A collaborative EDNAP exercise on SNaPshot™-based mtDNA control region typing

Weiler, Natalie; Baca, Katharyn M.; Ballard, David J.; Balsa, F.; Bogus, Magdalena; Børsting, Claus; Brisighelli, Francesca; Červenáková, J.; Chaitanya, Lakshmi; Coble, Michael D.; Decroyer, V.; Desmyter, Stijn; Gaag, Kristiaan J. van der; Gettings, Katherine B.; Haas, Cordula; Heinrich, Josephin; Porto, Maria João; Kal, Arnoud J.; Kayser, Manfred; Kúdelová, A.; Morling, Niels; Mosquera-Miguel, Ana; Noël, Fabrice; Parson, Walther; Pereira, Vânia; Schneider, Peter M.; Court, Denise Syndercombe; Turanská, M.; Vidaki, Athina; Woliński, P.; Zatkalíková, L.; Sijen, Titia

doi:10.1016/j.fsigen.2016.10.014

Cited by 5 publications

(2 citation statements)

References 25 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The application of FDSTools is not limited to the analysis of STRs. FDSTools has already been applied successfully to the analysis of multiplex assays of SNP fragments (manuscript in preparation) and complete mtDNA data [31]. Note that the minimum number of required reference samples for loci other than STRs will depend on the amount of variation observed in these loci.…”

Section: Discussionmentioning

confidence: 99%

FDSTools: A software package for analysis of massively parallel sequencing data with the ability to recognise and correct STR stutter and other PCR or sequencing noise

Hoogenboom

Gaag

Leeuw

et al. 2017

Forensic Science International: Genetics

View full text Add to dashboard Cite

Massively parallel sequencing (MPS) is on the advent of a broad scale application in forensic research and casework. The improved capabilities to analyse evidentiary traces representing unbalanced mixtures is often mentioned as one of the major advantages of this technique. However, most of the available software packages that analyse forensic short tandem repeat (STR) sequencing data are not well suited for high throughput analysis of such mixed traces. The largest challenge is the presence of stutter artefacts in STR amplifications, which are not readily discerned from minor contributions. FDSTools is an open-source software solution developed for this purpose. The level of stutter formation is influenced by various aspects of the sequence, such as the length of the longest uninterrupted stretch occurring in an STR. When MPS is used, STRs are evaluated as sequence variants that each have particular stutter characteristics which can be precisely determined. FDSTools uses a database of reference samples to determine stutter and other systemic PCR or sequencing artefacts for each individual allele. In addition, stutter models are created for each repeating element in order to predict stutter artefacts for alleles that are not included in the reference set. This information is subsequently used to recognise and compensate for the noise in a sequence profile. The result is a better representation of the true composition of a sample. Using Promega Powerseq™ Auto System data from 450 reference samples and 31 two-person mixtures, we show that the FDSTools correction module decreases stutter ratios above 20% to below 3%. Consequently, much lower levels of contributions in the mixed traces are detected. FDSTools contains modules to visualise the data in an interactive format allowing users to filter data with their own preferred thresholds.

show abstract

Section: Discussionmentioning

confidence: 99%

FDSTools: A software package for analysis of massively parallel sequencing data with the ability to recognise and correct STR stutter and other PCR or sequencing noise

Hoogenboom

Gaag

Leeuw

et al. 2017

Forensic Science International: Genetics

View full text Add to dashboard Cite

show abstract

“…While alignment software has simplified the analysis of MPS mtDNA profiles, sequence interpretation, especially heteroplasmy, can still be challenging and requires guidance and additional bioinformatic tools to ensure profiles are reported accurately (Just et al, 2014), including when assessing noise in MPS data (McElhoe, et al, 2020; Hoogenboom et al, 2017; Weiler et al, 2017).…”

Section: Massively Parallel Sequencingmentioning

confidence: 99%

The time is now for ubiquitous forensicmtMPSanalysis

Canale

Parson

Holland

2021

WIREs Forensic Science

View full text Add to dashboard Cite

Mitochondrial (mt) DNA sequence analysis is useful for assessing ancestral origin and migration, identifying human remains, and examining evidentiary material in forensic casework. Conventional Sanger‐type sequencing (STS) has been used for more than three decades to address these interests. This paper reviews the methodologies and merits of using a massively parallel sequencing (MPS) approach for mtDNA testing in forensic laboratories, as The Time is Now for Ubiquitous Forensic mtMPS Analysis. This article is categorized under: Forensic Biology > Haploid Markers Forensic Biology > Forensic DNA Technologies

show abstract

Forensically relevant SNaPshot® assays for human DNA SNP analysis: a review

2016

View full text Add to dashboard Cite

Short tandem repeats are the gold standard for human identification but are not informative for forensic DNA phenotyping (FDP). Single-nucleotide polymorphisms (SNPs) as genetic markers can be applied to both identification and FDP. The concept of DNA intelligence emerged with the potential for SNPs to infer biogeographical ancestry (BGA) and externally visible characteristics (EVCs), which together enable the FDP process. For more than a decade, the SNaPshot technique has been utilised to analyse identity and FDP-associated SNPs in forensic DNA analysis. SNaPshot is a single-base extension (SBE) assay with capillary electrophoresis as its detection system. This multiplexing technique offers the advantage of easy integration into operational forensic laboratories without the requirement for any additional equipment. Further, the SNP panels from SNaPshot assays can be incorporated into customised panels for massively parallel sequencing (MPS). Many SNaPshot assays are available for identity, BGA and EVC profiling with examples including the well-known SNPforID 52-plex identity assay, the SNPforID 34-plex BGA assay and the HIrisPlex EVC assay. This review lists the major forensically relevant SNaPshot assays for human DNA SNP analysis and can be used as a guide for selecting the appropriate assay for specific identity and FDP applications.

show abstract

A collaborative EDNAP exercise on SNaPshot™-based mtDNA control region typing

Cited by 5 publications

References 25 publications

FDSTools: A software package for analysis of massively parallel sequencing data with the ability to recognise and correct STR stutter and other PCR or sequencing noise

FDSTools: A software package for analysis of massively parallel sequencing data with the ability to recognise and correct STR stutter and other PCR or sequencing noise

The time is now for ubiquitous forensicmtMPSanalysis

Forensically relevant SNaPshot® assays for human DNA SNP analysis: a review

Contact Info

Product

Resources

About