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Evaluation of the Ion Torrent™ HID SNP 169-plex: A SNP typing assay developed for human identification by second generation sequencing.
Forensic Sci Int Genet. 2014 Sep; 12:144-54.FS

Abstract

The Ion Torrent™ HID SNP assay amplified 136 autosomal SNPs and 33 Y-chromosome markers in one PCR and the markers were subsequently typed using the Ion PGM™ second generation sequencing platform. A total of 51 of the autosomal SNPs were selected from the SNPforID panel that is routinely used in our ISO 17025 accredited laboratory. Concordance between the Ion Torrent™ HID SNP assay and the SNPforID assay was tested by typing 44 Iraqis twice with the Ion Torrent™ HID SNP assay. The same samples were previously typed with the SNPforID assay and the Y-chromosome haplogroups of the individuals were previously identified by typing 45 Y-chromosome SNPs. Full concordance between the assays were obtained except for the SNP genotypes of two SNPs. These SNPs were among the eight SNPs (rs2399332, rs1029047, rs10776839, rs4530059, rs8037429, rs430046, rs1031825 and rs1523537) with inconsistent allele balance among samples. These SNPs should be excluded from the panel. The optimal amount of DNA in the PCR seemed to be ≥0.5ng. Allele drop-outs were rare and only seen in experiments with <0.5ng input DNA and with a coverage of <50reads. No allele drop-in was observed. The great majority of the heterozygote allele balances were between 0.6 and 1.6, which is comparable to the heterozygote balances of STRs typed with PCR-CE. The number of reads with base calls that differed from the genotype call was typically less than five. This allowed detection of 1:100 mixtures with a high degree of certainty in experiments with a high total depth of coverage. In conclusion, the Ion PGM™ is a very promising platform for forensic genetics. However, the secondary sequence analysis software made wrong genotype calls from correctly sequenced alleles. These types of errors must be corrected before the platform can be used in case work. Furthermore, the sequence analysis software should be further developed and include quality settings for each SNP based on validation studies.

Authors+Show Affiliations

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark. Electronic address: sarah.fordyce@sund.ku.dk.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

24997319

Citation

Børsting, Claus, et al. "Evaluation of the Ion Torrent™ HID SNP 169-plex: a SNP Typing Assay Developed for Human Identification By Second Generation Sequencing." Forensic Science International. Genetics, vol. 12, 2014, pp. 144-54.
Børsting C, Fordyce SL, Olofsson J, et al. Evaluation of the Ion Torrent™ HID SNP 169-plex: A SNP typing assay developed for human identification by second generation sequencing. Forensic Sci Int Genet. 2014;12:144-54.
Børsting, C., Fordyce, S. L., Olofsson, J., Mogensen, H. S., & Morling, N. (2014). Evaluation of the Ion Torrent™ HID SNP 169-plex: A SNP typing assay developed for human identification by second generation sequencing. Forensic Science International. Genetics, 12, 144-54. https://doi.org/10.1016/j.fsigen.2014.06.004
Børsting C, et al. Evaluation of the Ion Torrent™ HID SNP 169-plex: a SNP Typing Assay Developed for Human Identification By Second Generation Sequencing. Forensic Sci Int Genet. 2014;12:144-54. PubMed PMID: 24997319.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Evaluation of the Ion Torrent™ HID SNP 169-plex: A SNP typing assay developed for human identification by second generation sequencing. AU - Børsting,Claus, AU - Fordyce,Sarah L, AU - Olofsson,Jill, AU - Mogensen,Helle Smidt, AU - Morling,Niels, Y1 - 2014/06/14/ PY - 2014/01/22/received PY - 2014/06/04/revised PY - 2014/06/06/accepted PY - 2014/7/6/entrez PY - 2014/7/6/pubmed PY - 2015/4/4/medline KW - Forensic genetics KW - Human identification KW - Ion PGM™ KW - SNP typing KW - SNPforID KW - Second generation sequencing SP - 144 EP - 54 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 12 N2 - The Ion Torrent™ HID SNP assay amplified 136 autosomal SNPs and 33 Y-chromosome markers in one PCR and the markers were subsequently typed using the Ion PGM™ second generation sequencing platform. A total of 51 of the autosomal SNPs were selected from the SNPforID panel that is routinely used in our ISO 17025 accredited laboratory. Concordance between the Ion Torrent™ HID SNP assay and the SNPforID assay was tested by typing 44 Iraqis twice with the Ion Torrent™ HID SNP assay. The same samples were previously typed with the SNPforID assay and the Y-chromosome haplogroups of the individuals were previously identified by typing 45 Y-chromosome SNPs. Full concordance between the assays were obtained except for the SNP genotypes of two SNPs. These SNPs were among the eight SNPs (rs2399332, rs1029047, rs10776839, rs4530059, rs8037429, rs430046, rs1031825 and rs1523537) with inconsistent allele balance among samples. These SNPs should be excluded from the panel. The optimal amount of DNA in the PCR seemed to be ≥0.5ng. Allele drop-outs were rare and only seen in experiments with <0.5ng input DNA and with a coverage of <50reads. No allele drop-in was observed. The great majority of the heterozygote allele balances were between 0.6 and 1.6, which is comparable to the heterozygote balances of STRs typed with PCR-CE. The number of reads with base calls that differed from the genotype call was typically less than five. This allowed detection of 1:100 mixtures with a high degree of certainty in experiments with a high total depth of coverage. In conclusion, the Ion PGM™ is a very promising platform for forensic genetics. However, the secondary sequence analysis software made wrong genotype calls from correctly sequenced alleles. These types of errors must be corrected before the platform can be used in case work. Furthermore, the sequence analysis software should be further developed and include quality settings for each SNP based on validation studies. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/24997319/Evaluation_of_the_Ion_Torrent���_HID_SNP_169_plex:_A_SNP_typing_assay_developed_for_human_identification_by_second_generation_sequencing_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(14)00122-7 DB - PRIME DP - Unbound Medicine ER -