Single nucleotide polymorphism genotyping by mini-primer allele-specific amplification with universal reporter primers for identification of degraded DNA

Analytical Biochemistry

Volumn 386, Issue 1, 2009, Pages 85-90

  Asari, Masaru ^a   Watanabe, Satoshi ^a   Matsubara, Kazuo ^a   Shiono, Hiroshi ^a   Shimizu, Keiko ^a  

^a ASAHIKAWA MEDICAL COLLEGE   (Japan)

Author keywords

Degraded DNA; Human identification; Mini primer; Single nucleotide polymorphism; URP ASA

Indexed keywords

CAPILLARY ELECTROPHORESIS; GENES; NUCLEOTIDES; POLYMORPHISM;

DEGRADED DNA; HUMAN IDENTIFICATION; MINI-PRIMER; SINGLE NUCLEOTIDE POLYMORPHISMS; URP/ASA;

DNA;

DNA;

ALLELE; ARTICLE; CAPILLARY ELECTROPHORESIS; DNA DEGRADATION; DNA DETERMINATION; GENE AMPLIFICATION; GENE FREQUENCY; GENE LOCUS; GENOME; GENOTYPE; HUMAN; HUMAN CELL; HUMAN TISSUE; INFANT; JAPANESE; PRIORITY JOURNAL; REPORTER GENE; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 58349089235     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2008.11.023     Document Type: Article

References (24)

1. Bar W., Kratzer A., Machler M., and Schmid W. Postmortem stability of DNA. Forensic Sci. Int. 39 (1988) 59-70
2. Wandeler P., Smith S., Morin P.A., Pettifor R.A., and Funk S.M. Patterns of nuclear DNA degeneration over time: a case study in historic teeth samples. Mol. Ecol. 12 (2003) 1087-1093
3. Miething F., Hering S., Hanschke B., and Dressler J. Effect of fixation to the degradation of nuclear and mitochondrial DNA in different tissues. J. Histochem. Cytochem. 54 (2006) 371-374
4. Gilbert M.T., Haselkorn T., Bunce M., Sanchez J.J., Lucas S.B., Jewell L.D., Van Marck E., and Worobey M. The isolation of nucleic acids from fixed, paraffin-embedded tissues: which methods are useful when?. PLoS ONE 2 (2007) e537
5. Urquhart A., Kimpton C.P., Downes T.J., and Gill P. Variation in short tandem repeat sequences: a survey of 12 microsatellite loci for use as forensic identification markers. Int. J. Legal Med. 107 (1994) 13-20
6. Tracey M. Short tandem repeat-based identification of individuals and parents. Croat. Med. J. 42 (2001) 233-238
7. Butler J.M. Genetics and genomics of core short tandem repeat loci used in human identity testing. J. Forensic Sci. 51 (2006) 253-265
8. Golenberg E.M., Bickel A., and Weihs P. Effect of highly fragmented DNA on PCR. Nucleic Acids Res. 24 (1996) 5026-5033
9. Gill P. An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. Int. J. Legal Med. 114 (2001) 204-210
10. Pakstis A.J., Speed W.C., Kidd J.R., and Kidd K.K. Candidate SNPs for a universal individual identification panel. Hum. Genet. 121 (2007) 305-317
11. Inagaki S., Yamamotoa Y., Doi Y., Tomoyo T., Ishikawa T., Imabayashi K., Yoshitomea K., Miyaishia S., and Ishizu H. A new 39-plex analysis method for SNPs including 15 blood group loci. Forensic Sci. Int. 144 (2004) 45-57
12. Sanchez J.J., Phillips C., Børsting C., Balogh K., Bogus M., Fondevila M., Harrison C.D., Musgrave-Brown E., Salas A., Syndercombe-Court D., Schneider P.M., Carracedo A., and Morling N. A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27 (2006) 1713-1724
13. Walker J.A., Hedges D.J., Perodeau B.P., Landry K.E., Stoilova N., Laborde M.E., Shewale J., Sinha S.K., and Batzer M.A. Multiplex polymerase chain reaction for simultaneous quantitation of human nuclear, mitochondrial, and male Y-chromosome DNA: application in human identification. Anal. Biochem. 337 (2005) 89-97
14. Mengel-Jørgensen J., Sanchez J.J., Børsting C., Kirpekar F., and Morling N. Typing of multiple single-nucleotide polymorphisms using ribonuclease cleavage of DNA/RNA chimeric single-base extension primers and detection by MALDI-TOF mass spectrometry. Anal. Chem. 77 (2005) 5229-5235
15. Divne A.M., and Allen M. A DNA microarray system for forensic SNP analysis. Forensic Sci. Int. 154 (2005) 111-121
16. Hussain J., Gill P., Long A., Dixon L., Hinton K., Hughes J., and Tully G. Rapid preparation of SNP multiplexes utilising universal reporter primers and their detection by gel electrophoresis and microfabricated arrays. Prog. Forensic Genet. 9 (2003) 5-8
17. Ayres K.L. The expected performance of single nucleotide polymorphism loci in paternity testing. Forensic Sci. Int. 154 (2005) 167-172
18. Krenke B.E., Tereba A., Anderson S.J., Buel E., Culhane S., Finis C.J., Tomsey C.S., Zachetti J.M., Masibay A., Rabbach D.R., Amiott E.A., and Sprecher C.J. Validation of a 16-locus fluorescent multiplex system. J. Forensic Sci. 47 (2002) 773-785
19. Kim K., Kim K.Y., Jeon E., Togloom A., Cho Y.O., Lee M.S., Lkhagvasuren G., Choi J.H., Tumen D., Ja Park A., Kim K.C., Park K.W., Kim J.H., Noh M., Yoo K.J., and Lee K.H. Technical note: Improved ancient DNA purification for PCR using ion-exchange columns. Am. J. Phys. Anthropol. 136 (2008) 114-121
20. Rohland N., and Hofreiter M. Comparison and optimization of ancient DNA extraction. BioTechniques 42 (2007) 343-352
21. Müller K., Klein R., Miltner E., and Wiegand P. Improved STR typing of telogen hair root and hair shaft DNA. Electrophoresis 28 (2007) 2835-2842
22. Gill P., Whitaker J., Flaxman C., Brown N., and Buckleton J. An investigation of the rigor of interpretation rules for STRs derived from less than 100 pg of DNA. Forensic Sci. Int. 112 (2000) 17-40
23. Aşicioglu F., Oguz-Savran F., and Ozbek U. Mutation rate at commonly used forensic STR loci: paternity testing experience. Dis. Markers 20 (2004) 313-315
24. Kikuchi S., Tachi N., Nozuka M., Ninomiya T., Lpbauasjo M., Horimoto Y., Uchida E., Sasaki K., Tatsumi H., and Takeda H. DNA extraction and sequencing using PCR from formalin-fixed samples. Sapporo Igaku Zasshi 74 (2005) 39-44 (in Japanese)