Technical Note

Estimating Individual Contributions to Complex DNA SNP Mixtures^†.^‡, ^§

Corresponding Author

Darrell O. Ricke Ph.D.

[email protected]

orcid.org/0000-0002-2842-2809

Bioengineering Systems & Technologies, Massachusetts Institute of Technology Lincoln Laboratory, 244 Wood Street, Lexington, MA

Corresponding author: Darrell O. Ricke, Ph.D. E-mail:[email protected]Search for more papers by this author

Philip Fremont-Smith M.S.,

Philip Fremont-Smith M.S.

orcid.org/0000-0002-2061-5809

Bioengineering Systems & Technologies, Massachusetts Institute of Technology Lincoln Laboratory, 244 Wood Street, Lexington, MA

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James Watkins B.S.,

James Watkins B.S.

Bioengineering Systems & Technologies, Massachusetts Institute of Technology Lincoln Laboratory, 244 Wood Street, Lexington, MA

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Sara Stankiewicz M.S.,

Sara Stankiewicz M.S.

orcid.org/0000-0003-3809-7883

Bioengineering Systems & Technologies, Massachusetts Institute of Technology Lincoln Laboratory, 244 Wood Street, Lexington, MA

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Tara Boettcher B.S.,

Tara Boettcher B.S.

orcid.org/0000-0003-3991-7193

Bioengineering Systems & Technologies, Massachusetts Institute of Technology Lincoln Laboratory, 244 Wood Street, Lexington, MA

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Eric Schwoebel Ph.D.,

Eric Schwoebel Ph.D.

Bioengineering Systems & Technologies, Massachusetts Institute of Technology Lincoln Laboratory, 244 Wood Street, Lexington, MA

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Darrell O. Ricke Ph.D.,

Corresponding Author

Darrell O. Ricke Ph.D.

[email protected]

orcid.org/0000-0002-2842-2809

Bioengineering Systems & Technologies, Massachusetts Institute of Technology Lincoln Laboratory, 244 Wood Street, Lexington, MA

Corresponding author: Darrell O. Ricke, Ph.D. E-mail:[email protected]Search for more papers by this author

Philip Fremont-Smith M.S.,

Philip Fremont-Smith M.S.

orcid.org/0000-0002-2061-5809

Bioengineering Systems & Technologies, Massachusetts Institute of Technology Lincoln Laboratory, 244 Wood Street, Lexington, MA

Search for more papers by this author

James Watkins B.S.,

James Watkins B.S.

Bioengineering Systems & Technologies, Massachusetts Institute of Technology Lincoln Laboratory, 244 Wood Street, Lexington, MA

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Sara Stankiewicz M.S.,

Sara Stankiewicz M.S.

orcid.org/0000-0003-3809-7883

Bioengineering Systems & Technologies, Massachusetts Institute of Technology Lincoln Laboratory, 244 Wood Street, Lexington, MA

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Tara Boettcher B.S.,

Tara Boettcher B.S.

orcid.org/0000-0003-3991-7193

Bioengineering Systems & Technologies, Massachusetts Institute of Technology Lincoln Laboratory, 244 Wood Street, Lexington, MA

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Eric Schwoebel Ph.D.,

Eric Schwoebel Ph.D.

Bioengineering Systems & Technologies, Massachusetts Institute of Technology Lincoln Laboratory, 244 Wood Street, Lexington, MA

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First published: 22 February 2019

https://doi.org/10.1111/1556-4029.14030

Citations: 8

^†

This material is based upon work supported under Air Force Contract No. FA8702-15-D-0001.

^‡

Any opinions, findings, conclusions, or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the U.S. Air Force.

^§

A patent application has been submitted that includes this work: Ricke, D. O. et al. Systems and Methods for Genetic Identification and Analysis. International Patent Application PCT/US2018/041081 (2018, July 6).

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Abstract

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.

