scholarly journals Progress in the implementation of massively parallel sequencing for forensic genetics: results of a European-wide survey among professional users

2021 ◽  
Author(s):  
Theresa E. Gross ◽  
Jan Fleckhaus ◽  
Peter M. Schneider
Keyword(s):  
Online Survey ◽  
Dna Analysis ◽  
Massively Parallel Sequencing ◽  
Forensic Genetics ◽  
Massively Parallel ◽  
Forensic Dna ◽  
Educational Training ◽  
Forensic Dna Analysis ◽  
Parallel Sequencing ◽  
Horizon 2020

AbstractA European-wide online survey was conducted to generate an overview on the state-of-the-art using massively parallel sequencing (MPS) platforms for forensic DNA analysis and DNA phenotyping among forensic practitioners in Europe. The survey was part of the dissemination activities of the “VISible Attributes through GEnomics – VISAGE” Horizon 2020 funded European research project [30], in preparation of a series of educational training activities. A total of 105 replies from 32 European countries representing participants from police, governmental, academic, and private laboratories providing professional services in the field of forensic genetics were included in the final analysis. Of these, 73% already own an MPS platform or are planning to acquire one within the next 1–2 years. One-third of the participants have already carried out MPS-based STR sequencing, identity, or ancestry SNP typing. A total of 23–40% of participants are planning to explore all FDP applications showing the overall very high interest in using MPS for the whole range of forensic MPS markers and applications. About 50% of the participants have previously gathered experience using forensic DNA phenotyping (FDP) markers based on conventional (i.e., not MPS-based) DNA typing methods. A total of 55% of the participants have attended training on the general use of MPS technology, but 36% have received no training whatsoever. Accordingly, 90% have expressed high or medium interest to attend training on the analysis and interpretation of DNA phenotyping data for predicting appearance, ancestry, and age. The results of our survey will provide valuable information for organizing relevant training workshops on all aspects of MPS-based DNA phenotyping for the forensic genetics scientific community.

scholarly journals A technique for setting analytical thresholds in massively parallel sequencing-based forensic DNA analysis

PLoS ONE ◽  
2017 ◽  
Vol 12 (5) ◽  
pp. e0178005 ◽  
Author(s):  
Brian Young ◽  
Jonathan L. King ◽  
Bruce Budowle ◽  
Luigi Armogida
Keyword(s):  
Dna Analysis ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Forensic Dna ◽  
Forensic Dna Analysis ◽  
Parallel Sequencing

Recent Developments in Forensic DNA Technology

2020 ◽  
pp. 105-127
Author(s):  
Henry Erlich ◽  
Cassandra Calloway ◽  
Steven B. Lee
Keyword(s):  
Mitochondrial Dna ◽  
Dna Analysis ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Degraded Dna ◽  
Forensic Dna ◽  
Current Standard ◽  
Forensic Dna Analysis ◽  
Str Loci ◽  
Recent Developments

The current standard of forensic DNA analysis is genotyping the length polymorphism of STR loci by capillary electrophoresis and analyzing the polymorphism of mitochondrial DNA by Sanger sequencing. However, the trend of dramatic technological developments begun in the mid 1980s has continued, with the most consequential recent innovations being (1) the development of next generation sequencing (NGS) or massively parallel sequencing (MPS) and (2) the implementation of commercial Rapid DNA instruments that automate genotyping of all CODIS core STR loci from sample to profile in 90 minutes. This chapter reviews the principles, benefits, and applications of NGS or MPS technology, with a focus on the critical features of massively parallel and clonal sequencing and the ability to perform quantitative analysis of mixtures. The potential to analyze degraded DNA by using NGS/MPS to sequence mitochondrial DNA and SNPs is discussed, as are the benefits and limitations of Rapid DNA instruments.

scholarly journals Developments in forensic DNA analysis

2021 ◽  
Author(s):  
Penelope R. Haddrill
Keyword(s):  
Dna Analysis ◽  
Massively Parallel Sequencing ◽  
Forensic Genetics ◽  
Snp Markers ◽  
Tissue Type ◽  
Forensic Dna ◽  
Forensic Dna Analysis ◽  
Dna Database ◽  
Forensic Practice ◽  
Potential Benefits

The analysis of DNA from biological evidence recovered in the course of criminal investigations can provide very powerful evidence when a recovered profile matches one found on a DNA database or generated from a suspect. However, when no profile match is found, when the amount of DNA in a sample is too low, or the DNA too degraded to be analysed, traditional STR profiling may be of limited value. The rapidly expanding field of forensic genetics has introduced various novel methodologies that enable the analysis of challenging forensic samples, and that can generate intelligence about the donor of a biological sample. This article reviews some of the most important recent advances in the field, including the application of massively parallel sequencing to the analysis of STRs and other marker types, advancements in DNA mixture interpretation, particularly the use of probabilistic genotyping methods, the profiling of different RNA types for the identification of body fluids, the interrogation of SNP markers for predicting forensically relevant phenotypes, epigenetics and the analysis of DNA methylation to determine tissue type and estimate age, and the emerging field of forensic genetic genealogy. A key challenge will be for researchers to consider carefully how these innovations can be implemented into forensic practice to ensure their potential benefits are maximised.

