Forensic SNP Information

[Assays] [General SNP Information] [Markers – IISNPs, AISNPs, PISNPs, Y-SNPs, mtDNA SNPs] [Typing Technologies] [Links to Other SNP Resources]

This site is intended to provide general information on single nucleotide polymorphism (SNP) markers that may be of interest in human identification applications. Many of these markers come from The SNP Consortium (TSC) efforts or are already present in the NCBI dbSNP database. To submit a SNP marker for inclusion on this forensic SNP site, please provide the requested information in a Microsoft Excel spreadsheet or a standardized SNP fact sheet (click here to download) to John Butler via email: john.butler@nist.gov.

For discussion regarding the potential role of SNPs in the future of forensic DNA typing, see

Gill, P., Werrett, D.J., Budowle, B. and Guerrieri, R. (2004) An assessment of whether SNPs will replace STRs in national DNA databases-Joint considerations of the DNA working group of the European Network of Forensic Science Institutes (ENFSI) and the Scientific Working Group on DNA Analysis Methods (SWGDAM). Science&Justice, 44(1): 51-53.

Butler, J.M., Coble, M.D., Vallone, P.M. (2007) STRs vs SNPs: thoughts on the future of forensic DNA testing. Forensic Sci. Med. Pathol. 3: 200-205.

Butler J.M., Budowle B., Gill P., Kidd K.K., Phillips C., Schneider P.M., Vallone P.M., Morling N. (2008) Report on ISFG SNP Panel Discussion. Forensic Sci Int Genet Supplement Series 1:471-472.

Update provided by the George Washington University Department of Forensic Sciences. Please send suggestions for future updates to butler_k@gwu.edu. Last Updated: 06/19/2010

Assays

35plex Y-SNP minisequencing assay - Sanchez et al. (2003) Forensic Sci. Int., 137(1):74-84

50 Y-SNPs in 8 multiplexes - Vallone and Butler (2004) J. Forensic Sci. 49(4): 723-732

11plex mtSNP minisequencing assay - Vallone et al. (2004) Int. J. Legal Med., 118: 147-157

21plex Autosomal IISNP assay - Dixon et al. (2005) Dixon, L.A. et al. (2005) Forensic Sci. Int. 154(1): 62-77 [links to individual SNP fact sheets]

29plex Y-SNP minisequencing assay – Brion et al. (2005) Electrophoresis 26: 4411-4420

52plex Autosomal IISNP assay - Sanchez et al. (2006) Electrophoresis 27(9): 1713-1724 [Supplementary material]

34plex AISNP assay – Phillips et al. (2007) Forensic Sci. Int. Genet. 1:273-280. [Supplementary material]

12plex mtSNP minisequencing assay – Nelson et al. (2007) Croat Med J. 48: 460-472.

90 Autosomal IISNPs in 2 multiplexes – Fang et al. (2009) Forensic Sci. Int. Genet. Supplement Series 2: 538-539

6plex PISNP assay for eye color - Walsh et al. (2010) Forensic Sci. Int. Genet. [In Press].

General SNP Information

Budowle, B. and van Daal, A. (2008) Forensically relevant SNP classes. Biotechniques 44(5): 603-610.

Sobrino, B., Brion, M., Carracedo, A. (2005) SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci. Int. 154(2-3):181-94.

Sobrino, B., Carracedo, A. (2005) SNP typing in forensic genetics: a review. Methods Mol. Biol. (Forensic DNA Typing Protocols) 297:107-126.

Markers

Individually Identifying SNPs

Dixon, L.A. et al. (2005) Validation of a 21-locus autosomal SNP multiplex for forensic identification purposes. Forensic Sci. Int. 154(1): 62-77.

