Estimation of the detection rate in STR analysis by determining the DNA degradation ratio using quantitative PCR

To date, there is no systematic investigation of the association of short tandem repeat (STR) typing success rate in soft tissues with different signs of putrefaction. Herein, putrefaction was rated using a newly developed 19-parameter system in soft tissues from a collective of 68 decaying bodies, and DNA yield was determined in 408 samples. DNA integrity was rated using a self-devised pentaplex PCR generating an "integrity score" (Si). STR typing success rate was then assessed for selected cases. DNA yield and Si differed significantly between tissues with kidney on average exhibiting the highest Si values. Statistical analysis revealed that nine parameters were significantly and positively correlated with Si . The observed values for each of these nine parameters were summed up to generate a putrefaction score (Sp) for each sample. Our results show that STR typing success rate can be predicted based on Sp before expensive multiplex STR profiling is performed.

Section: Discussionmentioning

confidence: 99%

Assessment of STR Typing Success Rate in Soft Tissues from Putrefied Bodies Based on a Quantitative Grading System for Putrefaction

Courts

Sauer

Hofmann

et al. 2015

“…The stored DNA of the Sample A was used in this study. This DNA sample was extracted from liquid blood using a MagNA Pure LC instrument (Roche Diagnostics, Basel, Switzerland) for the population studies and its 1/10 solution diluted with low TE buffer (TE −4 ) was quantified in real‐time PCR assay using the 207‐bp amplicon at D17Z1 locus in the same method described previously in the comparison study of DNA extraction instruments . The sample was used with the approval of the ethics committee at our institute.…”

Section: Methodsmentioning

confidence: 99%

D5S818 Typing Discrepancy Between PowerPlex^® Fusion and Other STR Kits Including GlobalFiler^® Caused by a One‐base Deletion in 31 Nucleotides Upstream of the Repeat Region

Fujii

Iwashima

Watahiki

et al. 2016

Self Cite

Short tandem repeat (STR) typing is widely used in forensic investigation. When the same DNA sample is analyzed with different STR typing kits, a typing discrepancy is occasionally observed. In this study, we examined the cause of a typing discrepancy in a sample at D5S818 locus. This sample was designated as 10, 12 using Identifiler(®) , Identifiler(®) Plus, GlobalFiler(®) , PowerPlex(®) 16HS, and PowerPlex(®) 18D, but as 9.3, 12 using PowerPlex(®) Fusion. Sequencing results indicated that the shorter allele in the sample had a deletion (U31Tdel) at 31 nucleotides upstream of the repeat region (AGAT)10 . This deletion was located in the binding site of the published D5S818 forward primer in PowerPlex(®) 16 and was only 9 and 11 nucleotides downstream of our estimated 5' end position of D5S818 forward primer in GlobalFiler(®) and PowerPlex(®) 18D, respectively. We also examined the effect of primer length on the heterozygous peak balance in this sample.

“…The selected primer target sites were compared to all of the available sequences using BLAST (http://www.ncbi.nlm.nih.gov/BLAST) and were confirmed as complementary to the target species, but not with other species. In addition, the primer set designed by Kitayama et al was used to detect and quantify human DNA. The sequences of all of the primers are shown in Table .…”

Section: Methodsmentioning

confidence: 99%

Screening Test for Shed Skin Cells by Measuring the Ratio of Human DNA to Staphylococcus epidermidisDNA

Nakanishi

Ohmori

Hara

et al. 2016

A novel screening method for shed skin cells by detecting Staphylococcus epidermidis (S. epidermidis), which is a resident bacterium on skin, was developed. Staphylococcus epidermidis was detected using real-time PCR. Staphylococcus epidermidis was detected in all 20 human skin surface samples. Although not present in blood and urine samples, S. epidermidis was detected in 6 of 20 saliva samples, and 5 of 18 semen samples. The ratio of human DNA to S. epidermidisDNA was significantly smaller in human skin surface samples than in saliva and semen samples in which S. epidermidis was detected. Therefore, although skin cells could not be identified by detecting only S. epidermidis, they could be distinguished by measuring the S. epidermidis to human DNA ratio. This method could be applied to casework touch samples, which suggests that it is useful for screening whether skin cells and human DNA are present on potential evidentiary touch samples.