Skip to main content
Erschienen in: Forensic Science, Medicine and Pathology 3/2007

01.09.2007 | Original Paper

STRs vs. SNPs: thoughts on the future of forensic DNA testing

verfasst von: John M. Butler, Michael D. Coble, Peter M. Vallone

Erschienen in: Forensic Science, Medicine and Pathology | Ausgabe 3/2007

Einloggen, um Zugang zu erhalten

Abstract

Largely due to technological progress coming from the Human Genome and International HapMap Projects, the issue has been raised in recent years within the forensic DNA typing community of the potential for single nucleotide polymorphism (SNP) markers as possible replacements of the currently used short tandem repeat (STR) loci. Our human identity testing project team at the U.S. National Institute of Standards and Technology (NIST) has explored numerous SNP and STR loci and assays as well as developing miniSTRs for degraded DNA samples. Based on their power of discrimination, use in deciphering mixture components, and ability to be combined in multiplex assays in order to recover information from low amounts of biological material, we believe that STRs rather than SNPs will fulfill the dominant role in human identity testing for the foreseeable future. However, SNPs may play a useful role in specialized applications such as mitochondrial DNA (mtDNA) testing, Y-SNPs as lineage markers, ancestry informative markers (AIMs), the prediction of phenotypic traits, and other potential niche forensic casework applications.
Literatur
1.
Zurück zum Zitat Butler JM. Forensic DNA typing: Biology, technology, and genetics of STR markers. 2nd ed. New York: Elsevier; 2005. Butler JM. Forensic DNA typing: Biology, technology, and genetics of STR markers. 2nd ed. New York: Elsevier; 2005.
2.
Zurück zum Zitat Gill P. Role of short tandem repeat DNA in forensic casework in the UK – past, present, and future perspectives. BioTechniques 2002;32:366–72.PubMed Gill P. Role of short tandem repeat DNA in forensic casework in the UK – past, present, and future perspectives. BioTechniques 2002;32:366–72.PubMed
3.
Zurück zum Zitat Butler JM. Genetics and genomics of core short tandem repeat loci used in human identity testing. J Forensic Sci 2006;51:253–65.PubMedCrossRef Butler JM. Genetics and genomics of core short tandem repeat loci used in human identity testing. J Forensic Sci 2006;51:253–65.PubMedCrossRef
5.
Zurück zum Zitat International HapMap Consortium. A haplotype map of the human genome. Nature 2005;437:1229–320. International HapMap Consortium. A haplotype map of the human genome. Nature 2005;437:1229–320.
7.
Zurück zum Zitat Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR. Whole-genome patterns of common DNA variation in three human populations. Science 2005;307:1072–9.PubMedCrossRef Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR. Whole-genome patterns of common DNA variation in three human populations. Science 2005;307:1072–9.PubMedCrossRef
8.
Zurück zum Zitat Budowle B. SNP typing strategies. Forensic Sci Int 2004;S139–42. Budowle B. SNP typing strategies. Forensic Sci Int 2004;S139–42.
9.
Zurück zum Zitat Sobrino B, Brion M, Carracedo A. SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int 2005;154:181–94.PubMedCrossRef Sobrino B, Brion M, Carracedo A. SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int 2005;154:181–94.PubMedCrossRef
10.
Zurück zum Zitat Chakraborty R, Stivers DN, Su Y, Budowle B. The utility of short tandem repeat loci beyond human identification: implications for development of new DNA typing systems. Electrophoresis 1999;20:1682–96.PubMedCrossRef Chakraborty R, Stivers DN, Su Y, Budowle B. The utility of short tandem repeat loci beyond human identification: implications for development of new DNA typing systems. Electrophoresis 1999;20:1682–96.PubMedCrossRef
11.
Zurück zum Zitat Krawczak M. Informativity assessment for biallelic single nucleotide polymorphisms. Electrophoresis 1999;20:1676–81.PubMedCrossRef Krawczak M. Informativity assessment for biallelic single nucleotide polymorphisms. Electrophoresis 1999;20:1676–81.PubMedCrossRef
12.
Zurück zum Zitat Gill P. An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. Int J Legal Med 2001;114:204–10.PubMedCrossRef Gill P. An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. Int J Legal Med 2001;114:204–10.PubMedCrossRef
13.
