Hi Kevin, all,
Brian or others might be able to correct my description of the technology but, as Bruce mentions, the T2T consortium has published the first complete sequence of the Y chromosome, unlocking the remaining 60% of our Y chromosomes that could not be sequenced until now. This is possible because of the longer chunks of DNA that these new technologies (HiFi, ultra-nanopone) can read.
Previous efforts (hg38, a.k.a. GRCh38) used shorter read technology, like the BigY itself, which cuts up the DNA into chunks of about 150 base pairs at a time. If you only have a small chunk, it's like only having small pieces in a jigsaw puzzle - you can't always be sure you are putting the jigsaw piece in the right part of the chromosome. Having a complete map of the chromosome from T2T is like being given the box the jigsaw came in: you can more clearly see what can go where, and where potential duplications might lie. This makes the mapping exercise of fitting the jigsaw pieces together a little simpler.
Aligning to T2T instead of hg38 therefore will let you correctly map more of your Y chromosome, but the differences aren't huge. They represent an extra few percent more on the size of the BigY test. Some SNPs can and have come out of this (the FTT series at FTDNA, including the FTT8 SNP that most of us have). You can pay the fee and have these SNPs tested in your own DNA for the sake of personal interest. However, the question remains what you do with these SNPs once you've discovered them. Unless the people around you upgrade, you have no idea whether they are positive or negative for most of these SNPs, so finding them becomes an increasingly academic exercise.
Some people will be happy to pay a small fee for these SNPs that (currently) have fairly limited use, some will not. The early adopters may encourage others to do so, or spur FTDNA to perform the realignment faster (they have already done some kits, hence the FTT SNPs). Most likely, the first tangible benefit that they'll see from this is that any new SNPs that may or may not be found will either remain private or become shared with others. In rare circumstances where SNPs are found and found to be shared where no other defining SNP occurs, this could lead to a new haplogroup at YFull, but would still take quite some time to end up in the Family Tree DNA system, Discover, etc. By that time, it's likely that FTDNA will have realigned more kits to the T2T reference anyway.
In the longer term, we're going to see more of this: more reference sequences that we could align to. The huge structural variations in the Y chromosome that appear to occur between different haplogroups could have a significant benefit if you align to a sequence close to your own haplogroup. For us, that would mean getting a T2T reference sequence within R-U106. That will likely happen eventually, and eventually we can hope that these tests become affordable for us consumers to get a T2T sequence of our own DNA. Until then, it's a gamble of what you get. Upgrading to a T2T alignment for €23 is a good way for YFull to make money - for consumers it's a long-odds gamble as to whether you'll get anything useful, but maybe that shouldn't stop some of us doing it for the curiosity or the fun.
Cheers,
Iain.
