Abstract
Since the development of DNA fingerprinting by Sir Alec Jeffery, the technique has always had a special relevance to forensic science. With the new emerging technologies, DNA fingerprinting has been performed through detection of specific DNA sequences within reference and query samples by techniques such as RFLP analysis and SSCP analysis to name a few. Recent advancement into determination of individuality includes the detection and analysis of Single Nucleotide Polymorphs (SNPs) within the samples. These analyses have proven significance due to their uniqueness within the genetic sequences by acting as biological markers. SNP detection protocols focus on highlighting the presence of the sequence modifications by using electrophoretic techniques, probes, primers, and high-throughput methods such as Sanger sequencing and NGS. The high-throughput techniques allow simultaneous multi-sample analysis through sequence by synthesis. With respect to individualization, these techniques have been adopted worldwide on regular basis for forensic investigation analysis of recent and cold cases.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Allio R, Donega S, Galtier N, Nabholz B (2017) Large variation in the ratio of mitochondrial to nuclear mutation rate across animals: implications for genetic diversity and the use of mitochondrial DNA as a molecular marker. Mol Biol Evol 34:2762–2772
Armentrout S. Using SNP genoty** to solve crimes: the cold case of April Tinsley warning: this presentation contains graphic sexual content. 2019
Arshad M, Bhatti A, John P (2018) Identification and in silico analysis of functional SNPs of human TAGAP protein: a comprehensive study. PLoS One 13:1–13
Bardan F. New forensic DNA profiling techniques for human identification. 2019
Barreiro LB, Laval G, Quach H, Patin E, Quintana-Murci L (2008) Natural selection has driven population differentiation in modern humans. Nat Genet 40:340–345
Bas Yavaser G, Hulya Yukseloglu E, Cavus Yonar F, Erkan I (2021) Assessment of 13 single nucleotide polymorphisms loci for identification in forensic sciences for Turkish population. Int J Biol Chem 14:56–63
Belmont JW, Boudreau A, Leal SM, Hardenbol P, Pasternak S, Wheeler DA et al (2005) A haplotype map of the human genome. Nature 437:1299–1320
Bogenhagen D, Clayton DA (1974) The number of mitochondrial deoxyribonucleic acid genomes in mouse L and human HeLa cells. Quantitative isolation of mitochondrial deoxyribonucleic acid. J Biol Chem 249:7991–7995
Breslin K, Wills B, Ralf A, Ventayol Garcia M, Kukla-Bartoszek M, Pospiech E et al (2019) HIrisPlex-S system for eye, hair, and skin color prediction from DNA: massively parallel sequencing solutions for two common forensically used platforms. Forensic Sci Int Genet 43:102152
Brookes AJ (1999) The essence of SNPs. Gene 234:177–186
Buetow KH, Edmonson MN, Cassidy AB (1999) Reliable identification of large numbers of candidate SNPs from public EST data. Nat Genet 21:323–325
Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, Patil N et al (1999) Characterization of single- nucleotide polymorphisms in coding regions of human genes [published erratum appears in Nat Genet 1999 Nov;23(3):373]. Nat Genet 22:231–238
Chen TJ, Boles RG, Wong LJ (1999) Detection of mitochondrial DNA mutations by temporal temperature gradient gel electrophoresis. Clin Chem 45:1162–1167
Cotton RG, Rodrigues NR, Campbell RD (1988) Reactivity of cytosine and thymine in single-base- pair mismatches with hydroxylamine and osmium tetroxide and its application to the study of mutations. Proc Natl Acad Sci U S A 85:4397–4401
Dario P, Ribeiro T, Dias D, Corte-Real F, Geada H (2011) Complex casework using single nucleotide polymorphisms. Forensic Sci Int Genet Suppl Ser 3:379–380
Darwin C (1859) On the origin of species by means of natural selection, or preservation of favoured races in the struggle for life. John Murray, London; 1809-1882
Fiatal S, Ádány R (2018) Application of single-nucleotide polymorphism-related risk estimates in identification of increased genetic susceptibility to cardiovascular diseases: a literature review. Front Public Heal 5:5
