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Author Topic: Need more STR + SNP results together.  (Read 1968 times)
geneticgenie
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« on: February 28, 2009, 08:05:37 PM »

For those people who have done both the SNP testing through either deCODEme or 23andMe and also have done STR testing through FTDNA,  please tell us if you have any of the following associated findings and are willing to report the results.

Now that I have seen more STR results, I would like to figure out if the bimodal distribution of STR is related to more of the SNP haplotypes.  We just need to know the SNPs which would be letters and the STRS which would be numbers.

For example, a low number (such as 7) at DXS10074 position 66,914,898, may be related to haplotype GCG*G   at 66,895,296 (rs1931545), 66,896,864 (rs5918768), 66,900,740 (rs1337082), 66,913,866 (rs12010636), 66,920,055 (rs5965443) but a high number (such as 20) may correlate with TCACG.  See examples at:

http://www.worldfamilies.net/geo/xdna/results?raw=1

Here is a new block to consider because it is associated with DXS 10066 position 145,619,628.

https://www.23andme.com/you/explorer/chr/?chr=X&pos_start=145556600

My parents are unlike each other both at the STR result and the SNP sequence.
I assume my XX has the following two sequences based on common male haplotypes:

TGTTTCAAGGTCTCCAGC
GTCCCTGGAACCCCCAGT

Here I counted 18 SNPs. My two associated STRs are 13 and 21.
But I don’t know if a high number in the STR is associated with haplotype 1 or haplotype 2. The hypothesis is that these are two different haplogroups and the STRS will fall into one or the other in a bimodal distriubution. One STR range is from 8 to 15 at DXS10066. The other would be (I am guessing) from 17 to 24.

For deCODEme users, if tested:
Gene Position  SNP Versions 

145556600  rs381365 G or T GT 
dbSNP Orientation: Minus
dbSNP Genotype: AC
 
145561012  rs370451 G or T GT 
dbSNP Orientation: Minus
dbSNP Genotype: AC
 
145583339  rs1794721 C or T CT 
dbSNP Orientation: Minus
dbSNP Genotype: AG
 
145614175  rs410329 C or T CT 
dbSNP Orientation: Minus
dbSNP Genotype: AG
 
145616651  rs381796 C or T CT 
dbSNP Orientation: Minus
dbSNP Genotype: AG
 
145625124  rs392247 C or T CT 
dbSNP Orientation: Minus
dbSNP Genotype: AG
 
145626675  rs404960 A or G AG 
dbSNP Orientation: Minus
dbSNP Genotype: CT
 
145631625  rs423514 A or G AG 
dbSNP Orientation: Minus
dbSNP Genotype: CT
 
145632815  rs6525733 A or G AG 
dbSNP Orientation: Plus
dbSNP Genotype: AG
 
145660212  rs1575093 A or G AG 
dbSNP Orientation: Minus
dbSNP Genotype: CT
 
145660351  rs1575091 C or T CT 
dbSNP Orientation: Minus
dbSNP Genotype: AG
 
145668986  rs5919734 C or T CC 
dbSNP Orientation: Plus
dbSNP Genotype: CC
 
145669261  rs997401 C or T CT 
dbSNP Orientation: Plus
dbSNP Genotype: CT
 
145673172  rs1590176 A or C CC 
dbSNP Orientation: Minus
dbSNP Genotype: GG
 
145679987  rs5920283 A or C CC 
dbSNP Orientation: Plus
dbSNP Genotype: CC
 
145716506  rs5920317 A or G AA 
dbSNP Orientation: Plus
dbSNP Genotype: AA
 
145723304  rs5966347 A or G GG 
dbSNP Orientation: Plus
dbSNP Genotype: GG
 
145724581  rs5919746 C or T CT
dbSNP Orientation: Plus
dbSNP Genotype: CT
 
I hope this is clear. Thanks.
Kathy
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Kathy J.
X Chromosomes: 75% English, 12.5% German, 6.25% Dutch, 3.125% Irish, 3.125% Scottish;
from Father's X: 43.75% English, 6.25% Dutch;
from Mother's X: 31.25% English, 12.5% German, 3.125% Irish, 3.125% Scottish
Seán MacGorman Powell
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« Reply #1 on: February 28, 2009, 11:40:32 PM »

Here is a new block to consider because it is associated with DXS 10066 position 145,619,628.

https://www.23andme.com/you/explorer/chr/?chr=X&pos_start=145556600

My parents are unlike each other both at the STR result and the SNP sequence.
I assume my XX has the following two sequences based on common male haplotypes:

<snip>

Thanks for posting the new block, Kathy.  I went ahead and added it to the X-SNP results chart, but unfortunately I can't upload it to the website because of the continuing glitches that WorldFamilies is experiencing with its recent upgrades.  I am getting the impression that this particular spreadsheet is too big for the new editor script to handle.  Hopefully Terry can get it fixed soon, and I'll keep trying.

