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January 20, 2018

South Asian Genotype Project, update

Filed under: South Asian Genetics,South Asian Genotype Project — Razib Khan @ 10:08 pm


I’ve been working on the South Asian Genotype Project. Again, if you are interested: send me a 23andMe, Ancestry, or Family Tree DNA raw genotype file to contactgnxp -at- gmail.com.

In the subject please put:

  1. “South Asian Genotype Project”
  2. The state/province your family is from
  3. Ethnolinguistic group
  4. If applicable, caste

I changed the reference populations because the earlier ones were too complicated. You can see the population averages from public data sets for some groups.  The results for project members are here. I re-ran everyone who has sent data in so far. I’ll leave commentary for later.

At this point, I think the easiest way to update project members is to create a mailing list. If you are have submitted genotypes, please join:

Subscribe to the South Asian Genotype Project

* indicates required




January 6, 2018

South Asian Genotype Project update

Just a quick update. I know I haven’t been responsive, but I’ve been traveling and spending time with the family and working a lot for the past few weeks. I’m going to make some revisions to my pipeline as well. I will get back to generating results soon (as in a week or so). So please keep sending data to contactgnxp@gmail.com.

December 2, 2017

South Asian Genotype Project

Filed under: Personal genomics,South Asian Genotype Project — Razib Khan @ 6:02 pm


It’s been a few years since I’ve done any serious “Genome Blogging.” Mostly I’ve been very busy and there isn’t much low-hanging fruit left as it is. But today I want to announce that I’ll be running the generically titled “South Asian Genotype Project.”

The way it works is simple: send me a 23andMe, Ancestry, or Family Tree DNA raw genotype file to contactgnxp -at- gmail.com (though 23andMe’s new chip has far less overlap with other platforms earlier, so probably best if you were typed before August 2017).

In the subject please put:

  1. “South Asian Genotype Project”
  2. The state/province your family is from
  3. Ethnolinguistic group
  4. If applicable, caste

In the body of the email you can put Y and mtDNA and any other information you want. Obviously your data is confidential and I won’t identify you by name, just ethnolinguistic group and such.

Since the last time I did this I have some scripts that make this a lot of easier, so hopefully I’ll be adding individuals to this spreadsheet every few days. I’ll give project members an ID and try to email them when the results are up.

The main motivator for this project on my part is that people still ask me questions about Sinhalese, Nasrani Christians, and other assorted groups which we don’t have answers to because current research projects haven’t focused on them.

Since Zack worked on the Harappa Ancestry Project we know a lot more about South Asian ancestry. Basically, there is an ANI-ASI cline, and some South Asians have exogenous ancestry off this cline. Indian Jews have Middle Eastern ancestry, while Bengalis have East Asian ancestry, and some groups in Pakistan have African ancestry. With that in mind I’ll be testing a smaller number of populations. The marker set is 240,000 SNPs by the way.

Below are some representative results. You can see that my results from three DTC services are basically the same. Also, some South Indian groups (see Pulliyar) show “Dai” ancestry, when I’m pretty sure it’s just that I didn’t sample as much on the extreme portion of the ASI-cline.

ID
Armenians
Belorussian
C_India
Dai
Nigerian
NWIndia
S_India
YemeniteJews
Balochi
34%
1%
0%
0%
0%
66%
0%
0%
Bangladesh_Razib (23andMe)
0%
0%
14%
14%
0%
15%
57%
0%
Bangladesh_Razib (Ancestry)
0%
0%
14%
14%
0%
15%
57%
0%
Bangladesh_Razib (ftDNA)
0%
0%
13%
14%
0%
15%
58%
0%
Chenchus
0%
0%
1%
1%
0%
0%
98%
0%
Dharkars
0%
0%
16%
2%
0%
38%
44%
0%
Dusadh
0%
0%
21%
1%
0%
2%
76%
0%
Iranians
65%
2%
1%
2%
0%
20%
0%
10%
Kallar
0%
0%
0%
0%
0%
0%
100%
0%
Kurumba
0%
0%
0%
0%
0%
4%
96%
0%
Meghawal
0%
0%
10%
0%
0%
26%
64%
0%
MumbaiJews
18%
0%
4%
0%
0%
39%
28%
11%
Naga
0%
0%
0%
90%
0%
0%
10%
0%
NorthKannadi
0%
0%
0%
2%
0%
0%
98%
0%
Pakistani
3%
7%
19%
6%
0%
38%
23%
4%
Pathan
12%
3%
1%
1%
0%
80%
3%
0%
TamilNadu_Iyer
0%
1%
2%
0%
0%
42%
54%
0%
TamilNadu_Nadar
0%
0%
0%
1%
0%
0%
99%
0%
UP_Kayastha
0%
0%
17%
2%
0%
42%
39%
0%
WestBengal_Kayastha
0%
2%
15%
6%
0%
14%
64%
0%
Pulliyar
0%
0%
0%
7%
0%
0%
93%
0%
DalitTN
0%
0%
0%
1%
0%
0%
99%
0%
Velama
0%
0%
9%
0%
0%
22%
68%
0%