Zurück zum Zitat Dixon LA, Dobbins AE, Pulker HK, Butler JM, Vallone PM, Coble MD, Parson W, Berger B, Grubwieser P, Mogensen HS, Morling N, Nielsen K, Sanchez JJ, Petkovski E, Carracedo A, Sanchez-Diz P, Ramos-Luis E, Brion M, Irwin JA, Just RS, Loreille O, Parsons TJ, Syndercombe-Court, Schmitter H, Stradmann-Bellinghausen B, Bender K, Gill P. Analysis of artificially degraded DNA using STRs and SNPs-results of a collaborative European (EDNAP) exercise. Forensic Sci Int 2006;164(1):33–44.PubMedCrossRef Dixon LA, Dobbins AE, Pulker HK, Butler JM, Vallone PM, Coble MD, Parson W, Berger B, Grubwieser P, Mogensen HS, Morling N, Nielsen K, Sanchez JJ, Petkovski E, Carracedo A, Sanchez-Diz P, Ramos-Luis E, Brion M, Irwin JA, Just RS, Loreille O, Parsons TJ, Syndercombe-Court, Schmitter H, Stradmann-Bellinghausen B, Bender K, Gill P. Analysis of artificially degraded DNA using STRs and SNPs-results of a collaborative European (EDNAP) exercise. Forensic Sci Int 2006;164(1):33–44.PubMedCrossRef
14.
Zurück zum Zitat Sanchez JJ, Phillips C, Borsting C, Balogh K, Bogus M, Fondevila M, Harrison CD, Musgrave-Brown E, Salas A, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N. A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 2006;27:1713–24.PubMedCrossRef Sanchez JJ, Phillips C, Borsting C, Balogh K, Bogus M, Fondevila M, Harrison CD, Musgrave-Brown E, Salas A, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N. A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 2006;27:1713–24.PubMedCrossRef
15.
Zurück zum Zitat Kidd KK, Pakstis AJ, Speed WC, Grigorenko EL, Kajuna SL, Karoma NJ, Kungulilo S, Kim JJ, Lu RB, Odunsi A, Okonofua F, Parnas J, Schulz LO, Zhukova OV, Kidd JR. Developing a SNP panel for forensic identification of individuals. Forensic Sci Int 2006;164(1):20–32.PubMedCrossRef Kidd KK, Pakstis AJ, Speed WC, Grigorenko EL, Kajuna SL, Karoma NJ, Kungulilo S, Kim JJ, Lu RB, Odunsi A, Okonofua F, Parnas J, Schulz LO, Zhukova OV, Kidd JR. Developing a SNP panel for forensic identification of individuals. Forensic Sci Int 2006;164(1):20–32.PubMedCrossRef
16.
Zurück zum Zitat Butler JM, Shen Y, McCord BR. The development of reduced size STR amplicons as tools for analysis of degraded DNA. J Forensic Sci 2003;48:1054–64.PubMed Butler JM, Shen Y, McCord BR. The development of reduced size STR amplicons as tools for analysis of degraded DNA. J Forensic Sci 2003;48:1054–64.PubMed
17.
Zurück zum Zitat Coble MD, Butler JM. Characterization of new miniSTR loci to aid analysis of degraded DNA. J Forensic Sci 2005;50:43–53.PubMedCrossRef Coble MD, Butler JM. Characterization of new miniSTR loci to aid analysis of degraded DNA. J Forensic Sci 2005;50:43–53.PubMedCrossRef
18.
Zurück zum Zitat Biesecker LG, Bailey-Wilson JE, Ballantyne J, Baum H, Bieber FR, Brenner C, Budowle B, Butler JM, Carmody G, Conneally PM, Duceman B, Eisenberg A, Forman L, Kidd KK, LeClair B, Niezgoda S, Parsons T, Pugh E, Shaler R, Sherry ST, Sozer A, Walsh A. DNA identifications after the 9/11 World Trade Center attack. Science 2005;310:1122–3.PubMedCrossRef Biesecker LG, Bailey-Wilson JE, Ballantyne J, Baum H, Bieber FR, Brenner C, Budowle B, Butler JM, Carmody G, Conneally PM, Duceman B, Eisenberg A, Forman L, Kidd KK, LeClair B, Niezgoda S, Parsons T, Pugh E, Shaler R, Sherry ST, Sozer A, Walsh A. DNA identifications after the 9/11 World Trade Center attack. Science 2005;310:1122–3.PubMedCrossRef
19.
Zurück zum Zitat Amorim A, Pereira L. Pros and cons in the use of SNPs in forensic kinship investigation: a comparative analysis with STRs. Forensic Sci Int 2005;150:17–21.PubMedCrossRef Amorim A, Pereira L. Pros and cons in the use of SNPs in forensic kinship investigation: a comparative analysis with STRs. Forensic Sci Int 2005;150:17–21.PubMedCrossRef
20.
Zurück zum Zitat Vallone PM, Decker AE, Butler JM. Allele frequencies for 70 autosomal SNP loci with U.S. Caucasian, African-American, and Hispanic samples. Forensic Sci Int 2005;149:279–86.PubMedCrossRef Vallone PM, Decker AE, Butler JM. Allele frequencies for 70 autosomal SNP loci with U.S. Caucasian, African-American, and Hispanic samples. Forensic Sci Int 2005;149:279–86.PubMedCrossRef
21.
Zurück zum Zitat Gut IG. Automation in genotyping of single nucleotide polymorphisms. Hum Mutat 2001;17:475–92.PubMedCrossRef Gut IG. Automation in genotyping of single nucleotide polymorphisms. Hum Mutat 2001;17:475–92.PubMedCrossRef
22.
Zurück zum Zitat Syvanen AC. Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet 2001;2:930–42.PubMedCrossRef Syvanen AC. Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet 2001;2:930–42.PubMedCrossRef
23.
