A multiple predictive tool approach for phenotypic and biogeographical ancestry inferences

References

• https://www.rcmp-grc.gc.ca/cc-afn/index-eng.htm
   Google Scholar
• Phillips C, Prieto L, Fondevila M, et al. Ancestry analysis in the 11-M Madrid bomb attack investigation. PLoS One. 2009;4(8):e6583.
   PubMed Web of Science ®Google Scholar
• Murphy E. Legal and ethical issues in forensic DNA phenotyping, NYU school of law. Public Law Research Paper No. 13–46; 2013;6–7. https://doi.org/http://dx.doi.org/10.2139/ssrn.2288204
   Google Scholar
• Gannett L. Biogeographical ancestry and race. Stud Hist Philos Biol Biomed Sci. 2014;47:173–184.
   PubMedGoogle Scholar
• Phillips C. Forensic genetic analysis of bio-geographical ancestry. Forensic Sci Int Genet. 2015;18:49–65.
   PubMed Web of Science ®Google Scholar
• Kayser M. Forensic DNA phenotyping: predicting human appearance from crime scene material for investigative purposes. Forensic Sci Int Genet. 2015;18:33–48.
   PubMed Web of Science ®Google Scholar
• Ambers A, Bus MM, King JL, et al. Forensic genetic investigation of human skeletal remains recovered from the La Belle shipwreck. Forensic Sci Int. 2020;306:110050.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• ForenSeqTM DNA Signature Prep Reference Guide. From VEROGEN Document #VD2018005 Rev A. 2018.
   Google Scholar
• Xavier C, de la Puente M, Mosquera-Miguel A, et al. Development and validation of the VISAGE AmpliSeq basic tool to predict appearance and ancestry from DNA. Forensic Sci Int Genet. 2020;48:102336.
   PubMed Web of Science ®Google Scholar
• Palencia-Madrid L, Xavier C, de la Puente M, et al. Evaluation of the VISAGE basic tool for appearance and ancestry prediction using PowerSeq Chemistry on the MiSeq FGx System. Genes. 2020;11(6):708.
   Web of Science ®Google Scholar
• https://hirisplex.erasmusmc.nl/
   Google Scholar
• HIrisPlex-S DNA Phenotyping Webtool User Manual Version 2.0. © of the department of genetic identification of Erasmus MC. Rotterdam: The Netherlands; 2018.
   Google Scholar
• http://mathgene.usc.es/snipper/
   Google Scholar
• Phillips C, Salas A, Sánchez JJ, SNPforID Consortium, et al. Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci Int Genet. 2007;1(3–4):273–280.
   PubMed Web of Science ®Google Scholar
• https://frog.med.yale.edu/
   Google Scholar
• Rajeevan H, Soundararajan U, Pakstis AJ, et al. Introducing the forensic research/reference on genetics knowledge base, FROG-kb. Investig Genet. 2012;3(1):18.
   PubMedGoogle Scholar
• Kidd KK, Soundararajan U, Rajeevan H, et al. The redesigned forensic research/reference on genetics-knowledge base, FROG-kb. Forensic Sci Int Genet. 2018;33:33–37.
   PubMed Web of Science ®Google Scholar
• Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155(2):945–959.
   PubMed Web of Science ®Google Scholar
• Porras-Hurtado L, Ruiz Y, Santos C, et al. An overview of STRUCTURE: applications, parameter settings, and supporting software. Front Genet. 2013;4:1–13.
   Google Scholar
• https://www12.statcan.gc.ca/census-recensement/2016/dp-pd/dv-vd/imm/index-eng.cfm
   Google Scholar
• ForenSeq™ Universal Analysis Software Guide. From VEROGEN Document # VD2018007 Rev A. 2018.
   Google Scholar
• Walsh S, Liu F, Wollstein A, et al. The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA. Forensic Sci Int Genet. 2013;7(1):98–115.
   PubMed Web of Science ®Google Scholar
• Walsh S, Chaitanya L, Clarisse L, et al. Developmental validation of the HIrisPlex system: DNA-based eye and hair colour prediction for forensic and anthropological usage. Forensic Sci Int Genet. 2014;9:150–161.
   PubMed Web of Science ®Google Scholar
• Frégeau CJ, Dalpé C. Simulated radioactive decontamination of biological samples using a portable DNA extraction instrument for rapid DNA profiling. Forensic Sci Int. 2016;259:161–178.
   PubMed Web of Science ®Google Scholar
• Frégeau CJ, Laurin N. The Qiagen Investigator® Quantiplex HYres as an alternative kit for DNA quantification. Forensic Sci Int Genet. 2015;16:148–162.
   PubMed Web of Science ®Google Scholar
• QIAGEN Investigator® Quantiplex HYres Handbook. From QIAGEN. Germany: Hilden; 2012 (Version dated March 2012).