Supporting Information

References

1Oldoni 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.
10.1016/j.fsigen.2016.07.002
CAS PubMed Web of Science® Google Scholar
2Kanokwongnuwut P, Martin B, Kirkbride KP, Linacre A. Shedding light on shedders. Forensic Sci Int Genet 2018; 36: 20–5.
10.1016/j.fsigen.2018.06.004
CAS PubMed Web of Science® Google Scholar
3Bleka 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.
10.1016/j.fsigen.2015.11.008
CAS PubMed Web of Science® Google Scholar
4Bleka 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.
10.1016/j.fsigss.2017.09.084
Web of Science® Google Scholar
5Bill 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.
10.1016/j.forsciint.2004.06.037
CAS PubMed Web of Science® Google Scholar
6Gill 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.
10.1016/S0379-0738(97)00174-6
CAS PubMed Web of Science® Google Scholar
7Cowell 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.
10.1111/rssc.12071
PubMed Web of Science® Google Scholar
8 ArmedXpert Support Site; www.armedxpert.com (accessed August 1, 2018).
Google Scholar
9 The DNA-VIEW^® mixture solution; http://dna-view.com/downloads/Mixture%20Solution%20poster.pdf (accessed August 8, 2018).
Google Scholar
10 qualitype. GenoProof Mixture 3; https://www.qualitype.de/en/solutions/products/evaluation-software/genoproof-mixture/(accessed August 1, 2018).
Google Scholar
11Inman 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.
10.1186/s12859-015-0740-8
PubMed Web of Science® Google Scholar
12Haned 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.
10.1016/j.fsigen.2012.08.008
CAS PubMed Web of Science® Google Scholar
13Taylor D, Bright J-A, Buckleton J. The interpretation of single source and mixed DNA profiles. Forensic Sci Int Genet 2013; 7(5): 516–28.
10.1016/j.fsigen.2013.05.011
CAS PubMed Web of Science® Google Scholar
14Perlin 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.
10.1111/j.1556-4029.2011.01859.x
CAS PubMed Web of Science® Google Scholar
15Voskoboinik L, Darvasi A. Forensic identification of an individual in complex DNA mixtures. Forensic Sci Int Genet 2011; 5(5): 428–35.
10.1016/j.fsigen.2010.09.002
CAS PubMed Web of Science® Google Scholar
16Isaacson 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.
10.1016/j.fsigen.2014.09.003
CAS PubMed Web of Science® Google Scholar
17Shcherbina 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.
Google Scholar
18Pakstis 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.
10.1007/s00439-009-0771-1
PubMed Web of Science® Google Scholar
19Nievergelt 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.
10.1186/2041-2223-4-13
PubMed Google Scholar
20Branicki 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.
10.1007/s00439-010-0939-8
PubMed Web of Science® Google Scholar
21Ricke DO, Shcherbina A, Michaleas A, Fremont-Smith P. GrigoraSNPs: optimized HTS DNA forensic SNP analysis. J Forensic Sci 2018; 63(6): 1841–5.
10.1111/1556-4029.13794
CAS PubMed Web of Science® Google Scholar
22 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).
Google Scholar
23Battelle. 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).
Google Scholar
24Woerner AE, King JL, Budowle B. Fast STR allele identification with STRait Razor 3.0. Forensic Sci Int Genet 2017; 30(Suppl C): 18–23.
10.1016/j.fsigen.2017.05.008
CAS PubMed Web of Science® Google Scholar
25Li 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.
10.1093/bioinformatics/btp352
CAS PubMed Web of Science® Google Scholar
26Ricke 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.
Google Scholar
27Lowe 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.
10.1016/S0379-0738(02)00207-4
CAS PubMed Web of Science® Google Scholar

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Volume64, Issue5

September 2019

Pages 1468-1474

Estimating Individual Contributions to Complex DNA SNP Mixtures^†.^‡, ^§

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Estimating Individual Contributions to Complex DNA SNP Mixtures^†.^‡, ^§