Next-generation sequencing approaches to short-tandem repeat sequence variation

Lead Research Organisation: University of Leicester
Department Name: Genetics

Abstract

Human short tandem repeats (STRs) have been widely used as markers in linkage and population-genetic studies, and remain the prime tools for forensic individual identification. However, remarkably little is known about STR sequence variation in human populations; this is due to genotyping via PCR fragment length, which ignores internal variants and STR-allele linkage to flanking variation, thus hiding alleles identical-by-descent (IBD) under apparent identity-by-state. The past decade has seen the emergence of next-generation sequencing (NGS), which can provide simultaneous sequence data for multiple PCR amplicons. This promises access to STR sequences and flanking variants, and thanks to its high throughput and suitability for fragmented DNA, is being developed for new forensic assays. Note that low-coverage whole-genome approaches yield only STR length information.

Publications

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Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M016706/1 01/10/2015 30/09/2019
1698175 Studentship BB/M016706/1 01/10/2015 30/09/2019
 
Description This study is applying next-generation sequencing to classical forensic marker analysis. With this improved technology the results give a higher resolution of genetic data for forensic purposes. The application of this new technology is currently in its start for real-life forensic investigations, as its full potential will be reached by applying the results of studies like this one for population statistics and analysis method evaluations. This study has generated essential data to review the applicability of the method both in laboratory and in the following bioinformatic analysis. The study confirmed the advantages of using next-generation sequencing compared to current gold standard methods (capillary electrophoresis). The ability to gather more information from the same or even less amount of genetic material is helping to deconvolute mixtures more efficiently and enables us to distinguish variants of genetic markers that were undistinguishable by standard technique, thus improving the certainty of genetic matches and decreasing the possibility of false inclusions. It has also proved to minimize the sample usage by multiplexing different type of forensic markers into one analysis, thus saving sample, which is extremely advantageous in the processing of forensic samples. Apart from direct forensic applications this study has also proved to be insightful on the evolutionary processes that are forming these markers. These characteristics can often be used to estimate broad geographic or phylogenetic origins of a sample.
Exploitation Route This study is now completed for a UK sample set, but the same type of population approach could be applied to any country or sub-population of a country to provide specific statistics that can be used as benchmarks for forensic reporting on genetic markers in the future..
Sectors Government, Democracy and Justice,Security and Diplomacy,Other

 
Title OREO 
Description As Other options are not offered: OREO is a bioinformatic tool which allows researchers to remove primer-derived bias from next generation sequencing data when using tiling amplicon sequencing approach from commercial kits, where primer sequences are proprietary. The tool is designed primarily for forensic studies, but can be used similarly in any other using tiling amplicon approaches, such as variant detection for cancer diagnostics and other similar health related areas. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? Yes  
Impact OREO approach is now available to the wider community to use it on their next generation sequencing data to remove primer bias in overlapping amplicon studies. 
 
Title OREO 
Description OREO is a bioinformatic tool which allows researchers to remove primer-derived bias from next generation sequencing data when using tiling amplicon sequencing approach from commercial kits, where primer sequences are proprietary. The tool is designed primarily for forensic studies, but can be used similarly in any other using tiling amplicon approaches, such as variant detection for cancer diagnostics and other similar health related areas. 
Type Of Material Data analysis technique 
Year Produced 2019 
Provided To Others? Yes  
Impact OREO approach is now available to the wider community to use it on their next generation sequencing data to remove primer bias in overlapping amplicon studies. 
 
