Liquid chromatography-electrospray ionization mass spectrometry for simultaneous detection of mtDNA length and nucleotide polymorphisms

International Journal of Legal Medicine

Volumn 121, Issue 1, 2007, Pages 57-67

  Oberacher, Herbert ^a   Niederstätter, Harald ^a   Parson, Walther ^a  

^a INNSBRUCK MEDICAL UNIVERSITY   (Austria)

Author keywords

Electrospray ionization; Length heteroplasmy; Mass spectrometry; Mitochondrial DNA; Screening method

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; AUSTRIA; CONTROLLED STUDY; DNA DETERMINATION; DNA POLYMORPHISM; DNA SEQUENCE; ELECTROSPRAY MASS SPECTROMETRY; FEMALE; HETEROPLASMY; HUMAN; ION PAIR CHROMATOGRAPHY; POLYMERASE CHAIN REACTION; POPULATION; PRIORITY JOURNAL; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; TIME OF FLIGHT MASS SPECTROMETRY;

AUSTRIA; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; COMPLEMENTARITY DETERMINING REGIONS; DNA FINGERPRINTING; DNA, MITOCHONDRIAL; FEMALE; HUMANS; INHERITANCE PATTERNS; POLYMORPHISM, SINGLE NUCLEOTIDE; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION;

EID: 33845808671     PISSN: 09379827     EISSN: 14371596     Source Type: Journal    
DOI: 10.1007/s00414-006-0117-7     Document Type: Article

References (45)

