Y chromosomal STR analysis using Pyrosequencing technology

Forensic Science International: Genetics

Volumn 3, Issue 2, 2009, Pages 119-124

  Edlund, Hanna ^a   Allen, Marie ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Forensic identification; Pyrosequencing; Y chromosome STR

Indexed keywords

ARTICLE; CHROMOSOME ANALYSIS; CONTROLLED STUDY; DNA DETERMINATION; FEMALE; FORENSIC GENETICS; FORENSIC IDENTIFICATION; GENETIC MARKER; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; MALE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PYROSEQUENCING; SEQUENCE ANALYSIS; SHORT TANDEM REPEAT; Y CHROMOSOME;

ALLELES; CHROMOSOMES, HUMAN, Y; DNA; DNA FINGERPRINTING; DNA PRIMERS; FORENSIC GENETICS; GENE FREQUENCY; GENETIC MARKERS; GENETIC VARIATION; HAPLOTYPES; HUMANS; MALE; MICROSATELLITE REPEATS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SWEDEN;

EID: 59649104925     PISSN: 18724973     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fsigen.2008.11.010     Document Type: Article

References (37)

1. Edwards A., Civitello A., Hammond H.A., and Caskey C.T. DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am. J. Hum. Genet. 49 (1991) 746-756
2. Gill P., Kimpton C.P., Urquhart A., Oldroyd N., Millican E.S., Watson S.K., and Downes T.J. Automated short tandem repeat (STR) analysis in forensic casework-a strategy for the future. Electrophoresis 16 (1995) 1543-1552
3. Kimpton C.P., Oldroyd N.J., Watson S.K., Frazier R.R., Johnson P.E., Millican E.S., Urquhart A., Sparkes B.L., and Gill P. Validation of highly discriminating multiplex short tandem repeat amplification systems for individual identification. Electrophoresis 17 (1996) 1283-1293
4. Prinz M., Boll K., Baum H., and Shaler B. Multiplexing of Y chromosome specific STRs and performance for mixed samples. Forensic Sci. Int. 85 (1997) 209-218
5. Prinz M., and Sansone M. Y chromosome-specific short tandem repeats in forensic casework. Croat. Med. J. 42 (2001) 288-291
6. Jobling M.A., Pandya A., and Tyler-Smith C. The Y chromosome in forensic analysis and paternity testing. Int. J. Legal Med. 110 (1997) 118-124
7. Kayser M., Caglia A., Corach D., Fretwell N., Gehrig C., Graziosi G., Heidorn F., Herrmann S., Herzog B., Hidding M., Honda K., Jobling M., Krawczak M., Leim K., Meuser S., Meyer E., Oesterreich W., Pandya A., Parson W., Penacino G., Perez-Lezaun A., Piccinini A., Prinz M., Schmitt C., Roewer L., et al. Evaluation of Y-chromosomal STRs: a multicenter study. Int. J. Legal Med. 110 (1997) 125-133 141-129
8. Corach D., Sala A., Penacino G., Iannucci N., Bernardi P., Doretti M., Fondebrider L., Ginarte A., Inchaurregui A., Somigliana C., Turner S., and Hagelberg E. Additional approaches to DNA typing of skeletal remains: the search for "missing" persons killed during the last dictatorship in Argentina. Electrophoresis 18 (1997) 1608-1612
9. Jobling M.A., and Tyler-Smith C. Fathers and sons: the Y chromosome and human evolution. Trends Genet. 11 (1995) 449-456
10. Jobling M.A., and Tyler-Smith C. The human Y chromosome: an evolutionary marker comes of age. Nat. Rev. Genet. 4 (2003) 598-612
11. Hall A., and Ballantyne J. The development of an 18-locus Y-STR system for forensic casework. Anal. Bioanal. Chem. 376 (2003) 1234-1246
12. Roewer L., Krawczak M., Willuweit S., Nagy M., Alves C., Amorim A., Anslinger K., Augustin C., Betz A., Bosch E., Caglia A., Carracedo A., Corach D., Dekairelle A.F., Dobosz T., Dupuy B.M., Furedi S., Gehrig C., Gusmao L., Henke J., Henke L., Hidding M., Hohoff C., Hoste B., Jobling M.A., Kargel H.J., de Knijff P., Lessig R., Liebeherr E., Lorente M., Martinez-Jarreta B., Nievas P., Nowak M., Parson W., Pascali V.L., Penacino G., Ploski R., Rolf B., Sala A., Schmidt U., Schmitt C., Schneider P.M., Szibor R., Teifel-Greding J., and Kayser M. Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes. Forensic Sci. Int. 118 (2001) 106-113
13. Ayub Q., Mohyuddin A., Qamar R., Mazhar K., Zerjal T., Mehdi S.Q., and Tyler-Smith C. Identification and characterisation of novel human Y-chromosomal microsatellites from sequence database information. Nucleic Acids Res. 28 (2000) e8
14. Grignani P., Peloso G., Fattorini P., and Previdere C. Highly informative Y-chromosomal haplotypes by the addition of three new STRs DYS437, DYS438 and DYS439. Int. J. Legal Med. 114 (2000) 125-129