Description Key Forensic Services Limited is the industrial partner on the iCASE studentship 
Organisation Key Forensic Services Ltd
Country United Kingdom 
Sector Private 
PI Contribution Provided lecture about the project and the new technology to staff at their Norwich site. Provided lecture to their law enforcement customers about the new technology at their Coventry site.
Collaborator Contribution Arranged for NPPV3 and SC clearances to be carried out. Arranged for accommodation during a two week visit at their Norwich site.
Impact Discussion on the adaptation of the new technology;considering adjustments related to nomenclature and reporting in practice for the near future.
Start Year 2015
 
Description Promega providing in-kind and financial support for the iCASE studentship 
Organisation Promega Corporation
Country Global 
Sector Private 
PI Contribution Testing of prototype products for next-generation technology. Feedback about the product. Generating manuscripts using the prototype product of the company. Giving talks about the product and the technology.
Collaborator Contribution Providing prototype products for next-generation technology. Support travel costs to conferences where presenting research about the prototype product.
Impact The main body of the PhD research is the result of this collaboration, this outcome may be categorized as multidisciplinary as this new field is building on genetics and bioinformatics equally. Two publications have been published in the field's main journal: Forensic Science International: Genetics and two talks were presented at international conferences. The research created a new bionformatic way to analyse data which in form of a simple software was published to be used by the community.
Start Year 2015
 
Description Walter Bodmer at the University of Oxford 
Organisation University of Oxford
Department Department of Oncology
Country United Kingdom 
Sector Academic/University 
PI Contribution Transport of samples and analysis using next-generation sequencing of forensic markers.
Collaborator Contribution The group of Walter Bodmer at the University of Oxford, Department of Oncology shared access to the People of The British Isles project DNA samples. Katarzyna Hutnik, provided assistance by preparing the UK specific samples.
Impact The samples provided were key to the UK specific part of the research project.
Start Year 2016
 
Description 13th Festival of Postgraduate Research at the University of Leicester, June 29, 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact The 13th Festival of Postgraduate research has selected the work "One step ahead: Fighting crime with new genomic technologies" to be displayed. The event was open to public and different fields of industry, involved presenting the poster to the public and to number of jurors during the day. The poster won the prize of Peer Review Prize. The engagement and interest in the topic from laymen was outstanding. The feedback highlighted the very suitable language used to connect with the public and interpret rather complicated scientific facts in simple understandable and relatable terms.
Year(s) Of Engagement Activity 2017
URL https://www2.le.ac.uk/staff/announcements/graduate-school-announces-winners-of-the-13th-festival-of-...
 
Description Taking about own research as a postgraduate researcher - invited by PubhD Leicester , 14 June, 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact The concept of PubhD events across the world is to present specialized knowledge in the simplest terms that is enjoyable for the general public in a relaxed environment. The talk gently summarized how the science works in forensic genetics and highlighted how applying new genomic technologies can improve it. Examples from the research project were used to explain the difference between these approaches using simple visual analogies.
Year(s) Of Engagement Activity 2016
 
Description Talk at the International Science Festival, Edinburgh, 3 April, 2017 - invited by The Edinburgh Skeptics Society 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact The talk "The science behind the fiction - Investigating with DNA" was given at the Edinburgh International Science Festival, invited by The Edinburgh Skeptics Society. The talk gave a general overview of how real life forensic work uses DNA as opposed to the public's perception from the media. Highlighted the emerging technologies, like next-generation sequencing and how they improve the strength of DNA evidence that are to be used in the near future. The audience noted the ease to follow the talk, as it was put in simple, understandable terms for the non-specialist audience with a general interest in science.
Year(s) Of Engagement Activity 2017
URL https://www.facebook.com/events/423275711348948/
 
Description Winter Showcase 2016 - The Forensic Society of University of Leicester, 7 Dec, 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact The Forensic Science Society of the University of Leicester invited specialists in different forensic fields to give talks about their expertise to their memebers. Prior to Christmas 2016 they organized a winter showcase to have a selection from several fields, this is where the talk, "Next-generation sequencing: Adding a new dimension to forensic DNA analysis" was given and it was aimed at undergraduate, postgraduate students or professionals pursuing a career in any forensic field, thus the audience's interest was forensic focussed, but not necessarily specialized in forensic genetics. The discussions afterwards showed good understanding of basic concepts even in an interdisciplinary setting.
Year(s) Of Engagement Activity 2016