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My-Forensic-Loci-queries (MyFLq) framework for analysis of forensic STR data generated by massive parallel sequencing

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Abstract
Forensic scientists are currently investigating how to transition from capillary electrophoresis (CE) to massive parallel sequencing (MPS) for analysis of forensic DNA profiles. MPS offers several advantages over CE such as virtually unlimited multiplexy of loci, combining both short tandem repeat (STR) and single nucleotide polymorphism (SNP) loci, small amplicons without constraints of size separation, more discrimination power, deep mixture resolution and sample multiplexing. We present our bioinformatic framework My-Forensic-Loci-queries (MyFLq) for analysis of MPS forensic data. For allele calling, the framework uses a MySQL reference allele database with automatically determined regions of interest (ROIs) by a generic maximal flanking algorithm which makes it possible to use any STR or SNP forensic locus. Python scripts were designed to automatically make allele calls starting from raw MPS data. We also present a method to assess the usefulness and overall performance of a forensic locus with respect to MPS, as well as methods to estimate whether an unknown allele, which sequence is not present in the MySQL database, is in fact a new allele or a sequencing error. The MyFLq framework was applied to an Illumina MiSeq dataset of a forensic Illumina amplicon library, generated from multilocus STR polymerase chain reaction (PCR) on both single contributor samples and multiple person DNA mixtures. Although the multilocus PCR was not yet optimized for MPS in terms of amplicon length or locus selection, the results show excellent results for most loci. The results show a high signal-to-noise ratio, correct allele calls, and a low limit of detection for minor DNA contributors in mixed DNA samples. Technically, forensic MPS affords great promise for routine implementation in forensic genomics. The method is also applicable to adjacent disciplines such as mitochondrial DNA research.
Keywords
MiSeq, Illumina, STR, Forensic loci, MPS, NGS, INTERNATIONAL SOCIETY, RECOMMENDATIONS, GENETICS, GENOMES

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Chicago
Van Neste, Christophe, Mado Vandewoestyne, Wim Van Criekinge, Dieter Deforce, and Filip Van Nieuwerburgh. 2014. “My-Forensic-Loci-queries (MyFLq) Framework for Analysis of Forensic STR Data Generated by Massive Parallel Sequencing.” Forensic Science International-genetics 9: 1–8.
APA
Van Neste, C., Vandewoestyne, M., Van Criekinge, W., Deforce, D., & Van Nieuwerburgh, F. (2014). My-Forensic-Loci-queries (MyFLq) framework for analysis of forensic STR data generated by massive parallel sequencing. FORENSIC SCIENCE INTERNATIONAL-GENETICS, 9, 1–8.
Vancouver
1.
Van Neste C, Vandewoestyne M, Van Criekinge W, Deforce D, Van Nieuwerburgh F. My-Forensic-Loci-queries (MyFLq) framework for analysis of forensic STR data generated by massive parallel sequencing. FORENSIC SCIENCE INTERNATIONAL-GENETICS. 2014;9:1–8.
MLA
Van Neste, Christophe, Mado Vandewoestyne, Wim Van Criekinge, et al. “My-Forensic-Loci-queries (MyFLq) Framework for Analysis of Forensic STR Data Generated by Massive Parallel Sequencing.” FORENSIC SCIENCE INTERNATIONAL-GENETICS 9 (2014): 1–8. Print.
@article{4416378,
  abstract     = {Forensic scientists are currently investigating how to transition from capillary electrophoresis (CE) to massive parallel sequencing (MPS) for analysis of forensic DNA profiles. MPS offers several advantages over CE such as virtually unlimited multiplexy of loci, combining both short tandem repeat (STR) and single nucleotide polymorphism (SNP) loci, small amplicons without constraints of size separation, more discrimination power, deep mixture resolution and sample multiplexing. We present our bioinformatic framework My-Forensic-Loci-queries (MyFLq) for analysis of MPS forensic data. For allele calling, the framework uses a MySQL reference allele database with automatically determined regions of interest (ROIs) by a generic maximal flanking algorithm which makes it possible to use any STR or SNP forensic locus. Python scripts were designed to automatically make allele calls starting from raw MPS data. We also present a method to assess the usefulness and overall performance of a forensic locus with respect to MPS, as well as methods to estimate whether an unknown allele, which sequence is not present in the MySQL database, is in fact a new allele or a sequencing error. The MyFLq framework was applied to an Illumina MiSeq dataset of a forensic Illumina amplicon library, generated from multilocus STR polymerase chain reaction (PCR) on both single contributor samples and multiple person DNA mixtures. Although the multilocus PCR was not yet optimized for MPS in terms of amplicon length or locus selection, the results show excellent results for most loci. The results show a high signal-to-noise ratio, correct allele calls, and a low limit of detection for minor DNA contributors in mixed DNA samples. Technically, forensic MPS affords great promise for routine implementation in forensic genomics. The method is also applicable to adjacent disciplines such as mitochondrial DNA research.},
  author       = {Van Neste, Christophe and Vandewoestyne, Mado and Van Criekinge, Wim and Deforce, Dieter and Van Nieuwerburgh, Filip},
  issn         = {1872-4973},
  journal      = {FORENSIC SCIENCE INTERNATIONAL-GENETICS},
  keyword      = {MiSeq,Illumina,STR,Forensic loci,MPS,NGS,INTERNATIONAL SOCIETY,RECOMMENDATIONS,GENETICS,GENOMES},
  language     = {eng},
  pages        = {1--8},
  title        = {My-Forensic-Loci-queries (MyFLq) framework for analysis of forensic STR data generated by massive parallel sequencing},
  url          = {http://dx.doi.org/10.1016/j.fsigen.2013.10.012},
  volume       = {9},
  year         = {2014},
}

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