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Evaluation of the iPLEX® Sample ID Plus Panel designed for the Sequenom MassARRAY® system. A SNP typing assay developed for human identification and sample tracking based on the SNPforID panel.
Forensic Sci Int Genet. 2013 Sep; 7(5):482-7.FS

Abstract

Sequenom launched the first commercial SNP typing kit for human identification, named the iPLEX(®) Sample ID Plus Panel. The kit amplifies 47 of the 52 SNPs in the SNPforID panel, amelogenin and two Y-chromosome SNPs in one multiplex PCR. The SNPs were analyzed by single base extension (SBE) and Matrix Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). In this study, we evaluated the accuracy and sensitivity of the iPLEX(®) Sample ID Plus Panel by comparing the typing results of the iPLEX(®) Sample ID Plus Panel with those obtained with our ISO 17025 accredited SNPforID assay. The average call rate for duplicate typing of any one SNPs in the panel was 90.0% when the mass spectra were analyzed automatically with the MassARRAY(®) TYPER 4.0 genotyping software in real time. Two reproducible inconsistencies were observed (error rate: 0.05%) at two different SNP loci. In addition, four inconsistencies were observed once. The optimal amount of template DNA in the PCR was ≥10ng. There was a relatively high risk of allele and locus drop-outs when ≤1ng template DNA was used. We developed an R script with a stringent set of "forensic analysis parameters" based on the peak height and the signal to noise data exported from the TYPER 4.0 software. With the forensic analysis parameters, all inconsistencies were eliminated in reactions with ≥10ng DNA. However, the average call rate decreased to 69.9%. The iPLEX(®) Sample ID Plus Panel was tested on 10 degraded samples from forensic case-work. Two samples could not be typed, presumably because the samples contained PCR and SBE inhibitors. The average call rate was generally lower for degraded DNA samples and the number of inconsistencies higher than for pristine DNA. However, none of the inconsistencies were reproduced and the highest match probability for the degraded samples typed with the panel was 1.7E-9 using the stringent forensic analysis parameters. Although the relatively low sensitivity of the iPLEX(®) Sample ID Plus Panel makes it inappropriate for typing of trace samples from crime scenes, the panel may be interesting for relationship testing and for identification of e.g. samples in biobanks because of the low reagent costs, the limited hands-on time of the iPLEX(®) assay and the automatic analysis of the mass spectra.

Authors+Show Affiliations

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark.No affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Comparative Study
Evaluation Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

23948317

Citation

Johansen, P, et al. "Evaluation of the iPLEX® Sample ID Plus Panel Designed for the Sequenom MassARRAY® System. a SNP Typing Assay Developed for Human Identification and Sample Tracking Based On the SNPforID Panel." Forensic Science International. Genetics, vol. 7, no. 5, 2013, pp. 482-7.
Johansen P, Andersen JD, Børsting C, et al. Evaluation of the iPLEX® Sample ID Plus Panel designed for the Sequenom MassARRAY® system. A SNP typing assay developed for human identification and sample tracking based on the SNPforID panel. Forensic Sci Int Genet. 2013;7(5):482-7.
Johansen, P., Andersen, J. D., Børsting, C., & Morling, N. (2013). Evaluation of the iPLEX® Sample ID Plus Panel designed for the Sequenom MassARRAY® system. A SNP typing assay developed for human identification and sample tracking based on the SNPforID panel. Forensic Science International. Genetics, 7(5), 482-7. https://doi.org/10.1016/j.fsigen.2013.04.009
Johansen P, et al. Evaluation of the iPLEX® Sample ID Plus Panel Designed for the Sequenom MassARRAY® System. a SNP Typing Assay Developed for Human Identification and Sample Tracking Based On the SNPforID Panel. Forensic Sci Int Genet. 2013;7(5):482-7. PubMed PMID: 23948317.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Evaluation of the iPLEX® Sample ID Plus Panel designed for the Sequenom MassARRAY® system. A SNP typing assay developed for human identification and sample tracking based on the SNPforID panel. AU - Johansen,P, AU - Andersen,J D, AU - Børsting,C, AU - Morling,N, Y1 - 2013/06/28/ PY - 2013/02/15/received PY - 2013/04/18/revised PY - 2013/04/24/accepted PY - 2013/8/17/entrez PY - 2013/8/21/pubmed PY - 2014/5/13/medline KW - Forensic genetics KW - Human identification KW - MassARRAY KW - Multiplex KW - SNPforID KW - SNPs KW - iPLEX(®) Sample ID Plus Panel SP - 482 EP - 7 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 7 IS - 5 N2 - Sequenom launched the first commercial SNP typing kit for human identification, named the iPLEX(®) Sample ID Plus Panel. The kit amplifies 47 of the 52 SNPs in the SNPforID panel, amelogenin and two Y-chromosome SNPs in one multiplex PCR. The SNPs were analyzed by single base extension (SBE) and Matrix Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). In this study, we evaluated the accuracy and sensitivity of the iPLEX(®) Sample ID Plus Panel by comparing the typing results of the iPLEX(®) Sample ID Plus Panel with those obtained with our ISO 17025 accredited SNPforID assay. The average call rate for duplicate typing of any one SNPs in the panel was 90.0% when the mass spectra were analyzed automatically with the MassARRAY(®) TYPER 4.0 genotyping software in real time. Two reproducible inconsistencies were observed (error rate: 0.05%) at two different SNP loci. In addition, four inconsistencies were observed once. The optimal amount of template DNA in the PCR was ≥10ng. There was a relatively high risk of allele and locus drop-outs when ≤1ng template DNA was used. We developed an R script with a stringent set of "forensic analysis parameters" based on the peak height and the signal to noise data exported from the TYPER 4.0 software. With the forensic analysis parameters, all inconsistencies were eliminated in reactions with ≥10ng DNA. However, the average call rate decreased to 69.9%. The iPLEX(®) Sample ID Plus Panel was tested on 10 degraded samples from forensic case-work. Two samples could not be typed, presumably because the samples contained PCR and SBE inhibitors. The average call rate was generally lower for degraded DNA samples and the number of inconsistencies higher than for pristine DNA. However, none of the inconsistencies were reproduced and the highest match probability for the degraded samples typed with the panel was 1.7E-9 using the stringent forensic analysis parameters. Although the relatively low sensitivity of the iPLEX(®) Sample ID Plus Panel makes it inappropriate for typing of trace samples from crime scenes, the panel may be interesting for relationship testing and for identification of e.g. samples in biobanks because of the low reagent costs, the limited hands-on time of the iPLEX(®) assay and the automatic analysis of the mass spectra. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/23948317/Evaluation_of_the_iPLEX®_Sample_ID_Plus_Panel_designed_for_the_Sequenom_MassARRAY®_system__A_SNP_typing_assay_developed_for_human_identification_and_sample_tracking_based_on_the_SNPforID_panel_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(13)00109-9 DB - PRIME DP - Unbound Medicine ER -