Genetic profiling variation caused by tissue type, error, and damage

Abstract

Genetic profiling variations caused by tissue type, error, and damage have been studied only minimally in the past. Even though it is well accepted that damage to the DNA molecule and PCR induced error occur, little focus has been given to their roles in generating variation within genetic profiles. Through the generation and compilation of mitochondrial DNA (mtDNA) sequence data, autosomal short tandem repeat (STR) data, and Y-chromosome STR (Y-STR) data, the incidence of damage, error and mutation was assessed during this study. Mitochondrial DNA sequence data was analyzed among 255 replicates from 42 aDNA samples in 9 populations. Intra-individual genetic profiling variations were observed in 28 replicates from 18 individuals, the majority of which can be explained by damage to the DNA molecule (hydrolytic and oxidative). In 15 replicates from 1 modem individual, no Y-STR profiling variations were observed. Conversely, ancient Y-STR data yielded multiple variations, all of which are attributable to PCR error. In 64 replicates from 6 individuals, only 4 alleles in total were observed to consistently amplify. The remaining loci exhibited variation among multiple replicates from each individual. To overcome such profiling problems, 8 hemi-nested Y-STR singleplexes were designed and optimized. For autosomal STRs, booster STR amplification was tested for its potential use, however, the results were unreliable. The data obtained throughout this study are consistent with previous reports pertaining to DNA damage. In addition, this research has shown that specific damage is acting on particular populations presumably due to their depositional environments. This research leads into future studies concerning DNA damage detection and repair for the recovery of low copy number DNA templates.