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Usefulness of Quantitative PCR in Forensic Genetics

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Handbook of DNA Profiling

Abstract

Although most DNA studies in forensic genetics are focused on the sample, including DNA extraction and amplification, sample quantification is an important step that is required to determine the optimal DNA input for amplification. In addition, the effective quantification of DNA can provide information regarding the degradation and inhibition of DNA to optimize the amplification strategy or the extraction method and can be used to inform the decision to analyze another sample of the same specimen. In this chapter, quantitative PCR (qPCR, also known as real-time PCR, RT-PCR) will be described after a brief history of quantification methods, PCR fundamentals, current applications in forensic genetics [including the sequencing of short-tandem repeats (STRs), single-nucleotide polymorphisms (SNPs), Y-chromosomes, mitochondrial DNA (mtDNA), and non-human DNA], and future perspectives for this technique.

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References

  • Ahn SJ, Costa J, Emanuel JR (1996) PicoGreen quantitation of DNA: effective evaluation of samples pre-or post-PCR. Nucleic Acids Res 24:2623–2625

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Alonso A (ed) (2012) DNA electrophoresis protocols for forensic genetics. Humana Press, London

    Google Scholar 

  • Alonso A, García O (2007) Real-time quantitative PCR in forensic science. In: Rapley R, Whitehouse D (eds) Molecular forensics. Wiley, Chinchester

    Google Scholar 

  • Alonso A, Martín P, Albarrán C et al (2003) Specific quantification of human genomes from low copy number DNA samples in forensic and ancient DNA studies. Croat Med J 44:273–280

    PubMed  Google Scholar 

  • Alonso A, Martín P, Albarrán C et al (2004) Real-time PCR designs to estimate nuclear and mitochondrial DNA copy number in forensic and ancient DNA studies. Forensic Sci Int 139:141–149

    Article  CAS  PubMed  Google Scholar 

  • Andréasson H, Allen M (2003) Rapid quantification and sex determination of forensic evidence materials. J Forensic Sci 48:1–8

    Article  Google Scholar 

  • Andréasson H, Gyllensten U, Allen M (2002) Real-time DNA quantification of nuclear and mitochondrial DNA in forensic analysis. BioTechniques 33:402–411

    Article  PubMed  Google Scholar 

  • Arenas M, Pereira F, Oliveira M et al (2017) Forensic genetics and genomics: much more than just a human affair. PLoS Genet 13:e1006960

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Baggesgaard Sterndorff E, Russel J, Jakobsen J et al (2020) The T-shirt microbiome is distinct between individuals and shaped by washing and fabric type. Environ Res 185:109449

    Article  CAS  Google Scholar 

  • Barta JL, Monroe C, Teisberg JE et al (2014) One of key characteristics of ancient DNA, low copy number, may be a product of its extraction. J Archeol Sci 46:281–289

    Article  CAS  Google Scholar 

  • BioCat Real Time PCR Dyes (2009) In: Genomics. https://www.biocat.com/genomics/real-time-pcr-dyes. Accessed 6 May 2016

  • Bunce M, Oskam CL, Alletoft ME (2012) Quantitative real-time PCR in aDNA research. In: Shapiro B, Hofreiter M (eds) Ancient DNA methods and protocols. Humana Press, New York, pp 121–133

    Chapter  Google Scholar 

  • Butler JM (2011) Advanced topics in forensic DNA typing: methodology. Academic Press, San Diego

    Google Scholar 

  • Cao L, Cui X, Hu J et al (2017) Advances in digital polymerase chain reaction (dPCR) and its emerging biomedical applications. Biosens Bioelectron 90:459–474

    Article  CAS  PubMed  Google Scholar 

  • Carracedo Á (ed) (2005) Forensic DNA typing. Humana Press, Totawa

    Google Scholar 

  • Editorial (2015) qPCR, dPCR, NGS – a journey. Biomol Detect Quantif 3:A1–A5

    Article  Google Scholar 

  • Ewing MM, Thompson JM, McLaren RS et al (2016) Human DNA quantification and sample quality assessment: developmental validation of the PowerQuant® system. Forensic Sci Int Genet 23:166–177

