PDA

View Full Version : YSEQ's Wish An SNP



Almagest
03-11-2016, 08:24 PM
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?

Huntergatherer1066
03-11-2016, 11:24 PM
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/?

KSDA
03-12-2016, 12:13 AM
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.

Almagest
03-12-2016, 06:17 AM
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/?


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.

mwauthy
07-24-2018, 09:13 PM
Do they let you know when the SNP is now available for testing? How long of a wait usually after you wish it?

RobertCasey
07-25-2018, 07:12 PM
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.

mwauthy
07-26-2018, 02:25 PM
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?

RobertCasey
07-27-2018, 12:15 AM
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.

mwauthy
07-27-2018, 05:28 AM
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.

Petr
07-27-2018, 11:47 AM
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.

mwauthy
07-27-2018, 03:37 PM
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.

So people that have already done Big Y could actually have twice as many snps than what is listed? How much coverage does FGC Elite 2.1 do? In the future do you think there will be more coverage? Is it best to wait a few years prior to doing deep Y chromosome testing in your opinion?

deadly77
07-27-2018, 03:59 PM
Comparison chart between Big Y and the YElite and WGS tests from FGC: https://isogg.org/wiki/Y-DNA_next_generation_sequencing although it doesn't seem to have been updated very recently (changing BigY to BigY-Y500, comparison with WGS from Dante, YSEQ, etc.). The R-U106 primer from Iain McDonald contains some head-to-head data on coverage here: http://www.jb.man.ac.uk/~mcdonald/genetics/report-2017-primer.pdf