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Insertion/deletion (INDEL) polymorphisms are diallelic markers with potential characteristics for use in forensics and biological anthropology, including: the simplicity of laboratory analysis, the possibility of genotyping many markers in a single PCR multiplex reaction, as well as analyzing markers with special inheritance types, such as those linked to the X chromosome (X-INDEL). In this work we developed a laboratory analysis methodology using a 33-INDEL marker panel for the X chromosome in a single PCR multiplex reaction, followed by a capillary electrophoresis run. We employed the panel to genotype a sample of 351 individuals of a mixed population from the Brazilian Amazon. The results demonstrate that the measurement of biostatistical parameters for forensic use in this population is compatible with prior estimates from other populations using current X-STR panels.

A new polymorphic INDEL was detected at the X-STR GATA172D05 flanking region, which corresponds to an 18-bp deletion, 141 bp upstream the TAGA repeat motif. This INDEL was found to be polymorphic in different population samples from Native Americans, Africans, and Europeans as well as in an admixed population from the Amazonia (Belém). Gene diversities varied between 37.5% in Native Americans and 49.9% in Africans. Comparison between human and chimpanzee sequences showed that the ancestral state corresponds to the presence of two copies of 18 bp, detected in both species; and the mutated allele has lost one of these two copies. The simultaneous analysis of the short tandem repeat (STR) and INDEL variation showed an association between the INDEL ancestral allele with the shorter STR alleles. High diversities were found in all population groups when combining the information provided by the INDEL and STR variation. Gene diversities varied between 76.7% in Native Americans and 80.6% in both Portugal and Belém.