    Article  CAS  PubMed  Google Scholar 

  • Fregel R, Almeida M, Betancor E et al (2011) Reliable nuclear and mitochondrial DNA quantification for low copy number and degraded forensic samples. Forensic Sci Int Genet Suppl Series 3:e303–e304

    Article  Google Scholar 

  • Gallimore JM, McElhoe JA, Holland MM (2018) Assessing heteroplasmic variant drift in the mtDNA control region of human hairs using an MPS approach. Forensic Sci Int Genet 32:7–17

    Article  CAS  PubMed  Google Scholar 

  • Giglio S, Monis PT, Saint CP (2003) Demonstration of preferential binding of SYBR green I to specific DNA fragments in real-time multiplex PCR. Nucleic Acids Res 31:e136

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Ginart S, Caputo M, Corach D, Sala A (2019) Human DNA degradation assessment and male DNA detection by quantitative-PCR followed by high-resolution melting analysis. Forensic Sci Int 295:1–7

    Article  CAS  PubMed  Google Scholar 

  • Habtom H, Pasternak Z, Matan O et al (2019) Applying microbial biogeography in soil forensics. Forensic Sci Int Genet 38:195–203

    Article  CAS  PubMed  Google Scholar 

  • Heid CA, Stevens J, Livak KJ, Williams PM (1996) Real time quantitative PCR. Genome Methods 6:986–994

    CAS  Google Scholar 

  • Heß SA, Trapani S, Boronat MDM et al (2021) Ribosomal DNA as target for the assessment of DNA degradation of human and canine DNA. Legal Med 48:101819

    Article  CAS  PubMed  Google Scholar 

  • Holland PM, Abramson RD, Watson R, Gelfand DH (1991) Detection of specific polymerase chain reaction product by utilizing the 5′→3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc Natl Acad Sci U S A 88:7276–7280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Holmes AS, Houston R, Elwick K et al (2018) Evaluation of four commercial quantitative real-time PCR kits with inhibited and degraded samples. Int J Legal Med 132:691–701

    Article  PubMed  Google Scholar 

  • Holt A, Wootton SC, Mulero JJ et al (2015) Developmental validation of the QuantifilerTM HP and Trio kits for human DNA quantification in forensic samples. Forensic Sci Int Genet 21:145–157

    Article  CAS  PubMed  Google Scholar 

  • Hopkins JF, Woodson SA (2005) Molecular beacons as probes of RNA unfolding under native conditions. Nucleic Acids Res 33:5763–5770

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Johnson CE, Premasuthan A, Tarsk JS, Kanthaswamy S (2013) Species identification of Cannabis sativa using real-time quantitative PCR (qPCR). J Forensic Sci 58:486–490

    Article  CAS  PubMed  Google Scholar 

  • Joseph LJ (2010) Setting up a laboratory. In: Weiss RE, Refetoff S (eds) Genetic diagnosis of endocrine disorders. Academic Press, MA, Burlington, pp 303–314

    Google Scholar 

  • Jung JY, Yoon HK, An S et al (2018) Rapid oral bacteria detection based on real-time PCR for the forensic identification of saliva. Sci Rep 8:10852

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kanthaswamy S, Premasuthan A, Ng J et al (2012) Quantitative real-time PCR (qPCR) assay for human-dog-cat species identification and nuclear DNA quantification. Forensic Sci Int Genet 6:290–295

    Article  CAS  PubMed  Google Scholar 

  • Kavlick MF (2019) Development of a triplex mtDNA qPCR assay to assess quantification, degradation, inhibition, and amplification target copy numers. Mitochondrion 46:41–50

    Article  CAS  PubMed  Google Scholar 

  • Klein D (2002) Quantification using real-time PCR technology: applications and limitations. Trends Mol Med 8:257–260

    Article  CAS  PubMed  Google Scholar 

  • Kocher TD, Thomas WK, Meyer A et al (1989) Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc Natl Acad Sci U S A 86:6196–6200

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Köhnemann S, Pennekamp P, Schmidt PF, Pfeiffer H (2010) qPCR and mtDNA SNP analysis of experimentally degraded hair samples in forensic casework. Int J Legal Med 124:337–342

    Article  PubMed  Google Scholar 

  • Köppel R, Zimmerly F, Breitenmoser A (2009) Heptaplex real-time PCR for the identification and quantification of DNA from beef, pork, chicken, Turkey, horse meat, sheep (mutton) and goat. Eur Food Res Technol 230:125–133

