Analysis of 30 INDEL Polymorphic Markers in the Panamanian Population: Gene Admixture Estimates, Population Structure and Forensic Parameters

Short tandem repeat (STR) loci have been successfully employed for forensic genetic, paternity and anthropological analyses in the admixed and Amerindian populations of Panamanian for several years. Nevertheless, reports indicate that the use of STRs might be limited in cases involving degraded DNA samples due to their PCR amplicon size and in paternity because of their relatively high mutation rates. Therefore, as a complement to STRs, markers with higher PCR efficiency, such as insertion/deletion (INDEL), have been developed. However, the genetic polymorphisms and distribution of INDELs in the Panamanian population was unknown. Using the Investigator® DIPplex kit (Qiagen), we report here for the first time the genetic profile of 30 INDEL markers in the Panamanian population. Gene admixture estimates and population structure indicated that the Panamanian population is differentially admixed highly polymorphic. Interestingly, admixture estimates where highly similar to our previous report using STR indicating Amerindian, African and European gene contributions. INDELs showed three gene clusters in these proportions: 0.46 (cluster 1), 0.24 (cluster 2) and 0.30 (cluster 3) versus 0.51 (Amerindian), 0.24 (African) and 0.25 (European) for STRs. We also found that both, INDELs and STRs indicated that ancestral gene distribution is heterogeneous among the provinces, across the country. Furthermore, allele frequency variation showed that all loci accomplished Hardy-Weinberg expectations and display high diversity as indicated by the average of observed heterozygosity (0.4477), expected heterozygosity (0.4553) and high similarity with reference U.S. and world populations. Additionally, forensic statistic parameters showed a strong significance in the combined power of discrimination (0.9999999999987) and the combined matching probability (1.27 × 10-12) but relatively lower significance in the combined power of exclusion (0.992655332). The forensic parameters calculated indicate that INDEL markers can be affectively applicable to the Panamanian population for forensic uses but should be complemented with additional markers, such as STRs for paternity analyses.