Tag Archives: jewish

June Update

I have a total of 123 participants in the project right now who have sent me their raw data. Six of those have relatives participating and thus have to be filtered out for most analysis other than individual admixture percentages etc where I divide participants into small groups.

The following groups are represented:

  • South Asian: 90
    • Tamil: 15
    • Punjab: 13
    • Bengal: 9
    • Karnataka: 7
    • Andhra Pradesh: 5
    • Uttar Pradesh: 5
    • Kerala: 5
    • Bihar: 5
    • Gujarati: 4
    • Sindhi: 4
    • Maharashtra: 3
    • Sri Lankan: 3
    • Caribbean Indian: 2
    • Kashmir: 2
    • Romani: 2
    • Goa: 1
    • Rajasthan: 1
    • Baloch: 1
    • Orissa: 1
    • Anglo-Indian: 1
    • Unknown: 1
  • Others: 33
    • Iran: 8
    • Assyrian: 3
    • Kurd: 2
    • Mexican: 2
    • Ashkenazi: 2
    • Northwest European: 2
    • Iraqi Arab: 2
    • Georgian: 1
    • Azeri: 1
    • Kazakh: 1
    • Brazilian: 1
    • Yemen: 1
    • Irish: 1
    • Egypt: 1
    • Gagauz Turk: 1
    • Afro-Belizean: 1
    • Iraqi Mandaean: 1
    • Egyptian/Iraqi Jew: 1
    • French/Madagascar/Indian: 1

Most are 23andme data while 4 are from FTDNA.

We are getting close to 100 South Asian participants.

April Update

I have a total of 97 participants in the project right now who have sent me their raw data. Six of those have relatives participating and thus have to be filtered out for most analysis other than individual admixture percentages etc where I divide participants into small groups.

The following groups are represented:

  • Tamil: 14
  • Punjab: 10
  • Bengal: 7
  • Iran: 7
  • Karnataka: 6
  • Andhra Pradesh: 4
  • Uttar Pradesh: 4
  • Gujarati: 3
  • Kerala: 3
  • Maharashtra: 3
  • Assyrian: 3
  • Bihar: 2
  • Caribbean Indian: 2
  • Kashmir: 2
  • Sindhi: 2
  • Sri Lankan: 2
  • Iraqi Arab: 2
  • Anglo-Indian: 1
  • Roma: 1
  • Goa: 1
  • Rajasthan: 1
  • Egyptian/Iraqi Jew: 1
  • Baloch: 1
  • Iraqi Kurd: 1
  • Georgian: 1
  • Azeri: 1
  • French/Madagascar/Indian: 1
  • Kazakh: 1
  • Ashkenazi: 1
  • Brazilian: 1
  • Mexican: 1
  • Unknown: 2

Let's try to get to hundred soon.

And yes, I am accepting FTDNA Family Finder (new Illumina chip) now.

Behar Bene Israel

As Razib and I were discussing, the four Bnei Menashe Jewish samples from Behar et al didn't look right since Bnei Menashe are from Mizoram in the northeast of India and thus should be expected to have some East Asian admixture.

When I tried to confirm the admixture/PCA results for Bnei Menashe in the Behar et al paper, I didn't find any mention of the group. Instead, the South Asian Jewish group they mentioned was Bene Israel. According to their admixture and PCA results, Bene Israel looked more like Pakistani populations than their Indian host populations. This is consistent with what my admixture runs show.

So I suspected that the four Bene Israel samples mentioned in the Behar et al paper were accidently labeled as Bnei Menashe in the dataset. I sent an email to the authors and they have confirmed that this was the case.

I have corrected all my spreadsheets so you should see Bene Israel instead of Bnei Menashe now. If you spot Bnei Menashe anywhere, please let me know.

PS. Also, it has been confirmed that three Paniya samples were mislabeled when the data was submitted to the GEO database. They are working on fixing it soon.

UPDATE: Mait Metspalu tells me that the database has been updated with the fixed version of the Behar et al dataset.

End of March Update

I have a total of 67 participants in the project right now who have sent me their raw data. This is not counting those who have relatives participating and thus have to be filtered out for most analysis other than individual admixture percentages etc where I divide participants into small groups.

The following groups are represented:

  • Tamil: 11
  • Punjab: 9
  • Iran: 7
  • Bengal: 5
  • Uttar Pradesh: 4
  • Andhra Pradesh: 3
  • Kerala: 3
  • Gujarati: 3
  • Bihar: 2
  • Karnataka: 2
  • Caribbean Indian: 2
  • Kashmir: 2
  • Sri Lankan: 2
  • Maharashtra: 2
  • Iraqi Arab: 2
  • Anglo-Indian: 1
  • Roma: 1
  • Goa: 1
  • Rajasthan: 1
  • Baloch: 1
  • Sindhi: 1
  • Iraqi Kurd: 1
  • Egyptian/Iraqi Jew: 1

I need to post analyses of Tamils, Bengalis and Punjabis soon.