Individual SNP Fact Sheets have been submitted for many of the FSS-selected SNP loci:

TSC 0252540 (submitted by Peter Gill) TSC 1342445 (submitted by Peter Gill)

TSC 0421768 (submitted by Peter Gill) TSC 0478751 (submitted by Peter Gill)

TSC 0320706 (submitted by Peter Gill) TSC 0155410 (submitted by Peter Gill)

TSC 0154197 (submitted by Peter Gill) TSC 0683201 (submitted by Peter Gill)

TSC 0739545 (submitted by Peter Gill) TSC 0131214 (submitted by Peter Gill)

TSC 0156245 (submitted by Peter Gill) TSC 0709016 (submitted by Peter Gill)

TSC 0078283 (submitted by Peter Gill)

Vallone, P.M., Decker, A.E., Butler, J.M. (2005) Allele frequencies for 70 autosomal SNP loci with U.S. Caucasian, African American, and Hispanic Samples. Forensic Sci. Int. 149: 279-286

Information on Orchid 70 IIM SNPs

Kidd, K.K., Pakstis, A.J., Speed, W.C., Grigorenko, E.L., Kajuna, S.L., Karoma, N.J., Kungulilo, S., Kim, J.J., Lu, R.B., Odunsi, A., Okonofua, F., Parnas, J., Schulz, L.O., Zhukova, O.V., Kidd, J.R. (2006) Developing a SNP panel for forensic identification of individuals. Forensic Sci. Int. 164(1):20-32.

Sanchez, J.J. et al. (2006) A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27(9): 1713-1724. [Supplementary material]

Information on 52 SNPs in SNPforID 52-plex assay (summarized from SNPforID website or supplied by Chris Phillips)

Pakstis, A.J., Speed, W.C., Kidd, J.R., Kidd, K.K. (2007) Candidate SNPs for a universal individual identification panel. Human Genet. 121(3-4):305-317.

Pakstis A.J., Speed W.C., Kidd J.R., Kidd K.K. (2008) SNPs for individual identification. Forensic Sci. Int. Genet. Supplement Series 1: 479-481.

Fang R., Pakstis A.J., Hyland F., Wang D., Shewale J., Kidd J.R., Kidd K.K., Furtado M.R. (2009) Multiplexed SNP detection panels for human identification. Forensic Sci. Int. Genet. Supplement Series 2: 538-539.

Ancestry Informative SNPs

Frudakis T., Venkateswarlu K., Thomas M.J., Gaskin Z., Ginjupalli S., Gunturi S., Ponnuswamy V., Natarajan S., Nachimuthu P.K. (2003) A Classifier for the SNP-Based Inference of Ancestry. J. Forensic Sci. 48(4):1-12.

Lao O., van Duijn K., Kersbergen P., de Knijff P., Kayser M. (2006) Proportioning Whole-Genome Single-Nucleotide–Polymorphism Diversity for the Identification of Geographic Population Structure and Genetic Ancestry. Am. J. Hum. Genet. 78:680-690.

Phillips C., Salas A., Sanchez J.J., Fondevila M., Gomez-Tato A., Alvarez-Dios J., Calaza M., Casares de Cal M., Ballard D., Lareu M.V., Carracedo A. (2007) Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci. Int. Genet. 1:273-280. [Supplementary material]

Halder I., Shriver M., Thomas M., Fernandez J.R., Frudakis T. (2008) A panel of Ancestry Informative Markers for Estimating Individual Biogeographical Ancestry and Admixture From Four Continents: Utility and Applications. Human Mutation 29: 648-658.

Kosoy R., Nassir R., Tian C., White P.A., Butler L.M., Silva G., Kittles R., Alarcon-Riquelme M.E., Gregersen P.K., Belmont J.W., De La Vega F.M., Seldin M.F. (2009) Ancestry Informative Marker Sets for Determining Continental Origin and Admixture Proportions in Common Populations in America. Human Mutation 30:69-78.

Halder I., Yang B.Z., Kranzler H.R., Stein M.B., Shriver M.D., Gelernter J. (2009) Measurement of admixture proportions and description of admixture structure in different U.S. populations. Human Mutation 30(9): 1299-1309. [Supplementary material]

Phenotype Informative SNPs

Branicki W., Brudnik U., Kupiec T., Wolanska-Nowak P., Wojas-Pelc A. (2007) Determination of Phenotype Associated SNPs in the MC1R Gene. J. Forensic Sci. 52(2):349-354.

Duffy D.L., Montgomery G.W., Chen W., Zhao Z.Z., Le L., James M.R., Hayward N.K., Martin N.G., Sturm R.A. (2007) A three single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation. Am. J. Hum. Genet. 80:241–252.

