Abstract
DNA profiling in forensic context has seen tremendous growth over the last almost four decades. Forensic DNA fingerprinting started with Alec Jefferey’s single and multilocus probes via autoradiography followed by fluorescence-based PCR-STRs. Lately, there has been a significant change in technology for human identification. Chip-based massively parallel sequencing is the most recent advancement. Drawing investigative leads, disaster victim identification, and unsolved cold cases created a requirement for more efficient ways of extraction, rapid DNA testing, and genetic genealogy. Pooling forensic genetic genealogy, mitochondrial DNA for challenging sample analysis and STR-SNP sequencing has opened more avenues to generate the data leading to identification. This chapter highlights some of the advanced methods adopted in forensic DNA profiling and a few appropriate cases incorporating such methods.
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Alonso A, Barrio PA, Müller P, Köcher S, Berger B, Martin P, Bodner M, Willuweit S, Parson W, Roewer L, Budowle B (2018) Current state-of-art of STR sequencing in forensic genetics. Electrophoresis 39;(21):2655–2668
Berglund EC, Kiialainen A, Syvänen AC (2011) Next-generation sequencing technologies and applications for human genetic history and forensics. Investig Genet 2(1):23
Børsting C, Morling N (2015) Next generation sequencing and its applications in forensic genetics. Forensic Sci Int Genet 18:78–89
Buscaino J, Barican A, Farrales L, Goldman B, Klevenberg J, Kuhn M, Lin F, Nguyen P, Salceda S, Schueren R, Smith C, Troup C, Tsou D, Vangbo M, King D (2018) Evaluation of a rapid DNA process with the RapidHIT® ID system using a specialized cartridge for extracted and quantified human DNA. Forensic Sci Int Genet 34:116–127
Butler JM (2015) The future of forensic DNA analysis. Philos Trans R Soc B Biol Sci 370(1674):20140252
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. Int Soc Microb Ecol 6(8):1621–1624
Chakravarty M, Pandya P, Raina A, Priyanka (2019) Resourcefulness of Str markers in forensic casework analysis. Int J Med Toxicol Legal Med 22(3–4):110–113
Churchill JD, Schmedes SE, King JL, Budowle B (2016) Evaluation of the Illumina® Beta version ForenSeq™ DNA signature prep kit for use in genetic profiling. Forensic Sci Int Genet 20:20–29
Coble MD, Bright JA (2019) Probabilistic genotyping software: an overview. Forensic Sci Int Genet 38:219–224
Court S. Denise (2018) Forensic genealogy: some serious concerns. Forensic Sci Int Genet 36:203–204
Dalsgaard S, Rockenbauer E, Gelardi C, Børsting C, Fordyce SL, Morling N (2013) Characterization of mutations and sequence variations in complex STR loci by second generation sequencing. Genet Suppl Serie Forensic Sci Int 4(1):e218–e219
Dash HR, Pankaj S, Surajit D (2020) RAPID DNA technology: a boon to forensic DNA. Typing 313–316
Dixit S, Pankaj S, Kumawat RK, Kaitholia K, Dash HR, Sharma H, Choubey G (2019) Forensic genetic analysis of population of Madhya Pradesh with PowerPlex fusion 6C ™ multiplex system. Int J Legal Med133(3):803–805
Fang C, Xu L, Jing Z, Bingbing X, Jialin Q, Wenli l, Baoming L, Xiaoli Z, Huijuan W, Jiangwei Y (2020) Age estimation using bloodstain MiRNAs based on massive parallel sequencing and machine learning: a pilot study. Forensic Sci Int Genet 47:102300
Fordyce SL, Ávila-Arcos MC, Rockenbauer E, Børsting C, Frank-Hansen R, Petersen FT, Willerslev E, Hansen AJ, Morling N, Gilbert TP (2011) High-throughput sequencing of Core STR loci for forensic genetic investigations using the Roche genome sequencer FLX platform. BioTechnique 51(2):127–133
Frégeau CJ, Marc Lett C, Fourney RM (2010) Validation of a DNA IQ™-based extraction method for TECAN robotic liquid handling workstations for processing casework. Forensic Sci Int Genet 4(5):292–304
