Objectives: Retrotransposable elements (REs), consisting of long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), are a group of markers that can be useful for human identity testing. Until now, however, due to the inherent size difference (up to 6 kb in some instances) associated with insertion and null alleles (or INNULs), the use of REs for facilitated population studies has not been sought or practical. The size of the insertion elements (from a few hundred to several thousand bp) has proven to limit their utility as a marker because of the inefficient amplicon yield with PCR. A novel primer design now facilitates INNUL marker testing. A preliminary panel of single-locus markers was developed to evaluate the potential of typing these insertion elements. Nine INNULs (5 Alu and 4 LINEs) were typed in three major North American populations and analyzed for population genetic features. In addition, the variation of each marker among the sample populations provides insight of its potential use as individual identification or ancestral marker. Methods: INNUL markers were developed into fluorescently labeled single-loci PCR. Nine markers were developed with amplicons that were less than 180 bp in length, and, depending on the locus amplicons of the INNULs, alleles varied in size from 50 to 1 bp. This allele size is noteworthy because the insertion alleles of the 9 loci range in size from 297 to 6,195 bp. The allele distribution of the INNULs was assessed and analyzed in three major North American populations. Results: Upon observation of the distribution of the alleles in three major North American populations, the markers generally met Hardy-Weinberg expectations, and there was little evidence of detectable levels of linkage disequilibrium. Due to varying distributions of the alleles in the major population groups tested, some of the markers might be better suited for use as an individual identification marker, while others are better suited for bio-ancestral studies. Conclusions: Using the primer design strategy described in our work, SINEs and (for the first time, to our knowledge) LINEs can be utilized as markers for studying population genetic variation that is more amenable to the limitations of the PCR technique. This study lays the foundation for future work of developing a multiplex panel of INNUL markers that can be used as a single-tube assay for human identity testing utilizing small amplicons (<180 bp), which could be useful for ancient or degraded forensic DNA samples.
© 2012 S. Karger AG, Basel
- Long interspersed nuclear elements
- Andersen JF, Greenhalgh MJ, Butler HR, et al: Further validation of a multiplex STR system for use in routine forensic identity testing. Forensic Sci Int 1996;78:47–64.
- Brinkmann B, Klintschar M, Neuhuber F, Hühne J, Rolf B: Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat. Am J Hum Genet 1998;62:1408–1415.
- Collins PJ, Hennessy LK, Leibelt CS, Roby RK, Reeder DJ, Foxall PA: Developmental validation of a single-tube amplification of the 13 CODIS STR loci, D2S1338, D19S433, and amelogenin: the AmpFISTR® Identifiler® PCR Amplification Kit. J Forensic Sci 2004;49:1265–1277.
- LaFountain MJ, Schwartz MB, Svete PA, Walkinshaw MA, Buel E: TWGDAM validation of the AmpFeSTR Profiler Plus and AmpFeSTR COfiler STR multiplex systems using capillary electrophoresis. J Forensic Sci 2001;46:1191–1198.
- Micka KA, Sprecher CJ, Lins AM, et al: Validation of multiplex polymorphic STR amplification sets developed for personal identification applications. J Forensic Sci 1996;41:582–590.
- Moretti T, Baumstark AL, Defenbaugh DA, Keys KM, Smerick JB, Budowle B: 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 2001;46:647–660.
- Smit AF: The origin of interspersed repeats in the human genome. Curr Opin Genet Dev 1996;6:743–748.
- Batzer MA, Deininger PL: Alu repeats and human genomic diversity. Nat Rev Genet 2002;3:370–379.
- Batzer MA, Stoneking M, Alegria-Hartman M, et al: African origin of human-specific polymorphic Alu insertions. Proc Natl Acad Sci USA 1994;91:12288–12292.
- Feng Q, Moran JV, Kazazian HH Jr, Boeke JD: Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 1996;87:905–916.
- Houck CM, Rinehart FP, Schmid CW: A ubiquitous family of repeated DNA sequences in the human genome. J Mol Biol 1979;132:289–306.
- Kazazian HH, Moran JV: The impact of L1 retrotransposons on the human genome. Nat Genet 1998;19:19–24.
- Ostertag EM, Kazazian HH Jr: Biology of mammalian L1 retrotransposons. Annu Rev Genet 2001;35:501–538.
- Ustyugova SV, Amosova AL, Lebedev YB, Sverdlov ED: Cell line fingerprinting using retroelement insertion polymorphism. Biotechniques 2005;38:561–565.
- Novick GE, Novick CC, Yunis J, et al: Polymorphic human specific Alu insertions as markers for human identification. Electrophoresis 1995;16:1596–1601.
- Mamedov IZ, Shaqina IA, Kurnikova MA, et al: A new set of markers for human identification based on 32 polymorphic Alu insertions. Eur J Hum Genet 2010;18:808–814.
- Lander ES, et al: Initial sequencing and analysis of the human genome. Nature 2001;409:860–921.
- Burger J, Hummel S, Hermann B, Henke W: DNA preservation: a microsatellite DNA study on ancient skeletal remains. Electrophoresis 1999;20:1722–1728.
