ABSTRACT
DNA extracts from challenged samples, such as environmentally insulted stains, bones, and other anthropological materials that are characterized by containing a low copy number of severely degraded DNA and/or the presence of polymerase chain reaction (PCR) inhibitors, may pose challenges to downstream DNA analyses. PCR amplification, a critical step in the DNA typing process, generates millions to billions of copies of targeted DNA sequences. These amplified products will be subjected to further analyses, e.g., sequencing or capillary electrophoresis (CE), to determine genotypes or haplotypes of the samples. Therefore, enhancing recovery of DNA, purifying extracts to remove inhibitors, and making PCR robust are crucial in successful DNA data generation. Several methods for enhancement of the efficacy of PCR with challenged DNA samples have been proposed. Some techniques target improvement of amplification of degraded DNA, while others enrich amplification when PCR inhibitors are co-extracted. Herein, methods that can improve the recovery of genetic information from challenged samples will be discussed. The examples primarily will focus on bones; however, the approaches apply equally well to biological stain evidence recovered from crime scenes. Each strategy should be applied with an understanding of the particular traits of challenged samples and the techniques, and each requires validation.
