Use of Next‐Generation Sequencing in Forensic Genetics

Abstract

The main purpose of forensic science institutions is to provide scientifically based investigations to the judicial system and assist society as a whole with objective analyses of evidence.

Ten years ago, the invention of clonal amplification by emulsion PCR or bridge PCR inspired a technical revolution in DNA sequencing commonly known as next‐generation sequencing (NGS). New methods and platforms were invented, all with the same purpose of sequencing massive numbers of DNA molecules simultaneously. These methods are of obvious interest to forensic genetic practitioners, who are frequently faced with the challenge of genotyping limited and degraded DNA material extracted from irreplaceable trace samples. NGS may be superior to the existing techniques and offers new exiting possibilities to the end users of forensic investigations.

Key Concepts

  • Next‐generation sequencing (NGS) is based on simultaneous clonal amplification of millions of individual DNA molecules and parallel sequencing of the generated products.
  • Fragment length analyses of PCR‐amplified short tandem repeats (STRs) have been the preferred method for human identification in forensic genetic case work for more than two decades.
  • The multiplexing capability of PCR‐NGS and sequencing capacity of NGS platforms make it possible to type different types of markers (STRs, SNPs and INDELs) in one assay, which increases the available information, saves time and reduces the overall cost of the investigation.
  • Human identification and forensic phenotyping may be accomplished simultaneously by typing human identification and phenotypical markers in one PCR‐NGS assay.
  • Detailed sequence information of STRs increases the statistical weight of the DNA evidence and may aid mixture interpretation.
  • Genome or transcriptome sequencing of samples from deceased makes it possible to combine forensic pathology with medical genetics and forensic toxicology with pharmacogenetics.

Keywords: next‐generation sequencing; massively parallel sequencing; PCR; forensic genetics; forensic genomics; human identification; human phenotyping; kinship testing; STR; SNP

Figure 1. An example of a DNA profile generated by PCR‐CE. The male individual was typed with the AmpFLSTR® NGM SElect™ PCR amplification Kit (ThermoFisher Scientific), and the PCR products were analysed by capillary electrophoresis. The electropherogram is divided into four images. Each image illustrates the detected PCR products carrying a specific fluorescent dye (blue, green, yellow (shown in black) and red). The abscissa indicates the length in nucleotides and the ordinate indicates the signal strength in relative fluorescent units. The expected size ranges of each locus are indicated by the grey boxes above the abscissa. The number of STR repeats for each product is indicated below the peak. ST = stutter. X and Y are the signals from the INDEL marker amelogenin. In the D10S1248 locus, the individual carry two alleles (13 and 15). Each of these alleles gave rise to a stutter (with a size of 12 and 14 repeats, respectively). In the D22S1045 locus, the individual is homozygous for allele 16 and two stutters are detected (with sizes of 15 and 17 repeats).
Figure 2. Three examples (blue, grey and brown eye colour) of digital eye images used for quantitative measurement of eye colour (Andersen et al., ). Among the pigmentary traits, eye colour has the highest heritability and phenotype predictability.
close

References

Andersen JD, Pietroni C, Johansen P, et al. (2016) Importance of non‐synonymous OCA2 variants in human eye colour prediction. Molecular Genetics & Genomic Medicine 4: 420–430.

Bekaert B, Kamalandua A, Zapico SC, et al. (2015) Improved age determination of blood and teeth samples using a selected set of DNA methylation markers. Epigenetics 10: 922–930.

Beleza S, Johnson NA, Candille SI, et al. (2013) Genetic architecture of skin and eye color in an African‐European admixed population. PLoS Genetics 9: e1003372.

Benschop CC, van der Beek CP, Meiland HC, et al. (2011) Low template STR typing: effect of replicate number and consensus method on genotyping reliability and DNA database search results. Forensic Science International: Genetics 5: 316–328.

Branicki W, Liu F, van Duijn K, et al. (2011) Model‐based prediction of human hair color using DNA variants. Human Genetics 129: 443–454.

Buchard A, Kampmann M, Poulsen L, et al. (2016) ISO17025 validation of a next generation sequencing assay for relationship testing. Electrophoresis 37: 2822–2831.

Budowle B, Moretti TR, Baumstark AL, et al. (1999) Population data on the thirteen CODIS core short tandem repeat loci in African Americans, U.S. Caucasians, Hispanics, Bahamians, Jamaicans, and Trinidadians. Journal of Forensic Science 44: 1277–1286.

Butler J (2015) U.S. initiatives to strengthen forensic science & international standards in forensic DNA. Forensic Science International: Genetics 18: 4–20.