- Fondevila M, et al: Challenging DNA: assessment of a range of genotyping approaches for highly degraded forensic samples. Forensic Sci Int Genet Suppl Ser 2008;1:26–28.
- Golenberg EM, Bickel A, Weihs P: Effect of highly fragmented DNA on PCR. Nucleic Acids Res 1996;24:5026–5033.
- Hughes-Stamm SR, Ashton KJ, van Daal A: Assessment of DNA degradation and the genotyping success of highly degraded samples. Int J Legal Med 2011;125:341–348.
- Zangenberg G, Saiki R, Reynolds R: Multiplex PCR: Optimization Guidelines. PCR Applications: Protocols for Functional Genomics. San Diego, Academic Press, 1999, pp 73–94.
- Budowle B: SNP typing strategies. Forensic Sci Int 2004;146:S139.
- Syvanen AC, Sajantila A, Lukka M: Identification of individuals by analysis of biallelic DNA markers, using PCR and solid-phase minisequencing. Am J Hum Genet 1993;52:46–59.
- LaRue BL, Ge J, King JL, Budowle B: A validation study of the Qiagen Investigator DIPplex® kit; an INDEL-based assay for human identification. Int J Legal Med 2012;126:533-540.
- Shriver MD, Smith MW, Lin L, Marcini A, Akey JM, Deka R, Ferrell RE: Ethnic-affiliation estimation by use of population-specific DNA markers. Am J Hum Genet 1997;60:957–964.
- Wang J, Song L, Grover D, Azrak S, Batzer MA, Liang P: dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans. Hum Mutat 2006;27:323–329.
- Benson DA, et al: GenBank. Nucleic Acids Res 2005;33(suppl 1):D34–D38.
- Cheung KH, Osier MV, Kidd JR, Pakstis AJ, Miller PL, Kidd KK: ALFRED: an allele frequency database for diverse populations and DNA polymorphisms. Nucleic Acids Res 2000;28:361.
- McGinnis S, Madden TL: BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 2004;32(suppl 2):W20–W25.
- Lewis PO, Zaykin D: Genetic Data Analysis: Computer Program for the Analysis of Allelic Data. Version 1.1, 2001.
- Excoffier L, Laval G, Schneider S: Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 2005;1:47–50.
- Weir B, Cockerham CC: Estimating F-statistics for the analysis of population structure. Evolution 1984;1358–1370.
- Falush D, Stephens M, Pritchard JK: Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 2003;164:1567–1587.
- Chakraborty R: Linkage disequilibrium: concept, utility and evolutionary dynamics in the context of the human genome variation. West Lafayette, DESTOBIO 2000, 2000.
- Fondevila M, Phillips C, Santos C, Pereira R, Gusmão L, Carracedo A, Butler JM, Lareu MV, Vallone PM: Forensic performance of two insertion-deletion marker assays. Int J Legal Med 2012;126:725–737.
- Li C, Zhao S, Zhang S, Li L, Liu Y, Chen J, Xue J: Genetic polymorphism of 29 highly informative InDel markers for forensic use in the Chinese Han population. Forensic Sci Int Genet 2011;5:e27–e30.
- Weber JL, David D, Heil J, Fan Y, Zhao C, Marth G: Human diallelic insertion/deletion polymorphisms. Am J Hum Genet 2002;71:854–862.
- Edelmann J, et al: Indel polymorphisms – an additional set of markers on the X-chromosome. Forensic Sci Int Genet Suppl Ser 2009;2:510–512.
- Pereira R, et al: Insertion/deletion polymorphisms: a multiplex assay and forensic applications. Forensic Sci Int Genet Suppl Ser 2009;2:513–515.
- Pereira R, Phillips C, Alves C, et al: A new multiplex for human identification using insertion/deletion polymorphisms. Electrophoresis 2009;30:3682–3690.
- Friis SL, Borsting C, Rockenbauer E, et al: Typing of 30 insertion/deletions in Danes using the first commercial indel kit – Mentype® DIPplex. Forensic Sci Int Genet 2012;6:e72–e74.
- Pakstis A, Speed WC, Kidd JR, Kidd KK: Candidate SNPs for a universal individual identification panel. Hum Genet 2007;121:305–317.
- Kidd KK, Pakstis AJ, Speed WC, et al: Developing a SNP panel for forensic identification of individuals. Forensic Sci Int 2006;164:20–32.
Institute of Applied Genetics
University of North Texas Health Science Center
Fort Worth, TX 76107 (USA)
Received: June 11, 2012
Accepted after revision: August 30, 2012
Published online: October 20, 2012
Number of Print Pages : 9
Number of Figures : 2, Number of Tables : 2, Number of References : 44
Additional supplementary material is available online - Number of Parts : 2
Human Heredity (International Journal of Human and Medical Genetics)
Vol. 74, No. 1, Year 2012 (Cover Date: November 2012)
Journal Editor: Devoto M. (Philadelphia, Pa./Rome)
ISSN: 0001-5652 (Print), eISSN: 1423-0062 (Online)
For additional information: http://www.karger.com/HHE
Copyright / Drug Dosage / Disclaimer
Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher or, in the case of photocopying, direct payment of a specified fee to the Copyright Clearance Center.
Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in goverment regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.
Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.