Zurück zum Zitat Coble MD, Just RS, O’Callaghan JE, Letmanyi IH, Peterson CT, Irwin JA, Parsons TJ. Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians. Int J Legal Med 2004;118:137–46.PubMedCrossRef Coble MD, Just RS, O’Callaghan JE, Letmanyi IH, Peterson CT, Irwin JA, Parsons TJ. Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians. Int J Legal Med 2004;118:137–46.PubMedCrossRef
24.
Zurück zum Zitat Coble MD, Vallone PM, Just RS, Diegoli TM, Smith BC, Parsons TJ. Effective strategies for forensic analysis in the mitochondrial DNA coding region. Int J Legal Med 2006;120:27–32.PubMedCrossRef Coble MD, Vallone PM, Just RS, Diegoli TM, Smith BC, Parsons TJ. Effective strategies for forensic analysis in the mitochondrial DNA coding region. Int J Legal Med 2006;120:27–32.PubMedCrossRef
25.
Zurück zum Zitat Brandstatter A, Parsons TJ, Parson W. Rapid screening of mtDNA coding region SNPs for the identification of west European Caucasian haplogroups. Int J Legal Med 2003;117(5):291–8.PubMedCrossRef Brandstatter A, Parsons TJ, Parson W. Rapid screening of mtDNA coding region SNPs for the identification of west European Caucasian haplogroups. Int J Legal Med 2003;117(5):291–8.PubMedCrossRef
26.
Zurück zum Zitat Vallone PM, Just RS, Coble MD, Butler JM, Parsons TJ. A multiplex allele-specific primer extension assay for forensically informative SNPs distributed throughout the mitochondrial genome. Int J Legal Med 2004;118:147–57.PubMedCrossRef Vallone PM, Just RS, Coble MD, Butler JM, Parsons TJ. A multiplex allele-specific primer extension assay for forensically informative SNPs distributed throughout the mitochondrial genome. Int J Legal Med 2004;118:147–57.PubMedCrossRef
27.
Zurück zum Zitat Vallone PM, Butler JM. Y-SNP typing of U.S. African American and Caucasian samples using allele-specific hybridization and primer extension. J Forensic Sci 2004;49:723–32.PubMedCrossRef Vallone PM, Butler JM. Y-SNP typing of U.S. African American and Caucasian samples using allele-specific hybridization and primer extension. J Forensic Sci 2004;49:723–32.PubMedCrossRef
28.
Zurück zum Zitat Wetton JH, Tsang KW, Khan H. Inferring the population of origin of DNA evidence within the UK by allele-specific hybridization of Y-SNPs. Forensic Sci Int 2005;152:45–53.PubMedCrossRef Wetton JH, Tsang KW, Khan H. Inferring the population of origin of DNA evidence within the UK by allele-specific hybridization of Y-SNPs. Forensic Sci Int 2005;152:45–53.PubMedCrossRef
29.
Zurück zum Zitat Shriver MD, Kittles RA. Genetic ancestry and the search for personalized genetic histories. Nat Rev Genet 2004;5(8):611–8.PubMedCrossRef Shriver MD, Kittles RA. Genetic ancestry and the search for personalized genetic histories. Nat Rev Genet 2004;5(8):611–8.PubMedCrossRef
30.
Zurück zum Zitat Frudakis T, Venkateswarlu K, Thomas MJ, Gaskin Z, Ginjupalli S, Gunturi S, Ponnuswamy V, Natarajan S, Nachimuthu PK. A classifier for the SNP-based inference of ancestry. J Forensic Sci. 2003;48(4):771–82.PubMed Frudakis T, Venkateswarlu K, Thomas MJ, Gaskin Z, Ginjupalli S, Gunturi S, Ponnuswamy V, Natarajan S, Nachimuthu PK. A classifier for the SNP-based inference of ancestry. J Forensic Sci. 2003;48(4):771–82.PubMed
31.
Zurück zum Zitat Grimes EA, Noake PJ, Dixon L, Urquhart A. Sequence polymorphism in the human melanocortin 1 receptor gene as an indicator of the red hair phenotype. Forensic Sci Int 2001;122:124–9.PubMedCrossRef Grimes EA, Noake PJ, Dixon L, Urquhart A. Sequence polymorphism in the human melanocortin 1 receptor gene as an indicator of the red hair phenotype. Forensic Sci Int 2001;122:124–9.PubMedCrossRef
32.
Zurück zum Zitat Sturm RA, Frudakis TN. Eye colour: portals into pigmentation genes and ancestry. Trends Genet 2004;20(8):327–32.PubMedCrossRef Sturm RA, Frudakis TN. Eye colour: portals into pigmentation genes and ancestry. Trends Genet 2004;20(8):327–32.PubMedCrossRef
33.
Zurück zum Zitat Gill P, Werrett DJ, Budowle B, Guerrieri R. 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). Sci Justice 2004;44:51–3.PubMedCrossRef Gill P, Werrett DJ, Budowle B, Guerrieri R. 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). Sci Justice 2004;44:51–3.PubMedCrossRef
Metadaten
Titel
STRs vs. SNPs: thoughts on the future of forensic DNA testing
verfasst von
John M. Butler
Michael D. Coble
Peter M. Vallone
Publikationsdatum
01.09.2007
Verlag
Humana Press Inc
Erschienen in
Forensic Science, Medicine and Pathology / Ausgabe 3/2007
Print ISSN: 1547-769X
Elektronische ISSN: 1556-2891
DOI
https://doi.org/10.1007/s12024-007-0018-1

