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Erschienen in: International Journal of Legal Medicine 6/2006

01.11.2006 | Technical Note

Quantification of mtDNA mixtures in forensic evidence material using pyrosequencing

verfasst von: H. Andréasson, M. Nilsson, B. Budowle, S. Frisk, M. Allen

Erschienen in: International Journal of Legal Medicine | Ausgabe 6/2006

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Abstract

Analysis of mtDNA variation using Sanger sequencing does not allow accurate quantification of the components of mtDNA mixtures. An alternative method to determine the specific mixture ratios in samples displaying heteroplasmy, consisting of DNA contributions from several individuals, or containing contamination would therefore be valuable. A novel quantification system for mtDNA mixture analysis has been developed based on pyrosequencing technology, in which the linear relationship between incorporated nucleotides and released light allows quantification of the components of a sample. Within five polymerase chain reaction fragments, seven variable positions in the mtDNA control and coding region were evaluated using this quantification analysis. For all single nucleotide polymorphisms quantified in this study, a linear relationship was observed between the measured and expected mixture ratios. This mtDNA quantification assay is an easy to use, fast and accurate quantification system, with the ability to resolve and interpret major and minor mtDNA components in forensic mixture samples.
Literatur
1.
Zurück zum Zitat Clayton TM, Whitaker JP, Sparkes R, Gill P (1998) Analysis and interpretation of mixed forensic stains using DNA STR profiling. Forensic Sci Int 91:55–70PubMedCrossRef Clayton TM, Whitaker JP, Sparkes R, Gill P (1998) Analysis and interpretation of mixed forensic stains using DNA STR profiling. Forensic Sci Int 91:55–70PubMedCrossRef
2.
Zurück zum Zitat Wilson MR, Polanskey D, Butler J, DiZinno JA, Replogle J, Budowle B (1995) Extraction, PCR amplification and sequencing of mitochondrial DNA from human hair shafts. Biotechniques 18:662–669PubMed Wilson MR, Polanskey D, Butler J, DiZinno JA, Replogle J, Budowle B (1995) Extraction, PCR amplification and sequencing of mitochondrial DNA from human hair shafts. Biotechniques 18:662–669PubMed
3.
Zurück zum Zitat Allen M, Engstrom AS, Meyers S et al (1998) Mitochondrial DNA sequencing of shed hairs and saliva on robbery caps: sensitivity and matching probabilities. J Forensic Sci 43:453–464PubMed Allen M, Engstrom AS, Meyers S et al (1998) Mitochondrial DNA sequencing of shed hairs and saliva on robbery caps: sensitivity and matching probabilities. J Forensic Sci 43:453–464PubMed
4.
Zurück zum Zitat Steighner RJ, Holland M (1998) Amplification and sequencing of mitochondrial DNA in forensic casework. Methods Mol Biol 98:213–223PubMed Steighner RJ, Holland M (1998) Amplification and sequencing of mitochondrial DNA in forensic casework. Methods Mol Biol 98:213–223PubMed
5.
Zurück zum Zitat Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467PubMedCrossRef Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467PubMedCrossRef
6.
Zurück zum Zitat Calloway CD, Reynolds RL, Herrin GL Jr, Anderson WW (2000) The frequency of heteroplasmy in the HVII region of mtDNA differs across tissue types and increases with age. Am J Hum Genet 66:1384–1397PubMedCrossRef Calloway CD, Reynolds RL, Herrin GL Jr, Anderson WW (2000) The frequency of heteroplasmy in the HVII region of mtDNA differs across tissue types and increases with age. Am J Hum Genet 66:1384–1397PubMedCrossRef
7.
Zurück zum Zitat Parker LT, Zakeri H, Deng Q, Spurgeon S, Kwok PY, Nickerson DA (1996) AmpliTaq DNA polymerase, FS dye-terminator sequencing: analysis of peak height patterns. Biotechniques 21:694–699PubMed Parker LT, Zakeri H, Deng Q, Spurgeon S, Kwok PY, Nickerson DA (1996) AmpliTaq DNA polymerase, FS dye-terminator sequencing: analysis of peak height patterns. Biotechniques 21:694–699PubMed
8.
