Use of standardized bioinformatics for the analysis of fungal DNA signatures applied to sample provenance

Allwood, Julia S.; Fierer, Noah; Dunn, Robert R.; Breen, Matthew; Reich, Brian J.; Laber, Eric B.; Clifton, Jesse; Grantham, Neal S.; Faith, Seth A.

doi:10.1016/j.forsciint.2020.110250

Cited by 12 publications

(7 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Fungal ITS1 minibarcode OTUs from over 900 WLOH dust samples from different U.S. locations, a subset of which were used in this study, enabled the estimation of geographic provenance with a median prediction margin of 230 km (36). A similar approach was used to determine the worldwide country of origin from dust samples (37,38). These approaches avoid many of the pitfalls of taxonomic identification and species distribution estimation but, unlike our approach, require generation of a new reference dataset.…”

Section: Discussionmentioning

confidence: 99%

Estimation of Geographic Origin from Dust Using Plant DNA Metabarcoding

Lennartz

Kurucar

Coppola

et al. 2021

Preprint

View full text Add to dashboard Cite

Information obtained from the analysis of dust, particularly biological particles such as pollen, plant parts, and fungal spores, has great utility in forensic geolocation. As an alternative to manual microscopic analysis, we developed a pipeline that utilizes the environmental DNA (eDNA) from plants in dust samples to estimate previous sample location(s). The species of plant-derived eDNA within dust samples were identified using metabarcoding and their geographic distributions were then derived from occurrence records in the USGS Biodiversity in Service of Our Nation (BISON) database. The distributions for all plant species identified in a sample were used to generate a probabilistic estimate of the sample source. With settled dust collected at four U.S. sites over a 15-month period, we demonstrated positive regional geolocation (within 600 km 2 of the collection point) with 47.6% (20 of 42) of the samples analyzed. Attribution accuracy and resolution was dependent on the number of plant species identified in a dust sample, which was greatly affected by the season of collection. In dust samples that yielded a minimum of 20 identified plant species, positive regional attribution improved to 66.7% (16 of 24 samples). Using dust samples collected from 31 different U.S. sites, trace plant eDNA provided relevant regional attribution information on provenance in 32.2%. This demonstrated that analysis of plant eDNA in dust can provide an accurate estimate regional provenance within the U.S., and relevant forensic information, for a substantial fraction of samples analyzed.

show abstract

Section: Discussionmentioning

confidence: 99%

Estimation of Geographic Origin from Dust Using Plant DNA Metabarcoding

Lennartz

Kurucar

Coppola

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…The importance of bioinformatic applications for NGS in forensic science has been recently underlined (Allwood et al 2020a;Allwood et al 2020b;Giampaoli et al 2018). The analysis of biological material, even from trace amounts in dust, has clear advantages for specific forensic applications, in particular, when we need to discern sample origin or geolocation (Allwood et al 2020a).…”

Section: Discussionmentioning

confidence: 99%

DNA metabarcoding of forensic mycological samples

Giampaoli

Vittori

Barni³

et al. 2021

Egypt J Forensic Sci

View full text Add to dashboard Cite

Background DNA metabarcoding and massive parallel sequencing are valuable molecular tools for the characterization of environmental samples. In forensic sciences, the analysis of the sample’s fungal population can be highly informative for the estimation of post-mortem interval, the ascertainment of deposition time, the identification of the cause of death, or the location of buried corpses. Unfortunately, metabarcoding data analysis often requires strong bioinformatic capabilities that are not widely available in forensic laboratories. Results The present paper describes the adoption of a user-friendly cloud-based application for the identification of fungi in typical forensic samples. The samples have also been analyzed through the QIIME pipeline, obtaining a relevant data concordance on top genus classification results (88%). Conclusions The availability of a user-friendly application that can be run without command line activities will increase the popularity of metabarcoding fungal analysis in forensic samples.

show abstract

“…This approach increases bias in abundance (favouring the most abundant taxa), and where indexes are introduced in the second step there is potential for undetectable cross-contamination as the amplified sequences cannot be traced to the original source. The use of internal controls for more accurate quantitative measures and inclusion of positive controls have been suggested [131,132], however, for processing low biomass samples such controls present a potential contamination risk and are not advised [133].…”

Section: Quality Controlsmentioning

confidence: 99%

“…Due to these inconsistencies, comparisons between multiple datasets becomes difficult. To resolve this, Allwood et al 2020 have proposed a standardised approach for fungi analysis in dust [132].…”

Section: Moving Towards a Likelihood Ratiomentioning

confidence: 99%

Massively parallel sequencing is unlocking the potential of environmental trace evidence

Young

Linacre

2021

Forensic Science International: Genetics

View full text Add to dashboard Cite

Massively parallel sequencing (MPS) has revolutionised the field of genomics enabling substantial advances in human DNA profiling. Further, the advent of MPS now allows biological signatures to be obtained from complex DNA mixtures and trace amounts of low biomass samples. Environmental samples serve as ideal forms of contact trace evidence as detection at a scene can establish a link between a suspect, location and victim. Many studies have applied MPS technology to characterise the biodiversity within high biomass environmental samples (such as soil and water) to address questions related to ecology, conservation, climate change and human health. However, translation of these tools to forensic science remains in its infancy, due in part to the merging of traditional forensic ecology practices with unfamiliar DNA technologies and complex datasets. In addition, people and objects also carry low biomass environmental signals which have recently been shown to reflect a specific individual or location. The sensitivity, and reducing cost, of MPS is now unlocking the power of both high and low biomass environmental DNA (eDNA) samples as useful sources of genetic information in forensic science. This paper discusses the potential of eDNA to forensic science by reviewing the most explored applications that are leading the integration of this technology into the field. We introduce novel areas of forensic ecology that could also benefit from these tools with a focus on linking a suspect to a scene or establishing provenance of an unknown sample and discuss the current limitations and validation recommendations to achieve translation of eDNA into casework.

show abstract

Use of standardized bioinformatics for the analysis of fungal DNA signatures applied to sample provenance

Cited by 12 publications

References 28 publications

Estimation of Geographic Origin from Dust Using Plant DNA Metabarcoding

Estimation of Geographic Origin from Dust Using Plant DNA Metabarcoding

DNA metabarcoding of forensic mycological samples

Massively parallel sequencing is unlocking the potential of environmental trace evidence

Contact Info

Product

Resources

About