Advertisement
Research Article| Volume 63, 102825, March 2023

Download started.

Ok

Comparative study of Rapid DNA versus conventional methods on compromised bones

Published:December 27, 2022DOI:https://doi.org/10.1016/j.fsigen.2022.102825

      Highlights

      • Conventional methods were more successful than Rapid methods for STR typing of compromised bones.
      • Erroneous and false homozygous genotypes were detected among bones run on the ANDE system.
      • Modified rapid analysis was required for genotyping of compromised bones with ANDE and RHID systems.
      • Optimization of bone processing time and quantity on the ANDE system did not improve genotyping success.

      Abstract

      Equivalent amounts of compromised bones were used to directly compare STR success of conventional and Rapid DNA methods. Conventional DNA extraction methods, including manual full demineralization and semi-automated PrepFiler BTA/ AutoMate Express (ThermoFisher Scientific), provided insights regarding the DNA quantity and extent of degradation of each compromised bone analyzed with ANDE 6C (ANDE Corp) and RapidHIT ID (ThermoFisher Scientific) Rapid systems. Full demineralization provided higher DNA yields than extraction with the AutoMate Express for quality control (QC) and environmentally challenged bones. The degradation indices ranged from ∼1.8 to 73. Both demineralization and AutoMate Express extracts benefited from additional clean-up with NucleoSpin XS devices, which usually resulted in more alleles being detected than without further clean-up. Complete “CODIS 20″ profiles could be obtained with bone QC1 with all methods. However, among the 14 compromised bones with low DNA content, complete CODIS 20 profiles were detected for 7, 4, and 0 bones analyzed with demineralization, AutoMate Express and ANDE methods, respectively. The RapidHIT ID was the least sensitive method, providing the fewest detectable alleles for the bones tested. Whereas extracted DNA of approximately 0.1 ng can yield complete GlobalFiler STR profiles, at least 30 ng was required for complete FlexPlex 27 profiles using the ANDE 6C Rapid DNA system. In addition to being less sensitive than conventional methods, the tested Rapid DNA approaches were less predictable when attempting to improve STR success and proved to be less reliable in genotyping accuracy.

      Keywords

      To read this article in full you will need to make a payment

      Purchase one-time access:

      Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
      One-time access price info
      • For academic or personal research use, select 'Academic and Personal'
      • For corporate R&D use, select 'Corporate R&D Professionals'

      Subscribe:

      Subscribe to Forensic Science International: Genetics
      Already a print subscriber? Claim online access
      Already an online subscriber? Sign in
      Institutional Access: Sign in to ScienceDirect

