Assessing PreCR™ repair enzymes for restoration of STR profiles from artificially degraded DNA for human identification

Robertson, James; Dineen, Shauna M.; Scott, Kristina A.; Lucyshyn, Jonathan; Saeed, Maria; Murphy, Devonie L.; Schweighardt, Andrew J.; Meiklejohn, Kelly A.

doi:10.1016/j.fsigen.2014.05.011

Cited by 19 publications

(8 citation statements)

References 29 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: 92%

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: 92%

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

et al. 2015

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“…Various studies over the last decade have elucidated the nature of some of the damage mechanisms associated with biological evidence (Hall and Ballantyne 2004;Gates 2009;Ballantyne 2009, 2010;Hall et al 2014). DNA damage with regard to forensic specimens has been widely studied; various methods exist that attempt to repair various forms of DNA damage (Evans and Nichols 2008;Diegoli et al 2012;Ambers et al 2014;Robertson et al 2014;Wallace 2014). Little is known, however, with regard to miRNA damage-in particular, with forensic specimens.…”

Section: Potential Limitationsmentioning

confidence: 99%

Potential applications of microRNA profiling to forensic investigations

Glynn

2019

RNA

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Within the forensic science community, there is a continued push to develop novel tools to aid in criminal investigations. microRNA (miRNA) analysis has been the focus of many researcher's attention in the biomedical field since its discovery in 1993; however, the forensic application of miRNA analysis has only been suggested within the last 10 years and has been gaining considerable traction recently. The primary focus of the forensic application of miRNA analysis has been on body fluid identification to provide confirmatory universal analysis of unknown biological stains obtained from crime scenes or evidence items. There are, however, other forensic applications of miRNA profiling that have shown potential, yet are largely understudied, and warrant further investigation such as organ tissue identification, donor age estimation, and more. This review paper aims to evaluate the current literature and future potential of miRNA analysis within the forensic science field.

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“…The PreCR repair mix we used in this study has been shown to repair a variety of DNA damages, including DNA nicks, gaps, modifications of DNA molecules such as oxidation, and deamination, loss of DNA bases, and pyrimidine‐dimer formation . In forensics, it was reported that the PreCR repair mix could restore short tandem repeat profiles from UV‐damaged DNA samples and artificially degraded DNA, mimicking the exposure of native DNA to oxidizing agents, hydrolytic conditions, and ionizing radiation . In archeology, it was used to recover heavily damaged ancient DNA samples .…”

Section: Discussionmentioning

confidence: 99%

“…To salvage the damaged DNA molecules, the use of PreCR repair mix, a commercial DNA repair kit, has been shown to be effective in recovering damaged DNA in forensics, archeology, and molecular diagnostics . We hypothesized that the PreCR repair mix could also be used to repair cfDNA in maternal plasma.…”

Section: Introductionmentioning

confidence: 99%

Enrichment of fetal and maternal long cell‐free DNA fragments from maternal plasma following DNA repair

et al. 2019

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Objective Cell‐free DNA (cfDNA) fragments in maternal plasma contain DNA damage and may negatively impact the sensitivity of noninvasive prenatal testing (NIPT). However, some of these DNA damages are potentially reparable. We aimed to recover these damaged cfDNA molecules using PreCR DNA repair mix. Methods cfDNA was extracted from 20 maternal plasma samples and was repaired and sequenced by the Illumina platform. Size profiles and fetal DNA fraction changes of repaired samples were characterized. Targeted sequencing of chromosome Y sequences was used to enrich fetal cfDNA molecules following repair. Single‐molecule real‐time (SMRT) sequencing platform was employed to characterize long (>250 bp) cfDNA molecules. NIPT of five trisomy 21 samples was performed. Results Size profiles of repaired libraries were altered, with significantly increased long (>250 bp) cfDNA molecules. Single nucleotide polymorphism (SNP)‐based analyses showed that both fetal‐ and maternal‐derived cfDNA molecules were enriched by the repair. Fetal DNA fractions in maternal plasma showed a small but consistent (4.8%) increase, which were contributed by a higher increment of long fetal cfDNA molecules. z ‐score values were improved in NIPT of all trisomy 21 samples. Conclusion Plasma DNA repair recovers and enriches long cfDNA molecules of both fetal and maternal origins in maternal plasma.

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Assessing PreCR™ repair enzymes for restoration of STR profiles from artificially degraded DNA for human identification

Cited by 19 publications

References 29 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

Potential applications of microRNA profiling to forensic investigations

Enrichment of fetal and maternal long cell‐free DNA fragments from maternal plasma following DNA repair

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