Using FastID to analyze complex SNP mixtures from indoor dust.
FastID
MPS
SNPs
indoor dust
interpretation of DNA mixtures
investigative leads
massively parallel sequencing
single nucleotide polymorphisms
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:
May 2023
May 2023
Historique:
revised:
10
03
2023
received:
09
12
2022
accepted:
20
03
2023
medline:
2
5
2023
pubmed:
4
4
2023
entrez:
3
4
2023
Statut:
ppublish
Résumé
Forensically relevant single nucleotide polymorphisms (SNPs) can provide valuable supplemental information to short tandem repeats (STRs) for investigative leads, and genotyping can now be streamlined using massively parallel sequencing (MPS). Dust is an attractive evidence source, as it accumulates on undisturbed surfaces, often is overlooked by perpetrators, and contains sufficient human DNA for analysis. To assess whether SNPs genotyped from indoor dust using MPS could be used to detect known household occupants, 13 households were recruited and provided buccal samples from each occupant and dust from five predefined indoor locations. Thermo Fisher Scientific Precision ID Identity and Ancestry Panels were utilized for SNP genotyping, and sequencing was completed using Illumina
Identifiants
pubmed: 37009755
doi: 10.1111/1556-4029.15246
doi:
Substances chimiques
DNA
9007-49-2
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
768-779Subventions
Organisme : North Carolina State University College of Veterinary Medicine
Informations de copyright
© 2023 The Authors. Journal of Forensic Sciences published by Wiley Periodicals LLC on behalf of American Academy of Forensic Sciences.
Références
Locard E. The analysis of dust traces. Part I. Am J Police Sci. 1930;1:276-98. https://doi.org/10.2307/1147154
Locard E, Larson DJ. The analysis of dust traces. Part II. Am J Police Sci. 1930;1:401-18. https://doi.org/10.2307/1147186
Locard E. The analysis of dust traces. Part III. Am J Police Sci. 1930;1:496-514. https://doi.org/10.2307/1147228
Barberán A, Ladau J, Leff JW, Pollard KS, Menninger HL, Dunn RR, et al. Continental-scale distributions of dust-associated bacteria and fungi. Proc Natl Acad Sci U S A. 2015;112:5756-61. https://doi.org/10.1073/pnas.1420815112
Barberán A, Dunn RR, Reich BJ, Pacifici K, Laber EB, Menninger HL, et al. The ecology of microscopic life in household dust. Proc R Soc B: Biol Sci. 2015;282:20151139. https://doi.org/10.1098/rspb.2015.1139
Craine J, Craine J, Barberán A, Barberán A, Lynch R, Lynch R, et al. Molecular analysis of environmental plant DNA in house dust across the United States. Aerobiologia. 2017;33:71-86. https://doi.org/10.1007/s10453-016-9451-5
Madden AA, Barberán A, Bertone MA, Menninger HL, Dunn RR, Fierer N. The diversity of arthropods in homes across the United States as determined by environmental DNA analyses. Mol Ecol. 2016;25:6214-24. https://doi.org/10.1111/mec.13900
Toothman MH, Kester KM, Champagne J, Cruz TD, Street WS, Brown BL. Characterization of human DNA in environmental samples. Forensic Sci Int. 2008;178:7-15. https://doi.org/10.1016/j.forsciint.2008.01.016
Bertone MA, Leong M, Bayless KM, Malow TLF, Dunn RR, Trautwein MD. Arthropods of the great indoors: characterizing diversity inside urban and suburban homes. PeerJ. 2016;4:e1582. https://doi.org/10.7717/peerj.1582
Ott CM, Bruce RJ, Pierson DL. Microbial characterization of free floating condensate aboard the Mir space station. Microb Ecol. 2004;47:133-6. https://doi.org/10.1007/s00248-003-1038-3
Çakan H, Kasım G, Çevik F, Demirci M, Kocazeybek B. Investigation of human DNA profiles in house dust mites: implications in forensic acarology. Rom J Leg Med. 2015;23:187-92. https://doi.org/10.4323/rjlm.2015.187
Farash K. Strategies for enhanced genetic analysis of trace DNA from touch DNA evidence and household dust [Dissertation]. Orlando: University of Central Florida; 2015.
