RT Journal Article
T1 Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the Ion PGM™
A1 Eduardoff, Mayra
A1 Santos, Carla
A1 Puente Vila, María del Carmen de la
A1 Gross, Theresa E.
A1 Fondevila, María Sonia
A1 Strobl, Christina
A1 Sobrino, Beatriz
A1 Ballard, David
A1 Schneider, Peter M.
A1 Carracedo Álvarez, Ángel
A1 Lareu Huidobro, María Victoria
A1 Parson, Walther
A1 Phillips, C.
K1 Next generation sequencing
K1 Massively parallel sequencing
K1 Ion PGM™
K1 Ion Torrent
K1 Identification SNPs
AB Next generation sequencing (NGS) offers the opportunity to analyse forensic DNA samples and obtain massively parallel coverage of targeted short sequences with the variants they carry. We evaluated the levels of sequence coverage, genotyping precision, sensitivity and mixed DNA patterns of a prototype version of the first commercial forensic NGS kit: the HID-Ion AmpliSeq™ Identity Panel with 169-markers designed for the Ion PGM™ system. Evaluations were made between three laboratories following closely matched Ion PGM™ protocols and a simple validation framework of shared DNA controls. The sequence coverage obtained was extensive for the bulk of SNPs targeted by the HID-Ion AmpliSeq™ Identity Panel. Sensitivity studies showed 90–95% of SNP genotypes could be obtained from 25 to 100pg of input DNA. Genotyping concordance tests included Coriell cell-line control DNA analyses checked against whole-genome sequencing data from 1000 Genomes and Complete Genomics, indicating a very high concordance rate of 99.8%. Discordant genotypes detected in rs1979255, rs1004357, rs938283, rs2032597 and rs2399332 indicate these loci should be excluded from the panel. Therefore, the HID-Ion AmpliSeq™ Identity Panel and Ion PGM™ system provide a sensitive and accurate forensic SNP genotyping assay. However, low-level DNA produced much more varied sequence coverage and in forensic use the Ion PGM™ system will require careful calibration of the total samples loaded per chip to preserve the genotyping reliability seen in routine forensic DNA. Furthermore, assessments of mixed DNA indicate the user’s control of sequence analysis parameter settings is necessary to ensure mixtures are detected robustly. Given the sensitivity of Ion PGM™, this aspect of forensic genotyping requires further optimisation before massively parallel sequencing is applied to routine casework.
PB Elsevier
YR 2015
FD 2015-04-15
LK https://hdl.handle.net/10347/45456
UL https://hdl.handle.net/10347/45456
LA eng
NO Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the Ion PGM™ . Eduardoff, M. et al. Forensic Science International: Genetics, Volume 17, 110 - 121
NO This work was funded by the European Union Seventh Framework Program (FP7/2007-2013) under grant agreement no. 285487 (EUROFORGEN-NoE) and the Austrian Science Fund (FWF) [P22880-B12]. CS is supported by funding awarded by the Portuguese Foundation for Science and Technology (FCT) and co- financed by the European Social Fund (Human Potential Thematic Operational Program SFRH/BD/75627/2010). MdlP is supported by funding awarded by the Consellería de Cultura, Educación e Ordenación Universitaria of the Xunta de Galicia as part of the Plan Galego de Investigación, Innovación e Crecemento 2011–2015 (Plan I2C). The authors wish to thank Jorge Amigo, Grupo de Medicina Xenómica (GMX), University of Santiago de Compostela and Matt Phipps of Life Technologies, for their helpful guidance with NGS data analysis.
DS Minerva
RD 23 abr 2026