Fullwood MJ, Wei CL, Liu ET, Ruan Y (2009) Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res 19(4):521–532
Gaag VD, Kristiaan J, De Leeuw RH, Hoogenboom J, Patel J, Storts DR, Laros JFJ, De Knijff P (2016) Massively parallel sequencing of short tandem repeats -- population data and mixture analysis results for the PowerSeq™ system. Forensic Sci Int Genet 24:86–96
Gettings KB, Aponte RA, Kiesler KM, Vallone PM (2015a) The next dimension in STR sequencing: polymorphisms in flanking regions and their allelic associations. Genet Suppl Serie Forensic Sci Int 5:e121–e123
Gettings KB, Kiesler KM, Vallone PM (2015b) Performance of a next generation sequencing SNP assay on degraded DNA. Forensic Sci Int Genet 19:1–9
Greytak EM, Moore CC, Armentrout SL (2019) Genetic genealogy for cold case and active investigations. Forensic Sci Int 299:103–113
Guo F, Yu J, Lu Z, Li J (2017) Massively parallel sequencing of forensic STRs and SNPs using the Illumina® ForenSeq™ DNA signature prep kit on the MiSeq FGx™ forensic genomics system. Forensic Sci Int Genet 31:135–141
Heather JM, Chain B (2016) The sequence of sequencers: the history of sequencing DNA. Genomics 107(1):1–8
Higuchi R, Von Beroldingen CH, Sensabaugh GF, Erlich HA (1988) DNA typing from single hairs. Nature 332(6164):543–546
Holland MM, Parsons TJ (1999) Mitochondrial DNA sequence analysis – validation and use for forensic casework. Forensic Sci Rev 11(1):21–50
Holland MM, Bonds RM, Holland CA, McElhoe JA (2019) Recovery of MtDNA from unfired metallic ammunition components with an assessment of sequence profile quality and DNA damage through MPS analysis. Forensic Sci Int Genet 39:86–96
Holland MM, Parson W (2011) GeneMarker® HID: a reliable software tool for the analysis of forensic STR data. J Forensic Sci 56(1):29–35
Hopwood AJ, Hurth C, Yang J, Cai Z, Moran N, Lee-Edghill JG, Nordquist A, Lenigk R, Estes MD, Haley JP, McAlister CR, Chen X, Brooks C, Smith S, Elliott K, Koumi P, Zenhausern F, Tully G (2010) Integrated microfluidic system for rapid forensic DNA analysis: sample collection to DNA profile. Anal Chem 82(16):6991–6999
Hyman ED (1988) A new method of sequencing DNA. Anal Biochem 174(2):423–436
Ingold S, Dørum G, Hanson E, Berti A, Branicki W, Brito P, Elsmore P, Gettings KB, Giangasparo F, Gross TE, Hansen S, Hanssen EN, Kampmann ML, Kayser M, Laurent FX, Morling N, Mosquera-Miguel A, Parson W, Phillips C, Porto MJ, Pośpiech E, Roeder AD, Schneider PM, Schulze Johann K, Steffen CR, Syndercombe-Court D, Trautmann M, van den Berge M, van der Gaag KJ, Vannier J, Verdoliva V, Vidaki A, Xavier C, Ballantyne J, Haas C (2018) Body fluid identification using a targeted MRNA massively parallel sequencing approach – results of a EUROFORGEN/EDNAP collaborative exercise. Forensic Sci Int Genet 34:105–115
Jiang L, Wei YL, Zhao L, Li N, Liu T, Liu HB, Ren LJ, Li JL, Hao HF, Li Q, Li CX (2018) Global analysis of population stratification using a smart panel of 27 continental ancestry-informative SNPs. Forensic Sci Int Genet 35:e10–e12
Kayser M (2015) Forensic DNA phenotyping: predicting human appearance from crime scene material for investigative purposes. Forensic Sci Int Genet 18:33–48
Kayser M, De Knijff P (2011) Improving human forensics through advances in genetics, genomics and molecular biology. Nature Rev Genet 12(3):179–192
Kidd KK, Kidd JR, Speed WC, Fang R, Furtado MR, Hyland FCL, Pakstis AJ (2012) Expanding data and resources for forensic use of SNPs in individual identification. Forensic Sci Int Genet 6(5):646–652
Kircher M, Sawyer S, Meyer M (2012) Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res 40(1):e3–e3
Kirsch S, Klein CA (2012) Sequence error storms and the landscape of mutations in Cancer. Proc Nat Acad Sci U S A 109(36):14289–14290
