Assessment of the role of DNA repair in damaged forensic samples

Ambers, Angie; Turnbough, Meredith; Benjamin, Robert C.; King, Jonathan L.; Budowle, Bruce

doi:10.1007/s00414-014-1003-3

Cited by 27 publications

(14 citation statements)

References 23 publications

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“…Whether this accounts for the increase in adapted molecules (Supplementary Figure S1) and endogenous DNA content (Figure 1) is unclear. The results presented here are consistent with previous STR-based evaluations, where peak height decrease or allelic drop-out was observed in more complex DNA samples equivalent to aDNA specimens (14,15). …”

Section: Resultssupporting

confidence: 95%

Surveying the Repair of Ancient DNA from Bones Via High-Throughput Sequencing

et al. 2015

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DNA damage in the form of abasic sites, chemically altered nucleotides, and strand fragmentation is the foremost limitation in obtaining genetic information from many ancient samples. Upon cell death, DNA continues to endure various chemical attacks such as hydrolysis and oxidation, but repair pathways found in vivo no longer operate. By incubating degraded DNA with specific enzyme combinations adopted from these pathways, it is possible to reverse some of the post-mortem nucleic acid damage prior to downstream analyses such as library preparation, targeted enrichment, and high-throughput sequencing. Here, we evaluate the performance of two available repair protocols on previously characterized DNA extracts from four mammoths. Both methods use endonucleases and glycosylases along with a DNA polymerase-ligase combination. PreCR Repair Mix increases the number of molecules converted to sequencing libraries, leading to an increase in endogenous content and a decrease in cytosine-to-thymine transitions due to cytosine deamination. However, the effects of Nelson Repair Mix on repair of DNA damage remain inconclusive.

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Section: Resultssupporting

confidence: 95%

Surveying the Repair of Ancient DNA from Bones Via High-Throughput Sequencing

et al. 2015

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“…Whole human blood samples were environmentally-damaged as described in [1]. All samples were anonymized and collected in accordance with methods approved by the Institutional Review Board of the University of North Texas Health Science Center in Fort Worth, Texas USA.…”

Section: Degraded/compromised Samplesmentioning

confidence: 99%

“…Contemporary skeletal remains consisted of 1 femur and 1 tibia from two different individuals. Historical bone samples included the 120-year-old skeletal remains (right femur, both tibiae, four teeth) of an exhumed American Civil War soldier [1,19] and the skeletal remains (femora and tibiae) of four Finnish World War II soldiers (provided by the Department of Forensic Medicine, University of Helsinki, Helsinki, Finland) [20].…”

Section: Degraded/compromised Samplesmentioning

confidence: 99%

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Modified DOP-PCR for improved STR typing of degraded DNA from human skeletal remains and bloodstains

et al. 2016

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Forensic and ancient DNA samples often are damaged and in limited quantity as a result of exposure to harsh environments and the passage of time. Several strategies have been proposed to address the challenges posed by degraded and low copy templates, including a PCR based whole genome amplification method called degenerate oligonucleotide-primed PCR (DOP-PCR). This study assessed the efficacy of four modified versions of the original DOP-PCR primer that retain at least a portion of the 5' defined sequence and alter the number of bases on the 3' end. The use of each of the four modified primers resulted in improved STR profiles from environmentally-damaged bloodstains, contemporary human skeletal remains, American Civil War era bone samples, and skeletal remains of WWII soldiers over those obtained by previously described DOP-PCR methods and routine STR typing. Additionally, the modified DOP-PCR procedure allows for a larger volume of DNA extract to be used, reducing the need to concentrate the sample and thus mitigating the effects of concurrent concentration of inhibitors.

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“…Analysis of various biomarkers in biofluids found at a crime scene can help in preliminary conclusions about the race, gender, age, etc., of possible suspects [35]. DNA typing for criminal suspects or victims can be extended to the DNA analysis of human remains [36], as well as to the analysis of DNA damage and repair in forensic samples [37]. In addition, while in most forensic analytical applications samples collected at the crime scene are sent to a specialized laboratory for sophisticated instrumental analysis, rapid on-site analysis of samples could be very beneficial for crime investigation, thus, representing another use of simple biosensors in forensic practice [38].…”

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confidence: 99%

Forensic Science - Multidisciplinary Approach

Katz¹

2015

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The word forensic originates from the Latin word forensis, which means: public, to the forum or public discussion. A modern definition of forensic is: relating to, used in, or suitable to a court of law [1]. Any science used for the purpose of law is a forensic science. Forensic sciences [2-4] concern the application of scientific knowledge to legal problems and they are vital tools in any legal proceeding. The forensic sciences, including forensic chemistry [5-8], forensic biology [9,10], forensic anthropology [11], forensic medicine [12], forensic materials science [13,14], forensic engineering [15], computational forensics [16], etc., are broadly used to resolve civil disputes, to justly enforce criminal laws and government regulations, and to protect public health. While novel methods used in natural sciences might have some allowance for limited reproducibility and questionable interpretations, adaptation to forensic science, requires absolute reproducibility and non-variability in terms of the results interpretation: evidence is not only a scientific, but legal issue. It should be kept in mind that forensic analysis is strongly regulated by the legal constraints which affect both the work implementation and the results. Forensic science is in a unique position among all other scientific fields because of its important social impact. Indeed, forensic science is at the intersection of the natural sciences and law in civil and criminal cases. Therefore, methods used in forensic science require not only rigorous scientific standards, but also high ethical standards, providing interpretation of obtained results without any possibility

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Assessment of the role of DNA repair in damaged forensic samples

Cited by 27 publications

References 23 publications

Surveying the Repair of Ancient DNA from Bones Via High-Throughput Sequencing

Surveying the Repair of Ancient DNA from Bones Via High-Throughput Sequencing

Modified DOP-PCR for improved STR typing of degraded DNA from human skeletal remains and bloodstains

Forensic Science - Multidisciplinary Approach

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