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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
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
Alonso A (ed) (2012) DNA electrophoresis protocols for forensic genetics. Humana Press, London
Alonso A, García O (2007) Real-time quantitative PCR in forensic science. In: Rapley R, Whitehouse D (eds) Molecular forensics. Wiley, Chinchester
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
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
Andréasson H, Allen M (2003) Rapid quantification and sex determination of forensic evidence materials. J Forensic Sci 48:1–8
Andréasson H, Gyllensten U, Allen M (2002) Real-time DNA quantification of nuclear and mitochondrial DNA in forensic analysis. BioTechniques 33:402–411
Arenas M, Pereira F, Oliveira M et al (2017) Forensic genetics and genomics: much more than just a human affair. PLoS Genet 13:e1006960
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
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
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
Butler JM (2011) Advanced topics in forensic DNA typing: methodology. Academic Press, San Diego
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
Carracedo Á (ed) (2005) Forensic DNA typing. Humana Press, Totawa
Editorial (2015) qPCR, dPCR, NGS – a journey. Biomol Detect Quantif 3:A1–A5
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
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
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
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
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
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
Habtom H, Pasternak Z, Matan O et al (2019) Applying microbial biogeography in soil forensics. Forensic Sci Int Genet 38:195–203
Heid CA, Stevens J, Livak KJ, Williams PM (1996) Real time quantitative PCR. Genome Methods 6:986–994
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
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
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
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
Hopkins JF, Woodson SA (2005) Molecular beacons as probes of RNA unfolding under native conditions. Nucleic Acids Res 33:5763–5770
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
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
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
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
Kavlick MF (2019) Development of a triplex mtDNA qPCR assay to assess quantification, degradation, inhibition, and amplification target copy numers. Mitochondrion 46:41–50
Klein D (2002) Quantification using real-time PCR technology: applications and limitations. Trends Mol Med 8:257–260
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
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
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
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
Kupiec T, Janula M, Doniec A (2018) Assessment of Y chromosome degradation level using the investigator® Quantiplex® pro RGQ kit. Kraków, Hilden, Germany
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
Lee SB, McCord B, Buel E (2015) Advances in forensic DNA quantification: a review. Electrophoresis 35:3044–3052
Lucy D (2005) Introduction to statistics for forensic scientists. Wiley, Chichester
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
Mandrekar MN, Erickson AM, Kopp K et al (2001) Development of a human DNA quantitation system. Croat Med J 42:336–339
Manoj P (2016) Droplet digital PCR technology promises new applications and research areas. Mitochondrial DNA A DNA Mapp Seq Anal 27:742–746
Nicklas JA, Buel E (2003a) Quantification of DNA in forensic samples. Anal Bioanal Chem 376:1160–1167
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
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
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
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
Ponchel F (2006) Real-time PCR using SYBR® green. In: Dorak MT (ed) Real-time PCR. Taylor & Francis, Abingdon, pp 139–153
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
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
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
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
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
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
Sidstedt M, Rådström P, Hedman J (2020) PCR inhibition in qPCR, dPCR and MPS—mechanisms and solutions. Anal Bioanal Chem 412:2009–2023
Sobrino B, Brión M, Carracedo A (2005) SNPs in forensic genetics: a review on SNPS typing methodologies. Forensic Sci Int 154:181–194
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
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
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
Untergasser A, Cutcutache I, Koressaar T et al (2012) Primer3 – new capabilities and interfaces. Nucleic Acids Res 40:e115
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
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
Walsh PS, Varlaro J, Reynolds R (1992) A rapid chemiluminescent method for quantitation of human DNA. Nucleic Acids Res 20:5061–5065
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
Whittle MR, Sumita DR (2008) Quadruplex real-time PCR for forensic DNA quantitation. Forensic Sci Int Genet Suppl Ser 1:86–88
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
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
Young ST, Moore JR, Bishop CP (2018) A rapid, confirmatory test for body fluid identification. J Forensic Sci 63:511–516
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 Springer Nature Singapore Pte Ltd.
About this entry
Cite this entry
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
Download citation
DOI: https://doi.org/10.1007/978-981-16-4318-7_39
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-16-4317-0
Online ISBN: 978-981-16-4318-7
eBook Packages: Biomedical and Life SciencesReference Module Biomedical and Life Sciences