Top

Published in:

01-07-2012 | Original Article

A validation study of the Qiagen Investigator DIPplex® kit; an INDEL-based assay for human identification

Authors: Bobby L. LaRue, Jianye Ge, Jonathan L. King, Bruce Budowle

Published in: International Journal of Legal Medicine | Issue 4/2012

Abstract

Marker sets that are based on small insertion/deletion (INDEL) alleles can serve as useful supplementary or stand-alone assays for human identification. A validation study has been performed on a human identification assay based on a panel of 30 INDELs and amelogenin using the Investigator DIPplex® kit (Qiagen). The assay was able to type DNA from a number of forensically relevant sample types and obtain full profiles with 62 pg of template DNA and partial profiles with as little as 16 pg of template DNA. The assay is reproducible, precise, and non-overlapping alleles from minor contributors were detectable in mixture analysis ranging from 6:1 to 19:1 mixtures. Population studies were performed on the 30 indels, and there were no significant departures from Hardy–Weinberg equilibrium or significant linkage disequilibrium between the markers (after correction for sampling). In all populations, the random match probability was 1.43 × 10⁻¹¹ or less, and the power of exclusion was greater than .999999999. We also discovered several microvariant alleles in our population samples. The data support that the Investigator DIPplex® kit provides a powerful supplement or stand-alone capability for human identity testing.

Available only for authorised users

Andersen JF, Greenhalgh M, Butler H, Kilpatrick S, Piercy R, Way K, Myhill H, Wright J, Hallett R, Parkin B (1996) Further validation of a multiplex STR system for use in routine forensic identity testing. Forensic Sci Int 78(1):47–64PubMedCrossRef

Brinkmann B, Klintschar M, Neuhuber F, Hühne J, Rolf B (1998) Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat. Am J Hum Genet 62(6):1408–1415PubMedCrossRef

Collins PJ, Hennessy LK, Leibelt CS, Roby RK, Reeder DJ, Foxall PA (2004) Developmental validation of a single-tube Amplification of the 13 CODIS STR loci, D2S1338, D19S433, and amelogenin: the AmpFSTR® Identifiler® PCR Amplification Kit. J Forensic Sci 49(6):1265–1277PubMedCrossRef

Gill P, Whitaker J, Flaxman C, Brown N, Buckleton J (2000) An investigation of the rigor of interpretation rules for STRs derived from less than 100 pg of DNA. Forensic Sci Int 112(1):17–40PubMedCrossRef

Junge A, Lederer T, Braunschweiger G, Madea B (2003) Validation of the multiplex kit genRESMPX-2 for forensic casework analysis. Int J Leg Med 117(6):317–325CrossRef

LaFountain MJ, Schwartz MB, Svete PA, Walkinshaw MA, Buel E (2001) TWGDAM validation of the AmpFeSTR Profiler Plus and AmpFeSTR COfiler STR multiplex systems using capillary electrophoresis. J Forensic Sci 46(5):1191–1198PubMed

Moretti T, Baumstark A, Defenbaugh D, Keys K, Smerick J, Budowle B (2001) Validation of short tandem repeats (STRs) for forensic usage: performance testing of fluorescent multiplex STR systems and analysis of authentic and simulated forensic samples. J Forensic Sci 46(3):647PubMed

Micka KA, Sprecher CJ, Lins AM, Comey CT, Koons BW, Crouse C, Endean D, Pirelli K, Lee SB, Duda N (1996) Validation of multiplex polymorphic STR amplification sets developed for personal identification applications. J Forensic Sci 41:582–590PubMed

Fondevila M, Phillips C, Naverán N, Cerezo M, Rodríguez A, Calvo R, Fernández L, Carracedo Á, Lareu M (2008) Challenging DNA: assessment of a range of genotyping approaches for highly degraded forensic samples. Forensic Sci Int: Genet Suppl Ser 1(1):26–28CrossRef

10.

Burger J, Hummel S, Herrmann B, Henke W (1999) DNA preservation: a microsatellite DNA study on ancient skeletal remains. Electrophoresis 20(8):1722–1728PubMedCrossRef

11.

Golenberg EM, Bickel A, Weihs P (1996) Effect of highly fragmented DNA on PCR. Nucleic Acids Res 24(24):5026–5033. doi:10.1093/nar/24.24.5026 PubMedCrossRef

12.

Forster L, Thomson J, Kutranov S (2008) Direct comparison of post-28-cycle PCR purification and modified capillary electrophoresis methods with the 34-cycle “low copy number” (LCN) method for analysis of trace forensic DNA samples. Forensic Sci Int: Genet 2(4):318–328CrossRef

13.

Kloosterman AD, Kersbergen P (2003) Efficacy and limits of genotyping low copy number DNA samples by multiplex PCR of STR loci. Int Congr Ser 1239:795–798CrossRef

14.

Budowle B, van Daal A (2008) Forensically relevant SNP classes. BioTechniques 44:603–610PubMedCrossRef

15.

Dixon LA, Murray CM, Archer EJ, Dobbins AE, Koumi P, Gill P (2005) Validation of a 21-locus autosomal SNP multiplex for forensic identification purposes. Forensic Sci Int 154(1):62–77PubMedCrossRef

16.

