X projects? Any third party sites etc?

[Boudicca]

Hi,
Does anyone know if any X projects still exist? I remember years ago there was one but I never sent any data. If there are any, can they help find geographical connections to certain parts of the world a bit like Y/MtDNA? As I have raw data from 3 companies it seems a shame not to use it :biggrin1:

[thetick]

Kathy Johnson, member of the ISOGG, had postings on the defunct dnaforums. I vaguely recall she identified and was investigating 2 or 3 different out of Africa groups. I don't think there was ever much more than that. 23andme is the only commercial company using the X chromosome (with Relative Finder/Ancestry finder results). FTDNA has X STRs with very little details available for the results. Family Finder does not even match on the X, but does provide the raw data. Finally Dr. McDonald provides the only X chromosome painting, but he has stated in various emails/forums the X Chromosome results are not as reliable as the other chromosome paintings.

[aajamilkhan]

I vaguely recall she identified and was investigating 2 or 3 different out of Africa groups. I don't think there was ever much more than that. 23andme is the only commercial company using the X chromosome (with Relative Finder/Ancestry finder results). FTDNA has X STRs with very little details available for the results.

[kjjohnston]

Kathy Johnson, member of the ISOGG, had postings on the defunct dnaforums. I vaguely recall she identified and was investigating 2 or 3 different out of Africa groups. I don't think there was ever much more than that. 23andme is the only commercial company using the X chromosome (with Relative Finder/Ancestry finder results). FTDNA has X STRs with very little details available for the results. Family Finder does not even match on the X, but does provide the raw data. Finally Dr. McDonald provides the only X chromosome painting, but he has stated in various emails/forums the X Chromosome results are not as reliable as the other chromosome paintings.

Hi everybody. I miss the defunct DNA Forums. A lot of information was lost.

We never got much interest in pursuing the X after that but the spread sheet is still being kept by Didier Vernade here:
https://sd-4.archive-host.com/membres/up/90261920431217746/X-23andme.zip
It was originally version 2, 23andMe so he has not been able to update it.

See:
http://1drv.ms/1eykBQY for previous work compiled by Sean MacGorman Powell

I still have an interest in certain out of Africa groups that migrated to Europe and I think this work would contribute a lot of information with historical significance. Citizen scientists could play a role in this work. I am not good with computers and spread sheets. I believe there are phylogenetic trees that can be built out of X markers though.

If you find you share a haplotype block of interest, there also are some uncommon terminal SNPs that are probably recent variants in European groups that can now be traced at
http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/

For example, in the spread sheet compiled by Sean above there is one located at position 75,904,338, rs182875. The C variant is uncommon whereas the common SNP is a T within the population. C is not found in Asians or in Africans. If we could get enough genetic genealogists interested, we could probably trace the origins in Europe of this "terminal" SNP. It appears higher in Iberians (14%) in the 1000 Genomes Project. It is easily identified when you have a colorized biogeographical block of markers.

Those who like to follow Y SNPs would be good at finding X SNPs as well. I never understood why this type of investigation has never caught on except that the Illumina chip used by the testing companies is rather SNP-poor these days. I have always been disappointed in the current chips. We are clearly sitting on a goldmine of information if the chips could be improved and if people would just become involved with their sharing partners in some of these regions of ancient origin.

[Táltos]

Hi everybody. I miss the defunct DNA Forums. A lot of information was lost.

We never got much interest in pursuing the X after that but the spread sheet is still being kept by Didier Vernade here:
https://sd-4.archive-host.com/membres/up/90261920431217746/X-23andme.zip
It was originally version 2, 23andMe so he has not been able to update it.

See:
http://1drv.ms/1eykBQY for previous work compiled by Sean MacGorman Powell

I still have an interest in certain out of Africa groups that migrated to Europe and I think this work would contribute a lot of information with historical significance. Citizen scientists could play a role in this work. I am not good with computers and spread sheets. I believe there are phylogenetic trees that can be built out of X markers though.

