Monday, October 20, 2014

Hinxton-4 DNA Analysis

I was processing the Hinxton-4 over the last few days and I am finally able to complete it today. I am happy to say it did had enough SNPs to upload to GEDMatch and I uploaded it as kit# F999925.

Admixture

MDLP K23b for Hinxton-4

Dodecad V3 for Hinxton-4

Eurogenes K13 for Hinxton-4


Runs of Homozygosity

RoH reveals the parents of Hinxton-4 are not related in his genealogical timeframe.

Eye Color



Telomere

The average length of telomere length from all runs is 2.24 kb, which means, Hinxton-4 died around the age 55.

Telomere length of 2.24 relates to age ~55
(Image adapted from http://learn.genetics.utah.edu/content/chromosomes/telomeres/)

Mt-DNA

Mitochondria haplogroup is H1ag1

y-DNA

Y-Haplogroup is R1b1a2a1a2c1g2a1 (R-DF25).


The kit# F999925 is available for 1-to-1 comparison. Please wait for a couple of days before doing 1-to-many comparison.

Saturday, October 18, 2014

Ajvide58 DNA Analysis

The authors had generated between 0.01 to 2.2-fold genome wide coverage for 6 neolithic hunter-gathers from pitted ware culture, 4 neolithic farmers from funnel beaker culture and 1 late Mesolithic hunter-gatherer. I converted the raw data of Ajvide58 from Pitted Ware Culture excavated in Sweden into formats familiar to genetic genealogists and uploaded here. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch as kit# F999924. The kit is tokenized and available for 1-to-1 comparision. Please wait a couple of days before checking for 1-to-many matches.

Admixture results


MDLP K23b Admixture Calculator

Dodecad V3 Admixture Calculator

Eurogenes K13 Admixture Calculator


Eye Color



Runs of Homozygosity

RoH reveals the the parents of Ajvide58 are 3rd cousins.

Telomere

The average length of telomere from all runs reveal it had 3.0857 which means the Ajvide58 died around the age of 35.

Telomere length of 3.057 kb relates to age 35.


Mt-DNA

Mitochondria haplogroup is U4d.

Y-DNA

The Y-Haplogroup is I-CTS772.

How to compare Ancient DNA with yours?

This is a small tutorial to compare your DNA with any of the ancient DNA with extremely low thresholds using Autosomal Segment Analyzer.

Open the Autosomal Segment Analyzer and wait until the map gets loaded (it will take a while on slow computers). Now, click File -> Open Files.

Open Files

Ancient DNA Settings
  • Do not tick 'Match no-calls'. Ancient DNA may have several no calls. So, don't check it.
  • Make sure Error radius is always -1. This will ensure the segment has no errors.
  • For SNP Threshold, you are free to put any low number of SNPs here. E.g., 10 SNPs
  • For cM Threshold, you are free to put any low decimal here. E.g, 0.1 cM
  • You can tick 'Ignore SNPs which are universal matches among populations'. Example, if only AA and AC is found among populations, then that SNP is a universal match. Hence, it will not be counted towards SNP count threshold.
  • Universal SNP match threshold can be tuned as well. For example, all universal matches have probability of 1. For example, if populations have AA, AC and CT, you have CT and it occurs so widely that the probability of that genotype occurrence is 75%, then you can ignore them towards SNP count by reducing the threshold to 0.60, thus further increasing the accuracy.
Matching Segments

Based on SNP/cM thresholds, when a segment matches, it will tell you in the status bar, how many accidental matches can occur for that segment, and gives you a clear picture of what is IBS noise and what are compound segments.

Once, you click 'OK', it will take a while for the processing to complete.

The output on the left pane has segment probability. On the right side, you have the probability of occurrence of the genotype for each SNP. The status will tell you if an accidental match can occur or not and even even tell you at what rate accidental matches can occur for that segment.

So, what does it mean? Any matching segment with says in description 'Accidental matches cannot occur', it means, the segment is compound and that ancient DNA does share the DNA segment through endogamy or cousin marriages. However, this does not mean you are related in any recent genealogical times. The IBS compound segment with low threshold could be thousands of years back in time. This tool only differentiates IBS noise from IBS compound segments at extremely low thresholds.

Let me know how you match compound segments or population matches with Ancient DNA.

Thursday, October 16, 2014

Ancient DNA upload files update

I got notified regarding the noise and duplicate SNPs in some of the upload files. I went ahead and investigated why is that the case. Because I merged the processed files from several sequence runs into one file, there seems to be a few negligible number of SNPs having different values in different runs and gets duplicated in the final file.

Below are the samples affected which are merged from multiple runs.

To solve this issue, I combined all the files processed from each run and took the genotype for those SNPs which occurs the most. The processed files for each run are untouched and can be accessed at the download links. Then file is then sorted by coordinates and re-uploaded. I also uploaded the filtered version having SNPs tested by DNA companies. I also re-upload Hinxton-2 and Hinxton-3 into GEDMatch with same kit number, i.e, F999921 and F999922 respectively.

Now, the files will have much less noise and properly sorted by coordinates. Future uploads will also follow the same procedure to make sure the uploads are with less noise and easy to use with sorted coordinates.

Wednesday, October 15, 2014

Hinxton-3 Analysis

I was processing the Hinxton-3 over the last few days and I am finally able to complete it today. I am happy to say it did had enough SNPs to upload to GEDMatch and I uploaded it as kit# F999922.

Admixture

MDLP K23b admixture for Hinxton-3 sample


Eurogenes K13 admixture for Hinxton-3 sample


Parent's Relationship

Based on Runs of Homozygosity, parents of Hinxton-3 are related as second cousins.


Eye Color

Eye Color in GEDMatch

Telomere Length

The average telomere length based on 10 runs is 1.367  which suggests she is in her 70s when she died.

Telomere length of 1.367 for Hinxton-3 sample
(Image adapted from http://learn.genetics.utah.edu/content/chromosomes/telomeres/)

Mt-DNA Analysis

Mitochondria haplogroup is K1a4a1a2b and the closest individual I can find so far is JQ701810 from the publicly available FMS samples.

New mutations in JQ701810 : T1189C, G5460A, A6752G, T9698C, C16189T, G5460A, A6752G
New mutations in Hixton-3: A4704G, C16184A, C16190T
Genetic Distance between these two individuals is 10 which is based on HVR1, HVR2 and CR.

The closest individual from FamilyTreeDNA projects is from mtDNA Haplogroup K (Katrine's Clan) project, FTDNA kit# 84833 for HVR1 and HVR2 comparisons who has a genetic distance of 7. Kit# 84833 is two HVR1 mutations and one HVR2 mutation away from the common ancestor with Hinxton-3 sample, while the sample is two HVR1 mutations and two HVR2 mutation away from the common ancestor.


The kit is available for 1-to-1 comparison. Please wait for atleast 2 days before checking for 1-to-many as batch processing is not yet complete. Let me know what you find.