    Article  CAS  Google Scholar 

  • Krenke BE, Nassif N, Sprecher CJ et al (2008) Developmental validation of a real-time PCR assay for the simultaneous quantification of total human and male DNA. Forensic Sci Int Genet 3:14–21

    Article  CAS  PubMed  Google Scholar 

  • Kupiec T, Janula M, Doniec A (2018) Assessment of Y chromosome degradation level using the investigator® Quantiplex® pro RGQ kit. Kraków, Hilden, Germany

    Google Scholar 

  • Kutyavin IV, Afonina IA, Mills A et al (2000) 3′-minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures. Nucleic Acids Res 28:655–661

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee SB, McCord B, Buel E (2015) Advances in forensic DNA quantification: a review. Electrophoresis 35:3044–3052

    Article  CAS  Google Scholar 

  • Lucy D (2005) Introduction to statistics for forensic scientists. Wiley, Chichester

    Google Scholar 

  • Maggi RG, Richardson T, Breitschwerdt EB, Miller JC (2020) Development and validation of a droplet digital PCR assay for the detection and quantification of Bartonella species within human clinical samples. J Microbiol Methods 176:106022

    Article  CAS  PubMed  Google Scholar 

  • Mandrekar MN, Erickson AM, Kopp K et al (2001) Development of a human DNA quantitation system. Croat Med J 42:336–339

    CAS  PubMed  Google Scholar 

  • Manoj P (2016) Droplet digital PCR technology promises new applications and research areas. Mitochondrial DNA A DNA Mapp Seq Anal 27:742–746

    Article  CAS  PubMed  Google Scholar 

  • Nicklas JA, Buel E (2003a) Quantification of DNA in forensic samples. Anal Bioanal Chem 376:1160–1167

    Article  CAS  PubMed  Google Scholar 

  • Nicklas JA, Buel E (2003b) Development of an Alu-based, real-time PCR method for quantitation of human DNA in forensic samples. J Forensic Sci 48:1–9

    Google Scholar 

  • Niederstätter H, Köchl S, Grubweiser P et al (2007) A modular real-time PCR concept for determining the quantity and quality of human nuclear and mitochondrial DNA. Forensic Sci Int Genet 1:29–34

    Article  CAS  PubMed  Google Scholar 

  • Phillips NR, Sprouse ML, Roby RK (2014) Simultaneous quantification of mitochondrial DNA copy number and deletion ratio: a multiplex real-time PCR assay. Sci Rep 4:1–7

    Google Scholar 

  • Pineda GM, Montgomery AH, Thompson R et al (2014) Development and validation of InnoQuantTM, a sensitive human DNA quantitation and degradation assessment method for forensic samples using high copy number mobile elements Alu and SVA. Forensic Sci Int Genet 13:224–235

    Article  CAS  PubMed  Google Scholar 

  • Ponchel F (2006) Real-time PCR using SYBR® green. In: Dorak MT (ed) Real-time PCR. Taylor & Francis, Abingdon, pp 139–153

    Google Scholar 

  • Prediger E (2013) How to design primers and probes for PCR and qPCR. Integrated DNA Technologies. https://eu.idtdna.com/pages/education/decoded/article/designing-pcr-primers-and-probes. Accessed 20 Aug 2018

  • Quan P-L, Sauzade M, Brouzes E (2018) dPCR: a technology review. Sensors (Basel) 18:1271

    Article  CAS  Google Scholar 

  • Refinetti P, Warren D, Morgenthaler S, Ekstrøm PO (2017) Quantifying mitochondrial DNA copy number using robust regression to interpret real time PCR results. BMC Res Notes 10:E1–E7

    Article  Google Scholar 

  • Richard ML, Frappier RH, Newman JC (2003) Developmental validation of a real-time quantitative PCR assay for automated quantification of human DNA. J Forensic Sci 48:1041–1046

    Article  CAS  PubMed  Google Scholar 

  • Ruijter JM, Ruiz-Villalba A, van den Hoff AJJ et al (2019) Removal of artifact bias from qPCR results using DNA melting curve analysis. FASEB J 33:14542–14555

