Population genetics of 30 insertion/deletion polymorphisms in the Bahraini population

Abstract

This paper evaluates the forensic utility of 30 insertion-deletion polymorphism (indel) markers in a sample from the Bahraini population using the Qiagen Investigator DIPplex Kit. Allele frequencies and forensic stats of the 30 indels were investigated in 293 unrelated individuals from different governorates of the Kingdom of Bahrain. None of the markers showed significant deviation from Hardy Weinberg equilibrium except for HLD88 locus and no linkage disequilibrium were detected between all possible pair of the indel loci, assuming that these markers are independent and their allele frequencies can be used to calculate the match probabilities in the Bahraini population. The high power of discrimination (CPD = 0.9999999999998110) and the low combined match probability (CPM = 1.89 × 10−13) indicate that these markers are informative and can be successfully used for human identification in terms of forensics and paternity. Genetic distances and relatedness were displayed through multidimensional plotting and phylogenetic tree using various populations in the region. Our study showed that the Bahraini population was clustered with neighboring countries such as Kuwait and Emirates which indicates that these closely geographical regions share similar allele frequencies and are more genetically related than other reference population studied.

Population Genetic Data of 30 Insertion-Deletion Markers in the Polish Population

“…The POPTREE2 software [ 17 ] was used to calculate sample bias corrected interpopulation FST distances [ 18 ] and also to reconstruct the neighbor-joining (NJ) phylogenetic tree [ 19 ] based on allelic frequency data. Twenty populations were included in the FST calculation: Poland (this study), Spain [ 20 ], Mexico (Chihuahua) [ 21 ], South Korea [ 22 ], Finland, Somalia [ 23 ], Pakistan (Punjab) [ 24 ], South Africa Afrikaner, Zulu) [ 25 ], Iraq, Lithuania, Slovenia, Turkey [ 26 ], Vietnam, Nigeria [ 27 ], Bahrain [ 28 ], immigrants from Angola and Mozambique in Lisbon, Portugal [ 29 ], Brazil [ 30 ], and China (Han) [ 31 ]. A multidimensional scaling analysis (MDS) plot on the pairwise FST distances was drawn using the SMACOF approach [ 32 ] in the R package v.4.1.1 [ 33 ].…”

Applications of massively parallel sequencing in forensic genetics

“…So far, more than 3.5 million InDels have been identified through massively parallel sequencing (The 1000 Genomes Project Consortium et al, 2015). When compared to STRs, DIPs present lower mutation rates (~2.9 x 10 -9 ) (Nachman and Crowell, 2000), and its amplification and sequencing result in shorter amplicons in a procedure that does not result in the production of stutter, which makes it an interesting marker for forensic purposes (Zaumsegel et al, 2013;Al-Snan et al, 2021). InDels have been successfully used for ancestry inference and human identification.…”

Identification of Male-Specific Molecular Markers by Recombination of RhoGEF10 Gene in Spotted Knifejaw (Oplegnathus punctatus)

“…Insertion/deletion polymorphism is a molecular marker, which is the second most frequent alteration at the DNA or protein sequence level after residue substitution, mainly manifested by the insertion or deletion of fragmented DNA of different sizes in the genome [ 18 ]. As an important member of the RhoGEF family, RhoGEF10 is involved in the normal development of peripheral nerves in vertebrates, influencing peripheral nerve conduction velocity and myelin sheath thickness [ 15 ].…”