Ancestry-informative marker (AIM) SNP panel for the Malay population
Padillah Yahya1, Sarina Sulong2, Azian Harun3
1Department of Paediatrics, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
International Journal of Legal Medicine
|November 25, 2019
Summary
This study developed three Malay Ancestry-Informative Marker (AIM) panels using different methods to accurately identify individuals of Malay ancestry. The developed AIM panels achieved up to 90% accuracy in distinguishing Malay individuals from other populations.
Area of Science:
- Population genetics
- Genomics
- Biomedical research
Background:
- Self-reported ethnicity can be inaccurate in biomedical research.
- Ancestry-informative markers (AIMs) are crucial for inferring individual ancestry.
- Developing population-specific AIMs enhances research accuracy.
Purpose of the Study:
- To develop and evaluate Ancestry-Informative Marker Single Nucleotide Polymorphism (SNP) panels for the Malay population.
- To compare the efficacy of different AIM selection strategies: pairwise FST, informativeness for assignment (In), and PCA-correlated SNPs (PCAIMs).
- To establish a reliable method for identifying Malay ancestry in genetic studies.
Main Methods:
- Extracted genotype data from 165 Malay individuals using SNP arrays (Affymetrix SNP-6, Illumina OMNI 2.5).
- Utilized the HapMap phase 3 database as a reference population (1397 individuals, 11 populations).
- Employed machine learning models (WEKA) to evaluate the accuracy of selected Malay AIM panels.
Main Results:
- A panel of 1250 SNPs achieved 90% accuracy in identifying Malay individuals against global populations.
- The pairwise FST method yielded a 157-SNP panel with 80% accuracy.
- Panels of 200 SNPs selected via In and PCAIMs demonstrated approximately 80% accuracy.
Conclusions:
- The developed Malay AIM panels are effective for identifying individuals of Malay ancestry.
- Different AIM selection strategies offer varying levels of accuracy and panel size.
- These AIM panels can improve the reliability of genetic research involving the Malay population.
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