Butler JM. The future of forensic DNA analysis. Philos Trans R Soc Lond B Biol Sci. 2015;370:20140252. https://doi.org/10.1098/rstb.2014.0252
Watkins DRL, Myers D, Xavier HE, Marciano MA. Revisiting single cell analysis in forensic science. Sci Rep. 2021;11:7054. https://doi.org/10.1038/s41598-021-86271-6
Budowle B, van Daal A. Forensically relevant SNP classes. Biotechniques. 2008;44:603-10. https://doi.org/10.2144/000112806
Osier MV, Cheung K-H, Kidd JR, Pakstis AJ, Miller PL, Kidd KK. ALFRED: an allele frequency database for anthropology. Am J Phys Anthropol. 2002;119:77-83. https://doi.org/10.1002/ajpa.10094
Rajeevan H, Soundararajan U, Pakstis AJ, Kidd KK. Introducing the forensic research/reference on genetics knowledge base, FROG-Kb. Investigative Genet. 2012;3:18. https://doi.org/10.1186/2041-2223-3-18
Pakstis A, Speed W, Fang R, Hyland F, Furtado M, Kidd J, et al. SNPs for a universal individual identification panel. Hum Genet. 2010;127:315-24. https://doi.org/10.1007/s00439-009-0771-1
Kidd KK, Kidd JR, Pakstis AJ, Speed WC, Grigorenko EL, Kajuna SLB, et al. Developing a SNP panel for forensic identification of individuals. Forensic Sci Int. 2006;164:20-32. https://doi.org/10.1016/j.forsciint.2005.11.017
Walsh S, Liu F, Ballantyne KN, van Oven M, Lao O, Kayser M. IrisPlex: a sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information. Forensic Sci Int Genet. 2011;5:170-80. https://doi.org/10.1016/j.fsigen.2010.02.004
Almalki N, Chow HY, Sharma V, Hart K, Siegel D, Wurmbach E. Systematic assessment of the performance of Illumina's MiSeq FGx™ forensic genomics system. Electrophoresis. 2017;38:846-54. https://doi.org/10.1002/elps.201600511
Just RS, Moreno LI, Smerick JB, Irwin JA. Performance and concordance of the ForenSeq™ system for autosomal and Y chromosome short tandem repeat sequencing of reference-type specimens. Forensic Sci Int Genet. 2017;28:1-9. https://doi.org/10.1016/j.fsigen.2017.01.001
Köcher S, Müller P, Berger B, Bodner M, Parson W, Roewer L, et al. Inter-laboratory validation study of the ForenSeq™ DNA signature prep kit. Forensic Sci Int Genet. 2018;36:77-85. https://doi.org/10.1016/j.fsigen.2018.05.007
Jäger AC, Alvarez ML, Davis CP, Guzmán E, Han Y, Way L, et al. Developmental validation of the MiSeq FGx forensic genomics system for targeted next generation sequencing in forensic DNA casework and database laboratories. Forensic Sci Int Genet. 2017;28:52-70. https://doi.org/10.1016/j.fsigen.2017.01.011
Xavier C, Parson W. Evaluation of the Illumina ForenSeq™ DNA signature prep kit - MPS forensic application for the MiSeq FGx™ benchtop sequencer. Forensic Sci Int Genet. 2017;28:188-94. https://doi.org/10.1016/j.fsigen.2017.02.018
Devesse L, Ballard D, Davenport L, Riethorst I, Mason-Buck G, Court D. Concordance of the ForenSeq™ system and characterisation of sequence-specific autosomal STR alleles across two major population groups. Forensic Sci Int Genet. 2018;34:57-61. https://doi.org/10.1016/j.fsigen.2017.10.012
Churchill JD, Schmedes SE, King JL, Budowle B. Evaluation of the Illumina® Beta version ForenSeq™ DNA signature prep kit for use in genetic profiling. Forensic Sci Int Genet. 2016;20:20-9. https://doi.org/10.1016/j.fsigen.2015.09.009
Guo F, Yu J, Zhang L, Li J. 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. 2017;31:135-48. https://doi.org/10.1016/j.fsigen.2017.09.003
Hussing C, Huber C, Bytyci R, Mogensen HS, Morling N, Børsting C. Sequencing of 231 forensic genetic markers using the MiSeq FGx™ forensic genomics system - an evaluation of the assay and software. Forensic Sci Res. 2018;3:111-23. https://doi.org/10.1080/20961790.2018.1446672