   Google Scholar
• Kidd KK, Speed WC, Pakstis AJ, et al. Progress toward an efficient panel of SNPs for ancestry inference. Forensic Sci Int Genet. 2014;10:23–32.
   PubMed Web of Science ®Google Scholar
• MiSeq FGx™ Instrument Reference Guide. From VEROGEN Document #VD2018006 Rev A. 2018.
   Google Scholar
• Technical Note: Introducing the MiSeq FGx™ Reagent Micro Kit for Forensic Applications. © 2018 Verogen Inc. Publication No. VD2018016. 2018.
   Google Scholar
• Liu F, van Duijn K, Vingerling JR, et al. Eye color and the prediction of complex phenotypes from genotypes. Curr Biol. 2009;19(5):R192–R193.
   PubMed Web of Science ®Google Scholar
• Walsh S, Liu F, Ballantyne KN, et al. 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(3):170–180.
   PubMed Web of Science ®Google Scholar
• Branicki W, Liu F, van Duijn K, et al. Model-based prediction of human hair color using DNA variants. Hum Genet. 2011;129(4):443–454.
   PubMed Web of Science ®Google Scholar
• Ruiz Y, Phillips C, Gómez-Tato A, et al. Further development of forensic eye color predictive tests. Forensic Sci Int Genet. 2013;7(1):28–40.
   PubMed Web of Science ®Google Scholar
• Freire-Aradas A, Ruiz Y, Phillips C, et al. Exploring iris colour prediction and ancestry inference in admixed populations of South America. Forensic Sci Int Genet. 2014;13:3–9.
   PubMed Web of Science ®Google Scholar
• Walsh S, Lindenbergh A, Zuniga SB, et al. Developmental validation of the IrisPlex system: determination of blue and brown iris colour for forensic intelligence. Forensic Sci Int Genet. 2011;5(5):464–471.
   PubMed Web of Science ®Google Scholar
• Pakstis AJ, Gurkan C, Dogan M, et al. Genetic relationships of European, Mediterranean, and SW Asian populations using a panel of 55 AISNPs. Eur J Hum Genet. 2019;27(12):1885–1893.
   PubMed Web of Science ®Google Scholar
• http://biology-assets.anu.edu.au/GenAlEx/Welcome.html
   Google Scholar
• Peakall R, Smouse PE. GenAlEx 6.5: genetic analysis in excel. Population genetic software for teaching and research-an update. Bioinformatics. 2012;28(19):2537–2539.
   PubMed Web of Science ®Google Scholar
• http://clumpak.tau.ac.il
   Google Scholar
• Kopelman NM, Mayzel J, Jakobsson M, et al. Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Resour. 2015;15(5):1179–1191.
   PubMed Web of Science ®Google Scholar
• Walsh S, Wollstein A, Liu F, et al. DNA-based eye colour prediction across Europe with the IrisPlex system. Forensic Sci Int Genet. 2012;6(3):330–340.
   PubMed Web of Science ®Google Scholar
• Bulbul O, Zorlu T, Filoglu G. Prediction of human eye colour using highly informative phenotype SNPs (PISNPs). Australian J Forensic Sci. 2020;52(1):27–37.
   Web of Science ®Google Scholar
• Yun L, Gu Y, Rajeevan H, et al. Application of six IrisPlex SNPs and comparison of two eye color prediction systems in diverse Eurasia populations. Int J Legal Med. 2014;128(3):447–453.
   PubMed Web of Science ®Google Scholar
• https://www12.statcan.gc.ca/census-recensement/2016/dp-pd/abpopprof/infogrph/infgrph.cfm?LANG=E&DGUID=2016A000011124&PR=01
   Google Scholar
• Butler Gettings K, Lai R, Johnson JL, et al. A 50-SNP assay for biogeographical ancestry and phenotype prediction in the U.S. population. Forensic Sci Int Genet. 2014;8(1):101–108.
   PubMed Web of Science ®Google Scholar
• Kastelic V, Pośpiech E, Draus-Barini J, et al. Prediction of eye color in the Slovenian population using the IrisPlex SNPs. Croat Med J. 2013;54(4):381–386.
   PubMed Web of Science ®Google Scholar
• Junker K, Staadig A, Sidstedt M, et al. Phenotype prediction accuracy – a Swedish perspective. Forensic Sci Int Genet Suppl Ser. 2019;7(1):384–386.
   Web of Science ®Google Scholar
• Meyer OS, Børsting C, Andersen JD. Perception of blue and brown eye colours for forensic DNA phenotyping. Forensic Sci Int Genet Suppl Ser. 2019;7(1):476–477.
   Web of Science ®Google Scholar
• Kukla-Bartoszek M, Pośpiech E, Spólnicka M, et al. Investigating the impact of age-depended hair colour darkening during childhood on DNA-based hair colour prediction with the HIrisPlex system . Forensic Sci Int Genet. 2018;36:26–33.
