SNP-minisequencing as an excellent tool for analysing degraded DNA recovered from archival tissues.

Bąbol-Pokora, Katarzyna; Berent, Jarosław

doi:10.18388/abp.2008_3045

Cited by 16 publications

(5 citation statements)

References 3 publications

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“…Traditional capillary electrophoresis (CE) assays are limited by the number and type of markers along with the fact that the amplicons must be separated both spatially and spectrally. Many SNPs can potentially be typed using very short recognition sequences and advances have been observed in relation to the typing of degraded samples . However, due to the biallelic nature of SNPs, a higher number of SNPs is required for analysis (using suitable analytical platforms) to allow the discrimination power to be equivalent to that currently observed for 13–15 short tandem repeat (STR) loci .…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Evaluation of the performance of Illumina's ForenSeq™ system on serially degraded samples

Zhang¹,

Zhou²,

Liu³

et al. 2018

Electrophoresis

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The use of next generation sequencing is increasing in the field of forensic genomics. This study assesses the performance of Illumina's MiSeq FGx System in the recovery of forensic genomic sequencing information from degraded and low-template DNA. The analysis involved a sensitivity study where a range of 1 ng to 5 pg of 2800M DNA was utilized. DNA was artificially and systematically degraded by incubating 2800 M DNA at 98°C for 10, 20, 30, 40, 50, 60, 70, 120 and 180 min (resulting in degradation index values ranging from 0.837 to 232.247). The results revealed the detected allele call frequencies were greater than 80% when the DNA input was > = 50 pg or the degradation index was lower than 72.28. The allele balance was lower than 0.6 when the samples were heated for more than 120 min or the input quantity was less than 25 pg. Our data also indicated that the stutter type and ratio depend on the specific locus, while the sequencing run was the most significant factor in noise occurrence. The results of this study will help laboratories to develop workflows for the analysis of challenging samples using the ForenSeq FGx system.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Evaluation of the performance of Illumina's ForenSeq™ system on serially degraded samples

Zhang¹,

Zhou²,

Liu³

et al. 2018

Electrophoresis

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“…The advantage of FFPE blocks is simple and relatively safe handling, cheap storage, wide availability and suitability for the application of immunohistochemical and other analyzes. Isolation of nucleic acids from archived biological material such as FFPE tissue blocks for PCR analysis is increasingly used in clinical practice [14] and is a signi cant source of DNA for use in forensics [15,16]. However, in retrospective studies and forensic analyzes, FFPE tissues are often the only and last available material for further molecular analysis [17].…”

Section: Discussionmentioning

confidence: 99%

The Quality of DNA Isolated from Autopsy FF and FFPE Tissues: Study of 1662 Samples

Vitošević

Todorović

Slović

et al. 2023

Preprint

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Background: There are enormous formalin fixed paraffin embedded tissue archives and constantly growing number of methods for molecular analyses but, isolation of DNA from this tissue is still challenging due to the damage effect of formalin on DNA. To determine the extent to which DNA purity, quantity and integrity depends on the process of fixation in formalin, and to what extent on the process of tissue paraffin embedding, we compared the quality of DNA isolated from fixed tissues and DNA isolated from tissues embedded in paraffin blocks after fixation. Methods and Results: Heart, liver and brain tissues obtained from healthy people who suddenly died a violent death were fixed in 10% buffered formalin as well as in 4% unbuffered formalin 6h, 1-7 days (every 24h), 10, 14, 28 days and 2 months. Also the same tissues were fixed in 4% unbuffered formalin and embedded in paraffin block and stored from few months to 30 years. Yield and purity of the DNA samples isolated from these tissues were measured using spectrophotomer The PCR amplification of the hTERT gene was performed to evaluate the degree of DNA molecule fragmentation. Although the purity of the DNA isolated from almost all tissue samples is satisfactory, the DNA yields changes significantly. Conclusion: The largest decrease in DNA yield was observed after tissue fixation in formalin, especially with prolonged formalin fixation, and additionally after paraffin embedding of tissue. DNA integrity also depends on time of tissue formalin fixation and the age of paraffin blocks.

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“…Latini and L.M. Castilho samples, including formalin-fixed paraffin-embedded tissues, 29 heat-degraded samples, 17 and DNA extracted from bones, teeth, muscles, organs, nails, semen-contaminated vaginal fluid, and aged dried blood on blood type test paper. 17,20 When SNaPshot costs are analyzed and compared with other methods, we conclude that it can be an excellent option.…”

Section: Strengths and Limitationsmentioning

confidence: 99%

An overview of the use of SNaPshot for predicting blood group antigens

Latini

Castilho²

2015

Immunohematology

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The use of SNaPshot (Applied Biosystems, Foster City, CA) for predicting blood group antigens has emerged as an alternative to hemagglutination testing and also to the current low-and highthroughput blood group genotyping methods. Several groups have developed multiplex-polymerase chain reaction SNaPshot assays to determine single nucleotide polymorphisms (SNPs) in blood group genes with the purpose of identifying clinically relevant antigens and rare alleles. The selection of SNPs is based on the population or laboratory reality and the purpose of the genotyping. Unlike high-throughput genotyping strategies that are provided as commercial platforms, the SNPs can be chosen to best meet the needs of the user, and the interpretation of the results do not depend on the manufacturer. Immunohematology 2015;31:53-57.

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SNP-minisequencing as an excellent tool for analysing degraded DNA recovered from archival tissues.

Cited by 16 publications

References 3 publications

Evaluation of the performance of Illumina's ForenSeq™ system on serially degraded samples

Evaluation of the performance of Illumina's ForenSeq™ system on serially degraded samples

The Quality of DNA Isolated from Autopsy FF and FFPE Tissues: Study of 1662 Samples

An overview of the use of SNaPshot for predicting blood group antigens

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