Sturm R.A., Duffy D.L., Zhao Z.Z., Leite F.P.N., Stark M.S., Hayward N.K., Martin N.G., Montgomery G.W. (2008) A single SNP in an evolutionary conserved region within Intron 86 of the HERC2 gene determines human blue-brown eye color. Am. J. Hum. Genet. 82:424–31.

Sturm R.A. (2009) Molecular genetics of human pigmentation diversity. Hum. Mol. Genet. 18: R9-R17.

Valenzuela R.K., Henderson M.S., Walsh M.H., Garrison N.A., Kelch J.T., Cohen-Barak O., Erickson D.T., Meaney F.J., Walsh J.B., Cheng K.C., Ito S., Wakamatsu K., Frudakis T., Thomas M., Brilliant M. (2010) Predicting Phenotype from Genotype: Normal Pigmentation. J. Forensic Sci. 55(2): 315-322.

Walsh S., Liu F., Ballantyne K.N., van Oven M., Lao O., Kayser M. (2010) IrisPlex: A sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information. Forensic Sci. Int. Genet. [In Press].

Y-Chromosome SNPs

Sanchez JJ et al. (2003) Multiplex PCR and minisequencing of SNPs—a model with 35 Y chromosome SNPs. Forensic Sci. Int., 137(1):74-84.

Information on 35plex Y-SNP minisequencing assay

Vallone, P.M. and Butler, J.M. (2004) Y-SNP typing of U.S. African American and Caucasian samples using allele-specific hybridization and primer extension. J. Forensic Sci. 49(4): 723-732.

Information on 50 Y-SNPs typed at NIST

Brion, M. et al. (2005) Introduction of an single nucleotide polymorphism-based "Major Y-chromosome haplogroup typing kit" suitable for predicting the geographical origin of male lineages. Electrophoresis 26: 4411-4420.

Information on 29 Y-SNPs useful for major Y-chromosome haplogroup determination

Bouakaze, C. et al. (2007) First successful assay of Y-SNP typing by SNaPshot minisequencing on ancient DNA. Int J Legal Med. 121: 493-499.

Mitochondrial DNA SNPs

Control region SNPs

Kline, M.C. et al. (2005) Mitochondrial DNA typing screens with control region and coding region SNPs. J. Forensic Sci. 50: 377-385.

Divne, M. et al. (2005) Forensic casework analysis using the HVI/HVII mtDNA linear array assay. J. Forensic Sci. 50(3):548-54.

Nelson, T.M. et al. (2007) Development of a Multiplex Single Base Extension Assay for Mitochondrial DNA Haplogroup Typing. Croat Med J. 48: 460-472.

Coding region SNPs

Coble, M.D. et al. (2004) Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians. Int. J. Legal Med., 118: 137-146.

Vallone, P.M. et al. (2004) A multiplex allele-specific primer extension assay for forensically informative SNPs distributed throughout the mitochondrial genome. Int. J. Legal Med., 118: 147-157.

Protocol for 11plex SNP assay developed at NIST [Genotyper macro for mtSNP 11plex]

Coble, M.D. et al. (2006) Effective strategies for forensic analysis in the mitochondrial DNA coding region. Int. J. Legal. Med. 120:27-32. [Supplementary Data]

SNP Typing Technologies

Helpful review articles on SNP typing technologies:

Sobrino, B., Brion, M., Carracedo, A. (2005) SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int. 154(2-3):181-94

Sobrino, B., Carracedo, A. (2005) SNP typing in forensic genetics: a review. Methods Mol Biol. (Forensic DNA Typing Protocols) 297:107-126

A brief summary of the following technologies will be included in the future: [COMING SOON]

Minisequencing/SNaPshot/Primer Extension assay

MALDI-TOF Mass Spectrometry with Primer Extension assay

TaqMan Real-time PCR assay

Luminex Bead Array with Allele-specific Hybridization assay

Pyrosequencing

Microarray technologies

Links to Other SNP Resources

SNPforID browser with allele frequency information: http://spsmart.cesga.es/snpforid.php

SNPforID publications: http://www.snpforid.org/publications.html

dbSNP Homepage at NCBI: http://www.ncbi.nlm.nih.gov/projects/SNP/

International HapMap Project: http://www.hapmap.org/