Tag Archives: singapore

HarappaWorld Tweaks

Posted by on May 29, 2012 18 comments

First of all, I wanted to draw your attention to the fact that I am using weighted means for population averages for HarappaWorld instead of just averaging all samples' results. The weighting gives less importance to outliers. I find this to be a better solution than a simple average or median. A median removes all outliers but it also rejects a lot of information.

An example of the weighted mean effect can be seen in the Behar et al Armenian samples. Four of the samples have higher NE European percentages than the rest. As you can see in the table below, the weighting makes their impact on the population results low.

Mean Weighted Mean
Ethnicity armenian armenian armenian armenian
Dataset behar yunusbayev behar yunusbayev
N 19 16 19 16
S Indian 0.37% 0.52% 0.41% 0.52%
Baloch 16.57% 17.73% 17.07% 17.65%
Caucasian 54.35% 56.43% 57.29% 56.61%
NE Euro 8.96% 2.98% 5.35% 2.95%
SE Asian 0.10% 0.12% 0.10% 0.13%
Siberian 0.49% 0.09% 0.29% 0.09%
NE Asian 0.14% 0.08% 0.16% 0.09%
Papuan 0.28% 0.27% 0.26% 0.27%
American 0.19% 0.18% 0.22% 0.18%
Beringian 0.26% 0.19% 0.23% 0.20%
Mediterranean 8.46% 8.37% 8.21% 8.40%
SW Asian 9.81% 13.03% 10.40% 12.91%
San 0.00% 0.00% 0.00% 0.00%
E African 0.02% 0.00% 0.01% 0.00%
Pygmy 0.00% 0.00% 0.00% 0.00%
W African 0.00% 0.00% 0.00% 0.00%

Another example is the Somali samples in Reich et al data. There is one sample (out of 6) who seems to be eastern Bantu. Let's compare the unweighted mean and weighted mean for Somalis in Reich et al and Harappa participants.

Mean Weighted Mean
Ethnicity somali somali somali somali
Dataset harappa reich harappa reich
N 2 6 2 6
S Indian 0.00% 1.62% 0.00% 1.49%
Baloch 0.00% 0.00% 0.00% 0.00%
Caucasian 2.76% 0.00% 2.76% 0.00%
NE Euro 0.00% 0.11% 0.00% 0.04%
SE Asian 0.27% 0.05% 0.27% 0.06%
Siberian 0.00% 0.04% 0.00% 0.05%
NE Asian 0.00% 0.41% 0.00% 0.46%
Papuan 0.26% 0.10% 0.26% 0.11%
American 0.14% 0.17% 0.14% 0.19%
Beringian 0.23% 0.33% 0.23% 0.38%
Mediterranean 2.12% 3.25% 2.12% 3.65%
SW Asian 31.73% 24.48% 31.73% 27.33%
San 1.96% 1.48% 1.96% 1.37%
E African 60.37% 56.75% 60.37% 60.13%
Pygmy 0.15% 1.78% 0.15% 1.23%
W African 0.00% 9.43% 0.00% 3.51%

Also, I have divided Singapore Indians into 4 groups (actually 3 groups and 1 outlier) since they are so heterogeneous. Here are the weighted mean admixture proportions for all Singapore Indians and the four subgroups.

Ethnicity singapore-indian singapore-indian-1 singapore-indian-2 singapore-indian-3 singapore-indian-4
Dataset sgvp sgvp sgvp sgvp sgvp
N 83 31 41 10 1
S Indian 53.57% 61.95% 50.39% 33.68% 27.81%
Baloch 33.97% 30.24% 36.00% 40.72% 14.27%
Caucasian 3.55% 1.92% 4.03% 9.32% 4.53%
NE Euro 2.93% 0.08% 3.89% 9.84% 35.38%
SE Asian 1.31% 1.30% 1.23% 0.63% 1.20%
Siberian 0.45% 0.47% 0.44% 0.43% 1.19%
NE Asian 0.92% 0.91% 0.80% 1.19% 3.26%
Papuan 0.72% 1.09% 0.50% 0.35% 0.62%
American 0.42% 0.35% 0.44% 0.69% 1.29%
Beringian 0.56% 0.38% 0.65% 0.76% 0.00%
Mediterranean 0.67% 0.40% 0.72% 1.33% 10.38%
SW Asian 0.90% 0.86% 0.87% 1.05% 0.06%
San 0.01% 0.00% 0.01% 0.00% 0.00%
E African 0.03% 0.02% 0.04% 0.00% 0.00%
Pygmy 0.00% 0.00% 0.00% 0.00% 0.00%
W African 0.01% 0.01% 0.00% 0.00% 0.00%