   PubMed Web of Science ®Google Scholar
• Bulbul O, Filoglu G, Zorlu T, et al. Inference of biogeographical ancestry across central regions of Eurasia. Int J Legal Med. 2016;130(1):73–79.
   PubMed Web of Science ®Google Scholar
• Bulbul O, Cherni L, Khodjet-el-Khil H, et al. Evaluating a subset of ancestry informative SNPs for discriminating among Southwest Asian and circum-Mediterranean populations. Forensic Sci Int Genet. 2016;23:153–158.
   PubMed Web of Science ®Google Scholar
• Bulbul O, Speed WC, Gurkan C, et al. Improving ancestry distinctions among Southwest Asian populations. Forensic Sci Int Genet. 2018;35:14–20.
   PubMed Web of Science ®Google Scholar
• Phillips C, McNevin D, Kidd KK, et al. MAPlex – A massively parallel sequencing ancestry analysis multiplex for Asia-Pacific populations. Forensic Sci Int Genet. 2019;42:213–226.
   PubMed Web of Science ®Google Scholar
• Sharma V, Jani K, Khosla P, et al. Evaluation of ForenSeq™ Signature Prep Kit B on predicting eye and hair coloration as well as biogeographical ancestry by using Universal Analysis Software (UAS) and available web-tools. Electrophoresis. 2019;40(9):1353–1364.
   PubMed Web of Science ®Google Scholar
• Cheung EYY, Gahan ME, McNevin D. Prediction of biogeographical ancestry in admixed individuals. Forensic Sci Int Genet. 2018;36:104–111.
   PubMed Web of Science ®Google Scholar
• Lawson DJ, van Dorp L, Falush D. A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots. Nat Commun. 2018;9(1):3258.
   PubMedGoogle Scholar
• Cheung EYY, Gahan ME, McNevin D. Predictive DNA analysis for biogeographical ancestry. Aust J Forensic Sci. 2018;50:1–658.
   Web of Science ®Google Scholar
• McNevin D, Santos C, Gómez-Tato A, et al. An assessment of Bayesian and multinomial logistic regression classification systems to analyse admixed individuals. Forensic Sci Int Genet Suppl Ser. 2013;4(1):e63–e64.
   Google Scholar
• Prestes PR, Mitchell RJ, Santos C, et al. The SNPforID 34-plex—Its ability to infer level of admixture in individuals. Forensic Sci Int Genet Suppl Ser. 2013;4(1):e13–e14.
   Google Scholar
• Liu Y, Nyunoya T, Leng S, et al. Softwares and methods for estimating genetic ancestry in human populations. Hum Genomics. 2013;7:1.
   PubMed Web of Science ®Google Scholar
• Pereira R, Phillips C, Pinto N, et al. Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing. PLoS One. . 2012;7(1):e29684.
   PubMed Web of Science ®Google Scholar
• Guo Y-X, Jin X-Y, Xia Z-Y, et al. A small NGS-SNP panel of ancestry inference designed to distinguish African, European, East, and South Asian populations. Electrophoresis. 2020;41(9):649–656.
   PubMed Web of Science ®Google Scholar
• Pereira V, Mogensen HS, Børsting C, et al. Evaluation of the precision ID ancestry panel for crime case work: a SNP typing assay developed for typing of 165 ancestral informative markers. Forensic Sci Int Genet. 2017;28:138–145.
   PubMed Web of Science ®Google Scholar
• Jin S, Chase M, Henry M, et al. Implementing a biogeographic ancestry inference service for forensic casework. Electrophoresis. 2018;39(21):2757–2765.
   PubMed Web of Science ®Google Scholar
• De la Puente M, Santos C, Fondevila M, EUROFORGEN-NoE Consortium, et al. The Global AIMs Nano set: a 31-plex SNaPshot assay of ancestry-informative SNPs. Forensic Sci Int Genet. 2016;22:81–88.
   PubMed Web of Science ®Google Scholar
• Phillips C, Parson W, Lundsberg B, EUROFORGEN-NoE Consortium, et al. Building a forensic ancestry panel from the ground up: the EUROFORGEN Global AIM-SNP set. Forensic Sci Int Genet. 2014;11:13–25.
   PubMed Web of Science ®Google Scholar
• Wang S, Lewis CM, JrJakobsson M, et al. Genetic variation and population structure in Native Americans. PLoS Genet. 2007;3(11):e185.
   PubMed Web of Science ®Google Scholar
• Ramani A, Wong Y, Zhen Tan S, et al. Ancestry prediction in Singapore population samples using the Illumina ForenSeq kit. Forensic Sci Int Genet. 2017;31:171–179.
   PubMed Web of Science ®Google Scholar