Fischer SG, Lerman LS (1983) DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc Natl Acad Sci U S A 80:1579–1583
Gao Y, He Z, He X, Zhang H, Weng J, Yang X et al (2019) Dual-color emissive AIEgen for specific and label-free double-stranded DNA recognition and single-nucleotide polymorphisms detection. J Am Chem Soc 141:20097–20106
Glazier AM, Nadeau JH, Aitman TJ (2002) Genetics: finding genes that underline complex traits. Science 298(80):2345–2349
Gunter LE, Kochert G, Giannasi DE (1994) Phylogenetic relationships of the Juglandaceae. Plant Syst Evol 192:11–29
Hayatsu H, Atsumi G, Nawamura T, Kanamitsu S, Negishi K, Maeda M (1991) Permanganate oxidation of nucleic acid components: a reinvestigation. Nucleic Acids Symp Ser 25:77–78
Higasa K, Kukita Y, Baba S, Hayashi K (2002) Software for machine-independent quantitative interpretation of SSCP in capillary array electrophoresis (QUISCA). BioTechniques 33:1342–1348
Hillier LDW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D et al (2008) Whole-genome sequencing and variant discovery in C. elegans. Nat Methods 5:183–188
Huchard E, Cowlishaw G, Raymond M, Weill M, Knapp LA (2006) Molecular study of Mhc-DRB in wild chacma baboons reveals high variability and evidence for trans-species inheritance. Immunogenetics 58:805–816
Inazuka M, Tahira T, Hayashi K (1996) One-tube post-PCR fluorescent labeling of DNA fragments. Genome Res 6:551–557
International HapMap Consortium. International HapMap consortium. The International HapMap Project Nature 2003; 426: 789–796
Ito M, Tran Le S, Chaudhari D, Higashimoto T, Maslim A, Boles RG (2001) Screening for mitochondrial DNA heteroplasmy in children at risk for mitochondrial disease. Mitochondrion 1:269–278
Kikuta E, Murata M, Katsube N, Koike T, Kimura E (1999) Novel recognition of thymine base in double-stranded DNA by zinc(II)- macrocyclic tetraamine complexes appended with aromatic groups. J Am Chem Soc 121:5426–5436
Kikuta E, Aoki S, Kimura E (2002) New potent agents binding to a poly(dT) sequence in double- stranded DNA: Bis(Zn2+−cyclen) and tris(Zn2+−cyclen) complexes. J Biol Inorg Chem 7:473–482
Kinoshita E, Kinoshita E, Koike T. Chapter 10 Zn (II)– Cyclen polyacrylamide gel electrophoresis for SNP. 2009
Kinoshita-Kikuta E, Kinoshita E, Koike T (2002) Erratum: a novel procedure for simple and efficient genoty** of single nucleotide polymorphisms by using the Zn2+−cyclen complex (nucleic acids research (2002) vol. 30 (e126)). Nucleic Acids Res 30:5593
Kruglyak L, Nickerson DA (2001) Variation is the spice of life. Nat Genet 27:234–236
Kukita Y, Tahira T, Sommer SS, Hayashi K (1997) SSCP analysis of long DNA fragments in low pH gel. Hum Mutat 10:400–407
Kukita Y, Higasa K, Baba S, Nakamura M, Manago S, Suzuki A et al (2002) A single-strand conformation polymorphism method for the large-scale analysis of mutations/polymorphisms using capillary electrophoresis. Electrophoresis 23:2259–2266
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J et al (2001) Erratum: initial sequencing and analysis of the human genome: international human genome sequencing consortium (nature (2001) 409 (860-921)). Nature 412:565–566
Liu W, Smith DI, Rechtzigel KJ, Thibodeau SN, James CD (1998) Denaturing high performance liquid chromatography (DHPLC) used in the detection of germline and somatic mutations. Nucleic Acids Res 26:1396–1400
Lohrer HD, Tangen U (2000) Investigations into the molecular effects of single nucleotide polymorphism. Pathobiology 68:283–290
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380
Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, Zakeri H et al (1999) A general approach to single- nucleotide polymorphism discovery. Nat Genet 23:452–456
Morin PA, Luikart G, Wayne RK (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19:208–216
Myers RM, Maniatis T, Lerman LS (1987) Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol 155:501–527
Ning C, Li T, Wang K, Zhang F, Li T, Wu X et al (2020) Ancient genomes from Northern China suggest links between subsistence changes and human migration. Nat Commun 11:1–9
Oldoni F, Kidd KK, Podini D (2019) Microhaplotypes in forensic genetics. Forensic Sci Int Genet 38:54–69
