scholarly journals FastID: Extremely Fast Forensic DNA Comparisons

2017 ◽  
Author(s):  
Darrell O. Ricke

AbstractRapid analysis of DNA forensic samples can have a critical impact on time sensitive investigations. Analysis of forensic DNA samples by massively parallel sequencing is creating the next gold standard for DNA forensic analysis. This technology enables the expansion of forensic profiles from the current 20 short tandem repeat (STR) loci to tens of thousands of single nucleotide polymorphism (SNP) loci. A forensic search scales by the product of the number of loci and the number of profile comparisons. This paper introduces a method (FastID) to address the need for rapid scalable analysis of DNA forensic samples (patent pending)[1]. FastID can search a profile of 2,500 SNP loci against 20 million profiles in 5.08 seconds using a single computational thread on a laptop (Intel i7 4.0 GHz).

Author(s):  
Ashley M. Cooley ◽  
Kelly A. Meiklejohn ◽  
Natalie Damaso ◽  
James M. Robertson ◽  
Tracey Dawson Cruz

Thermo Fisher Scientific released the Precision ID Ancestry Panel, a 165-single-nucleotide polymorphism (SNP) panel for ancestry prediction that was initially compatible with the manufacturer’s massively parallel sequencer, the Ion Torrent Personal Genome Machine (PGM). The semiautomated workflow using the panel with the PGM involved several time-consuming manual steps across three instruments, including making templating solutions and loading sequencing chips. In 2014, the manufacturer released the Ion Chef robot, followed by the Ion S5 massively parallel sequencer in late 2015. The robot performs the templating with reagent cartridges and loads the chips, thus creating a fully automated workflow across two instruments. The objective of the work reported here is to compare the performance of two massively parallel sequencing systems and ascertain if the change in the workflow produces different ancestry predictions. For performance comparison of the two systems, forensic-type samples ( n = 16) were used to make libraries. Libraries were templated either with the Ion OneTouch 2 system (for the PGM) or on the Ion Chef robot (for the S5). Sequencing results indicated that the ion sphere particle performance metrics were similar for the two systems. The total coverages per SNP and SNP quality were both higher for the S5 system. Ancestry predictions were concordant for the mock forensic-type samples sequenced on both massively parallel sequencing systems. The results indicated that automating the workflow with the Ion Chef system reduced the labor involved and increased the sequencing quality.


2020 ◽  
pp. 105-127
Author(s):  
Henry Erlich ◽  
Cassandra Calloway ◽  
Steven B. Lee

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.


Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 636
Author(s):  
Jennifer Daniels-Higginbotham ◽  
Erin M. Gorden ◽  
Stephanie K. Farmer ◽  
Brian Spatola ◽  
Franklin Damann ◽  
...  

In 1990 in Griswold, Connecticut, archaeologists excavated a burial found in a “skull and crossbones” orientation. The lid of the 19th century coffin had brass tacks that spelled “JB55”, the initials of the person lying there and age at death. JB55 had evidence of chronic pulmonary infection, perhaps tuberculosis. It is possible that JB55 was deemed a vampire due to his disease, and therefore had to be “killed” by mutilating his corpse. In an attempt to reveal the identity of JB55, DNA testing was performed. Ancestry informative single nucleotide polymorphism (SNP) analysis using the Precision ID Ancestry Panel indicated European ancestry. A full Y-chromosomal short tandem repeat (Y-STR) profile was obtained, belonging to haplogroup R1b. When the Y-STR profile was searched in the publicly accessible FamilyTreeDNA R1b Project website, the two closest matches had the surname “Barber”. A search of historical records led to a death notice mentioning John Barber, whose son Nathan Barber was buried in Griswold in 1826. The description of Nathan Barber closely fits the burial of “NB13,” found near JB55. By applying modern forensic DNA tools to a historical mystery, the identity of JB55 as John Barber, the 19th century Connecticut vampire, has been revealed.


2018 ◽  
Vol 27 (3) ◽  
pp. 400-407 ◽  
Author(s):  
Rick H. de Leeuw ◽  
Dominique Garnier ◽  
Rosemarie M. J. M. Kroon ◽  
Corinne G. C. Horlings ◽  
Emile de Meijer ◽  
...  

Biomics ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 321-346
Author(s):  
R.R. Garafutdinov ◽  
D.A. Chemeris ◽  
A.R. Sakhabutdinova ◽  
Ya.I. Alexeev ◽  
G.A. Gerashchenkov ◽  
...  

The application of mini- and microsatellite polymorphisms of dog DNA, also referred to as VNTR- and STR-loci, respectively, in dog breeding and criminalistics is considered. Their use in dog breeding is shown to clarify pedigrees, establish paternity and purebred, as well as to differentiate breeds mainly in the form of microsatellite DNA polymorphism. In criminalistics, dogs can be both participants in crime scenes in the form of attacks on humans or pets, and some witnesses through whose DNA extracted from their fur or feces, by DNA identification of a particular dog, it may be help to get out to the perpetrator or at least to the crime scene, which is also a good help in its disclosure. At the same time, population studies of dogs, during which the prevalence of certain alleles of marker traits in the form of STR loci in different territories is established, contribute to making the right decisions. The databases on STR-polymorphism of dog DNA or their prototypes are briefly described. Attention is paid to the sources of forensic canine DNA, as well as methods of its extraction and preliminary evaluation of isolated preparations. The use of VNTR polymorphism was rather short-lived, and was quickly replaced by STR polymorphism. There are some trends in the introduction of new polymorphic traits in this area in the form of single-nucleotide polymorphism or SNPs, potentially providing more accurate information, including for DNA identification of individuals. The issues of universal DNA certification of dogs are discussed, which can contribute to improving the culture of keeping dogs and will allow the elimination of stray dogs in the future, which will be humanistic character and potentially reduce the number of aggressor dogs.


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