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Haplogroup H

For people who are in mtDNA Haplogroup H

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Why we need to get our DNA results to Genebank 5 Replies

Started by Peiternella Suzzanna Hymen. Last reply by Kay Fordham May 10, 2010.

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Comment by Peiternella Suzzanna Hymen on May 10, 2010 at 7:03pm
AHHH crap!, I put a 1 on the end of H6a1a. Actually this sequence is at genbank as a H6a1. This is quite new as I saw it on Ian Logans reports to Genealogy DNA newsletter
HM124476 FTDNA Haplogroup H6a1 26-APR-2010
T195C T239C A263G 315.1C A750G A1438G G3915A A4727G A4769G A8860G
G9380A T10237C T11204C T11253C A15326G T16362C A16482G.
Now my partner treats the back mutations as:
if they have all the mutations that are in a particular Haplogroup sub branch but are missing that sub branch defining code
ie I have an H3 that shares nearly all the mutations with Hf but is missing 93G and they also share a unique private mutation, so he has classed it among the HF but still named it H3 as he says the phylotree changes as new data comes in. So far I have not come across a major sub branch mutation back-mutation but my partner has had a couple and he showed me their position on his data base. He said you can see the pattern of the mutations and that they are from that particular branch. When they are laid out you see patterns. Our H mutations on Phylotree are a mess-would you not agree?
This was a FTDNA sequence not 23andme.
Comment by Mardon Erbland on May 10, 2010 at 5:26pm
Hi Peiternella,

I'd like to understand better why you've put that haplotype into H6a1a1 instead of stopping at H6a1a*. Can you explain that part a little more?

For mtDNA haplotypes that have an upstream SNP missing when it 'should' be present according to the known downstream SNPs, I'd think first about the possibility of a data error.

I know from personal experience that SNP calls produced by genechip technology are subject to error rates large enough that they cannot be ignored. My mtDNA calls generated from the Illumina HumanHap550+ beadchip that 23andME uses contained several errors when compared to the direct sequencing done by FTDNA for my mtFullSequence test. If you are including data in your database that comes from genechip calls, then I think you can expect some incorrect calls. As I understand it, mtDNA is especially problematic for genechips.

Another possibility is that a human has made a transcription error somewhere in the path between the laboratory and the results that eventually get sent to you.

Your point about back mutations is an interesting one. I don't know how back mutations are supposed to be treated within the mtDNA Haplogroup Tree. I would suppose if a child of a person who was H6a1a developed a back mutation for rCRS position 3915, thereby putting position 3915 back to G from A, then the tree ought to show such a person in a new subclade of H6a1a and not in a new subclade of H6. That's just what seems logical to me. I don't have any idea if there are 'rules' as how back mutation are to be handled in the tree. Do you know?

Mardon
Comment by Peiternella Suzzanna Hymen on May 10, 2010 at 4:34pm
I got that too.But it is not submitted to Genbank as that !!!!. I put that sequence into my data base as H6a1a1 but not because it did not have 5460- they don't have 7325G, 9362 or at least one of them. I see a few sequences that do not have a all or even a branch mutation but can have all the clade mutations- you see a pattern when they are all in a group so it sticks out like a 'horses bottom' when they are or not. I have allowed for back mutation as my partner (has been guiding me) likes to point out that back mutations are not to uncommon and he has also found many wrong branch defining in his W group. Pete has a science degree in Geology but also did a year in Univesity intermediate biology so has a fantastic grasp of the subject. I feel so dumb sometime or actually most the time when he goes on about the maths side of DNA and much much moreLOl
Comment by Mardon Erbland on May 10, 2010 at 6:47am
Is this a 'trick' question? :)

Here's how I'd figure it (without even assuming that the H6 you've provided is correct):

Start at rCRS
A263G, A8860G, A15326G ---> H2a2
A750G ---> H2a
A4769G ---> H2
A1438G ---> H
T16362C ---> H6/H8
T239C, A16482G ---> H6
G3915A ---> H6a
A4727G, G9380A ---> H6a1
T11253C ---> H6a1a

This leaves SNPs T10237C and T11204C unaccounted for.

H6a1a1 requires an SNP at rCRS 5460 so this haplotype is NOT that subclade.

I therefore conclude that the haplotype you've provided is for a yet-to-be-defined subclade of H6a1a. Am I close of have I missed something?
Comment by Peiternella Suzzanna Hymen on May 10, 2010 at 2:35am
Heres an interesting exercise , guess what branch of H6 this following sequence is
using FTDNA mutation list and phylotree
T195C T239C A263G 315.1C A750G A1438G G3915A A4727G A4769G A8860G G9380A T10237C T11204C T11253C A15326G T16362C A16482G
Comment by Maria on April 21, 2010 at 6:39am
Well, I won't do a full sequence as I could just test around the 4336 mutation which is diagnostic for H5a according to Achilli et al. 2004.
Here's what's interesting: my boss appears to be H12 so I'll check for 3936 to make sure. I've been researching the publications on H12 and found nothing. We are a weird bunch!
Comment by Peiternella Suzzanna Hymen on April 20, 2010 at 11:28pm
Hi Maria, marine organisms hey! Interesting stuff. Handy you can do your own test...jealous LOL.Mardons comments below cover what you need to test for yourself so you can find out what H5 sub branch or clade you maybe in. H5 is cool, not to many of them guys around.Good luck in the lab and keep us posted. I am most interested to hear what you are. CHeers
Comment by Peiternella Suzzanna Hymen on April 20, 2010 at 11:20pm
Hi E Collins, I think you are wondering how the Genograhic Project defined you as an H is because you dint have the mutations 2706A, 7028C which all other haplogroups tested people have.
Your mutation 16093c is one of the
H1f 4452C, 7309C, 9066G, 16093C, 16189C however you need 3010A (this mutation defines H1. You need a full sequence, as Mardon has mentioned, to actually find out what sub branch you are in. Hope this has helped some.
Comment by Maria on April 20, 2010 at 10:24am
ok, for HVR1 i have 16111A 16304C which puts me right on H5! I did HVR2 and have the obvious 263G and 373G which is not diagnostic for anything. I'll have to get some SNPs to see if I'm H5a.
Best web I found for finding haplogroups by entering mutations is Ian Logan's!
http://www.ianlogan.co.uk/haplogroup/finder.htm
Now, I don't know about dogs as I work with marine organisms :)
Comment by Mardon Erbland on April 20, 2010 at 9:14am
E. Collins: The Genographic Project page at:
https://genographic.nationalgeographic.com/genographic/lan/en/parti...
describes that they only test HyperVariable Region 1 (HVR1, positions 16001 to 16569). They do not test HyperVariable Region 2 (HVR2, positions 00001 to 00574) nor the coding Region (CR, positions 00575 to 16000). Without a full sequence test of all the positions in your mitochondrial DNA, you will not be able to tell in which mtDNA H-subclade (if any) you belong. If you want a full sequence mtDNA test you will have to buy it from one of the labs that offers this service. I got mine at FamilyTreeDNA.com
Mardon
 

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