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Evaluation of the Illumina(®) Beta Version ForenSeq™ DNA Signature Prep Kit for use in genetic profiling.
Forensic Sci Int Genet. 2016 Jan; 20:20-29.FS

Abstract

While capillary electrophoresis-based technologies have been the mainstay for human identity typing applications, there are limitations with this methodology's resolution, scalability, and throughput. Massively parallel sequencing (MPS) offers the capability to multiplex multiple types of forensically-relevant markers and multiple samples together in one run all at an overall lower cost per nucleotide than traditional capillary electrophoresis-based methods; thus, addressing some of these limitations. MPS also is poised to expand forensic typing capabilities by providing new strategies for mixture deconvolution with the identification of intra-STR allele sequence variants and the potential to generate new types of investigative leads with an increase in the overall number and types of genetic markers being analyzed. The beta version of the Illumina ForenSeq DNA Signature Prep Kit is a MPS library preparation method with a streamlined workflow that allows for targeted amplification and sequencing of 63 STRs and 95 identity SNPs, with the option to include an additional 56 ancestry SNPs and 22 phenotypic SNPs depending on the primer mix chosen for amplification, on the MiSeq desktop sequencer (Illumina). This study was divided into a series of experiments that evaluated reliability, sensitivity of detection, mixture analysis, concordance, and the ability to analyze challenged samples. Genotype accuracy, depth of coverage, and allele balance were used as informative metrics for the quality of the data produced. The ForenSeq DNA Signature Prep Kit produced reliable, reproducible results and obtained full profiles with DNA input amounts of 1ng. Data were found to be concordant with current capillary electrophoresis methods, and mixtures at a 1:19 ratio were resolved accurately. Data from the challenged samples showed concordant results with current DNA typing methods with markers in common and minimal allele drop out from the large number of markers typed on these samples. This set of experiments indicates the beta version of the ForenSeq DNA Signature Prep Kit is a valid tool for forensic DNA typing and warrants full validation studies of this MPS technology.

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Publisher Full Text (DOI)

Authors+Show Affiliations

Churchill JD
Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA. Electronic address: Jennifer.Churchill@unthsc.edu.
Schmedes SE
Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.
King JL
Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.
Budowle B
Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.

MeSH

AllelesDNA FingerprintingElectrophoresis, CapillaryForensic GeneticsGenetic MarkersGenotypeHigh-Throughput Nucleotide SequencingHumansMicrosatellite RepeatsMultiplex Polymerase Chain ReactionPolymorphism, Single NucleotideReagent Kits, DiagnosticReproducibility of Results

Pub Type(s)

Evaluation Study
Journal Article

Language

eng

PubMed ID

26433485

Citation

Churchill, Jennifer D., et al. "Evaluation of the Illumina(®) Beta Version ForenSeq™ DNA Signature Prep Kit for Use in Genetic Profiling." Forensic Science International. Genetics, vol. 20, 2016, pp. 20-29.
Churchill JD, Schmedes SE, King JL, et al. Evaluation of the Illumina(®) Beta Version ForenSeq™ DNA Signature Prep Kit for use in genetic profiling. Forensic Sci Int Genet. 2016;20:20-29.
Churchill, J. D., Schmedes, S. E., King, J. L., & Budowle, B. (2016). Evaluation of the Illumina(®) Beta Version ForenSeq™ DNA Signature Prep Kit for use in genetic profiling. Forensic Science International. Genetics, 20, 20-29. https://doi.org/10.1016/j.fsigen.2015.09.009
Churchill JD, et al. Evaluation of the Illumina(®) Beta Version ForenSeq™ DNA Signature Prep Kit for Use in Genetic Profiling. Forensic Sci Int Genet. 2016;20:20-29. PubMed PMID: 26433485.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Evaluation of the Illumina(®) Beta Version ForenSeq™ DNA Signature Prep Kit for use in genetic profiling. AU - Churchill,Jennifer D, AU - Schmedes,Sarah E, AU - King,Jonathan L, AU - Budowle,Bruce, Y1 - 2015/09/21/ PY - 2015/06/30/received PY - 2015/09/01/revised PY - 2015/09/17/accepted PY - 2015/10/5/entrez PY - 2015/10/5/pubmed PY - 2016/10/12/medline KW - ForenSeq KW - Illumina MiSeq KW - Massively parallel sequencing (MPS) KW - SNPs KW - STRs SP - 20 EP - 29 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 20 N2 - While capillary electrophoresis-based technologies have been the mainstay for human identity typing applications, there are limitations with this methodology's resolution, scalability, and throughput. Massively parallel sequencing (MPS) offers the capability to multiplex multiple types of forensically-relevant markers and multiple samples together in one run all at an overall lower cost per nucleotide than traditional capillary electrophoresis-based methods; thus, addressing some of these limitations. MPS also is poised to expand forensic typing capabilities by providing new strategies for mixture deconvolution with the identification of intra-STR allele sequence variants and the potential to generate new types of investigative leads with an increase in the overall number and types of genetic markers being analyzed. The beta version of the Illumina ForenSeq DNA Signature Prep Kit is a MPS library preparation method with a streamlined workflow that allows for targeted amplification and sequencing of 63 STRs and 95 identity SNPs, with the option to include an additional 56 ancestry SNPs and 22 phenotypic SNPs depending on the primer mix chosen for amplification, on the MiSeq desktop sequencer (Illumina). This study was divided into a series of experiments that evaluated reliability, sensitivity of detection, mixture analysis, concordance, and the ability to analyze challenged samples. Genotype accuracy, depth of coverage, and allele balance were used as informative metrics for the quality of the data produced. The ForenSeq DNA Signature Prep Kit produced reliable, reproducible results and obtained full profiles with DNA input amounts of 1ng. Data were found to be concordant with current capillary electrophoresis methods, and mixtures at a 1:19 ratio were resolved accurately. Data from the challenged samples showed concordant results with current DNA typing methods with markers in common and minimal allele drop out from the large number of markers typed on these samples. This set of experiments indicates the beta version of the ForenSeq DNA Signature Prep Kit is a valid tool for forensic DNA typing and warrants full validation studies of this MPS technology. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/26433485/Evaluation_of_the_Illumina_®__Beta_Version_ForenSeq™_DNA_Signature_Prep_Kit_for_use_in_genetic_profiling_ DB - PRIME DP - Unbound Medicine ER -