R1b-ZZ87
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AlMcCord
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R1b-ZZ87
My understanding is that the clade ZZ87 is believed to be the defining clade of the Ui Niall. I looked it up on www.ybrowse.org and it gives 2 possible loci. I understand that it is in a region where the nucleotides read the same forward and backward. It seems it is similar to the wave/particle paradox, "It might be there if your not looking"----
Last edited by Webmaster on Tue, 2021-May-18 5:11 pm, edited 1 time in total.
Reason: Title clarification.
Reason: Title clarification.
Al
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Webmaster
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Re: R1b-ZZ87
AI,
Yes, all the data so far indicates that. And unfortunately, it is in one of the problematic regions; but Alex is very good and doesn't call a mutation unless there is solid evidence. Commercial companies like FTDNA and YFull won't call it because of the potential conflicts.
Some of the following is repeat info, but hopefully will help put the problem in perspective. A lot of the reason for these problematic regions is how they actually do the testing. They literally chop up the entire Y chromosome for WGS tests, or a selected region of it for targeted NGS tests like the BigY, into 100 to 300 base pair long segments. Considering the Y chromosome is about 59 million base pairs long, that is a LOT of segments.
They then read each of these segments to determine the values of the base pairs. THEN they reassemble all these segments back into a long chain again; except they cannot do that perfectly because sometimes the segments are just too short and they look the same. And sometimes they just cannot get a good determination of a particular base pairs value. So, they have a giant jigsaw puzzle they are trying to put together with the added difficulty some pieces are identical.
To help with this, like having the original picture of the jigsaw puzzle as a guide, they have a reference Y chromosome they use in the reassembly. Currently, this is the hg38 reference; but the reference genome is constantly being updated itself every few years. To top it off, only about 1/3 of the Y chromosome has been mapped, so the reference only covers that 1/3. Further, the reference Y chromosome is artificially constructed from volunteer donors in an attempt to be universal; where all test results can be compared against it.
They are constantly trying to improve the sequencing technology. There have been several different methods designed to get longer read segments, but nothing has yet reached a reasonably priced test; although YSEQ now offers a WGS test with 400 base pair long read segments for US$399. There is even talk of building clade specific Y chromosome references, so that reassembly does not have to worry about all the upstream mutations above the clade because they are included in the reference already.
This explains why WGS tests are "future proof". Even though current reassembly methods only have a reference for 1/3 of the Y chromosome now, as that reference is updated, the raw WGS results can be reanalyzed against the new reference without requiring a whole new test like a targeted NGS test would require. And clade specific references would eliminate that issue completely.
The next few years will be exciting in the field of genetic genealogy. Hopefully, in the not too distant future we will have reasonably priced tests that will sequence the entire Y chromosome to a high degree of accuracy for true comparisons. There will probably be new problems introduced, of course, but hopefully not of an unsolvable nature.
Yes, all the data so far indicates that. And unfortunately, it is in one of the problematic regions; but Alex is very good and doesn't call a mutation unless there is solid evidence. Commercial companies like FTDNA and YFull won't call it because of the potential conflicts.
Some of the following is repeat info, but hopefully will help put the problem in perspective. A lot of the reason for these problematic regions is how they actually do the testing. They literally chop up the entire Y chromosome for WGS tests, or a selected region of it for targeted NGS tests like the BigY, into 100 to 300 base pair long segments. Considering the Y chromosome is about 59 million base pairs long, that is a LOT of segments.
They then read each of these segments to determine the values of the base pairs. THEN they reassemble all these segments back into a long chain again; except they cannot do that perfectly because sometimes the segments are just too short and they look the same. And sometimes they just cannot get a good determination of a particular base pairs value. So, they have a giant jigsaw puzzle they are trying to put together with the added difficulty some pieces are identical.
To help with this, like having the original picture of the jigsaw puzzle as a guide, they have a reference Y chromosome they use in the reassembly. Currently, this is the hg38 reference; but the reference genome is constantly being updated itself every few years. To top it off, only about 1/3 of the Y chromosome has been mapped, so the reference only covers that 1/3. Further, the reference Y chromosome is artificially constructed from volunteer donors in an attempt to be universal; where all test results can be compared against it.
They are constantly trying to improve the sequencing technology. There have been several different methods designed to get longer read segments, but nothing has yet reached a reasonably priced test; although YSEQ now offers a WGS test with 400 base pair long read segments for US$399. There is even talk of building clade specific Y chromosome references, so that reassembly does not have to worry about all the upstream mutations above the clade because they are included in the reference already.
This explains why WGS tests are "future proof". Even though current reassembly methods only have a reference for 1/3 of the Y chromosome now, as that reference is updated, the raw WGS results can be reanalyzed against the new reference without requiring a whole new test like a targeted NGS test would require. And clade specific references would eliminate that issue completely.
The next few years will be exciting in the field of genetic genealogy. Hopefully, in the not too distant future we will have reasonably priced tests that will sequence the entire Y chromosome to a high degree of accuracy for true comparisons. There will probably be new problems introduced, of course, but hopefully not of an unsolvable nature.
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AlMcCord
- Fochloc Senchada
- Posts: 11
- Joined: Fri, 2020-Aug-14 11:12 pm
- Location: Morgantown, West Virginia
Re: R1b-ZZ87
I really appreciate your explanation. Some of the info I did not know. I read somewhere that the new technology for reading those larger segments of chopped up dna is called nanopore. If I remember correctly, they use bacteria or something similar, and give it an electrical charge. The segments are then thread through the microscopic nanopore and read according to how each nucleotide responds to the signal. I am really amazed at how fast they are advancing things as well. It looks like WGS is the way to go. 400 base pairs is defiantly better compared to NGS limitations. I did learn new information from your post concerning the reference genome, and how they process the dna at the lab. For that I thank you.
Best,
Best,
Al
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Webmaster
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Re: R1b-ZZ87
AI,
My pleasure.
Nanopore technology is one way, but there are others, from what I understand. To me it seems like they could use 4 biochemical solutions, each one of which bonds to a specific nucleotide, either A, C, G, or T, and emits a specific light frequency. Then use a high-powered microscope that can "see" the individual nucleotides and then use light frequency processing to get all the base pairs accurately. Or something like that, so they don't have destructive sampling like they currently do. Reassembly is as much an art as it is a science. Maybe one day...
My pleasure.
Nanopore technology is one way, but there are others, from what I understand. To me it seems like they could use 4 biochemical solutions, each one of which bonds to a specific nucleotide, either A, C, G, or T, and emits a specific light frequency. Then use a high-powered microscope that can "see" the individual nucleotides and then use light frequency processing to get all the base pairs accurately. Or something like that, so they don't have destructive sampling like they currently do. Reassembly is as much an art as it is a science. Maybe one day...