Forensic Science International: Genetics
Volume 3, Issue 2 , Pages 119-124 , March 2009

Y chromosomal STR analysis using Pyrosequencing technology

Received 26 August 2008 ,Revised 19 November 2008 ,Accepted 19 November 2008.

References 

  1. Edwards A, Civitello A, Hammond HA, Caskey CT. DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am. J. Hum. Genet. 1991;49:746–756
  2. Gill P, Kimpton CP, Urquhart A, Oldroyd N, Millican ES, Watson SK, et al. Automated short tandem repeat (STR) analysis in forensic casework—a strategy for the future. Electrophoresis. 1995;16:1543–1552
  3. Kimpton CP, Oldroyd NJ, Watson SK, Frazier RR, Johnson PE, Millican ES, et al. Validation of highly discriminating multiplex short tandem repeat amplification systems for individual identification. Electrophoresis. 1996;17:1283–1293
  4. Prinz M, Boll K, Baum H, Shaler B. Multiplexing of Y chromosome specific STRs and performance for mixed samples. Forensic Sci. Int. 1997;85:209–218
  5. Prinz M, Sansone M. Y chromosome-specific short tandem repeats in forensic casework. Croat. Med. J. 2001;42:288–291
  6. Jobling MA, Pandya A, Tyler-Smith C. The Y chromosome in forensic analysis and paternity testing. Int. J. Legal Med. 1997;110:118–124
  7. Kayser M, Caglia A, Corach D, Fretwell N, Gehrig C, Graziosi G, et al Evaluation of Y-chromosomal STRs: a multicenter study. Int. J. Legal Med. 1997;110:125–133141–129
  8. Corach D, Sala A, Penacino G, Iannucci N, Bernardi P, Doretti M, et al. Additional approaches to DNA typing of skeletal remains: the search for “missing” persons killed during the last dictatorship in Argentina. Electrophoresis. 1997;18:1608–1612
  9. Jobling MA, Tyler-Smith C. Fathers and sons: the Y chromosome and human evolution. Trends Genet. 1995;11:449–456
  10. Jobling MA, Tyler-Smith C. The human Y chromosome: an evolutionary marker comes of age. Nat. Rev. Genet. 2003;4:598–612
  11. Hall A, Ballantyne J. The development of an 18-locus Y-STR system for forensic casework. Anal. Bioanal. Chem. 2003;376:1234–1246
  12. Roewer L, Krawczak M, Willuweit S, Nagy M, Alves C, Amorim A, et al. Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes. Forensic Sci. Int. 2001;118:106–113
  13. Ayub Q, Mohyuddin A, Qamar R, Mazhar K, Zerjal T, Mehdi SQ, et al. Identification and characterisation of novel human Y-chromosomal microsatellites from sequence database information. Nucleic Acids Res. 2000;28:e8
  14. Grignani P, Peloso G, Fattorini P, Previdere C. Highly informative Y-chromosomal haplotypes by the addition of three new STRs DYS437, DYS438 and DYS439. Int. J. Legal Med. 2000;114:125–129
  15. Butler JM, Schoske R, Vallone PM, Kline MC, Redd AJ, Hammer MF. A novel multiplex for simultaneous amplification of 20 Y chromosome STR markers. Forensic Sci. Int. 2002;129:10–24
  16. Krenke BE, Viculis L, Richard ML, Prinz M, Milne SC, Ladd C, et al. Validation of a male-specific, 12-locus fluorescent short tandem repeat (STR) multiplex. Forensic Sci. Int. 2005;148:1–14
  17. Mulero JJ, Chang CW, Calandro LM, Green RL, Li Y, Johnson CL, et al. Development and validation of the AmpFlSTR Yfiler PCR amplification kit: a male specific, single amplification 17 Y-STR multiplex system. J. Forensic Sci. 2006;51:64–75
  18. Budowle B, Adamowicz M, Aranda XG, Barna C, Chakraborty R, Cheswick D, et al. Twelve short tandem repeat loci Y chromosome haplotypes: genetic analysis on populations residing in North America. Forensic Sci. Int. 2005;150:1–15
