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Comparison of manual and automated AmpliSeq™ workflows in the typing of a Somali population with the Precision ID Identity Panel.
Forensic Sci Int Genet. 2017 11; 31:118-125.FS

Abstract

The Precision ID Identity Panel was used to type 109 Somali individuals in order to obtain allele frequencies for the Somali population. These frequencies were used to establish a Somali HID-SNP database, which will be used for the biostatistic calculations in family and immigration cases. Genotypes obtained with the Precision ID Identity Panel were found to be almost in complete concordance with genotypes obtained with the SNPforID PCR-SBE-CE assay. In seven SNP loci, silent alleles were identified, of which most were previously described in the literature. The project also set out to compare different AmpliSeq™ workflows to investigate the possibility of using automated library building in forensic genetic case work. In order to do so, the SNP typing of the Somalis was performed using three different workflows: 1) manual library building and sequencing on the Ion PGM™, 2) automated library building using the Biomek®3000 and sequencing on the Ion PGM™, and 3) automated library building using the Ion Chef™ and sequencing on the Ion S5™. AmpliSeq™ workflows were compared based on coverage, locus balance, noise, and heterozygote balance. Overall, the Ion Chef™/Ion S5™ workflow was found to give the best results and required least hands-on time in the laboratory. However, the Ion Chef™/Ion S5™ workflow was also the most expensive. The number of libraries that may be constructed in one Ion Chef™ library building run was limited to eight, which is too little for high throughput workflows. The Biomek®3000/Ion PGM™ workflow was found to perform similarly to the manual/Ion PGM™ workflow. This argues for the use of automated library building in forensic genetic case work. Automated library building decreases the workload of the laboratory staff, decreases the risk of pipetting errors, and simplifies the daily workflow in forensic genetic laboratories.

Authors+Show Affiliations

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark. Electronic address: claus.boersting@sund.ku.dk.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.

Pub Type(s)

Comparative Study
Journal Article

Language

eng

PubMed ID

28938152

Citation

van der Heijden, Suzanne, et al. "Comparison of Manual and Automated AmpliSeq™ Workflows in the Typing of a Somali Population With the Precision ID Identity Panel." Forensic Science International. Genetics, vol. 31, 2017, pp. 118-125.
van der Heijden S, de Oliveira SJ, Kampmann ML, et al. Comparison of manual and automated AmpliSeq™ workflows in the typing of a Somali population with the Precision ID Identity Panel. Forensic Sci Int Genet. 2017;31:118-125.
van der Heijden, S., de Oliveira, S. J., Kampmann, M. L., Børsting, C., & Morling, N. (2017). Comparison of manual and automated AmpliSeq™ workflows in the typing of a Somali population with the Precision ID Identity Panel. Forensic Science International. Genetics, 31, 118-125. https://doi.org/10.1016/j.fsigen.2017.09.009
van der Heijden S, et al. Comparison of Manual and Automated AmpliSeq™ Workflows in the Typing of a Somali Population With the Precision ID Identity Panel. Forensic Sci Int Genet. 2017;31:118-125. PubMed PMID: 28938152.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Comparison of manual and automated AmpliSeq™ workflows in the typing of a Somali population with the Precision ID Identity Panel. AU - van der Heijden,Suzanne, AU - de Oliveira,Susanne Juel, AU - Kampmann,Marie-Louise, AU - Børsting,Claus, AU - Morling,Niels, Y1 - 2017/09/14/ PY - 2017/07/26/received PY - 2017/09/11/revised PY - 2017/09/12/accepted PY - 2017/9/25/pubmed PY - 2017/12/12/medline PY - 2017/9/23/entrez KW - Automation KW - Forensic genetics KW - Library building KW - Next-generation sequencing KW - Precision ID Identity Panel KW - Single nucleotide polymorphism KW - Somali population SP - 118 EP - 125 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 31 N2 - The Precision ID Identity Panel was used to type 109 Somali individuals in order to obtain allele frequencies for the Somali population. These frequencies were used to establish a Somali HID-SNP database, which will be used for the biostatistic calculations in family and immigration cases. Genotypes obtained with the Precision ID Identity Panel were found to be almost in complete concordance with genotypes obtained with the SNPforID PCR-SBE-CE assay. In seven SNP loci, silent alleles were identified, of which most were previously described in the literature. The project also set out to compare different AmpliSeq™ workflows to investigate the possibility of using automated library building in forensic genetic case work. In order to do so, the SNP typing of the Somalis was performed using three different workflows: 1) manual library building and sequencing on the Ion PGM™, 2) automated library building using the Biomek®3000 and sequencing on the Ion PGM™, and 3) automated library building using the Ion Chef™ and sequencing on the Ion S5™. AmpliSeq™ workflows were compared based on coverage, locus balance, noise, and heterozygote balance. Overall, the Ion Chef™/Ion S5™ workflow was found to give the best results and required least hands-on time in the laboratory. However, the Ion Chef™/Ion S5™ workflow was also the most expensive. The number of libraries that may be constructed in one Ion Chef™ library building run was limited to eight, which is too little for high throughput workflows. The Biomek®3000/Ion PGM™ workflow was found to perform similarly to the manual/Ion PGM™ workflow. This argues for the use of automated library building in forensic genetic case work. Automated library building decreases the workload of the laboratory staff, decreases the risk of pipetting errors, and simplifies the daily workflow in forensic genetic laboratories. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/28938152/Comparison_of_manual_and_automated_AmpliSeq™_workflows_in_the_typing_of_a_Somali_population_with_the_Precision_ID_Identity_Panel_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(17)30197-7 DB - PRIME DP - Unbound Medicine ER -