      References

        • Hochmeister M.N.
        • Budowle B.
        • Borer U.V.
        • Eggmann U.
        • Comey C.T.
        • Dirnhofer R.
        Typing of deoxyribonucleic acid (DNA) extracted from compact bone from human remains.
        J. Forensic Sci. 1991; 36: 1649-1661
        • Colon E.M.
        • Hernandez M.
        • Candelario M.
        • Melendez M.
        • Dawson Cruz T.
        Evaluation of a freezer mill for bone pulverization prior to DNA extraction: an improved workflow for STR analysis.
        J. Forensic Sci. 2018; 63: 530-535
        • Davoren J.
        • Vanek D.
        • Konjhodzic R.
        • Crews J.
        • Huffine E.
        • Parsons T.J.
        Highly effective DNA extraction method for nuclear short tandem repeat testing of skeletal remains from mass graves.
        Croat. Med. J. 2007; 48: 478-485
        • Rucinski C.
        • Malaver A.L.
        • Yunis E.J.
        • Yunis J.J.
        Comparison of two methods for isolating DNA from human skeletal remains for STR Analysis.
        Forensic Sci. 2012; 57: 706-712
        • Ambers A.
        • Gill-King H.
        • Dirkmaat D.
        • Benjamin R.
        • King J.
        • Budowle B.
        Autosomal and Y-STR analysis of degraded DNA from the 120-year-old skeletal remains of Ezekiel Harper.
        Forensic Sci. Int.: Genet. 2014; 9: 33-41
        • Amory S.
        • Huel R.
        • Bilic A.
        • Loreille O.
        • Parsons T.J.
        Automatable full demineralization DNA extraction procedure from degraded skeletal remains.
        Forensic Sci. Int. Genet. 2012; 6: 398-406
        • Hasap L.
        • Chotigeat W.
        • Pradutkanchana J.
        • Vongvatcharanon U.
        • Kitpipit T.
        • Thanakiatkrai P.
        A novel, 4-h DNA extraction method for STR typing of casework bone samples.
        Int. J. Leg. Med. 2020; 134: 461-471
        • Jakubowska J.
        • Maciejewska A.
        • Pawłowski R.
        Comparison of three methods of DNA extraction from human bones with different degrees of degradation.
        Int. J. Leg. Med. 2012; 126: 173-178
        • Lee H.Y.
        • Park M.J.
        • Kim N.Y.
        • Sim J.E.
        • Yang W.I.
        • Shin K.J.
        Simple and highly effective DNA extraction methods from old skeletal remains using silica columns.
        Forensic Sci. Int.: Genet. 2010; 4: 275-280
        • Loreille O.M.
        • Diegoli T.M.
        • Irwin J.A.
        • Coble M.D.
        • Parsons T.J.
        High efficiency DNA extraction from bone by total demineralization.
        Forensic Sci. Int.: Genet. 2007; 1: 191-195
        • Pajnic I.Z.
        • Debska M.
        • Pogorelc B.G.
        • Mohorcic K.V.
        • Balazic J.
        • Zupanc T.
        • Stefanc B.
        • Gersak K.
        Highly efficient automated extraction of DNA from old and contemporary skeletal remains.
        J. Forensic Leg. Med. 2016; 37: 78-86
        • Zupanc T.
        • Podovsovnik E.
        • Obal M.
        • Zupanic Pajnic I.
        High DNA yield from metatarsal and metacarpal bones from Slovenian Second World War skeletal remains.
        Forensic Sci. Int.: Genet. 2021; 51102426
        • Barbaro A.
        • Samar S.
        • Falcone G.
        • La Marca A.
        Highly efficient and automated extraction of DNA from human remains using a modified EZ1 protocol.
        Forensic Sci. Res. 2021; 6: 59-66https://doi.org/10.1080/20961790.2020.1848138
        • Davis C.P.
        • King J.L.
        • Budowle B.
        • Eisenberg A.J.
        • Turnbough M.A.
        Extraction platform evaluations: a comparison of Automate Express™, EZ1® Advanced XL, and Maxwell® 16 bench-top DNA extraction systems.
        Leg. Med. 2012; 14: 36-39
        • Silva D.A.
        • Cavalcanti P.
        • Freitas H.
        • de Carvalho E.F.
        High quality DNA from human remains obtained by using the Maxwell 16 automated methodology.
        Forensic Sci. Int.: Genet. 2013; 4: e248-e249
        • Duijs F.E.
        • Sijen T.
        A rapid and efficient method for DNA extraction from bone powder.
        Forensic Sci. Int: Rep. 2020; 2100099
        • Liu J.Y.
        • Zhong C.
        • Holt A.
        • Lagace R.
        • Harrold M.
        • Dixon A.B.
        • Brevnov M.G.
        • Shewale J.G.
        • Hennessy L.K.
        AutoMate Express™ Forensic DNA extraction system for the extraction of genomic DNA from biological samples.
        J. Forensic Sci. 2012; 57: 1022-1030
      1. M. Mize, A semi-automated methodology for the extraction of DNA from human skeletal remains [thesis]. Texas (TX): Univ. of North Texas Health Science Center, 2013.

        • Vlahovic M.K.
        • Kubat M.
        DNA extraction method from bones using Maxwell 16.
        Leg. Med. 2012; 14: 272-275
        • Turingan R.S.
        • Tan E.
        • Jiang H.
        • Brown J.
        • Estari Y.
        • Krautz-Peterson G.
        • Selden R.F.
        Developmental validation of the ANDE 6C system for rapid DNA analysis of forensic casework and DVI samples.
        J. Forensic Sci. 2020; 65: 1056-1071https://doi.org/10.1111/1556-4029.14286
      2. ThermoFisher Scientific Applied Biosystems, RapidHIT ID system; Evaluation for processing of skeletal remains. 〈https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FGSD%2FReference-Materials%2Fdna-evaluation-skeletal-remains-presentation.pdf〉.

      3. ThermoFisher Scientific Applied Biosystems, Application note, Bone sample processing on the RapidHIT ID system with Rapid INTEL cartridges 2020. 〈https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FGSD%2FApplication-Notes%2FBone-sample-processing-RapidHIT-ID-system-RapidINTEL-cartridges-application-note.pdf〉.

        • Gin K.
        • Tovar J.
        • Bartelink E.J.
        • Kendell A.
        • Milligan C.
        • Willey P.
        • Wood J.
        • Tan E.
        • Turingan, R.S R.S.
        • Selden R.F.
        The 2018 california wildfires: integration of rapid DNA to dramatically accelerate victim identification.
        J. Forensic Sci. 2020; 65: 791-799https://doi.org/10.1111/1556-4029.14284
        • Turingan R.S.
        • Vasantgadkar S.
        • Palombo L.
        • Hogan C.
        • Jiang H.
        • Tan E.
        • Selden R.F.
        Rapid DNA analysis for automated processing and interpretation of low DNA content samples.
        Investig. Genet. 2016; 7: 2-12
      4. R.S. Turingan., J. Brown, L. Kaplun, J. Smith, J. Watson, D.A. Boyd, D. Wolfe Steadman, R.F. Selden, Identification of human remains using Rapid DNA analysis (2019) Int. J. Legal Med. https://doi.org/10.1007/s00414–019-02186-y.

