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Evaluation of the Qiagen 140-SNP forensic identification multiplex for massively parallel sequencing.
Forensic Sci Int Genet. 2017 05; 28:35-43.FS

Abstract

A new forensic 140-SNP genotyping system from Qiagen, designed for massively parallel sequencing (MPS) analysis, was evaluated using the Ion PGM™ MPS system. Assessments consisted of the sequencing of: established control DNAs that had been previously genotyped with alternative PCR and library preparation kits supplied by Thermo Fisher Scientific for the Ion PGM™ system; a simple set of artificial DNA mixtures; DNA extracted from a degraded femur; and a dilution series to gauge forensic sensitivity. In addition to the reagents for the DNA target capture PCR and library preparation, Qiagen offer an alternative sequence analysis software system (Workbench), which was assessed alongside the Ion PGM™ Genotyper software for forensic MPS analysis. The Qiagen SNP genotyping system produced full genotyping concordance with previous data obtained with a similar SNP panel on the Ion PGM™ and in comparison to genotypes listed for 139 of the 140 SNPs in 1000 Genomes. The workbench software was as reliable as Genotyper in calling genotypes, although scrutiny of sequence data with IGV revealed the problem of sequence misalignment plagues a small proportion of the 140 SNPs in the Qiagen panel, a problem already recognized in multiple MPS studies of the same markers in alternative kits. The potential for genotype miscalls from sequence misalignment in certain SNPs will require manual inspection in cases where low-level or degraded DNA reduces the sequence coverage to a point where misalignment influences individual SNP genotype quality.

Authors+Show Affiliations

Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain. Electronic address: c.phillips@mac.com.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain; Grupo de Medicina Xenómica (GMX), Faculty of Medicine, University of Santiago de Compostela, Spain; Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain.

Pub Type(s)

Evaluation Study
Journal Article

Language

eng

PubMed ID

28160618

Citation

de la Puente, M, et al. "Evaluation of the Qiagen 140-SNP Forensic Identification Multiplex for Massively Parallel Sequencing." Forensic Science International. Genetics, vol. 28, 2017, pp. 35-43.
de la Puente M, Phillips C, Santos C, et al. Evaluation of the Qiagen 140-SNP forensic identification multiplex for massively parallel sequencing. Forensic Sci Int Genet. 2017;28:35-43.
de la Puente, M., Phillips, C., Santos, C., Fondevila, M., Carracedo, Á., & Lareu, M. V. (2017). Evaluation of the Qiagen 140-SNP forensic identification multiplex for massively parallel sequencing. Forensic Science International. Genetics, 28, 35-43. https://doi.org/10.1016/j.fsigen.2017.01.012
de la Puente M, et al. Evaluation of the Qiagen 140-SNP Forensic Identification Multiplex for Massively Parallel Sequencing. Forensic Sci Int Genet. 2017;28:35-43. PubMed PMID: 28160618.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Evaluation of the Qiagen 140-SNP forensic identification multiplex for massively parallel sequencing. AU - de la Puente,M, AU - Phillips,C, AU - Santos,C, AU - Fondevila,M, AU - Carracedo,Á, AU - Lareu,M V, Y1 - 2017/01/27/ PY - 2016/08/06/received PY - 2017/01/05/revised PY - 2017/01/23/accepted PY - 2017/2/6/pubmed PY - 2017/7/8/medline PY - 2017/2/5/entrez KW - Forensic identification KW - Massively parallel sequencing (MPS) KW - Qiagen SNP-ID panel KW - SNPs SP - 35 EP - 43 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 28 N2 - A new forensic 140-SNP genotyping system from Qiagen, designed for massively parallel sequencing (MPS) analysis, was evaluated using the Ion PGM™ MPS system. Assessments consisted of the sequencing of: established control DNAs that had been previously genotyped with alternative PCR and library preparation kits supplied by Thermo Fisher Scientific for the Ion PGM™ system; a simple set of artificial DNA mixtures; DNA extracted from a degraded femur; and a dilution series to gauge forensic sensitivity. In addition to the reagents for the DNA target capture PCR and library preparation, Qiagen offer an alternative sequence analysis software system (Workbench), which was assessed alongside the Ion PGM™ Genotyper software for forensic MPS analysis. The Qiagen SNP genotyping system produced full genotyping concordance with previous data obtained with a similar SNP panel on the Ion PGM™ and in comparison to genotypes listed for 139 of the 140 SNPs in 1000 Genomes. The workbench software was as reliable as Genotyper in calling genotypes, although scrutiny of sequence data with IGV revealed the problem of sequence misalignment plagues a small proportion of the 140 SNPs in the Qiagen panel, a problem already recognized in multiple MPS studies of the same markers in alternative kits. The potential for genotype miscalls from sequence misalignment in certain SNPs will require manual inspection in cases where low-level or degraded DNA reduces the sequence coverage to a point where misalignment influences individual SNP genotype quality. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/28160618/Evaluation_of_the_Qiagen_140_SNP_forensic_identification_multiplex_for_massively_parallel_sequencing_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(17)30021-2 DB - PRIME DP - Unbound Medicine ER -