Weitere Artikel der Ausgabe 3/2007

Forensic Science, Medicine and Pathology 3/2007 Zur Ausgabe

Ba´alat

Báalat 6

Neu im Fachgebiet Pathologie

Molekularpathologische Untersuchungen im Wandel der Zeit

Open Access Biomarker Leitthema

Um auch an kleinen Gewebeproben zuverlässige und reproduzierbare Ergebnisse zu gewährleisten ist eine strenge Qualitätskontrolle in jedem Schritt des Arbeitsablaufs erforderlich. Eine nicht ordnungsgemäße Prüfung oder Behandlung des …

Vergleichende Pathologie in der onkologischen Forschung

Pathologie Leitthema

Die vergleichende experimentelle Pathologie („comparative experimental pathology“) ist ein Fachbereich an der Schnittstelle von Human- und Veterinärmedizin. Sie widmet sich der vergleichenden Erforschung von Gemeinsamkeiten und Unterschieden von …

Gastrointestinale Stromatumoren

Open Access GIST CME-Artikel

Gastrointestinale Stromatumoren (GIST) stellen seit über 20 Jahren ein Paradigma für die zielgerichtete Therapie mit Tyrosinkinaseinhibitoren dar. Eine elementare Voraussetzung für eine mögliche neoadjuvante oder adjuvante Behandlung bei …

Personalisierte Medizin in der Onkologie

Aufgrund des erheblichen technologischen Fortschritts in der molekularen und genetischen Diagnostik sowie zunehmender Erkenntnisse über die molekulare Pathogenese von Krankheiten hat in den letzten zwei Jahrzehnten ein grundlegender …