Contents lists available at ScienceDirect Forensic Science International: Genetics Supplement Series journal homepage: www.elsevier.com/locate/fsigss GENETIC PORTRAIT OF THE PUNJABI POPULATION FROM PAKISTAN USING THE PRECISION ID ANCESTRY PANEL Muhammad Adnan Shan a,b, *, Mie Refn a , Niels Morling a , Claus Børsting a , Vania Pereira a a Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark b Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan ARTICLE INFO Keywords: AIMs Ancestry Punjabi PCA plot Geno geographer ABSTRACT Prediction of geographical ancestry using genetic markers has a great potential in forensic genetics and may be used as an investigative lead in crime casework or missing person identification. Exploration of AIMs in Pakistan is interesting due to the distinct subpopulations with multidirectional ancestry from different groups. In the current study, 87 individuals from the Punjabi population from Pakistan were investigated using the Precision ID Ancestry Panel (Thermo Fisher Scientific) to assess whether it was possible to diff ;erentiate Punjabi individuals from other populations. With this panel, it is revealed that Punjabis are admixed and cannot be distinguished from other populations in South Central Asia and the Middle East. 1. Introduction Genetic markers that present marked allele frequency differences among populations can be used as ancestry informative markers (AIMs). Prediction of geographical ancestry using AIMs has a great potential in forensic genetics and may be used as an investigative lead in crime casework or missing person identification [1–3]. Exploration of AIMs in Pakistan is interesting due to the distinct subpopulations with multidirectional ancestry from neighbouring states and native groups [4,5]. Punjab is the second largest and most populous of the four provinces of Pakistan. It has a population of more than 90 million corresponding to 46 % of the Pakistani population [6]. Punjab is lo- cated in the north-western part of the Indian plate at the Indus River system. The Punjabi population is the largest ethnic group in Pakistan. It consists of a heterogeneous population group with various tribes, clans, and communities. The native language of the province is Punjabi. Various ethnic groups settled in this region and formed the Indus Valley Civilization in the bronze age 3,300 to 1,300 BCE [4–5]. In this work, the Precision ID Ancestry Panel (Thermo Fisher Scientific) [7,8] was used to genotype Punjabi individuals and estimate their ancestry. The panel includes 165 autosomal AIMs for genoogeo- graphic prediction. The marker set is a combination of 55 SNPs of the Kidd AISNP panel [9] and 123 AISNPs from the Seldin panel [10,11] with 13 SNPs overlapping [12]. The most likely population of origin was investigated with GenoGeographer [13,14], a tool that calculates the population likelihoods of a profile for each reference population included in the database (Sub-Saharan Africa, Somalia, North Africa, Europe, Middle East, South Central Asia, and Greenland). 1.1. Materials and methods A total of 87 unrelated Punjabi individuals were typed for 165 an- cestry informative markers using the Precision ID Ancestry Panel (Thermo Fisher Scientific). The Arlequin v.3.5.2.2 software [15] was used to estimate deviations from Hardy-Weinberg equilibrium (HWE). Data were compared to those of populations studied for the same markers (data kindly provided by the Kidd Lab, assembled from pub- licly available data). The SNP rs10954737 was excluded from the inter- population comparisons due to lack of data of the reference popula- tions. Principal component analysis (PCA) was performed using an in- house developed Python script. The software GenoGeographer was used to calculate z-scores, likelihoods and likelihood ratios to infer the most likely population of Punjabis. 2. Results and Discussion All studied 165 AIMs markers were in HWE after Bonferroni cor- rection for multiple testing, except for one locus (rs310644; p- value_0.0001). Punjabis clustered with individuals from South Central Asia and the Middle East as visualised in the PCA plot (Fig. 1). The https://doi.org/10.1016/j.fsigss.2019.09.034 Received 11 September 2019; Accepted 22 September 2019 ⁎ Corresponding author at: Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. E-mail address: muhammad.shan@sund.ku.dk (M.A. Shan). Forensic Science International: Genetics Supplement Series 7 (2019) 87–89 Available online 17 October 2019 1875-1768/ © 2019 Elsevier B.V. All rights reserved. T