Børsting C, Rockenbauer E and Morling N (2009) Validation of a single nucleotide polymorphism (SNP) typing assay with 49 SNPs for forensic genetic testing in a laboratory accredited according to the ISO 17025 standard. Forensic Science International: Genetics 4: 34–42.

Børsting C, Mogensen HS and Morling N (2013) Forensic genetic SNP typing of low‐template DNA and highly degraded DNA from crime case samples. Forensic Science International: Genetics 7: 345–352.

Chan SL, Suo C, Lee SC, et al. (2012) Translational aspects of genetic factors in the prediction of drug response variability: a case study of warfarin pharmacogenomics in a multi‐ethnic cohort from Asia. The Pharmacogenomics Journal 12: 312–318.

Christiansen SL, Hertz CL, Ferrero‐Miliani L, et al. (2016) Genetic investigation of 100 heart genes in sudden unexplained death victims in a forensic setting. European Journal of Human Genetics 24: 1797–1802.

Churchill JD, Schmedes SE, King JL, et al. (2016) Evaluation of the Illumina® beta version ForenSeq™ DNA signature prep kit for use in genetic profiling. Forensic Science International: Genetics 20: 20–29.

Cox MJ, Cookson WO and Moffatt MF (2013) Sequencing the human microbiome in health and disease. Human Molecular Genetics 22: R88–R94.

Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics 5: 435–445.

Fedurco M, Romieu A, Williams S, et al. (2006) BTA, a novel reagent for DNA attachment on glass and efficient generation of solid‐phase amplified DNA colonies. Nucleic Acids Research 34: e22.

Flusberg BA, Webster DR, Lee JH, et al. (2010) Direct detection of DNA methylation during single‐molecule, real‐time sequencing. Nature Methods 7: 461–465.

Fordyce S, Ávila‐Arcos MC, Rockenbauer E, et al. (2011) High‐throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform. Biotechniques 51: 127–133.

Freire‐Aradas A, Phillips C, Mosquera‐Miguel A, et al. (2016) Development of a methylation marker set for forensic age estimation using analysis of public methylation data and the Agena Bioscience EpiTYPER system. Forensic Science International: Genetics 24: 65–74.

Friis SL, Buchard A, Rockenbauer E, et al. (2016) Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs. Forensic Science International: Genetics 21: 68–75.

Gelardi C, Rockenbauer E, Dalsgaard S, et al. (2014) Second generation sequencing of three STRs D3S1358, D12S391 and D21S11 in Danes and a new nomenclature for sequenced STR allelles. Forensic Science International: Genetics 12: 38–41.

Gettings KB, Kiesler KM, Faith SA, et al. (2016) Sequence variation of 22 autosomal STR loci detected by next generation sequencing. Forensic Science International: Genetics 21: 15–21.

Giampaoli S, Berti A, Di Maggio RM, et al. (2014) The environmental biological signature: NGS profiling for forensic comparison of soils. Forensic Science International 240: 41–47.

Gill P, Haned H, Bleka O, et al. (2015) Genotyping and interpretation of STR‐DNA: low‐template, mixture and database matches‐twenty years of research and development. Forensic Science International: Genetics 18: 100–117.

Grandell I, Samara R and Tillmar AO (2016) A SNP panel for identity and kinship testing using massive parallel sequencing. International Journal of Legal Medicine 130: 905–914.

Guo F, Zhou Y, Song H, et al. (2016) Next generation sequencing of SNPs using the HID‐Ion AmpliSeq™ identity panel on the ion torrent PGM™ platform. Forensic Science International: Genetics 25: 73–84.

Hauther KA, Cobaugh KL, Jantz LM, et al. (2015) Estimating time since death from postmortem human gut microbial communities. Journal of Forensic Sciences 60: 1234–1240.

Horvath S (2013) DNA methylation age of human tissues and cell types. Genome Biology 14: R115.

Jeffreys AJ, Wilson V and Thein SL (1985) Individual‐specific ‘fingerprints’ of human DNA. Nature 316: 76–79.

Kidd KK, Speed WC, Pakstis AJ, et al. (2014) Progress toward an efficient panel of SNPs for ancestry inference. Forensic Science International: Genetics 10: 23–32.

Kim EH, Lee HY, Yang IS, et al. (2016) Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons. Forensic Science International: Genetics 22: 1–7.

Kosoy R, Nassir R, Tian C, et al. (2009) Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Human Mutation 30: 69–78.

Liu F, van Duijn K, Vingerling JR, et al. (2009) Eye color and the prediction of complex phenotypes from genotypes. Current Biology 19: R192–R193.