  19. Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P. Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem. 1996;242:84–89
  20. Ronaghi M, Uhlen M, Nyren P. A sequencing method based on real-time pyrophosphate. Science. 1998;281:363;365
  21. Ahmadian A, Ehn M, Hober S. Pyrosequencing: history, biochemistry and future. Clin. Chim. Acta. 2006;363:83–94
  22. Ahmadian A, Gharizadeh B, Gustafsson AC, Sterky F, Nyren P, Uhlen M, et al. Single-nucleotide polymorphism analysis by pyrosequencing. Anal. Biochem. 2000;280:103–110
  23. Nordstrom T, Ronaghi M, Forsberg L, de Faire U, Morgenstern R, Nyren P. Direct analysis of single-nucleotide polymorphism on double-stranded DNA by pyrosequencing. Biotechnol. Appl. Biochem. 2000;31(Pt 2):107–112
  24. Andreasson H, Asp A, Alderborn A, Gyllensten U, Allen M. Mitochondrial sequence analysis for forensic identification using pyrosequencing technology. Biotechniques. 2002;32:124–126128, 130-123
  25. Miller SA, Dykes DD, Polesky HF. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 1988;16:1215
  26. Walsh PS, Metzger DA, Higuchi R. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques. 1991;10:506–513
  27. Holmlund G, Nilsson H, Karlsson A, Lindblom B. Y-chromosome STR haplotypes in Sweden. Forensic Sci. Int. 2006;160:66–79
  28. Hedman M, Pimenoff V, Lukka M, Sistonen P, Sajantila A. Analysis of 16 Y STR loci in the Finnish population reveals a local reduction in the diversity of male lineages. Forensic Sci. Int. 2004;142:37–43
  29. Hallenberg C, Nielsen K, Simonsen B, Sanchez J, Morling N. Y-chromosome STR haplotypes in Danes. Forensic Sci. Int. 2005;155:205–210
  30. Schoske R, Vallone PM, Kline MC, Redman JW, Butler JM. High-throughput Y-STR typing of U.S. populations with 27 regions of the Y chromosome using two multiplex PCR assays. Forensic Sci. Int. 2004;139:107–121
  31. Carracedo A, Beckmann A, Bengs A, Brinkmann B, Caglia A, Capelli C, et al. Results of a collaborative study of the EDNAP group regarding the reproducibility and robustness of the Y-chromosome STRs DYS19, DYS389 I and II, DYS390 and DYS393 in a PCR pentaplex format. Forensic Sci. Int. 2001;119:28–41
  32. Willuweit S, Roewer L. Y chromosome haplotype reference database (YHRD): update. Forensic Sci. Int.: Genet. 2007;1:83–87
  33. Andreasson H, Gyllensten U, Allen M. Real-time DNA quantification of nuclear and mitochondrial DNA in forensic analysis. Biotechniques. 2002;33:402–404407–411
  34. Tschentscher F, Frey UH, Bajanowski T. Amelogenin sex determination by pyrosequencing of short PCR products. Int. J. Legal Med. 2008;122:333–335
  35. Butler JM, Shen Y, McCord BR. The development of reduced size STR amplicons as tools for analysis of degraded DNA. J. Forensic Sci. 2003;48:1054–1064
  36. Chung DT, Drabek J, Opel KL, Butler JM, McCord BR. A study on the effects of degradation and template concentration on the amplification efficiency of the STR Miniplex primer sets. J. Forensic Sci. 2004;49:733–740
  37. Coble MD, Butler JM. Characterization of new miniSTR loci to aid analysis of degraded DNA. J. Forensic Sci. 2005;50:43–53

PII: S1872-4973(08)00183-X

doi: 10.1016/j.fsigen.2008.11.010

Forensic Science International: Genetics
Volume 3, Issue 2 , Pages 119-124 , March 2009