      5. ThermoFisher Scientific Applied Biosystems customer profile: Kaua’I poly DNA technology disaster victim identification. 〈https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FGSD%2FReference-Materials%2FKauai-police-dna-technology-disaster-victim-identification.pdf〉.

        • Manzella A.M.
        • Carte K.M.
        • King S.L.
        • Moreno L.I.
        Assessment of the ANDE 6C Rapid DNA system and investigative biochip for the processing of calcified and muscle tissue.
        Forensic Sci. Int.: Genet. 2021; 53102526
        • Bowman Z.
        • Daniel R.
        • Gerostamoulos D.
        • Woodford N.
        • Hartman D.
        Rapid DNA from a distaster victim identification perspective: Is it a game changer?.
        Forensic Sci. Int.: Genet. 2022; 102684
        • Mapes A.A.
        • Kloosterman A.D.
        • de Poot C.J.
        • van Marion V.
        Objective data on DNA success rates can aid the selection process of crime samples for analysis by rapid mobile DNA technologies.
        Forensic Sci. Int. 2016; 264: 28-33
      6. ThermoFisher Scientific Applied Biosystems, PrepFiler Express™ and PrepFiler Express BTA™ forensic DNA extraction kits, User guide. 2017. 〈https://tools.thermofisher.com/content/sfs/manuals/cms_081933.pdf〉.

      7. ThermoFisher Scientific Applied Biosystems, AutoMate Express Instrument, User guide. 〈https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2F4441982_AutoMateExp_UG.pdf〉.

      8. Macherey Nagel, NucleoSpin® gDNA Clean-up XS, User manual. 2014 〈https://www.mn-net.com/media/pdf/c5/74/47/Instruction-NucleoSpin-gDNA-Clean-up-XS.pdf〉.

        • Faber K.L.
        • Person E.C.
        • Hudlow W.,R.
        PCR inhibitor removal using the NucleoSpin DNA Clean-Up XS kit.
        Forensic Sci. Int.: Genet. 2013; 7: 209-213
      9. ThermoFisher Scientific Applied Biosystems Quantifiler HP and Trio DNA quantification kits, User guidehttps://www.thermofisher.com/document-connect/document-connect.html?url=〈https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2F4485354.pdf〉.

      10. ThermoFisher Scientific Applied Biosystems, Globalfiler and GlobalFiler IQC PCR Amplification kits, User guide, Rev F, 2019 〈https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2F4477604.pdf〉.

      11. ThermoFisher Scientific Applied Biosystems. RapidHIT ID system 1.3.1, User guide, 〈https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2FMAN0018938_RapidHIT_ID_System_v1_3_1_UG.pdf〉.

      12. Applied Biosystems, RapidINTEL sample cartridge for blood and saliva samples. User bulletin (2019). 〈https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2FMAN0018979_RapidINTEL_RHIT_v1_1_3_Validation_UB.pdf〉.

        • Rohland N.
        • Hofreiter M.
        Comparison and optimization of ancient DNA extraction.
        BioTechniques. 2007; 42: 343-352
        • Emmons A.L.
        • Davoren J.
        • DeBruyn J.M.
        • Mundorff A.Z.
        Inter and intra-individual variation in skeletal DNA preservation in buried remains.
        Forensic Sci. Int. Genet. 2020; 44102193
        • Mundorff A.Z.
        • Bartelink E.J.
        • Mar-Cash E.
        DNA preservation in skeletal elements from the world trade center disaster: recommendations for mass fatality management.
        J. Forensic Sci. 2009; 54 (pgs 739-745): 739-745https://doi.org/10.1111/j.1556-4029.2009.01045.x
        • Grdina S.
        • Friša E.L.
        • Podovšovnik E.
        • Zupanc T.
        • Zupanič Pajnic I.
        Storage of Second World War bone samples: Bone fragments versus bone powder.
        Forensic Sci. Int.: Genet. 2019; 7: 175-176
        • Hofreiter M.
        • Sneberger J.
        • Pospisek M.
        • Vanek D.
        Progress in forensic bone DNA analysis: Lessons learned from ancient DNA.
        Forensic Sci. Int. Genet. 2021; 102538
        • Hares D.R.
        • Kneppers A.
        • Onorato A.J.
        • Kahn S.
        Rapid DNA for crime scene use: enhancements and data needed to consider use on forensic evidence for State and National DNA Databasing – an agreed position statement by ENFSI, SWGDAM and the Rapid DNA Crime Scene Technology Advancement Task Group.
        Forensic Sci. Int: Genet. 2020; 48102349