Mardis ER (2008) Next‐generation DNA sequencing methods. Annual Review of Genomics and Human Genetics 9: 387–402.

Margulies M, Egholm M, Altman WE, et al. (2005) Genome sequencing in microfabricated high‐density picolitre reactors. Nature 437: 376–380.

Methner DNR, Scherer SE, Welch K, et al. (2016) Postmortem genetic screening for the identification, verification, and reporting of genetic variants contributing to the sudden death of the young. Genome Research 26: 1170–1177.

Metzker ML (2010) Sequencing technologies‐the next generation. Nature Reviews Genetics 11: 31–46.

Pakstis AJ, Speed WC, Fang R, et al. (2010) SNPs for a universal individual identification panel. Human Genetics 127: 315–324.

Park J, Kim JH, Seo E, et al. (2016) Identification and evaluation of age‐correlated DNA methylation markers for forensic use. Forensic Science International: Genetics 23: 64–70.

Pfeifer CM, Klein‐Unseld R, Klintschar M, et al. (2012) Comparison of different interpretation strategies for low template DNA mixtures. Forensic Science International: Genetics 6: 716–722.

Phillips C (2015) Forensic genetic analysis of bio‐geographical ancestry. Forensic Science International: Genetics 18: 49–65.

Sanchez JJ, Phillips C, Børsting C, et al. (2006) A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27: 1713–1724.

Schreiber J, Wescoe ZL, Abu‐Shumays R, et al. (2013) Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands. Proceedings of the National Academy of Sciences of the United States of America 110: 18910–18915.

Sullivan D, Pinsonneault JK, Papp AC, et al. (2013) Dopamine transporter DAT and receptor DRD2 variants affect risk of lethal cocaine abuse: a gene‐gene‐environment interaction. Translational Psychiatry 3: e222.

Themudo GE, Mogensen HS, Børsting C, et al. (2016) Frequencies of HID‐Ion ampliseq ancestry panel markers among Greenlanders. Forensic Science International: Genetics 24: 60–64.

Tomas C, Mogensen HS, Friis SL, et al. (2014) Concordance study and population frequencies for 16 autosomal STRs analysed with PowerPlex® ESI 17 and AmpFlSTR® NGM SElect™ in Somalis, Danes and Greenlanders. Forensic Science International: Genetics 11: e18–e21.

Umer M and Herceg Z (2013) Deciphering the epigenetic code: an overview of DNA methylation analysis methods. Antioxidants & Redox Signaling 18: 1972–1986.

Van der Gaag KJ, de Leeuw RH, Hoogenboom J, et al. (2016) Massively parallel sequencing of short tandem repeats‐population data and mixture analysis results for the PowerSeq™ system. Forensic Science International: Genetics 24: 86–96.

Welch LA, Gill P, Phillips C, et al. (2012) European network of forensic science institutes (ENFSI): evaluation of new commercial STR multiplexes that include the European Standard Set (ESS) of markers. Forensic Science International: Genetics 6: 819–826.

Westen AA, Kraaijenbrink T, Robles de Medina EA, et al. (2014) Comparing six commercial autosomal STR kits in a large Dutch population sample. Forensic Science International: Genetics 10: 55–63.

Further Reading

Brion M, Sobrino B, Martinez M, et al. (2015) Massive parallel sequencing applied to the molecular autopsy in sudden cardiac death in the young. Forensic Science International: Genetics 18: 160–170.

Butler J (2005) Forensic DNA Typing: Biology, Technology and Genetics of STR Markers, 2nd edn. Burlington, MA: Elsevier Academic Press.

Butler J (2012) Advanced Topics in Forensic DNA Typing: Interpretation, 2nd edn. San Diego, CA: Elsevier Academic Press.

Børsting C and Morling N (2015) Next generation sequencing and its applications in forensic genetics. Forensic Science International: Genetics 18: 78–89.

Egeland T, Kling D and Mostad P (2016) Relationship Inference with Familias and R, 1st edn. San Diego, CA: Elsevier Academic Press.

Gill P (2014) Misleading DNA Evidence, 1st edn. Burlington, MA: Elsevier Academic Press.

Laird PW (2010) Principles and challenges of genome‐wide DNA methylation analysis. Nature Reviews Genetics 11: 191–203.

Phillips C, Gelabert‐Besada M, Fernandez‐Formoso L, et al. (2014) “New turns from old STaRs”: enhancing the capabilities of forensic short tandem repeat analysis. Electrophoresis 35: 3173–3187.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Børsting, Claus, and Morling, Niels(Apr 2017) Use of Next‐Generation Sequencing in Forensic Genetics. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0027106]