Orita M, Iwahana H, Kanazawa H, Hayashi K, Sekiya T (1989a) Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci U S A 86:2766–2770
Orita M, Suzuki Y, Sekiya T, Hayashi K (1989b) Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction. Genomics 5:874–879
Ota M, Fukushima H, Kulski JK, Inoko H (2007) Single nucleotide polymorphism detection by polymerase chain reaction-restriction fragment length polymorphism. Nat Protoc 2:2857–2864
Paris PL, Langenhan JM, Kool ET (1998) Probing DNA sequences in solution with a monomer- excimer fluorescence color change. Nucleic Acids Res 26:3789–3793
Ratan A, Miller W, Guillory J, Stinson J, Seshagiri S, Schuster SC (2013) Comparison of sequencing platforms for single nucleotide variant calls in a human sample. PLoS One 8:1–10
Robert F, Pelletier J (2018) Exploring the impact of single-nucleotide polymorphisms on translation. Front Genet 9:1–11
Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G et al (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928–933
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467
Schürch AC, Arredondo-Alonso S, Willems RJL, Goering RV (2018) Whole genome sequencing options for bacterial strain ty** and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene–based approaches. Clin Microbiol Infect 24:350–354
Sham P, Bader JS, Craig I, O’Donovan M, Owen M (2002) DNA pooling: a tool for large-scale association studies. Nat Rev Genet 3:862–871
Sheffield VC, Cox DR, Lerman LS, Myers RM (1989) Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc Natl Acad Sci U S A 86:232–236
Shionoya M, Shirot M (1993) A New Ternary Zinc(II)Complex with [12]aneN4 (= 1, 4, 7, 10-tetraazacyclododecane) and AZT (= 3'-azido-3'-deoxythymidine). Highly selective recognition of thymidine and its related nucleosides by a zinc (II) macrocyclic tetraamine complex with novel complementary associations. J Am Chem Soc 4:6730–6737
Theophilus BDM, Latham T, Grabowski GA, Smith FI (1989) Comparison of RNase a, a chemical cleavage and GC-clamped denaturing gradient gel electrophoresis for the detection of mutations in exon 9 of the human acid β-glucosidase gene. Nucleic Acids Res 17:7707–7722
Tillmar A, Sturk-Andreaggi K, Daniels-Higginbotham J, Thomas JT, Marshall C (2021) The FORCE panel: an all-in-one SNP marker set for confirming investigative genetic genealogy leads and for general forensic applications. Genes (Basel) 12:12
Tully LA, Parsons TJ, Steighner RJ, Holland MM, Marino MA, Prenger VL (2000) A sensitive denaturing gradient-gel electrophoresis assay reveals a high frequency of heteroplasmy in hypervariable region 1 of the human mtDNA control region. Am J Hum Genet 67:432–443
Tyagi S, Kramer FR (1996) Molecular beacon probes that fluoresce on hybridiztion. Nature 14:303–308
van Oorschot RAH, Ballantyne KN (2013) Capillary electrophoresis in forensic biology. In: Encyclopedia of forensic sciences: second edition, 2nd edn. Elsevier Ltd, London
Varona M, Anderson JL (2019) Visual detection of single-nucleotide polymorphisms using molecular beacon loop-mediated isothermal amplification with centrifuge-free DNA extraction. Anal Chem 91:6991–6995
Wong L-JC, Chen T-J, Tan D-J (2004) Detection of mitochondrial DNA mutations using temporal temperature gradient gel electrophoresis. Electrophoresis 25:2602–2610
Yamana K, Iwai T, Ohtani Y, Sato S, Nakamura M, Nakano H (2002) Bis-pyrene-labeled oligonucleotides: sequence specificity of excimer and monomer fluorescence changes upon hybridization with DNA. Bioconjug Chem 13:1266–1273
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2024 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Misra, S., Sharma, P., Mishra, A., Gondhali, U., Chauhan, T. (2024). Single Nucleotide Polymorphism as Evolutionary Evidence of Individuality. In: Puri, A., Mahalakshmi, N., Chauhan, T., Mishra, A., Bhatnagar, P. (eds) Fundamentals of Forensic Biology. Springer, Singapore. https://doi.org/10.1007/978-981-99-3161-3_21
Download citation
DOI: https://doi.org/10.1007/978-981-99-3161-3_21
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-99-3160-6
Online ISBN: 978-981-99-3161-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)