Friday, 16 December 2016

L2 MHT - Recommendations for further SNP Testing

So far in Lineage II, we have SNP marker data from 10 "Big Y" tests - the tenth one came in last week and is currently being assessed (member G65, 371202, MGG). Together with the STR marker data (i.e. the Y-DNA-37 test most people took when joining the project), this has allowed us to group people into separate branches of the Mutation History Tree for Lineage II (the L2 MHT for short; as discussed in the recent posts).(1) The pioneers of Lineage II who undertook this Big Y testing have paved the way for a more cost-effective, money-saving SNP testing strategy for the rest of the group, so a debt of gratitude is owed to these project members. Thank you, guys! 

As a result, only in rare circumstances will it be necessary for new members to do Big Y testing ... this will only happen if there is a new distant outlier to the rest of the Lineage II group. And this will happen from time to time as more people join our group.

The new SNP Testing Strategy involves collaboration with another DNA testing company - YSEQ. This is a specialist company headed by husband and wife team, Thomas and Astrid Krahn. Both of them used to work at FamilyTreeDNA but left to form their own company to address a gap in the market. Their niche company offers bespoke SNP testing. In discussions with Thomas, we have come up with a highly cost-effective strategy for further SNP testing in Lineage II. This will allow us to achieve our goals and save money at the same time.

The SNP Testing Strategy is in three phases:
  • Phase 1 - the YSEQ Z255 SNP Panel
  • Phase 2 - SNP Block testing
  • Phase 3 - Private SNP testing
All three phases are fluid and a person may jump between Phases 2 and 3 depending on what the results of new testing reveal.

Phase 1 - the YSEQ Z255 SNP Panel
This will be the starting point for most new members, for most people who have only tested to the 37 marker level, and for the 9 members who are currently ungrouped in our L2 MHT.  The YSEQ Z255 SNP Panel includes 6 SNP markers that are immediately relevant to Gleeson Lineage II.

First off, YSEQ is offering us discounted testing with their Z255 SNP Panel. Luckily for us, their Z255 SNP Panel offers more Lineage II-relevant SNP markers than the corresponding Z255 SNP Pack from FTDNA. YSEQ's Panel covers all the six "most downstream" branches identified so far for Lineage II. These branches are represented by the SNPs in the green boxed portion of the diagram below, namely A5631 (aka Y17108), A5628 (aka Y17112), A660, Y16880, A10634 (aka BY5706), & A10640 (aka BY5707). In addition, new branches can be added to this panel over time, so it will adapt as Gleeson Lineage II grows.

YSEQ's Z255 SNP Panel covers all 6 confirmed branches of Lineage II
FTDNA's Z255 SNP Panel (Dec 2016) - only covers 1 of the 6 branches of Lineage II

The usual price of the YSEQ Z255 SNP Panel is $88 (cheaper than FTDNA's panel) but we are getting it for a considerable discount. Not everyone within Lineage II needs to do this as the revised Mutation History Tree predicts which branch many people are likely to fall on. And simply doing a single SNP test with YSEQ (for $17.50 or less) might be all that is needed to confirm the prediction. More money savings! 

So only the following people need do the Z255 Panel (because their placement on the tree is uncertain and needs clarification):
  • the 9 people who are currently ungrouped in the L2 MHT - see footnote (2)
  • Branch E - any one of the 3 members (G91, G75, G84) could do the test - this will tell us whether or not this Branch is more closely related to Branch B or Branch C
  • Branch F - one of G97 or G98 could do the test to confirm or refute their supposed close connection to G65 (371202, MGG)
So at the moment, the recommendation is for 11 people in total to take the YSEQ Z255 SNP Panel. I will be writing to these people individually over the course of the next week in order to organise funding and ordering of the new kits (they will have to swab again as it is a different company).

Phase 2 - SNP Block Testing
For those people whose sub-branch is easily predicted from their STR results, the Z255 SNP Panel is not necessary. Instead they can jump straight to single SNP testing to confirm which of the 6 major branches they belong to. Once this has been confirmed, the next step would be to test for any "phylo-equivalent SNPs" - in other words, SNPs that occur in the same "SNP block" ... and there are 4 of these in Lineage II, highlighted in the diagram below. This stage of the testing is likely to split these 4 blocks into smaller blocks or even single SNPs, and in this way the number of branches associated with Lineage II will increase, possibly to as many as 18 unique "Gleeson" branches.

The 4 current SNP Blocks of Lineage II

Branch A of the L2 MHT
Currently, there are two people in the project that are at this stage of testing, both of them in Branch A (G54 & G79). These two people are predicted to belong to Branch A (both in the L2 MHT & the SAPP Tree). Both members should test for the single SNP A660 and if positive (95% probability) they should then go on to test for the remaining five SNPs in that particular SNP Block. The chances are that they will be positive for some of them and negative for others. This will "split" the block into two pieces. For example, G54 & G79 may test positive for the first 3 SNPs and negative for the other three. The block will thus be split into 1 section with the first 3 SNPs (with G54 & G79 sitting underneath it) and a second section beneath that with the last 3 SNPs, and the current members (the 3 brothers - G39, G51, G73) sitting underneath that.