Kidd KK, Pakstis AJ, Speed WC, Grigorenko EL, Kajuna SLB, Karoma NJ, Kungulilo S, Kim J-J, Lu R-B, Odunsi A, Okonofua F, Parnas J, Schulz LO, Zhukova OV, Kidd JR (2006) Developing a SNP panel for forensic identification of individuals. Forensic Sci Int 164(1):20–32PubMedCrossRef

17.

Phillips C, Fang R, Ballard D, Fondevila M, Harrison C, Hyland F, Musgrave-Brown E, Proff C, Ramos-Luis E, Sobrino B, Carracedo A, Furtado MR, Court DS, Schneider PM (2007) Evaluation of the Genplex SNP typing system and a 49plex forensic marker panel. Forensic Sci Int: Genet 1(2):180–185CrossRef

18.

Divne A-M, Allen M (2005) A DNA microarray system for forensic SNP analysis. Forensic Sci Int 154(2–3):111–121PubMedCrossRef

19.

Sanchez JJ, Phillips C, Børsting C, Balogh K, Bogus M, Fondevila M, Harrison CD, Musgrave-Brown E, Salas A, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N (2006) A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27(9):1713–1724. doi:10.1002/elps.200500671 PubMedCrossRef

20.

Edelmann J, Hering S, Augustin C, Szibor R (2009) Indel polymorphisms—an additional set of markers on the X-chromosome. Forensic Sci Int: Genet Suppl Ser 2(1):510–512CrossRef

21.

Francez PAdC, Ribeiro-Rodrigues EM, dos Santos SEB (2012) Allelic frequencies and statistical data obtained from 48 AIM INDEL loci in an admixed population from the Brazilian Amazon. Forensic Sci Int: Genet 6(1):132–135CrossRef

22.

Li C, Zhao S, Zhang S, Li L, Liu Y, Chen J, Xue J (2011) Genetic polymorphism of 29 highly informative InDel markers for forensic use in the Chinese Han population. Forensic Sci Int: Genet 5(1):e27–e30CrossRef

23.

Pereira R, Phillips C, Alves C, Amorim A, Carracedo Á, Gusmão L (2009) Insertion/deletion polymorphisms: a multiplex assay and forensic applications. Forensic Sci Int: Genet Suppl Ser 2(1):513–515CrossRef

24.

Lewis PO, Zaykin D (1999) Genetic Data Analysis: computer program for the analysis of allelic data, version 1.0 (d13). Free program distributed by the authors over the internet from the GDA homepage at http://chee.unm.edu/gda/

25.

Jones DA (1972) Blood samples: probability of discrimination. J Forensic Sci Soc 12(2):355–359PubMedCrossRef

26.

Weir B, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38(6):1358–1370CrossRef

27.

Chakraborty R (2000) Linkage disequilibrium: concept, utility and evolutionary dynamics in the context of the human genome variation. In: Destobio 2000, West Lafayette, IND

28.

Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164(4):1567PubMed

29.

Weir BS (1996) Genetic data analysis II, vol 2. Sinauer Associates, Sunderland

30.

Weber JL, David D, Heil J, Fan Y, Zhao C, Marth G (2002) Human diallelic insertion/deletion polymorphisms. Am J Hum Genet 71(4):854–862PubMedCrossRef

31.

Friis SL, Børsting C, Rockenbauer E, Poulsen L, Fredslund SF, Tomas C, Morling N (2012) Typing of 30 insertion/deletions in Danes using the first commercial indel kit—Mentype® DIPplex. Forensic Sci Int: Genet (in press)

32.

Alvarez MF PR, Gusmao L, Phillips C, Butler J, Lareu MV, Carracedo A, Vallone PM (2011) Forensic Performance of Short Amplicon Insertion-Deletion (INDEL) Markers. In: 22nd International Symposium on Human Identification, National Harbor, MD, 5 October 2011

Title: A validation study of the Qiagen Investigator DIPplex® kit; an INDEL-based assay for human identification
Authors: Bobby L. LaRue
Jianye Ge
Jonathan L. King
Bruce Budowle
Publication date: 01-07-2012
Publisher: Springer-Verlag
Published in: International Journal of Legal Medicine / Issue 4/2012
Print ISSN: 0937-9827
Electronic ISSN: 1437-1596
DOI: https://doi.org/10.1007/s00414-012-0667-9

Keynote webinar | Spotlight on medication adherence

Springer Medicine

A validation study of the Qiagen Investigator DIPplex® kit; an INDEL-based assay for human identification

Abstract

Keynote webinar | Spotlight on medication adherence

Springer Medicine

Abstract

Please log in to get access to this content

Other articles of this Issue 4/2012

The application of traditional and geometric morphometric analyses for forensic quantification of sexual dimorphism: preliminary investigations in a Western Australian population

Forensic and phylogeographic characterisation of mtDNA lineages from Somalia

The validation of a 15 STR multiplex PCR for Cannabis species

Combined radio-colour contrast in the examination of ballistic head models

Development and validation of a postmortem radiological alteration index: the RA-Index

Fifteen non-CODIS autosomal short tandem repeat loci multiplex data from nine population groups living in Taiwan