scholarly journals Laboratory Verification of a BRCA1 and BRCA2 Massively Parallel Sequencing Assay from Wet Bench to Bioinformatics for Germline DNA Analysis

2021 ◽  
Author(s):  
Kok-Siong Poon ◽  
Lily Chiu ◽  
Karen Mei-Ling Tan
Keyword(s):  
Genetic Testing ◽  
Sanger Sequencing ◽  
Dna Analysis ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Brca1 And Brca2 ◽  
Clinical Diagnostic Laboratory ◽  
Parallel Sequencing ◽  
Miseq Platform ◽  
Brca Genetic Testing

Abstract Introduction A robust genetic test for BRCA1 and BRCA2 genes is necessary for the diagnosis, prognosis, and treatment of patients with hereditary breast and ovarian cancer. We evaluated a commercial amplicon-based massively parallel sequencing (MPS) assay, BRCA MASTR Plus on the MiSeq platform, for germline BRCA genetic testing. Methods This study was performed on 31 DNA from cell lines and proficiency testing samples to establish the accuracy of the assay. A reference cell line DNA, NA12878 was used to determine the reproducibility of the assay. Discordant MPS result was resolved orthogonally by the current gold-standard Sanger sequencing method. Results The analytical accuracy, sensitivity, and specificity for variant detection were 93.55, 92.86, and 100.00%, respectively. Both sequencing depth and variant allele frequencies were highly reproducible by comparing the NA12878 DNA tested in three separate runs. The single discordant result, later confirmed by Sanger sequencing was due to the inability of the MASTR Reporter software to identify a 40-bp deletion in BRCA1. Conclusion The BRCA MASTR Plus assay on the MiSeq platform is accurate and reproducible for germline BRCA genetic testing, making it suitable for use in a clinical diagnostic laboratory. However, Sanger sequencing may still serve as a confirmatory method to improve diagnostic capability of the MPS assay.

scholarly journals High-Resolution Profiling of Fetal DNA Clearance from Maternal Plasma by Massively Parallel Sequencing

2013 ◽  
Vol 59 (8) ◽  
pp. 1228-1237 ◽  
Author(s):  
Stephanie CY Yu ◽  
Shara WY Lee ◽  
Peiyong Jiang ◽  
Tak Y Leung ◽  
KC Allen Chan ◽  
...  
Keyword(s):  
High Resolution ◽  
Half Life ◽  
Dna Analysis ◽  
Massively Parallel Sequencing ◽  
Maternal Plasma ◽  
Massively Parallel ◽  
Slow Phase ◽  
Parallel Sequencing ◽  
Fetal Dna ◽  
Circulating Fetal Dna

BACKGROUND With the advent of massively parallel sequencing (MPS), DNA analysis can now be performed in a genomewide manner. Recent studies have demonstrated the high precision of MPS for quantifying fetal DNA in maternal plasma. In addition, paired-end sequencing can be used to determine the size of each sequenced DNA fragment. We applied MPS in a high-resolution investigation of the clearance profile of circulating fetal DNA. METHODS Using paired-end MPS, we analyzed serial samples of maternal plasma collected from 13 women after cesarean delivery. We also studied the transrenal excretion of circulating fetal DNA in 3 of these individuals by analyzing serial urine samples collected after delivery. RESULTS The clearance of circulating fetal DNA occurred in 2 phases, with different kinetics. The initial rapid phase had a mean half-life of approximately 1 h, whereas the subsequent slow phase had a mean half-life of approximately 13 h. The final disappearance of circulating fetal DNA occurred at about 1 to 2 days postpartum. Although transrenal excretion was involved in the clearance of circulating fetal DNA, it was not the major route. Furthermore, we observed significant changes in the size profiles of circulating maternal DNA after delivery, but we did not observe such changes in circulating fetal DNA. CONCLUSIONS MPS of maternal plasma and urinary DNA permits high-resolution study of the clearance profile of circulating fetal DNA.

Increasing the reach of forensic genetics with massively parallel sequencing

2017 ◽  
Vol 13 (3) ◽  
pp. 342-349 ◽  
Author(s):  
Bruce Budowle ◽  
Sarah E. Schmedes ◽  
Frank R. Wendt
Keyword(s):  
Massively Parallel Sequencing ◽  
Forensic Genetics ◽  
Massively Parallel ◽  
Parallel Sequencing
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