Zurück zum Zitat Parker LT, Deng Q, Zakeri H, Carlson C, Nickerson DA, Kwok PY (1995) Peak height variations in automated sequencing of PCR products using Taq dye-terminator chemistry. Biotechniques 19:116–121PubMed Parker LT, Deng Q, Zakeri H, Carlson C, Nickerson DA, Kwok PY (1995) Peak height variations in automated sequencing of PCR products using Taq dye-terminator chemistry. Biotechniques 19:116–121PubMed
9.
Zurück zum Zitat Walker JA, Garber RK, Hedges DJ, Kilroy GE, Xing J, Batzer MA (2004) Resolution of mixed human DNA samples using mitochondrial DNA sequence variants. Anal Biochem 325:171–173PubMedCrossRef Walker JA, Garber RK, Hedges DJ, Kilroy GE, Xing J, Batzer MA (2004) Resolution of mixed human DNA samples using mitochondrial DNA sequence variants. Anal Biochem 325:171–173PubMedCrossRef
10.
Zurück zum Zitat LaBerge GS, Shelton RJ, Danielson PB (2003) Forensic utility of mitochondrial DNA analysis based on denaturing high-performance liquid chromatography. Croat Med J 44:281–288PubMed LaBerge GS, Shelton RJ, Danielson PB (2003) Forensic utility of mitochondrial DNA analysis based on denaturing high-performance liquid chromatography. Croat Med J 44:281–288PubMed
11.
Zurück zum Zitat Lutz S, Weisser HJ, Heizmann J, Pollak S (2000) Mitochondrial heteroplasmy among maternally related individuals. Int J Legal Med 113:155–161PubMedCrossRef Lutz S, Weisser HJ, Heizmann J, Pollak S (2000) Mitochondrial heteroplasmy among maternally related individuals. Int J Legal Med 113:155–161PubMedCrossRef
12.
Zurück zum Zitat Lutz-Bonengel S, Sanger T, Pollak S, Szibor R (2004) Different methods to determine length heteroplasmy within the mitochondrial control region. Int J Legal Med 118:274–281PubMedCrossRef Lutz-Bonengel S, Sanger T, Pollak S, Szibor R (2004) Different methods to determine length heteroplasmy within the mitochondrial control region. Int J Legal Med 118:274–281PubMedCrossRef
13.
Zurück zum Zitat Niederstatter H, Coble MD, Grubwieser P, Parsons TJ, Parson W (2005) Characterization of mtDNA SNP typing and mixture ratio assessment with simultaneous real-time PCR quantification of both allelic states. Int J Legal Med 120:18–23PubMedCrossRef Niederstatter H, Coble MD, Grubwieser P, Parsons TJ, Parson W (2005) Characterization of mtDNA SNP typing and mixture ratio assessment with simultaneous real-time PCR quantification of both allelic states. Int J Legal Med 120:18–23PubMedCrossRef
14.
Zurück zum Zitat Gruber JD, Colligan PB, Wolford JK (2002) Estimation of single nucleotide polymorphism allele frequency in DNA pools by using pyrosequencing. Hum Genet 110:395–401PubMedCrossRef Gruber JD, Colligan PB, Wolford JK (2002) Estimation of single nucleotide polymorphism allele frequency in DNA pools by using pyrosequencing. Hum Genet 110:395–401PubMedCrossRef
15.
Zurück zum Zitat Wasson J, Skolnick G, Love-Gregory L, Permutt MA (2002) Assessing allele frequencies of single nucleotide polymorphisms in DNA pools by pyrosequencing technology. Biotechniques 32:1144–1146, 1148, 1150 passimPubMed Wasson J, Skolnick G, Love-Gregory L, Permutt MA (2002) Assessing allele frequencies of single nucleotide polymorphisms in DNA pools by pyrosequencing technology. Biotechniques 32:1144–1146, 1148, 1150 passimPubMed
16.
Zurück zum Zitat Uhlmann K, Brinckmann A, Toliat MR, Ritter H, Nurnberg P (2002) Evaluation of a potential epigenetic biomarker by quantitative methyl–single nucleotide polymorphism analysis. Electrophoresis 23:4072–4079PubMedCrossRef Uhlmann K, Brinckmann A, Toliat MR, Ritter H, Nurnberg P (2002) Evaluation of a potential epigenetic biomarker by quantitative methyl–single nucleotide polymorphism analysis. Electrophoresis 23:4072–4079PubMedCrossRef
17.
Zurück zum Zitat Soderback E, Zackrisson AL, Lindblom B, Alderborn A (2005) Determination of CYP2D6 gene copy number by pyrosequencing. Clin Chem 51:522–531PubMedCrossRef Soderback E, Zackrisson AL, Lindblom B, Alderborn A (2005) Determination of CYP2D6 gene copy number by pyrosequencing. Clin Chem 51:522–531PubMedCrossRef
