Concordance of the ForenSeq™ system and characterisation of sequence-specific autosomal STR alleles across two major population groups.

By using sequencing technology to genotype loci of forensic interest it is possible to simultaneously target autosomal, X and Y STRs as well as identity, ancestry and phenotypic informative SNPs, resulting in a breadth of data obtained from a single run that is considerable when compared to that generated with standard technologies. It is important however that this information aligns with the genotype data currently obtained using commercially available kits for CE-based investigations such that results are compatible with existing databases and hence can be of use to the forensic community. In this work, 400 samples were typed using commercially available STR kits and CE, as well as using the Ilumina ForenSeq™ DNA Signature Prep Kit and MiSeq® FGx to assess concordance of autosomal STRs and population variability. Results show a concordance rate between the two technologies exceeding 99.98% while numerous novel sequence based alleles are described. In order to make use of the sequence variation observed, sequence specific allele frequencies were generated for White British and British Chinese populations.

[1]  M. Scarpetta,et al.  Identification and characterization of variant alleles at CODIS STR loci. , 2005, Journal of forensic sciences.

[2]  Lilliana I Moreno,et al.  Performance and concordance of the ForenSeq™ system for autosomal and Y chromosome short tandem repeat sequencing of reference-type specimens. , 2017, Forensic science international. Genetics.

[3]  N. Morling,et al.  Characterization of mutations and sequence variants in the D21S11 locus by next generation sequencing. , 2014, Forensic science international. Genetics.

[4]  Peter M Vallone,et al.  Sequence variation of 22 autosomal STR loci detected by next generation sequencing. , 2016, Forensic science international. Genetics.

[5]  P. Gill,et al.  Encoded evidence: DNA in forensic analysis , 2004, Nature Reviews Genetics.

[6]  Niels Morling,et al.  Next generation sequencing and its applications in forensic genetics. , 2015, Forensic science international. Genetics.

[7]  Niels Morling,et al.  Second generation sequencing of three STRs D3S1358, D12S391 and D21S11 in Danes and a new nomenclature for sequenced STR alleles. , 2014, Forensic science international. Genetics.

[8]  John M. Butler,et al.  STRBase: a short tandem repeat DNA database for the human identity testing community , 2001, Nucleic Acids Res..

[9]  W. Parson,et al.  New sequence data of allelic variants at the STR loci ACTBP2 (SE33), D21S11, FGA, vWA, CSF1PO, D2S1338, D16S539, D18S51 and D19S433 in Caucasoids , 2004 .

[10]  Laurent Excoffier,et al.  Arlequin (version 3.0): An integrated software package for population genetics data analysis , 2005, Evolutionary bioinformatics online.

[11]  Bruce Budowle,et al.  Characterization of genetic sequence variation of 58 STR loci in four major population groups. , 2016, Forensic science international. Genetics.

[12]  Peter M Vallone,et al.  STR allele sequence variation: Current knowledge and future issues. , 2015, Forensic science international. Genetics.

[13]  J. Butler,et al.  STR sequence analysis for characterizing normal, variant, and null alleles. , 2011, Forensic science international. Genetics.

[14]  Bruce Budowle,et al.  Evaluation of the Illumina(®) Beta Version ForenSeq™ DNA Signature Prep Kit for use in genetic profiling. , 2016, Forensic science international. Genetics.

[15]  N. Morling,et al.  Characterization of mutations and sequence variations in complex STR loci by second generation sequencing , 2013 .

[16]  D. Deforce,et al.  Forensic STR analysis using massive parallel sequencing. , 2012, Forensic science international. Genetics.

[17]  Bruce Budowle,et al.  Genetic analysis of the Yavapai Native Americans from West-Central Arizona using the Illumina MiSeq FGx™ forensic genomics system. , 2016, Forensic science international. Genetics.

[18]  Jocelyne Bruand,et al.  Developmental validation of the MiSeq FGx Forensic Genomics System for Targeted Next Generation Sequencing in Forensic DNA Casework and Database Laboratories. , 2017, Forensic science international. Genetics.

[19]  Douglas R Storts,et al.  Massively parallel sequencing of short tandem repeats-Population data and mixture analysis results for the PowerSeq™ system. , 2016, Forensic science international. Genetics.

[20]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[21]  Ashley L. Silvia,et al.  A preliminary assessment of the ForenSeq™ FGx System: next generation sequencing of an STR and SNP multiplex , 2016, International Journal of Legal Medicine.

[22]  Walther Parson,et al.  Evaluation of the Illumina ForenSeq™ DNA Signature Prep Kit - MPS forensic application for the MiSeq FGx™ benchtop sequencer. , 2017, Forensic science international. Genetics.

[23]  Niels Morling,et al.  Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs. , 2016, Forensic science international. Genetics.

[24]  Niels Morling,et al.  High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform. , 2011, BioTechniques.

[25]  Bruce Budowle,et al.  Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements. , 2016, Forensic science international. Genetics.

[26]  P. Grubwieser,et al.  Unusual variant alleles in commonly used short tandem repeat loci , 2005, International Journal of Legal Medicine.