Another Update

I have a total of 51 participants in the project right now who have sent me their raw data. This is not counting three people who have relatives participating and thus have to be filtered out for most analysis other than individual admixture percentages etc where I divide participants into small groups.

The following groups are represented:

  • Punjab: 7
  • Iran: 7
  • Tamil: 6
  • Bengal: 5
  • Andhra Pradesh: 2
  • Bihar: 2
  • Karnataka: 2
  • Caribbean Indian: 2
  • Kashmir: 2
  • Uttar Pradesh: 2
  • Sri Lankan: 2
  • Kerala: 2
  • Iraqi Arab: 2
  • Anglo-Indian: 1
  • Roma: 1
  • Goa: 1
  • Rajasthan: 1
  • Baloch: 1
  • Unknown: 1
  • Egyptian/Iraqi Jew: 1
  • Maharashtra: 1

I haven't received data from any new participants for more than a week which is the longest lull since I started Harappa Ancestry Project. So go out there and get people to send me their 23andme raw data.

Also, does anyone know if there are a significant number of South Asians who have done FamilyTreeDNA's Family Finder test? Is there a good overlap of SNPs between their test and 23andme's?

We have enough Punjabis, Iranians, Tamil and Bengalis that they deserve separate analysis posts.

Project Update

I have a total of 42 participants in the project right now who have sent me their raw data. This is not counting two people who have relatives participating and thus have to be filtered out for most analysis other than individual admixture percentages etc where I divide participants into small groups.

The following groups are represented:

  • Punjab: 7
  • Iran: 6
  • Tamil: 5
  • Andhra Pradesh: 2
  • Bengal: 2
  • Bihar: 2
  • Karnataka: 2
  • Caribbean Indian: 2
  • Kashmir: 2
  • Anglo-Indian: 1
  • Roma: 1
  • Goa: 1
  • Uttar Pradesh: 1
  • Sri Lankan: 1
  • Rajasthan: 1
  • Kerala: 1
  • Baloch: 1
  • Unknown: 1

The unknown is Manu Sporny who has put his genetic data in the public domain and I have drafted him into our project.

In addition, out of curiosity, I have accepted data from the following:

  • Iraqi Arab: 2
  • Egyptian/Iraqi Jew: 1

I know a bunch of you have done a lot to make this project known and gotten people to submit their data. But we really do need more participants of every ethnicity and geographic region in and around South Asia. So keep on!

I am working on K=12 admixture runs for the batches we have already done. In addition, the reference I dataset will be used for even higher values of K admixture components to see where the limit is.

Also, I am looking into doing chromosome by chromosome admixture (and other analysis). I have done some experimental runs and once I have pored over that data, I'll have something to report.

As we have seen, even with the removal of the San and Pygmy, the Africans take up 3 ancestral components and most South Asians (excepting me of course) do not have any African admixture. So I am working on a reference dataset without any Africans. I have my own take on how to do that which I'll share in the next few days.

In short, my home computer is running admixture, plink, eigensoft, etc. 24x7.

Behar et al Data

In their paper "The genome-wide structure of the Jewish people", Behar et al analyzed the genomes of some Jewish groups. More important than the Jewish samples (which include two South Asian Jewish groups) for us are the different South Asian, Middle Eastern, and European groups they sampled:

Ethnic group Count
Saudis 20
Jordanians 20
Georgians 20
Turks 19
Iranians 19
Hungarians 19
Ethiopians 19
Armenians 19
Lezgins 18
Chuvashs 17
Syrians 16
Romanians 16
Uzbeks 15
Spaniards 12
Egyptians 12
Cypriots 12
Moroccans 10
Lithuanians 10
North Kannadi 9
Belorussian 9
Yemenese 8
Lebanese 7
Sakilli 4
Paniya 4
Cochin Jews 4
Bene Israel 4
Samaritians 2
Russian 2
Malayan 2

Of the 466 samples, I excluded 8 because they were either duplicates or too similar in their genomes to others.

The series matrix files that I downloaded were in a somewhat different format. To convert them to Plink format, I had to look up the platform file for the Illumina genotyping BeadChip they used. Also, Illumina used an A/B alleles and Top/Bot strands system instead of the regular ACGT alleles and forward/reverse strands. This Illumina Technote explained it and I found a Perl script to convert between the two.