Senst A, Caliebe A, Scheurer E, Schulz I. Validation and beyond: next generation sequencing of forensic casework samples including challenging tissue samples from altered human corpses using the MiSeq FGx system. J Forensic Sci. 2022;67(4):1382-98. https://doi.org/10.1111/1556-4029.15028
Steffen CR, Huszar TI, Borsuk LA, Vallone PM, Gettings KB. A multi-dimensional evaluation of the ‘NIST 1032’ sample set across four forensic Y-STR multiplexes. Forensic Sci Int Genet. 2022;57:102655. https://doi.org/10.1016/j.fsigen.2021.102655
Frégeau CJ. Validation of the Verogen ForenSeq™ DNA signature prep kit/primer mix B for phenotypic and biogeographical ancestry predictions using the micro MiSeq® flow cells. Forensic Sci Int Genet. 2021;53:102533. https://doi.org/10.1016/j.fsigen.2021.102533
Fattorini P, Previderé C, Carboni I, Marrubini G, Sorçaburu-Cigliero S, Grignani P, et al. Performance of the ForenSeq™ DNA signature prep kit on highly degraded samples. Electrophoresis. 2017;38:1163-74. https://doi.org/10.1002/elps.201600290
Liu J, Wang Z, He G, Zhao X, Wang M, Luo T, et al. Massively parallel sequencing of 124 SNPs included in the precision ID identity panel in three east Asian minority ethnicities. Forensic Sci Int Genet. 2018;35:141-8. https://doi.org/10.1016/j.fsigen.2018.05.002
García O, Ajuriagerra JA, Alday A, Alonso S, Pérez JA, Soto A, et al. Frequencies of the precision ID ancestry panel markers in Basques using the Ion Torrent PGM™ platform. Forensic Sci Int Genet. 2017;31:e1-4. https://doi.org/10.1016/j.fsigen.2017.09.006
van der Heijden S, de Oliveira SJ, Kampmann M-L, Børsting C, Morling N. Comparison of manual and automated AmpliSeq™ workflows in the typing of a Somali population with the Precision ID Identity Panel. Forensic Sci Int Genet. 2017;31:118-25. https://doi.org/10.1016/j.fsigen.2017.09.009
Lee JH, Cho S, Kim M-Y, Shin DH, Rakha A, Shinde V, et al. Genetic resolution of Applied Biosystems™ Precision ID Ancestry Panel for seven Asian populations. Leg Med (Tokyo). 2018;34:41-7. https://doi.org/10.1016/j.legalmed.2018.08.007
Al-Asfi M, McNevin D, Mehta B, Power D, Gahan ME, Daniel R. Assessment of the Precision ID Ancestry Panel. Int J Leg Med. 2018;132:1581-94. https://doi.org/10.1007/s00414-018-1785-9
Meiklejohn KA, Robertson JM. Evaluation of the Precision ID Identity Panel for the Ion Torrent™ PGM™ sequencer. Forensic Sci Int Genet. 2017;31:48-56. https://doi.org/10.1016/j.fsigen.2017.08.009
Wang Z, He G, Luo T, Zhao X, Liu J, Wang M, et al. Massively parallel sequencing of 165 ancestry informative SNPs in two Chinese Tibetan-Burmese minority ethnicities. Forensic Sci Int Genet. 2018;34:141-7. https://doi.org/10.1016/j.fsigen.2018.02.009
Voskoboinik L, Darvasi A. Forensic identification of an individual in complex DNA mixtures. Forensic Sci Int Genet. 2011;5:428-35. https://doi.org/10.1016/j.fsigen.2010.09.002
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. https://doi.org/10.1016/j.fsigen.2014.09.003
Ricke DO. FastID: extremely fast forensic DNA comparisons. In: Proceedings of the 21st annual IEEE high performance extreme computing conference (HPEC); 2017 Sept 12-14; Waltham, MA. Piscataway, NJ: IEEE; 2017: 1-4 https://doi.org/10.1109/HPEC.2017.8091056
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. https://doi.org/10.1016/j.fsigen.2015.11.008
Hwa H-L, Chung W-C, Chen P-L, Lin C-P, Li H-Y, Yin H-I, et al. A 1204-single nucleotide polymorphism and insertion-deletion polymorphism panel for massively parallel sequencing analysis of DNA mixtures. Forensic Sci Int Genet. 2018;32:94-101. https://doi.org/10.1016/j.fsigen.2017.11.002