Kling D, Tillmar A (2019) Forensic genealogy—a comparison of methods to infer distant relationships based on dense SNP data. Forensic Sci Int Genet 42:113–124
Li M, Schönberg A, Schaefer M, Schroeder R, Nasidze I, Stoneking M (2010) Detecting Heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. Am J Hum Genet 87(2):237–249
Liu J, Weian D, Wang M, Liu C, Wang S, He G, Zheng W (2020) Forensic features, genetic diversity and structure analysis of three Chinese populations using 47 autosomal InDels. Forensic Sci Int Genet 45:102227
Ma Y, Kuang JZ, Nie TG, Zhu W, Yang Z (2016) Next generation sequencing: improved resolution for paternal/maternal duos analysis. Forensic Sci Int Genet 24:83–85
Mardis ER (2017) DNA sequencing technologies: 2006–2016. Nat Protoc 12(2):213–218
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Lei D, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density Picolitre reactors. Nature 437(7057):376–380
Martín P, García O, Albarrán C, García P, Alonso A (2006) Application of mini-STR loci to severely degraded casework samples. Int Cong Series 1288:522–525
Maxam AM, Gilbert W (1977) A new method for sequencing DNA. Proc Nat Acad Sci 74(2):560–564
McCarthy JJ, McLeod HL, Ginsburg GS (2013) Genomic medicine: a decade of successes, challenges, and opportunities. Sci Trans Med 5(189):189sr4–189sr4
Montano EA, Bush JM, Garver AM, Larijani MM, Wiechman SM, Baker CH, Wilson MR, Guerrieri RA, Benzinger EA, Gehres DN, Dickens ML (2018) Optimization of the Promega PowerSeq™ auto/Y system for efficient integration within a forensic DNA laboratory. Forensic Sci Int Genet 32:26–32
Müller P, Alonso A, Barrio PA, Berger B, Bodner M, Martin P, Parson W (2018) Systematic evaluation of the early access applied Biosystems precision ID Globalfiler mixture ID and Globalfiler NGS STR panels for the ion S5 system. Forensic Sci Int Genet 36:95–103
Niedringhaus TP, Milanova D, Kerby MB, Snyder MP, Barron AE (2011) Landscape of next-generation sequencing technologies. Anal Chem 83(12):4327–4341
Parson W, Huber G, Moreno L, Madel MB, Brandhagen MD, Nagl S, Xavier C, Eduardoff M, Callaghan TC, Irwin JA (2015) Massively parallel sequencing of complete mitochondrial genomes from hair shaft samples. Forensic Sci Int Genet 15:8–15
Parson W, Strobl C, Huber G, Zimmermann B, Gomes SM, Souto L, Fendt L, Delport R, Langit R, Wootton S, Lagacé R, Irwin J (2013) Evaluation of next generation MtGenome sequencing using the ion torrent personal genome machine (PGM). Forensic Sci Int Genet 7(5):543–549
Payne BAI, Wilson IJ, Yu-Wai-Man P, Coxhead J, Deehan D, Horvath R, Taylor RW, Samuels DC, Santibanez-Koref M, Chinnery PF (2013) Universal Heteroplasmy of human mitochondrial DNA. Hum Mol Genet 22(2):384–390
Petrovick MS, Boettcher T, Fremont-Smith P, Peragallo C, Ricke DO, Watkins J, Schwoebel E (2020) Analysis of complex DNA mixtures using massively parallel sequencing of SNPs with low minor allele frequencies. Forensic Sci Int Genet 46:102234
Phillips C, McNevin D, Kidd KK, Lagacé R, Wootton S, de la Puente M, Freire-Aradas A, Mosquera-Miguel A, Eduardoff M, Gross T, Dagostino L, Power D, Olson S, Hashiyada M, Oz C, Parson W, Schneider PM, Lareu MV, Daniel R (2019) MAPlex – A massively parallel sequencing ancestry analysis multiplex for Asia-Pacific populations. Forensic Sci Int Genet 42:213–226
Phillips C, Salas A, Sánchez JJ, Fondevila M, Gómez-Tato A, Álvarez-Dios J, Calaza M, Casares de Cal M, Ballard D, Lareu MV, Carracedo Á (2007) Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci Int Genet 1(3–4):273–280
Phillips C (2015) Forensic genetic analysis of bio-geographical ancestry. Forensic Sci Int Genet 18:49–65
Phillips C (2018) The Golden state killer investigation and the nascent field of forensic genealogy. Forensic Sci Int Genet 36:186–188