In addition, this would identify a new branching point within Branch A, and one (or more) of the defining SNPs could then be added to YSEQ's Z255 SNP Panel. This would benefit future testers.

Phase 3 - Private SNP testing
The third phase is testing of Private / Unique SNPs (i.e. SNPs that are currently unique to one or more specific individuals). These Unique SNPs have been identified via a collaborative effort of many individuals, including Thomas Krahn himself, Alex Williamson, James Kane, the teams at FTDNA and YFULL, various Haologroup Project Administrators, and many others. You can read previous blog posts of how these SNPs were identified below:

The current set of Unique SNPs associated with Lineage II members (3)
(red dots indicate SNPs covered by YSEQ's Z255 SNP Panel)

Currently, there is no one in the project at this phase of testing. But if the Z255 Panel testing of Branch F members confirms a connection between G65 (371202, MGG) and either G97 (524241, PG) or G98 (437908, WG), then G97 & G98 would undertake single SNP testing of the Private / Unique SNPs of G65 (our 10th & most recent Big Y tester). He appears to have 9 Private SNPs (based on preliminary analyses). Testing all 9 SNPs individually would usually cost $351 at FTDNA ($39 per SNP), and $157.50 at YSEQ ($17.50 per SNP = 55% cheaper) but Thomas is offering substantial reductions from the usual YSEQ price if we order in bulk. This SNP Testing Strategy is a lot less expensive than doing the Big Y test at FTDNA (usually $575).

Similarly, if any of the 9 currently-ungrouped individuals (doing the Z255 Panel) test positive for BY5706 as a terminal SNP (and therefore fall into Branch D), they can start single SNP testing of the Private SNPs of members G05 (86192, RLG) & G68 (411177, CG). G68 has 5 Private SNPs and G05 has 1, so it would usually cost $234 at FTDNA, and $105 at YSEQ, but again, Thomas is offering a substantial discount on the usual YSEQ prices if we order in bulk.

Thomas proposes to test for these SNPs sequentially, as this will allow substantial reductions in the cost of doing these tests. And the more people who test, the greater the reductions will be.

Thomas will not test all the SNPs at once. Instead he does sequential testing of single SNPs, usually 1 SNP every 1-2 weeks, and thus the results will trickle in over the course of several weeks or months, and decisions on further testing of the group will be based on the results of the previous test.

In addition, Thomas will add every reasonable new branch to the YSEQ Z255 Panel where new results (e.g. from additional Big Y testing or the above SNP Testing Strategy)  identify at least two people who share the same new branching point (characterised by a new SNP discovery) and are different in at least one other SNP.

So to recap, the new SNP Testing Strategy involves the following potential steps:
  1. Test with the YSEQ Z255 SNP Panel for those whose predicted placement on the Mutation History Tree for Lineage II needs further clarification
  2. Test for phylo-equivalent SNPs (within the same SNP Block) - this may split the block
  3. Test for Private / Unique SNPs - this may identify new downstream branching points
I will write to all 29 Lineage II project members individually with a bespoke testing plan for each member. I will calculate the price, ask all project members (who are willing to take part) to pay the relevant amount to the General Fund, and then I will pay for the tests via bulk order to get the maximum discount. Thomas will then send new (YSEQ) kits to the relevant people so that they can swab their cheeks and get tested.

In this way, the MHT for Lineage II will continue to grow progressively and will increase in complexity and accuracy. This will allow people to see how closely they are related to everyone else within the group and at what timepoint the common ancestor they share with any of the other members is likely to have been born. This information will facilitate more focussed genealogical research using documentary records. (4)

I will also be writing to individual project members to review the genealogical information they have supplied. Now is a good time for everyone to update that information. At the very least everyone should have supplied their basic MDKA information and their Gleeson pedigree. But to really optimise the chances of breaking through your Brick Wall, you should have the information detailed in my previous post about the MDKA Profile. I will review this information with each project member over the course of the next several weeks.

Maurice Gleeson
Dec 2016

(1) the current pdf version of the L2 MHT is available in three parts:

(2) Here are the 9 currently-ungrouped members who should test with the YSEQ Z255 SNP Panel (listed by G-number, kit number, and initials for ease of reference):
  • G99 ... 437986 ... MIG
  • G81 ... 458407 ... BEG
  • G89 ... 498597 ... OMG
  • G77 ... B78262 ... SG
  • G70 ... 371145 ... DG
  • G78 ... 446153 ... AG
  • G92 ... 438324 ... TOG
  • G95 ... 437988 ... TEG
  • G94 ... 437987 ... GMG

(3) These are based on Alex Williamson's analysis from the Big Tree 

(4) Incidentally, Judy has rearranged the order of project members displayed on the DNA Results page of our WFN website to match the current new groupings in the L2 MHT. See below ... 

The DNA Results table for Lineage II on our WorldFamilie.Net website
(click to enlarge)

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