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Forensic massively parallel sequencing data analysis tool: Implementation of MyFLq as a standalone web- and Illumina BaseSpace(®)-application.
Forensic Sci Int Genet. 2015 Mar; 15:2-7.FS

Abstract

Routine use of massively parallel sequencing (MPS) for forensic genomics is on the horizon. The last few years, several algorithms and workflows have been developed to analyze forensic MPS data. However, none have yet been tailored to the needs of the forensic analyst who does not possess an extensive bioinformatics background. We developed our previously published forensic MPS data analysis framework MyFLq (My-Forensic-Loci-queries) into an open-source, user-friendly, web-based application. It can be installed as a standalone web application, or run directly from the Illumina BaseSpace environment. In the former, laboratories can keep their data on-site, while in the latter, data from forensic samples that are sequenced on an Illumina sequencer can be uploaded to Basespace during acquisition, and can subsequently be analyzed using the published MyFLq BaseSpace application. Additional features were implemented such as an interactive graphical report of the results, an interactive threshold selection bar, and an allele length-based analysis in addition to the sequenced-based analysis. Practical use of the application is demonstrated through the analysis of four 16-plex short tandem repeat (STR) samples, showing the complementarity between the sequence- and length-based analysis of the same MPS data.

Authors+Show Affiliations

Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.Biobix, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium. Electronic address: Filip.VanNieuwerburgh@UGent.be.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

25457631

Citation

Van Neste, Christophe, et al. "Forensic Massively Parallel Sequencing Data Analysis Tool: Implementation of MyFLq as a Standalone Web- and Illumina BaseSpace(®)-application." Forensic Science International. Genetics, vol. 15, 2015, pp. 2-7.
Van Neste C, Gansemans Y, De Coninck D, et al. Forensic massively parallel sequencing data analysis tool: Implementation of MyFLq as a standalone web- and Illumina BaseSpace(®)-application. Forensic Sci Int Genet. 2015;15:2-7.
Van Neste, C., Gansemans, Y., De Coninck, D., Van Hoofstat, D., Van Criekinge, W., Deforce, D., & Van Nieuwerburgh, F. (2015). Forensic massively parallel sequencing data analysis tool: Implementation of MyFLq as a standalone web- and Illumina BaseSpace(®)-application. Forensic Science International. Genetics, 15, 2-7. https://doi.org/10.1016/j.fsigen.2014.10.006
Van Neste C, et al. Forensic Massively Parallel Sequencing Data Analysis Tool: Implementation of MyFLq as a Standalone Web- and Illumina BaseSpace(®)-application. Forensic Sci Int Genet. 2015;15:2-7. PubMed PMID: 25457631.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Forensic massively parallel sequencing data analysis tool: Implementation of MyFLq as a standalone web- and Illumina BaseSpace(®)-application. AU - Van Neste,Christophe, AU - Gansemans,Yannick, AU - De Coninck,Dieter, AU - Van Hoofstat,David, AU - Van Criekinge,Wim, AU - Deforce,Dieter, AU - Van Nieuwerburgh,Filip, Y1 - 2014/10/14/ PY - 2014/08/16/received PY - 2014/09/19/revised PY - 2014/10/03/accepted PY - 2014/12/3/entrez PY - 2014/12/3/pubmed PY - 2015/9/26/medline KW - Forensic loci KW - Illumina KW - MPS KW - MiSeq KW - NGS KW - STR SP - 2 EP - 7 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 15 N2 - Routine use of massively parallel sequencing (MPS) for forensic genomics is on the horizon. The last few years, several algorithms and workflows have been developed to analyze forensic MPS data. However, none have yet been tailored to the needs of the forensic analyst who does not possess an extensive bioinformatics background. We developed our previously published forensic MPS data analysis framework MyFLq (My-Forensic-Loci-queries) into an open-source, user-friendly, web-based application. It can be installed as a standalone web application, or run directly from the Illumina BaseSpace environment. In the former, laboratories can keep their data on-site, while in the latter, data from forensic samples that are sequenced on an Illumina sequencer can be uploaded to Basespace during acquisition, and can subsequently be analyzed using the published MyFLq BaseSpace application. Additional features were implemented such as an interactive graphical report of the results, an interactive threshold selection bar, and an allele length-based analysis in addition to the sequenced-based analysis. Practical use of the application is demonstrated through the analysis of four 16-plex short tandem repeat (STR) samples, showing the complementarity between the sequence- and length-based analysis of the same MPS data. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/25457631/Forensic_massively_parallel_sequencing_data_analysis_tool:_Implementation_of_MyFLq_as_a_standalone_web__and_Illumina_BaseSpace_®__application_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(14)00222-1 DB - PRIME DP - Unbound Medicine ER -