Alex Williamson's BigTree is another great source for R1b as well. For the HG I, YFULL is good for parts of HG I and FTDNA is probably dramatically improved as well. Unfortunately, the BigTree is currently limited to R1b (recently expanded to include U106). The ISOGG haplotree is rapidly becoming very dated due to its laborious requirements to qualify YSNP branches and its lack of support for recent branches which are not allowed (they should remove Genealogy from their name for this). With FTDNA, they except YSNP branches in complex areas and are very responsive to admin requests. The only minor issues remaining: they will not change the leading YSNP once established, routinely change branch equivalents to branches (much less these days) and require proof from FTDNA data (reasonable). They will add a YSNP branch to be tested individually discovered by YSEQ/FGC testing which is a major improvement that allows their haplotree to keep current.
    Last edited by RobertCasey; 07-27-2018 at 12:23 AM.

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     C J Wyatt III (07-27-2018)

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    Quote Originally Posted by RobertCasey View Post
    YSEQ (who offers individual YSNPs for testing) will reject YSNPs found in complex areas. These can be more problematic but this discards a lot of useful YSNPs. The ISOGG haplotree is separate for YSEQ's YBrowser (which is maintained by Thomas Krahn). The criteria and requirements make the ISOGG haplotree not very relevant these days (but it is still very handy for older branches). FTDNA has really improved for their haplotrees and is your best source (at least for R1b and probably HG I). Alex Williamson's BigTree is another great source for R1b as well. For the HG I, YFULL is good for parts of HG I and FTDNA is probably dramatically improved as well. Unfortunately, the BigTree is currently limited to R1b (recently expanded to include U106). The ISOGG haplotree is rapidly becoming very dated due to its laborious requirements to qualify YSNP branches and its lack of support for recent branches which are not allowed (they should remove Genealogy from their name for this). With FTDNA, they except YSNP branches in complex areas and are very responsive to admin requests. The only minor issues remaining: they will not change the leading YSNP once established, routinely change branch equivalents to branches (much less these days) and require proof from FTDNA data (reasonable). They will add a YSNP branch to be tested individually discovered by YSEQ/FGC testing which is a major improvement that allows their haplotree to keep current.
    Ftdna definitely has the most comprehensive haplotree underneath I-FGC24357 compared to Isogg or YFull. However, ftdna doesnít list any TMRCAís for the branches and the snp map feature seems to be inconsistent or doesnít work properly when I try to use it. As a result, itís hard to put the newer snps into any type of historical perspective or to find geographical correlations. I still donít understand why a red dot doesnít appear on the snp map for my location for my haplogroup.

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    FTDNA has the most test results, but their Big Y test has the length coverage 45 % only, so many branches and SNPs are missing.

    Regarding Sanger testing - FTDNA offers testing of SNPs that are rejected by YSEQ, but the result is often wrong. FTDNA returned my money several times when it turned out they could not do the test.
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
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