I have updated the spreadsheet as well as HarappaWorld Oracle.

Reich et al and Pan-Asian Datasets

Posted by on March 17, 2011 16 comments

I got access to the Reich et al (Nature 2009) dataset used in their paper "Reconstructing Indian population history".

It has the following populations:

Aonaga Aus Bhil
Chenchu Great_Andamanese Hallaki
Kamsali Kashmiri_Pandit Kharia
Kurumba Lodi Madiga
Mala Meghawal Naidu
Nysha Onge Sahariya
Santhal Satnami Siddi
Somali Srivastava Tharu
Vaish Velama Vysya

There are 141 individuals with 587,753 SNPs in their dataset which conveniently is in PED format.

Also, Blaise pointed me to the Pan-Asian SNP data used in the Dec 2009 Science paper "Mapping Human Genetic Diversity in Asia".

It includes the following 71 populations:

Maya Auca Quechua Karitiana Pima
Ami Atayal Melanesians Zhuang Han_Cantonese
Hmong Jiamao Jinuo Han_Shanghai Uyghur
Wa Alorese Dayak Javanese Batak_Karo
Lamaholot Lembata Malay Mentawai Manggarai
Kambera Sunda Batak_Toba Toraja Andhra_Pradesh
Karnataka Bengali-Assamese Rajasthan Uttaranchal Uttar Pradesh
Haryana Spiti Bhili Marathi Japanese
Ryukyuan Korean Bidayuh Jehai Kelantan
Kensiu Temuan Ayta Agta Ati
Iraya Minanubu Mamanwa Filipino Singapore_Chinese
Singapore_Indian Singapore_Malay Hmong (Miao) Karen Lawa
Mlabri Mon Paluang Plang Tai_Khuen
Tai_Lue H'tin Tai_Yuan Tai_Yong Yao
Hakka Minnan

It has 1,719 individuals with 54,794 SNPs. I wish it had more SNPs considering the wealth of populations.

Also, the Pan-Asian data is in the form of minor allele counts, so I need to convert that back to A/C/G/T. Since there are some HapMap populations included in the dataset, that shouldn't be too hard.

I am going to include both these datasets into my big reference set.

Singapore Indians

Posted by on March 11, 2011 8 comments

In the South Asian PCA plot, we saw that Singapore Indian samples from the SGVP dataset had a lot of diversity. Let's zoom into that plot so it's not dominated by the distinctiveness of the Kalash.

Eigenvector 1 explains 1.45 times the variation compared to eigenvector 2.

We see that Singapore Indians are spread in the whole region from Sindhis to North Kanaddi.

Now let's look at the individual admixture results (at K=12 ancestral populations) for the Singapore Indians. I have added some South Asian reference population averages so you can place them in context.

You can click on the legend to the right of the bar chart to sort by different ancestral components.

From these results, a majority of the Singapore Indian samples look South Indian but there are definitely a few from the northwest of the subcontinent (Punjabis or Sindhis?) There are also a few who could be from the Hindi belt.

There are 2-3 samples who have a significant amount of Southeast Asian. Could they be originally from Bengal? Or could they have partial Singapore Malay ancestry?

SGVP

Posted by on January 26, 2011 4 comments

SGVP is the Singapore Genome Variation Project. It sampled the following groups:

Ethnicity Sample Count SNP Count
Singapore Chinese 96 1,405,417
Singapore Malay 89 1,402,256
Singapore Indian 83 1,404,699

Singapore Indians are generally likely to be South Indians, especially Tamils.

These 268 samples were easy to convert to Plink format