15. Butler J.M., Schoske R., Vallone P.M., Kline M.C., Redd A.J., and Hammer M.F. A novel multiplex for simultaneous amplification of 20 Y chromosome STR markers. Forensic Sci. Int. 129 (2002) 10-24
16. Krenke B.E., Viculis L., Richard M.L., Prinz M., Milne S.C., Ladd C., Gross A.M., Gornall T., Frappier J.R., Eisenberg A.J., Barna C., Aranda X.G., Adamowicz M.S., and Budowle B. Validation of a male-specific, 12-locus fluorescent short tandem repeat (STR) multiplex. Forensic Sci. Int. 148 (2005) 1-14
17. Mulero J.J., Chang C.W., Calandro L.M., Green R.L., Li Y., Johnson C.L., and Hennessy L.K. Development and validation of the AmpFlSTR Yfiler PCR amplification kit: a male specific, single amplification 17 Y-STR multiplex system. J. Forensic Sci. 51 (2006) 64-75
18. Budowle B., Adamowicz M., Aranda X.G., Barna C., Chakraborty R., Cheswick D., Dafoe B., Eisenberg A., Frappier R., Gross A.M., Ladd C., Lee H.S., Milne S.C., Meyers C., Prinz M., Richard M.L., Saldanha G., Tierney A.A., Viculis L., and Krenke B.E. Twelve short tandem repeat loci Y chromosome haplotypes: genetic analysis on populations residing in North America. Forensic Sci. Int. 150 (2005) 1-15
19. Ronaghi M., Karamohamed S., Pettersson B., Uhlen M., and Nyren P. Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem. 242 (1996) 84-89
20. Ronaghi M., Uhlen M., and Nyren P. A sequencing method based on real-time pyrophosphate. Science 281 (1998) 363 365
21. Ahmadian A., Ehn M., and Hober S. Pyrosequencing: history, biochemistry and future. Clin. Chim. Acta 363 (2006) 83-94
22. Ahmadian A., Gharizadeh B., Gustafsson A.C., Sterky F., Nyren P., Uhlen M., and Lundeberg J. Single-nucleotide polymorphism analysis by pyrosequencing. Anal. Biochem. 280 (2000) 103-110
23. Nordstrom T., Ronaghi M., Forsberg L., de Faire U., Morgenstern R., and Nyren P. Direct analysis of single-nucleotide polymorphism on double-stranded DNA by pyrosequencing. Biotechnol. Appl. Biochem. 31 Pt 2 (2000) 107-112
24. Andreasson H., Asp A., Alderborn A., Gyllensten U., and Allen M. Mitochondrial sequence analysis for forensic identification using pyrosequencing technology. Biotechniques 32 (2002) 124-126 128, 130-123
25. Miller S.A., Dykes D.D., and Polesky H.F. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16 (1988) 1215
26. Walsh P.S., Metzger D.A., and Higuchi R. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10 (1991) 506-513
27. Holmlund G., Nilsson H., Karlsson A., and Lindblom B. Y-chromosome STR haplotypes in Sweden. Forensic Sci. Int. 160 (2006) 66-79
28. Hedman M., Pimenoff V., Lukka M., Sistonen P., and 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. 142 (2004) 37-43
29. Hallenberg C., Nielsen K., Simonsen B., Sanchez J., and Morling N. Y-chromosome STR haplotypes in Danes. Forensic Sci. Int. 155 (2005) 205-210
30. Schoske R., Vallone P.M., Kline M.C., Redman J.W., and Butler J.M. High-throughput Y-STR typing of U.S. populations with 27 regions of the Y chromosome using two multiplex PCR assays. Forensic Sci. Int. 139 (2004) 107-121
31. Carracedo A., Beckmann A., Bengs A., Brinkmann B., Caglia A., Capelli C., Gill P., Gusmao L., Hagelberg C., Hohoff C., Hoste B., Kihlgren A., Kloosterman A., Myhre Dupuy B., Morling N., O'Donnell G., Parson W., Phillips C., Pouwels M., Scheithauer R., Schmitter H., Schneider P.M., Schumm J., Skitsa I., Stradmann-Bellinghausen B., Stuart M., Syndercombe Court D., and Vide C. 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. 119 (2001) 28-41
32. Willuweit S., and Roewer L. Y chromosome haplotype reference database (YHRD): update. Forensic Sci. Int.: Genet. 1 (2007) 83-87
33. Andreasson H., Gyllensten U., and Allen M. Real-time DNA quantification of nuclear and mitochondrial DNA in forensic analysis. Biotechniques 33 (2002) 402-404 407-411
34. Tschentscher F., Frey U.H., and Bajanowski T. Amelogenin sex determination by pyrosequencing of short PCR products. Int. J. Legal Med. 122 (2008) 333-335
35. Butler J.M., Shen Y., and McCord B.R. The development of reduced size STR amplicons as tools for analysis of degraded DNA. J. Forensic Sci. 48 (2003) 1054-1064
36. Chung D.T., Drabek J., Opel K.L., Butler J.M., and McCord B.R. A study on the effects of degradation and template concentration on the amplification efficiency of the STR Miniplex primer sets. J. Forensic Sci. 49 (2004) 733-740
37. Coble M.D., and Butler J.M. Characterization of new miniSTR loci to aid analysis of degraded DNA. J. Forensic Sci. 50 (2005) 43-53