Ricke DO, Fremont-Smith P, Watkins J, Boettcher T, Schwoebel E. Estimating individual contributions to complex DNA SNP mixtures. bioRxiv. 2018;391086. https://doi.org/10.1101/391086
Scheible MK, Timpano EK, Boggs LM, Meiklejohn KA. An alternate workflow for preparing precision ID ancestry and identity panel libraries for Illumina sequencing. Int J Leg Med. 2021;135:1717-26. https://doi.org/10.1007/s00414-021-02549-4
Vlachos NT, Meiklejohn KA, Robertson JM. An automated independent workflow for the analysis of massively parallel sequence data from forensic SNP assays. Electrophoresis. 2018;39:2752-6. https://doi.org/10.1002/elps.201800085
Ricke DO, Watkins J, Fremont-Smith P, Michaleas A. IdPrism: rapid analysis of forensic DNA samples using MPS SNP profiles. In: Proceedings of the 23rd annual IEEE high performance extreme computing conference (HPEC); 2019 Sept 24-26; Waltham, MA. Piscataway, NJ: IEEE; 2019: 1-5 https://doi.org/10.1109/HPEC.2019.8916521
Ricke D, Schwartz S. Fast P(RMNE): fast forensic DNA probability of random man not excluded calculation [version 2; peer review: peer review discontinued]. F1000Res. 2018;6:2154. https://doi.org/10.12688/f1000research.13349.2
National Cancer Institute Division of Cancer Epidemiology & Genetics. LDlink API access. [cited 2023 Mar 20]. Available from: https://ldlink.nci.nih.gov/?tab=apiaccess
Federal Bureau of Investigation Laboratory. DNA procedures manual: Procedure for the quantification of human and male nuclear DNA. 2022 [cited 2023 Jan 18]. Available from: https://fbilabqsd.fbi.gov/file-repository/dna/casework/bio-520-00-quantification-of-human-and-male-nuclear-dna.pdf/view
New York City Office of the Chief Medical Examiner. Forensic biology protocols for forensic STR analysis: Quantifiler® Trio DNA Quantification kit. 2022 [cited 2023 Jan 18]. Available from: https://www1.nyc.gov/assets/ocme/downloads/pdf/technical-manuals/forensic-biology-technical-manuals/quantifiler_trio_quantification_062822.pdf
National Library of Medicine National Center for Biotechnology Information. dbSNP. [cited 2023 Mar 20]. Available from: https://www.ncbi.nlm.nih.gov/snp/
Fonneløp AE, Ramse M, Egeland T, Gill P. The implications of shedder status and background DNA on direct and secondary transfer in an attack scenario. Forensic Sci Int Genet. 2017;29:48-60. https://doi.org/10.1016/j.fsigen.2017.03.019
Goray M, van Oorschot RAH. Shedder status: exploring means of determination. Sci Justice. 2021;61:391-400. https://doi.org/10.1016/j.scijus.2021.03.004
Allen RW, Pogemiller J, Joslin J, Gulick M, Pritchard J. Identification through typing of DNA recovered from touch transfer evidence: parameters affecting yield of recovered human DNA. J Forensic Identif. 2008;58:33-41.
Poetsch M, Bajanowski T, Kamphausen T. Influence of an individual's age on the amount and interpretability of DNA left on touched items. Int J Leg Med. 2013;127:1093-6. https://doi.org/10.1007/s00414-013-0916-6
Manoli P, Antoniou A, Bashiardes E, Xenophontos S, Photiades M, Stribley V, et al. Sex-specific age association with primary DNA transfer. Int J Leg Med. 2016;130:103-12. https://doi.org/10.1007/s00414-015-1291-2
Petrovick MS, Boettcher T, Fremont-Smith P, Peragallo C, Ricke DO, Watkins J, et al. Analysis of complex DNA mixtures using massively parallel sequencing of SNPs with low minor allele frequencies. Forensic Sci Int Genet. 2020;46:102234. https://doi.org/10.1016/j.fsigen.2020.102234