1. Whitehouse CM, Dreyer RN, Yamashita M, Fenn JB (1985) Electrospray interface for liquid chromatographs and mass spectrometers. Anal Chem 57:675-679
2. Karas M, Hillenkamp F (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 60:2299-2301
3. Butler JM, Devaney JM, Marino MA, Vallone PM (2001) Quality control of PCR primers used in multiplex STR amplification reactions. Forensic Sci Int 119:87-96
4. Fountain KJ, Gilar M, Gebler JC (2004) Electrospray ionization mass spectrometric analysis of nucleic acids using high-throughput on-line desalting. Rapid Commun Mass Spectrom 18:1295-1302
5. Oberacher H, Niederstätter H, Parson W (2005) Characterization of synthetic nucleic acids by electrospray ionization quadrupole time-of-flight mass spectrometry. J Mass Spectrom 40:932-945
6. Butler JM, Li J, Shaler TA, Monforte JA, Becker CH (1998) Reliable genotyping of short tandem repeat loci without an allelic ladder using time-of-flight mass spectrometry. Int J Legal Med 112:45-49
7. Butler JM, Levin BC (1998) Forensic applications of mitochondrial DNA. Trends Biotechnol 16:158-162
8. Oberacher H, Parson W, Mühlmann R, Huber CG (2001) Analysis of polymerase chain reaction products by on-line liquid chromatography-mass spectrometry for genotyping of polymorphic short tandem repeat loci. Anal Chem 73:5109-5115
9. Null AP, Muddiman DC (2001) Perspectives on the use of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for short tandem repeat genotyping in the post-genome era. J Mass Spectrom 36:589-606
10. Null AP, Hannis JC, Muddiman DC (2001) Genotyping of simple and compound short tandem repeat loci using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem 73:4514-4521
11. Hannis JC, Muddiman DC (2001) Genotyping short tandem repeats using flow injection and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun Mass Spectrom 15:348-350
12. Oberacher H, Oefner PJ, Parson W, Huber CG (2001) On-line liquid chromatography mass spectrometry: a useful tool for the detection of DNA sequence variation. Angew Chem Int Ed Engl 40:3828-3830
13. Pusch W, Wurmbach JH, Thiele H, Kostrzewa M (2002) MALDITOF mass spectrometry-based SNP genotyping. Pharmacogenomics 3:537-548
14. Tost J, Gut IG (2002) Genotyping single nucleotide polymorphisms by mass spectrometry. Mass Spectrom Rev 21:388-418
15. Berger B, Hölzl G, Oberacher H, Niederstätter H, Huber CG, Parson W (2002) Single nucleotide polymorphism genotyping by on-line liquid chromatography-mass spectrometry in forensic science with the Y-chromosomal locus M9. J Chromatogr B Analyt Technol Biomed Life Sci 782:89-97
16. Oberacher H, Oefner PJ, Hölzl G, Premstaller A, Huber CG (2002) Re-sequencing of multiple single nucleotide polymorphisms by liquid chromatography-electrospray ionization mass spectrometry. Nucleic Acids Res 30:e67
17. Oberacher H, Huber CG, Oefner PJ (2003) Mutation scanning by ion-pair reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry (ICEMS). Hum Mutat 21:86-95
18. Van Ert MN, Hofstadler SA, Jiang Y et al (2004) Mass spectrometry provides accurate characterization of two genetic marker types in Bacillus anthracis. Biotechniques 37:642-648
19. Oberacher H, Niederstätter H, Casetta B, Parson W (2005) Detection of DNA sequence variations in homo- and heterozygous samples via molecular mass measurements by electrospray ionization time-of-flight mass spectrometry. Anal Chem 77:4999-5008
20. Hall TA, Budowle B, Jiang Y et al (2005) Base composition analysis of human mitochondrial DNA using electrospray ionization mass spectrometry: a novel tool for the identification and differentiation of humans. Anal Biochem 344:53-69
21. Fei Z, Ono T, Smith LM (1998) MALDI-TOF mass spectrometric typing of single nucleotide polymorphisms with mass-tagged ddNTPs. Nucleic Acids Res 26:2827-2828
22. Shahgholi M, Garcia BA, Chiu NH, Heaney PJ, Tang K (2001) Sugar additives for MALDI matrices improve signal allowing the smallest nucleotide change (A:T) in a DNA sequence to be resolved. Nucleic Acids Res 29:e91
23. Mengel-Jorgensen J, Sanchez JJ, Borsting C, Kirpekar F, Morling N (2004) MALDI-TOF mass spectrometric detection of multiplex single base extended primers. A study of 17 Y-chromosome single-nucleotide polymorphisms. Anal Chem 76:6039-6045
24. Graber JH, Smith CL, Cantor CR (1999) Differential sequencing with mass spectrometry. Genet Anal 14:215-219
25. Jurinke C, Oeth P, van den Boom D (2004) MALDI-TOF mass spectrometry: a versatile tool for high-performance DNA analysis. Mol Biotechnol 26:147-164
26. Muddiman DC, Anderson GA, Hofstadler SA, Smith RD (1997) Length and base composition of PCR-amplified nucleic acids using mass measurements from electrospray ionization mass spectrometry. Anal Chem 69:1543-1549
27. Null AP, George LT, Muddiman DC (2002) Evaluation of sample preparation techniques for mass measurements of PCR products using ESI-FT-ICR mass spectrometry. J Am Soc Mass Spectrom 13:338-344
28. Oberacher H, Parson W, Hölzl G, Oefner PJ, Huber CG (2004) Optimized suppression of adducts in polymerase chain reaction products for semi-quantitative SNP genotyping by liquid chromatography-mass spectrometry. J Am Soc Mass Spectrom 15:1897-1906
29. Stults JT, Marsters JC (1991) Improved electrospray ionization of synthetic oligodeoxynucleotides. Rapid Commun Mass Spectrom 5:359-363
30. Portier N, Van Dorsselaer A, Cordier Y, Roch O, Bischoff R (1994) Negative electrospray ionization mass spectrometry of synthetic and chemically modified oligonucleotides. Nucleic Acids Res 22:3895-3903
31. Walters JJ, Muhammad W, Fox KF et al (2001) Genotyping single nucleotide polymorphisms using intact polymerase chain reaction products by electrospray quadrupole mass spectrometry. Rapid Commun Mass Spectrom 15:1752-1759
32. Gilar M, Belenky A, Wang BH (2001) High-throughput biopolymer desalting by solid-phase extraction prior to mass spectrometric analysis. J Chromatogr A 921:3-13
33. Jiang Y, Hofstadler SA (2003) A highly efficient and automated method of purifying and desalting PCR products for analysis by electrospray ionization mass spectrometry. Anal Biochem 316:50-57
34. Huber CG, Buchmeiser MR (1998) On-line cation-exchange for suppression of adduct formation in negative-ion electrospray mass spectrometry of nucleic acids. Anal Chem 70:5288-5295
35. Bendall KE, Sykes BC (1995) Length heteroplasmy in the first hypervariable segment of the human mtDNA control region. Am J Hum Genet 57:248-256
36. Hauswirth WW, Clayton DA (1985) Length heterogeneity of a conserved displacement-loop sequence in human mitochondrial DNA. Nucleic Acids Res 13:8093-8104
37. Brandstätter A, Niederstätter H, Parson W (2004) Monitoring the inheritance of heteroplasmy by computer-assisted detection of mixed basecalls in the entire human mitochondrial DNA control region. Int J Legal Med 118:47-54
38. Köchl S, Niederstätter H, Parson W (2005) DNA extraction and quantitation of forensic samples using the phenol-chloroform method and real-time PCR. In: Carracedo A (ed) Forensic DNA typing protocols (methods in molecular biology). Humana, Totowa, pp 13-29
39. Premstaller A, Oberacher H, Huber CG (2000) High-performance liquid chromatography-electrospray ionization mass spectrometry of single- and double stranded nucleic acids using monolithic capillary columns. Anal Chem 72:4386-4393
40. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23:147
41. Pfeiffer H, Brinkmann B, Hühne J et al (1999) Expanding the forensic German mitochondrial DNA control region database: genetic diversity as a function of sample size and microgeography. Int J Legal Med 112:291-298
42. Tagliabracci A, Turchi C, Buscemi L, Sassaroli C (2001) Polymorphism of the mitochondrial DNA control region in Italians. Int J Legal Med 114:224-228
43. Zupanic Pajnic I, Balazic J, Komel R (2004) Sequence polymorphism of the mitochondrial DNA control region in the Slovenian population. Int J Legal Med 118:1-4
44. Vanecek T, Vorel F, Sip M (2004) Mitochondrial DNA D-loop hypervariable regions: Czech population data. Int J Legal Med 118:14-18
45. 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 118:274-281