South Asian Genotype Project

Filed under: Personal genomics,South Asian Genotype Project — Razib Khan @ 6:02 pm


It’s been a few years since I’ve done any serious “Genome Blogging.” Mostly I’ve been very busy and there isn’t much low-hanging fruit left as it is. But today I want to announce that I’ll be running the generically titled “South Asian Genotype Project.”

The way it works is simple: send me a 23andMe, Ancestry, or Family Tree DNA raw genotype file to contactgnxp -at- gmail.com (though 23andMe’s new chip has far less overlap with other platforms earlier, so probably best if you were typed before August 2017).

In the subject please put:

  1. “South Asian Genotype Project”
  2. The state/province your family is from
  3. Ethnolinguistic group
  4. If applicable, caste

In the body of the email you can put Y and mtDNA and any other information you want. Obviously your data is confidential and I won’t identify you by name, just ethnolinguistic group and such.

Since the last time I did this I have some scripts that make this a lot of easier, so hopefully I’ll be adding individuals to this spreadsheet every few days. I’ll give project members an ID and try to email them when the results are up.

The main motivator for this project on my part is that people still ask me questions about Sinhalese, Nasrani Christians, and other assorted groups which we don’t have answers to because current research projects haven’t focused on them.

Since Zack worked on the Harappa Ancestry Project we know a lot more about South Asian ancestry. Basically, there is an ANI-ASI cline, and some South Asians have exogenous ancestry off this cline. Indian Jews have Middle Eastern ancestry, while Bengalis have East Asian ancestry, and some groups in Pakistan have African ancestry. With that in mind I’ll be testing a smaller number of populations. The marker set is 240,000 SNPs by the way.

Below are some representative results. You can see that my results from three DTC services are basically the same. Also, some South Indian groups (see Pulliyar) show “Dai” ancestry, when I’m pretty sure it’s just that I didn’t sample as much on the extreme portion of the ASI-cline.

ID
Armenians
Belorussian
C_India
Dai
Nigerian
NWIndia
S_India
YemeniteJews
Balochi
34%
1%
0%
0%
0%
66%
0%
0%
Bangladesh_Razib (23andMe)
0%
0%
14%
14%
0%
15%
57%
0%
Bangladesh_Razib (Ancestry)
0%
0%
14%
14%
0%
15%
57%
0%
Bangladesh_Razib (ftDNA)
0%
0%
13%
14%
0%
15%
58%
0%
Chenchus
0%
0%
1%
1%
0%
0%
98%
0%
Dharkars
0%
0%
16%
2%
0%
38%
44%
0%
Dusadh
0%
0%
21%
1%
0%
2%
76%
0%
Iranians
65%
2%
1%
2%
0%
20%
0%
10%
Kallar
0%
0%
0%
0%
0%
0%
100%
0%
Kurumba
0%
0%
0%
0%
0%
4%
96%
0%
Meghawal
0%
0%
10%
0%
0%
26%
64%
0%
MumbaiJews
18%
0%
4%
0%
0%
39%
28%
11%
Naga
0%
0%
0%
90%
0%
0%
10%
0%
NorthKannadi
0%
0%
0%
2%
0%
0%
98%
0%
Pakistani
3%
7%
19%
6%
0%
38%
23%
4%
Pathan
12%
3%
1%
1%
0%
80%
3%
0%
TamilNadu_Iyer
0%
1%
2%
0%
0%
42%
54%
0%
TamilNadu_Nadar
0%
0%
0%
1%
0%
0%
99%
0%
UP_Kayastha
0%
0%
17%
2%
0%
42%
39%
0%
WestBengal_Kayastha
0%
2%
15%
6%
0%
14%
64%
0%
Pulliyar
0%
0%
0%
7%
0%
0%
93%
0%
DalitTN
0%
0%
0%
1%
0%
0%
99%
0%
Velama
0%
0%
9%
0%
0%
22%
68%
0%

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