If you find you share a haplotype block of interest, there also are some uncommon terminal SNPs that are probably recent variants in European groups that can now be traced at
http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/

For example, in the spread sheet compiled by Sean above there is one located at position 75,904,338, rs182875. The C variant is uncommon whereas the common SNP is a T within the population. C is not found in Asians or in Africans. If we could get enough genetic genealogists interested, we could probably trace the origins in Europe of this "terminal" SNP. It appears higher in Iberians (14%) in the 1000 Genomes Project. It is easily identified when you have a colorized biogeographical block of markers.

Those who like to follow Y SNPs would be good at finding X SNPs as well. I never understood why this type of investigation has never caught on except that the Illumina chip used by the testing companies is rather SNP-poor these days. I have always been disappointed in the current chips. We are clearly sitting on a goldmine of information if the chips could be improved and if people would just become involved with their sharing partners in some of these regions of ancient origin.

Interesting stuff! I checked all my kits at 23andme. At rs182875 we all have the common variant of T.

[Salkin]

For example, in the spread sheet compiled by Sean above there is one located at position 75,904,338, rs182875. The C variant is uncommon whereas the common SNP is a T within the population. C is not found in Asians or in Africans. If we could get enough genetic genealogists interested, we could probably trace the origins in Europe of this "terminal" SNP. It appears higher in Iberians (14%) in the 1000 Genomes Project. It is easily identified when you have a colorized biogeographical block of markers.

Neat - I'm rs182875 C. So it's not only my Y and mitochondria that are weird. :)

[kjjohnston]

Thanks for responding.
In the 1000 genomes project the rs182875 C is found in Great Britain at 10% but only 7% in Finns.
At ALFRED, this SNP rs182875 C is highest in one of the the Italian groups at 25%. Bedouins have 14%. Russians have 12%.
It is read there as G instead of C because the opposite strand in the double helix is read. There, the common variant is read as A.

http://alfred.med.yale.edu/alfred/mvograph.asp?siteuid=SI274513W

My feeling is that if you have a pileup of X matches in a small region on one of your chromosomes, you should look at the SNPs to determine if there is a biogeographical origin; look for terminal or less common SNPs that could indicate a more recent mutation. Instead of just figuring the frequency of a marker in isolation, we should be looking at haplotypes of individuals who match others in regions that do not undergo crossover recombination as frequently. I am not a population biologist, so I'm not sure if I am on the right track, but it seems to make sense as a citizen scientist. I have noticed that the region of 70 million to 80 million on the X looks like a pileup region where lots of people have matches of 1 cM and this is a potential phylogenetic tree region based on previous work we did several years ago. Now we have more populations to compare.

Kathy

[Táltos]

This might be of interest to some. Unfortunately you have to pay to read more. http://informahealthcare.com/doi/abs/10.3109/03014460.2014.944215

Mirandese language and genetic differentiation in Iberia: a study using X chromosome markers

January 2015, Vol. 42, No. 1 , Pages 20-25 (doi:10.3109/03014460.2014.944215)
Permissions
Supplemental Material
J. C. Pinto, V. Pereira, S. L. Marques, A. Amorim, L. Alvarez, and M. J. Prata
1Faculty of Sciences, University of Porto, Porto, Portugal,
2IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal,
3CIBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal, and
4Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
Correspondence: Joana Correia Pinto, IPATIMUP – Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal. Tel: +351 919099342. E-mail: [email protected]

Abstract

Background: In the Iberian Peninsula, the Mirandese dialect, spoken in Miranda do Douro (Portugal) close to the north-eastern border with Spain, has attracted much attention.

Aim, subjects and methods: This study focuses on providing further insight into the connections forged between Miranda do Douro and regions in the nearby Province of Zamora. This is in order to better assess the extent to which such relations could have been detained by the current patterns of genetic diversity of the populations, whilst contributing to refining the knowledge on patterns of micro-differentiation within the Peninsula. The genetic characterization of both populations was performed through the analysis of X-chromosomal markers: X-STRs and X-indels.

Results and conclusion: The results showed that Miranda do Douro tended to present slightly lower levels of diversity in comparison to the other studied regions, which can be a discreet sign of isolation of that population over the years that might have led the way to the preservation of a language not spoken anywhere else in the country. The analysis of X-STRs particularly brought to light the presence of a subtle population sub-structure at the micro-geographical area encompassing the north-eastern border, which seems to portray the importance of the political border as a mechanism withholding gene flow between the two countries.