I am a little wary of posting deduced haplotypes (i.e., guesses based on a few other people's results) in the project's X-SNP results chart, as that is opening up a big can of worms.  With this particular block, after I examined it closely in Ben's spreadsheet, there is clearly quite a lot of recombination going on, and a deduced phasing could easily turn out to be incorrect at one or more marker positions.  So I'll continue to be consistent and enter heterozygous results for females with asterisks in the spreadsheet, at least until I've given this some further thought.

Sean
« Last Edit: March 01, 2009, 09:54:38 AM by GhostX » Logged

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A.Hunt
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« Reply #2 on: March 01, 2009, 12:14:56 AM »

Well for what it is worth I am a male and mine is the same as the bottom one you posted.

GTCCCTGGAACCCCCAGT
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Seán MacGorman Powell
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« Reply #3 on: March 01, 2009, 10:04:33 AM »

Well for what it is worth I am a male and mine is the same as the bottom one you posted.

GTCCCTGGAACCCCCAGT


Thanks A.H., I'll get that added to the project's results chart as soon as I am able.

It would be helpful if you and other new contributors would calculate and post your ancestry percentages, for your X-chromosome only, or else post "unknown ancestry" if you have no way of figuring it (e.g., if you are adopted, or other reason).  Below are some charts to help you figure it out:

Use these charts for either males or females:

http://freepages.genealogy.rootsweb.ancestry.com/~hulseberg/DNA/xinheritance.html

Males may find this chart easier to use:

http://www.thegeneticgenealogist.com/2009/01/12/more-x-chromosome-charts/
« Last Edit: March 01, 2009, 10:14:22 AM by GhostX » Logged

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« Reply #4 on: March 01, 2009, 11:11:31 AM »

For those people who have done both the SNP testing through either deCODEme or 23andMe and also have done STR testing through FTDNA,  please tell us if you have any of the following associated findings and are willing to report the results.

Now that I have seen more STR results, I would like to figure out if the bimodal distribution of STR is related to more of the SNP haplotypes.  We just need to know the SNPs which would be letters and the STRS which would be numbers.

For example, a low number (such as 7) at DXS10074 position 66,914,898, may be related to haplotype GCG*G   at 66,895,296 (rs1931545), 66,896,864 (rs5918768), 66,900,740 (rs1337082), 66,913,866 (rs12010636), 66,920,055 (rs5965443) but a high number (such as 20) may correlate with TCACG.  See examples at:

http://www.worldfamilies.net/geo/xdna/results?raw=1

Here is a new block to consider because it is associated with DXS 10066 position 145,619,628.

https://www.23andme.com/you/explorer/chr/?chr=X&pos_start=145556600

My parents are unlike each other both at the STR result and the SNP sequence.
I assume my XX has the following two sequences based on common male haplotypes:

TGTTTCAAGGTCTCCAGC
GTCCCTGGAACCCCCAGT

Here I counted 18 SNPs. My two associated STRs are 13 and 21.
But I don’t know if a high number in the STR is associated with haplotype 1 or haplotype 2. The hypothesis is that these are two different haplogroups and the STRS will fall into one or the other in a bimodal distriubution. One STR range is from 8 to 15 at DXS10066. The other would be (I am guessing) from 17 to 24.


mine is:
GGTTTCAAGGTTTCAAGT

and DXS 10066=9
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Seán MacGorman Powell
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« Reply #5 on: March 01, 2009, 11:22:12 AM »

mine is:
GGTTTCAAGGTTTCAAGT

and DXS 10066=9

On other thing...

It would be very helpful if people would delineate their results with spaces, like this...

G G T T T C A A G G T T T C A A G T

...otherwise I can't import it directly into a spreadsheet, and it makes more work for me.

Thanks!
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geneticgenie
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« Reply #6 on: March 01, 2009, 03:23:42 PM »

 
[/quote]

mine is:
GGTTTCAAGGTTTCAAGT

and DXS 10066=9
[/quote]

Thank you.  It looks like *GTTTCA.. will be associated with the low numbers, so I would guess the higher numbers in the STRs would be associated with the *TCCCTG. There are a fair number of people who would have the *TCTCAG as well.
I will wait to hear from more people. 
Kathy J.
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Kathy J.
X Chromosomes: 75% English, 12.5% German, 6.25% Dutch, 3.125% Irish, 3.125% Scottish;
from Father's X: 43.75% English, 6.25% Dutch;
from Mother's X: 31.25% English, 12.5% German, 3.125% Irish, 3.125% Scottish
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