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Combining results of forensic STR kits: HDplex validation including allelic association and linkage testing with NGM and Identifiler loci

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Abstract

The autosomal short tandem repeat (STR) kits that are currently used in forensic science have a high discrimination power. However, this discrimination power is sometimes not sufficient for complex kinship analyses or decreases when alleles are missing due to degradation of the DNA. The Investigator HDplex kit contains nine STRs that are additional to the commonly used forensic markers, and we validated this kit to assist human identification. With the increasing number of markers it becomes inevitable that forensic and kinship analyses include two or more STRs present on the same chromosome. To examine whether such markers can be regarded as independent, we evaluated the 30 STRs present in NGM, Identifiler and HDplex. Among these 30 markers, 17 syntenic STR pairs can be formed. Allelic association between these pairs was examined using 335 Dutch reference samples and no linkage disequilibrium was detected, which makes it possible to use the product rule for profile probability calculations in unrelated individuals. Linkage between syntenic STRs was studied by determining the recombination fraction between them in five three-generation CEPH families. The recombination fractions were compared to the physical and genetic distances between the markers. For most types of pedigrees, the kinship analyses can be performed using the product rule, and for those cases that require an alternative calculation method (Gill et al., Forensic Sci Int Genet 6:477–486, 2011), the recombination fractions as determined in this study can be used. Finally, we calculated the (combined) match probabilities, for the supplementary genotyping results of HDplex, NGM and Identifiler.

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Acknowledgements

This study was supported by a grant from the Netherlands Genomics Initiative/Netherlands Organization for Scientific Research (NWO) within the framework of the Forensic Genomics Consortium Netherlands. The authors are grateful for the voluntary cooperation of the DNA donors for the Dutch reference set. We would like to thank Klaas Slooten and Ate Kloosterman for valuable discussions and Arnoud Kal for critically reading the manuscript.

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Authors and Affiliations

  1. Department of Human Biological Traces (R&D), Netherlands Forensic Institute, P.O. Box 24044, 2490 AA, The Hague, The Netherlands

    Antoinette A. Westen, Hinda Haned, Laurens J. W. Grol, Joyce Harteveld & Titia Sijen

  2. Forensic Laboratory for DNA Research, Leiden University Medical Centre, P.O. Box 9503, 2300 RA, Leiden, The Netherlands

    Kristiaan J. van der Gaag & Peter de Knijff

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  1. Antoinette A. Westen
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  2. Hinda Haned
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  6. Peter de Knijff
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  7. Titia Sijen
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Correspondence to Titia Sijen.

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Supplementary Fig 1

HDplex performance. a Comparison between two methods to sensitise low template DNA profiling of a dilution series of pristine DNA007 in threefold. Black bars show the average percentage of detected alleles for the standard setting with 30 PCR cycles and 3 kV CE. Dark grey bars represent 30 PCR cycles with 9 kV CE and light grey bars 32 PCR cycles with 3 kV CE. Error bars show the standard deviation. b Comparison between NGM (dark grey bars) and HDplex (light grey bars) for time-wise UV-degraded hDNA. The experiment is performed in duplicate, and the average percentage of detected alleles is plotted against the UV degradation time. Error bars represent the standard deviation (when present) (JPEG 2829 kb)

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Supplementary Fig. 2

Inter-locus balance (a) and intra-locus peak height ratio (b). Loci are ordered from shorter (left) to longer (right) amplicon sizes. Circles represent the median of the data points, boxes indicate the first to the third quartile and whiskers show the minimum and maximum values. The colour in which the markers are presented indicates the dye-channel (blue = 6-FAM, green = BTG and black = BTY). The horizontal line (at 1) in (a) represents perfect balance between loci, and the line in (b) indicates the preferred value (of 0.7) above which the data points should reside (JPEG 3583 kb)

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Westen, A.A., Haned, H., Grol, L.J.W. et al. Combining results of forensic STR kits: HDplex validation including allelic association and linkage testing with NGM and Identifiler loci. Int J Legal Med 126, 781–789 (2012). https://doi.org/10.1007/s00414-012-0724-4

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