18.
Zurück zum Zitat Pielberg G, Day AE, Plastow GS, Andersson L (2003) A sensitive method for detecting variation in copy numbers of duplicated genes. Genome Res 13:2171–2177PubMedCrossRef Pielberg G, Day AE, Plastow GS, Andersson L (2003) A sensitive method for detecting variation in copy numbers of duplicated genes. Genome Res 13:2171–2177PubMedCrossRef
19.
Zurück zum Zitat Sun A, Ge J, Siffert W, Frey UH (2005) Quantification of allele-specific G-protein beta3 subunit mRNA transcripts in different human cells and tissues by pyrosequencing. Eur J Hum Genet 13:361–369PubMedCrossRef Sun A, Ge J, Siffert W, Frey UH (2005) Quantification of allele-specific G-protein beta3 subunit mRNA transcripts in different human cells and tissues by pyrosequencing. Eur J Hum Genet 13:361–369PubMedCrossRef
20.
Zurück zum Zitat Andreasson H, Asp A, Alderborn A, Gyllensten U, Allen M (2002) Mitochondrial sequence analysis for forensic identification using pyrosequencing technology. Biotechniques 32:124–126, 128, 130–133PubMed Andreasson H, Asp A, Alderborn A, Gyllensten U, Allen M (2002) Mitochondrial sequence analysis for forensic identification using pyrosequencing technology. Biotechniques 32:124–126, 128, 130–133PubMed
21.
Zurück zum Zitat Miller SA, Dykes DD, Polesky HF (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 16:1215PubMed Miller SA, Dykes DD, Polesky HF (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 16:1215PubMed
22.
Zurück zum Zitat Andreasson H, Gyllensten U, Allen M (2002) Real-time DNA quantification of nuclear and mitochondrial DNA in forensic analysis. Biotechniques 33:402–404, 407–411PubMed Andreasson H, Gyllensten U, Allen M (2002) Real-time DNA quantification of nuclear and mitochondrial DNA in forensic analysis. Biotechniques 33:402–404, 407–411PubMed
23.
Zurück zum Zitat Balitzki-Korte B, Anslinger K, Bartsch C, Rolf B (2005) Species identification by means of pyrosequencing the mitochondrial 12S rRNA gene. Int J Legal Med 119:291–294PubMedCrossRef Balitzki-Korte B, Anslinger K, Bartsch C, Rolf B (2005) Species identification by means of pyrosequencing the mitochondrial 12S rRNA gene. Int J Legal Med 119:291–294PubMedCrossRef
24.
Zurück zum Zitat Budowle B, Wilson MR, DiZinno JA et al (1999) Mitochondrial DNA regions HVI and HVII population data. Forensic Sci Int 103:23–35PubMedCrossRef Budowle B, Wilson MR, DiZinno JA et al (1999) Mitochondrial DNA regions HVI and HVII population data. Forensic Sci Int 103:23–35PubMedCrossRef
25.
Zurück zum Zitat Budowle B, Allard MW, Wilson MR (2002) Critique of interpretation of high levels of heteroplasmy in the human mitochondrial DNA hypervariable region I from hair. Forensic Sci Int 126:30–33PubMedCrossRef Budowle B, Allard MW, Wilson MR (2002) Critique of interpretation of high levels of heteroplasmy in the human mitochondrial DNA hypervariable region I from hair. Forensic Sci Int 126:30–33PubMedCrossRef
26.
Zurück zum Zitat Jehaes E, Gilissen A, Cassiman JJ, Decorte R (1998) Evaluation of a decontamination protocol for hair shafts before mtDNA sequencing. Forensic Sci Int 94:65–71PubMedCrossRef Jehaes E, Gilissen A, Cassiman JJ, Decorte R (1998) Evaluation of a decontamination protocol for hair shafts before mtDNA sequencing. Forensic Sci Int 94:65–71PubMedCrossRef
27.
Zurück zum Zitat Weir BS, Triggs CM, Starling L, Stowell LI, Walsh KA, Buckleton J (1997) Interpreting DNA mixtures. J Forensic Sci 42:213–222PubMed Weir BS, Triggs CM, Starling L, Stowell LI, Walsh KA, Buckleton J (1997) Interpreting DNA mixtures. J Forensic Sci 42:213–222PubMed
Metadaten
Titel
Quantification of mtDNA mixtures in forensic evidence material using pyrosequencing
verfasst von
H. Andréasson
M. Nilsson
B. Budowle
S. Frisk
M. Allen
Publikationsdatum
01.11.2006
Verlag
Springer-Verlag
Erschienen in
International Journal of Legal Medicine / Ausgabe 6/2006
Print ISSN: 0937-9827
Elektronische ISSN: 1437-1596
DOI
https://doi.org/10.1007/s00414-005-0072-8

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