Estimating Individual Contributions to Complex DNA SNP Mixtures.
DNA forensics
forensic science
high-throughput sequencing
massively parallel sequencing
mixture analysis
single nucleotide polymorphism
Journal
Journal of forensic sciences
ISSN: 1556-4029
Titre abrégé: J Forensic Sci
Pays: United States
ID NLM: 0375370
Informations de publication
Date de publication:
Sep 2019
Sep 2019
Historique:
received:
11
10
2018
revised:
18
01
2019
accepted:
28
01
2019
pubmed:
26
2
2019
medline:
18
12
2019
entrez:
26
2
2019
Statut:
ppublish
Résumé
High-throughput sequencing (HTS) of large panels of single nucleotide polymorphisms (SNPs) provides an alternative or complimentary approach to short tandem repeats (STRs) panels for the analysis of complex DNA mixture forensic samples. For STRs, methods to estimate individual contribution concentrations compare capillary electrophoresis peak heights, peak areas, or HTS allele read counts within a mixture. This article introduces three approaches (mean, median, and slope methods) for estimating individual DNA contributions to forensic mixtures for HTS/massively parallel sequencing (MPS) SNP panels. For SNPs, the major:minor allele ratios or counts, unique to each contributor, were compared to estimate contributor proportion within the mixture using the mean, median, and slope intercept for these alleles. The estimates for these three methods were typically within 5% of planned experimental contributions for defined mixtures.
Identifiants
pubmed: 30801728
doi: 10.1111/1556-4029.14030
doi:
Substances chimiques
DNA
9007-49-2
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1468-1474Subventions
Organisme : Air Force
ID : FA8702-15-D-0001
Informations de copyright
Published 2019. This article is a U.S. Government work and is in the public domain in the USA.
Références
Oldoni F, Castella V, Hall D. Shedding light on the relative DNA contribution of two persons handling the same object. Forensic Sci Int Genet 2016;24:148-57.
Kanokwongnuwut P, Martin B, Kirkbride KP, Linacre A. Shedding light on shedders. Forensic Sci Int Genet 2018;36:20-5.
Bleka Ø, Storvik G, Gill P. EuroForMix: an open source software based on a continuous model to evaluate STR DNA profiles from a mixture of contributors with artefacts. Forensic Sci Int Genet 2016;21:35-44.
Bleka Ø, Eduardoff M, Santos C, Phillips C, Parson W, Gill P. Using EuroForMix to analyse complex SNP mixtures, up to six contributors. Forensic Sci Int Genet 2017;6(Genet Suppl):e277-9.
Bill M, Gill P, Curran J, Clayton T, Pinchin R, Healy M, et al. PENDULUM-a guideline-based approach to the interpretation of STR mixtures. Forensic Sci Int 2005;148(2):181-9.
Gill P, Sparkes R, Pinchin R, Clayton T, Whitaker J, Buckleton J. Interpreting simple STR mixtures using allele peak areas. Forensic Sci Int 1998;91(1):41-53.
Cowell RG, Graversen T, Lauritzen SL, Mortera J. Analysis of forensic DNA mixtures with artefacts. J R Stat Soc Ser C Appl Stat 2015;64(1):1-48.
ArmedXpert Support Site; www.armedxpert.com (accessed August 1, 2018).
The DNA-VIEW® mixture solution; http://dna-view.com/downloads/Mixture%20Solution%20poster.pdf (accessed August 8, 2018).
qualitype. GenoProof Mixture 3; https://www.qualitype.de/en/solutions/products/evaluation-software/genoproof-mixture/(accessed August 1, 2018).
Inman K, Rudin N, Cheng K, Robinson C, Kirschner A, Inman-Semerau L, et al. Lab Retriever: a software tool for calculating likelihood ratios incorporating a probability of drop-out for forensic DNA profiles. BMC Bioinformatics 2015;16(1):298.
Haned H, Slooten K, Gill P. Exploratory data analysis for the interpretation of low template DNA mixtures. Forensic Sci Int Genet 2012;6(6):762-74.
Taylor D, Bright J-A, Buckleton J. The interpretation of single source and mixed DNA profiles. Forensic Sci Int Genet 2013;7(5):516-28.
Perlin MW, Legler MM, Spencer CE, Smith JL, Allan WP, Belrose JL, et al. Validating TrueAllele® DNA mixture interpretation. J Forensic Sci 2011;56(6):1430-47.
Voskoboinik L, Darvasi A. Forensic identification of an individual in complex DNA mixtures. Forensic Sci Int Genet 2011;5(5):428-35.
Isaacson J, Schwoebel E, Shcherbina A, Ricke D, Harper J, Petrovick M, et al. Robust detection of individual forensic profiles in DNA mixtures. Forensic Sci Int Genet 2015;14:31-7.
Shcherbina A, Ricke DO, Schwoebel E, Boettcher T, Zook C, Bobrow J, et al. KinLinks: software toolkit for kinship analysis and pedigree generation from HTS datasets. In: Proceedings of the 2016 IEEE International Symposium on Technologies for Homeland Security (HST); 2016 May 10-12; Waltham, MA. Piscataway, NJ: Institute of Electrical and Electronics Engineers, 2016.
Pakstis AJ, Speed WC, Fang R, Hyland FCL, Furtado MR, Kidd JR, et al. SNPs for a universal individual identification panel. Human Genet 2010;127(3):315-24.
Nievergelt CM, Maihofer AX, Shekhtman T, Libiger O, Wang X, Kidd KK, et al. Inference of human continental origin and admixture proportions using a highly discriminative ancestry informative 41-SNP panel. Investig Genet 2013;4(1):13.
Branicki W, Liu F, van Duijn K, Draus-Barini J, Pośpiech E, Walsh S, et al. Model-based prediction of human hair color using DNA variants. Hum Genet 2011;129(4):443-54.
Ricke DO, Shcherbina A, Michaleas A, Fremont-Smith P. GrigoraSNPs: optimized HTS DNA forensic SNP analysis. J Forensic Sci 2018;63(6):1841-5.
Illumina. Human identification with STRs and SNPs; http://www.illumina.com/areas-of-interest/forensic-genomics/forensic-analysis-methods/snp-str-analysis.html (accessed September 22, 2018).
Battelle. ExactID® technical specifications; https://www.battelle.org/government-offerings/homeland-security-public-safety/security-law-enforcement/forensic-genomics/exactid/technical-specifications (accessed September 15, 2018).
Woerner AE, King JL, Budowle B. Fast STR allele identification with STRait Razor 3.0. Forensic Sci Int Genet 2017;30(Suppl C):18-23.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009;25(16):2078-9.
Ricke DO. FastID: extremely fast forensic DNA comparisons. In: Proceedings of the 2017 IEEE High Performance Extreme Computing Conference (HPEC); 2017 Sept 12-14; Waltham, MA. Waltham, MA. Piscataway, NJ: Institute of Electrical and Electronics Engineers, 2017;1-4.
Lowe A, Murray C, Whitaker J, Tully G, Gill P. The propensity of individuals to deposit DNA and secondary transfer of low level DNA from individuals to inert surfaces. Forensic Sci Int 2002;129(1):25-34.