Poinar HN, Schwarz C, Qi J, Shapiro B, MacPhee RDE, Buigues B, Tikhonov A, Huson DM, Tomsho LP, Auch A, Rampp M, Miller M, Schuster SC (2006) Metagenomics to Paleogenomics: large-scale sequencing of mammoth DNA. Science 311(5759):392–394
Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, De Filippo C, Li H, Mallick S, Dannemann M, Qiaomei F, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PLF, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S (2014) The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505(7481):43–49
Riman S, Iyer H, Borsuk LA, Vallone PM (2020) Understanding the characteristics of sequence-based single-source DNA profiles. Forensic Sci Int Genet 44:102192
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with Chain-terminating inhibitors. Proc Nat Acad Sci U S A 74(12):5463–5467
Shackleton D, Pagram J, Andrews N, Malsom S, Ives L, Vanhinsbergh D (2019) Development of enhanced sensitivity protocols on the RapidHIT™ 200 with a view to processing casework material. Sci Justice 59(4):411–417
Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26(10):1135–1145
Shrivastava P, Trivedi VB, Singh AK, Mishra N (2012) Application of DNA fingerprinting technology in Forensic Investigation. Int J Scient Res Publ 2(1):2250–3153
Srivastava V, Prabhakar Rao K, Surekha Rani H, Kumawat RK, Mishra A, Shrivastava P (2020) Genomic diversity in the Goud population of Telangana, India inferred using twenty-three autosomal marker PowerPlex® fusion 6C system. Meta Gene 25:100718
Tang S, Wang J, Zhang VW, Li FY, Landsverk M, Cui H, Truong CK, Wang G, Chen LC, Graham B, Scaglia F, Schmitt ES, Craigen WJ, Wong LJC (2013) Transition to next generation analysis of the whole mitochondrial genome: a summary of molecular defects. Hum Mutat 34(6):882–893
Tillmar A, Sjölund P, Lundqvist B, Klippmark T, Älgenäs C, Green H (2020) Whole-genome sequencing of human remains to enable genealogy DNA database searches – a case report. Forensic Sci Int Genet 46:102233
Tozzo P, D’angiolella G, Brun P, Castagliuolo I, Gino S, Caenazzo L (2020) Skin microbiome analysis for forensic human identification: what do we know so far? Microorganisms 8(6):873
Weber-Lehmann J, Schilling E, Gradl G, Richter DC, Wiehler J, Rolf B (2014) Finding the needle in the haystack: differentiating ‘identical’ twins in paternity testing and forensics by ultra-deep next generation sequencing. Forensic Sci Int Genet 9:42–46
Wickenheiser RA (2019) Forensic genealogy, bioethics and the Golden state killer case. Forensic Sci Int Synergy 1:114–125
Woerner AE, King JL, Budowle B (2017) Fast STR allele identification with STRait razor 3.0. Forensic Sci Int Genet 30:18–23
Xavier C, de la Puente M, Phillips C, Eduardoff M, Heidegger A, Mosquera-Miguel A, Freire-Aradas A, Lagace R, Wootton S, Power D, Parson W, Lareu MV, Daniel R (2020b) Forensic evaluation of the Asia Pacific ancestry-informative MAPlex assay. Forensic Sci Int Genet 48:102344
Xavier C, de la Puente M, Mosquera-Miguel A, Freire-Aradas A, Kalamara V, Vidaki A, Gross TE, Revoir A, Pośpiech E, Kartasińska E, Spólnicka M, Branicki W, Ames CE, Schneider PM, Hohoff C, Kayser M, Phillips C, Parson W (2020a) Development and validation of the VISAGE AmpliSeq basic tool to predict appearance and ancestry from DNA. Forensic Sci Int Genet 48:102336
Yang Y, Xie B, Yan J (2014) Application of next-generation sequencing Technology in Forensic Science. Genom Proteom Bioinform 12(5):190–197
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Chakravarty, M., Pandya, P. (2021). Introduction to Forensic DNA Typing and Current Trends. In: Dash, H.R., Shrivastava, P., Lorente, J.A. (eds) Handbook of DNA Profiling. Springer, Singapore. https://doi.org/10.1007/978-981-15-9364-2_1-1
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