    Article  CAS  PubMed  Google Scholar 

  • Thermo Fisher Scientific Digital PCR (2014) Polymerase Chain Reaction. https://www.thermofisher.com/es/es/home/life-science/pcr/digital-pcr.html

  • Shipley GL (2007) An introduction to real-time PCR. In: Dorak MT (ed) Real-time PCR. Taylor & Francis, Abingdon, pp 1–39

    Google Scholar 

  • Sidstedt M, Steffen CR, Kiesler KM et al (2019) The impact of common PCR inhibitors on forensic MPS analysis. Forensic Sci Int Genet 40:182–191

    Article  CAS  PubMed  Google Scholar 

  • Sidstedt M, Rådström P, Hedman J (2020) PCR inhibition in qPCR, dPCR and MPS—mechanisms and solutions. Anal Bioanal Chem 412:2009–2023

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sobrino B, Brión M, Carracedo A (2005) SNPs in forensic genetics: a review on SNPS typing methodologies. Forensic Sci Int 154:181–194

    Article  CAS  PubMed  Google Scholar 

  • Svec D, Tichopad A, Novosadova V (2015) How good is a PCR efficiency estimate: recommendations for precise and robust qPCR efficiency assessments. Biomol Detect Quantif 3:9–16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Swango KL, Timken MD, Chong MD, Buoncristiani MR (2006) A quantitative PCR assay for the assessment of DNA degradation in forensic samples. Forensic Sci Int 158:14–26

    Article  CAS  PubMed  Google Scholar 

  • ThermoFisher Scientific (2007) Top Ten Pitfalls in quantitative real-time PCR PRimer probe design and use. In: Sample Preparation for PCR, Real time PCR RT-PCR. https://www.thermofisher.com/es/es/home/references/ambion-tech-support/rtpcr-analysis/general-articles/top-ten-pitfalls-in-quantitative-real-time-pcr-primer.html

  • Tyagi S, Kramer FR (1996) Molecular beacons: probes that fluorescence upon hybridization. Nat Biotechnol 14:303–308

    Article  CAS  PubMed  Google Scholar 

  • Untergasser A, Cutcutache I, Koressaar T et al (2012) Primer3 – new capabilities and interfaces. Nucleic Acids Res 40:e115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vernarecci S, Ottaviani E, Agostino A et al (2015) Quantifiler® trio kit and forensic samples management: a matter of degradation. Forensic Sci Int Genet 16:77–85

    Article  CAS  PubMed  Google Scholar 

  • Vraneš M, Scherer M, Elliott K (2017) Development and validation of the investigator® Quantiplex pro kit for qPCR-based examination of the quantity and quality of human DNA in forensic samples. Forensic Sci Int Genet Suppl Ser 6:e518–e519

    Article  Google Scholar 

  • Walsh PS, Varlaro J, Reynolds R (1992) A rapid chemiluminescent method for quantitation of human DNA. Nucleic Acids Res 20:5061–5065

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Keith M, Leyme A et al (2019) Monitoring long-term DNA storage via absolute copy number quantification by ddPCR. Anal Biochem 583:113363

    Article  CAS  PubMed  Google Scholar 

  • Whittle MR, Sumita DR (2008) Quadruplex real-time PCR for forensic DNA quantitation. Forensic Sci Int Genet Suppl Ser 1:86–88

    Google Scholar 

  • Xavier C, Eduardoff M, Strobl C, Parsons W (2019) SD quants-sensitive detection tetraplex-system for nuclear and mitochondrial DNA quantification and degradation inference. Forensic Sci Int Genet 42:39–44

    Article  CAS  PubMed  Google Scholar 

  • Ye J, Coulouris G, Zaretskaya I et al (2012) Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinfor 13:134

    Article  CAS  Google Scholar 

  • Young ST, Moore JR, Bishop CP (2018) A rapid, confirmatory test for body fluid identification. J Forensic Sci 63:511–516

    Article  CAS  PubMed  Google Scholar 

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Correspondence to M. J. Alvarez-Cubero .

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Haarkötter, C., Alvarez-Cubero, M.J., Alvarez, J.C., Saiz, M. (2022). Usefulness of Quantitative PCR in Forensic Genetics. In: Dash, H.R., Shrivastava, P., Lorente, J.A. (eds) Handbook of DNA Profiling. Springer, Singapore. https://doi.org/10.1007/978-981-16-4318-7_39

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