Back
HIrisPlex-S system for eye, hair, and skin color prediction from DNA: Massively parallel sequencing solutions for two common forensically used platforms.
Journal article

HIrisPlex-S system for eye, hair, and skin color prediction from DNA: Massively parallel sequencing solutions for two common forensically used platforms.

  • Breslin K Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indiana, United States.
  • Wills B Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indiana, United States.
  • Ralf A Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.
  • Ventayol Garcia M Department of Human Biological Traces, Netherlands Forensic Institute, The Hague, The Netherlands.
  • Kukla-Bartoszek M Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
  • Pospiech E Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.
  • Freire-Aradas A Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
  • Xavier C Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
  • Ingold S Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland.
  • de La Puente M Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain; Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
  • van der Gaag KJ Department of Human Biological Traces, Netherlands Forensic Institute, The Hague, The Netherlands.
  • Herrick N Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indiana, United States.
  • Haas C Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland.
  • Parson W Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, United States.
  • Phillips C Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
  • Sijen T Department of Human Biological Traces, Netherlands Forensic Institute, The Hague, The Netherlands.
  • Branicki W Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland; Central Forensic Laboratory of the Police, Warsaw, Poland.
  • Walsh S Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indiana, United States. Electronic address: walshsus@iupui.edu.
  • Kayser M Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands. Electronic address: m.kayser@erasmusmc.nl.
Show more…
  • 2019-09-14
Published in:
  • Forensic science international. Genetics. - 2019
Bioinformatics pipeline
Eye color
Forensic DNA phenotyping
Forensic developmental validation
HIrisplex-S
Hair color
Ion torrent
Massively parallel sequencing
MiSeq
Skin color
Animals
DNA
Eye Color
Genotype
Genotyping Techniques
Hair Color
High-Throughput Nucleotide Sequencing
Humans
Phenotype
Polymerase Chain Reaction
Polymorphism, Single Nucleotide
Skin Pigmentation
Species Specificity
English Forensic DNA Phenotyping (FDP) provides the ability to predict externally visible characteristics from minute amounts of crime scene DNA, which can help find unknown perpetrators who are typically unidentifiable via conventional forensic DNA profiling. Fundamental human genetics research has led to a better understanding of the specific DNA variants responsible for physical appearance characteristics, particularly eye, hair, and skin color. Recently, we introduced the HIrisPlex-S system for the simultaneous prediction of eye, hair, and skin color based on 41 DNA variants generated from two forensically validated SNaPshot multiplex assays using capillary electrophoresis (CE). Here we introduce massively parallel sequencing (MPS) solutions for the HIrisPlex-S (HPS) system on two MPS platforms commonly used in forensics, Ion Torrent and MiSeq, that cover all 41 DNA variants in a single assay, respectively. Additionally, we present the forensic developmental validation of the two HPS-MPS assays. The Ion Torrent MPS assay, based on Ion AmpliSeq technology, illustrated the successful generation of full HIrisPlex-S genotypic profiles from 100 pg of input control DNA, while the MiSeq MPS assay based on an in-house design yielded complete profiles from 250 pg of input DNA. Assessing simulated forensic casework samples such as saliva, hair (bulb), blood, semen, and low quantity touch DNA, as well as artificially damaged DNA samples, concordance testing, and samples from numerous species, all illustrated the ability of both versions of the HIrisPlex-S MPS assay to produce results that motivate forensic applications. By also providing an integrated bioinformatics analysis pipeline, MPS data can now be analyzed and a file generated for upload to the publically accessible HIrisPlex online webtool (https://hirisplex.erasmusmc.nl). In addition, we updated the website to accept VCF input data for those with genome sequence data. We thus provide a user-friendly and semi-automated MPS workflow from DNA sample to individual eye, hair, and skin color prediction probabilities. Furthermore, we present a 2-person mixture separation tool that not only assesses genotype reliability with regards genotyping confidence but also provides the most fitting mixture scenario for both minor and major contributors, including profile separation. We envision this MPS implementation of the HIrisPlex-S system for eye, hair, and skin color prediction from DNA as a starting point for further expanding MPS-based forensic DNA phenotyping. This may include the future addition of SNPs predictive for more externally visible characteristics, as well as SNPs for bio-geographic ancestry inference, provided the statistical framework for DNA prediction of these traits is in place.
Language
  • English
Open access status
closed
Identifiers
Persistent URL
https://sonar.ch/global/documents/258784
Statistics
Document views: 54 File downloads: