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Ancestry-informative marker (AIM) SNP panel for the Malay population

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Abstract

Ancestry-informative markers (AIMs) can be used to infer the ancestry of an individual to minimize the inaccuracy of self-reported ethnicity in biomedical research. In this study, we describe three methods for selecting AIM SNPs for the Malay population (Malay AIM panel) using different approaches based on pairwise FST, informativeness for assignment (In), and PCA-correlated SNPs (PCAIMs). These Malay AIM panels were extracted from genotype data stored in SNP arrays hosted by the Malaysian node of the Human Variome Project (MyHVP) and the Singapore Genome Variation Project (SGVP). In particular, genotype data from a total of 165 Malay individuals were analyzed, comprising data on 117 individual genotypes from the Affymetrix SNP-6 SNP array platform and data on 48 individual genotypes from the OMNI 2.5 Illumina SNP array platform. The HapMap phase 3 database (1397 individuals from 11 populations) was used as a reference for comparison with the Malay genotype data. The accuracy of each resulting Malay AIM panel was evaluated using a machine learning “ancestry-predictive model” constructed by using WEKA, a comprehensive machine learning platform written in Java. A total of 1250 SNPs were finally selected, which successfully identified Malay individuals from other world populations with an accuracy of 90%, but the accuracy decreased to 80% using 157 SNPs according to the pairwise FST method, while a panel of 200 SNPs selected using In and PCAIMs could be used to identify Malay individuals with an accuracy of approximately 80%.

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Acknowledgments

We would like to thank all participants who contributed samples for this study. All authors contributed to aspects of the conception or design of the experimental work, analysis of data, and review and approval the final content of the manuscript.

Funding

This work was supported by a Universiti Sains Malaysia Apex Grant: 1002/PPSP/910343and an NTU Grant (Muhammed Ariff Research Grant (MAS): 304.PPSP.6150148.N119.

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Authors and Affiliations

  1. Department of Paediatrics, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia

    Padillah Yahya & Bin Alwi Zilfalil

  2. Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia

    Sarina Sulong

  3. Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia

    Azian Harun

  4. National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Khlong Luang District, Pathum Thani, 12120, Thailand

    Pongsakorn Wangkumhang, Alisa Wilantho, Chumpol Ngamphiw & Sissades Tongsima

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  1. Padillah Yahya
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Corresponding author

Correspondence to Bin Alwi Zilfalil.

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The humane and ethical research standards recommended by Universiti Sains Malaysia were followed in this study. All participants signed the written informed consents before sample collection. This study was approved by Universiti Sains Malaysia ethics committee.

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Supplement Fig. 1.

Method overview: We propose AIM selection methods (See Method Section for details) including quality control (QC), population clustering using ipPCA, and three approaches for selecting AIMs. In particular, we apply standard QC steps to the Malaysian population and 11 world populations from HapMap and population data from three Singaporean ethnic groups. We perform population clustering using ipPCA and obtain 11 subpopulations (SP1-SP11) as a result. We apply the AIM selection methods among the 11 subpopulations, including pairwise Fst (we selected the top 5 and top 50 SNPs from each SP), informativeness for assignment (200 SNPs) and PCAIMs (200 SNPs). Finally, we assess each model’s performance via ROC analysis using WEKA. (PNG 325 kb)

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Supplement Fig. 2

The performance of the SNPs selected based on In in classifying Malay individuals into their correct group. (PNG 324 kb)

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Supplement Fig. 3

The performance of the 100 SNPs selected based on In as shown by ADMIXTURE analysis. (PNG 20934 kb)

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Supplement Fig. 4

The performance of the 100 SNPs selected based on PCAIMs (k=3) as shown by ADMIXTURE analysis. (PNG 26171 kb)

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Supplement Fig. 5

Comparison of the performance of the PCAIMs and In method. (PNG 877 kb)

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Supplement data 6

Comparison of AIM model based on WEKA analysis. (XLSX 46 kb)

Supplement Fig. 7

Genetic structure of the Malay population using a set of 555 AIMs. (PNG 4704 kb)

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Supplement Fig. 8

Classification assessment via ROC analysis for 200 SNPs selected using PCAIMs (k=3). (PNG 4637 kb)

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Supplement Fig. 9

Classification assessment via ROC analysis for 1250 SNPs selected using Fst. (PNG 4501 kb)

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Supplement Fig. 10

Classification assessment via ROC analysis for 200 SNPs selected using In. (PNG 4791 kb)

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Supplement Fig. 11

Classification assessment via ROC analysis for 157 SNPs selected using Fst. (PNG 4526 kb)

High resolution image (TIFF 14768 kb)

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Yahya, P., Sulong, S., Harun, A. et al. Ancestry-informative marker (AIM) SNP panel for the Malay population. Int J Legal Med 134, 123–134 (2020). https://doi.org/10.1007/s00414-019-02184-0

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