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Steady Improvement in Techniques for the Analysis of Degraded DNA

by Douglas Ankney

DNA, while remarkably resilient, may be degraded by exposure to ultraviolet radiation, extreme temperatures, humidity, and microbial activity. These exposures may result in “single-strand and double-strand breaks, depurination, deamination, and crosslinks.” Consequently, the DNA “becomes fragmented, diminishing its suitability for traditional forensic analysis methods that rely on intact, high-quality genetic material.”

Short tandem repeat (“STR”) analysis is the gold standard of forensic profiling. Specific DNA sequences that appear along the human genome—the lengths of which vary between individuals—are represented by the STRs. But analysis of STRs in degraded samples is difficult and may be misleading.

DNA that is degraded often leads to “allele dropout” (where particular markers fail to amplify), resulting in “incomplete profiles” and compromising the integrity of forensic analysis. Additionally, there is the possibility of “allele drop-in” (where random DNA fragments erroneously amplify) “introducing noise into the analysis.”

The first obstacle in forensic analysts’ attempts to analyze degraded DNA is extracting usable DNA. While traditional extraction methods often fall short, advanced DNA extraction techniques have proven effective when the DNA is degraded. Specialized kits, including magnetic bead technologies that selectively bind to DNA molecules, enable forensic analysts to extract more genetic material from heavily damaged specimens.

After extraction, the next step in DNA analysis is “PCR amplification.” PCR amplification “produces numerous copies of specific DNA regions, generating sufficient genetic material for analysis.” But severely damaged DNA doesn’t always amplify properly for traditional STR analysis because of fragmentation.

But now, forensic analysts have at their disposal “mini-STRs,” which are compact versions of traditional STR loci, representing shorter repeat units and smaller amplicon sizes. These characteristics make mini-STRs more likely to amplify from degraded DNA samples, as shorter fragments are less susceptible to degradation. Mini-STRs are “invaluable for obtaining usable DNA profiles from highly compromised or fragmented samples.” The enhanced resilience of mini-STRs to degradation “enables forensic experts to bridge gaps in traditional STR analysis, preserving the integrity of the genetic information.”

The inclusion of additional dye channels has also provided a more comprehensive and sophisticated approach to DNA profiling via “increasing the number of loci that can be simultaneously analyzed within a single reaction, including mini-STRs.” Each additional dye channel enables forensic analysts and genetic analysts to amplify and detect greater numbers of STR loci in single reaction, “enhancing the discriminatory power of DNA profiling. The broader spectrum of colors minimizes overlap between peaks, reducing the likelihood of allele dropout and improving the ability to distinguish between alleles, especially in complex mixtures.”   

 

Source: forensicmag.com

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