Testing and evaluation of 43 "Noncore" Y chromosome markers for forensic casework applications

Journal of Forensic Sciences

Volumn 51, Issue 6, 2006, Pages 1298-1314

  Hanson, Erin K ^a,b   Berdos, Paulina N ^b   Ballantyne, Jack ^a,b  

^a UNIVERSITY OF CENTRAL FLORIDA   (United States)

^b National Center for Forensic Science   (United States)

Author keywords

Forensic science; MPIII; MPIV; MPV; Multiplex; SWGDAM validation; Y chromosome STR

Indexed keywords

DNA;

ACCURACY; ALLELE; ARTICLE; BLOOD SAMPLING; CHROMOSOME MAP; CHROMOSOME MARKER; CIGARETTE SMOKING; CROSS REACTION; DISCRIMINANT ANALYSIS; DNA EXTRACTION; FEMALE; FORENSIC IDENTIFICATION; GENE FREQUENCY; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; HUMAN CHROMOSOME; MALE; POPULATION RESEARCH; PRIORITY JOURNAL; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SHORT TANDEM REPEAT; SIMULATION; SPECIES DIFFERENCE; TIME; UTERINE CERVIX CYTOLOGY; Y CHROMOSOME;

ANIMALS; BLOOD; CHROMOSOMES, HUMAN, Y; DNA; DNA FINGERPRINTING; DNA PRIMERS; DNA, BACTERIAL; FEMALE; FORENSIC GENETICS; GENETIC MARKERS; HUMANS; MALE; POLYMERASE CHAIN REACTION; SPECIES SPECIFICITY; SPERMATOZOA; TANDEM REPEAT SEQUENCES;

EID: 33845581805     PISSN: 00221198     EISSN: 15564029     Source Type: Journal    
DOI: 10.1111/j.1556-4029.2006.00263.x     Document Type: Article

References (49)

1. de Knijff P, Kayser M, Caglia A, Corach D, Fretwell N, Gehrig C, et al. Chromosome Y microsatellites: population genetic and evolutionary aspects. Int J Legal Med 1997;110(3):134-49.
2. 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(3):125-9.
3. Corach DF, Filgueira Risso L, Marino M, Penacino G, Sala A. Routine Y-STR typing in forensic casework. Forensic Sci Int 2001;118(2-3):131-5.
4. Daniels DL, Hall AM, Ballantyne J. SWGDAM developmental validation of a 19-locus Y-STR system for forensic casework. J Forensic Sci 2004;49(4):668-83.
5. Hall A, Ballantyne J. The development of an 18-locus Y-STR system for forensic casework. Anal Bioanal Chem 2003;376(8):1234-46.
6. Kayser M, Brauer S, Willuweit S, Schadlich H, Batzer MA, Zawacki J, et al. Online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for U.S. populations. J Forensic Sci 2002;47(3):513-9.
7. Prinz M, Ishii A, Coleman A, Baum HJ, Shaler RC. Validation and casework application of a Y chromosome specific STR multiplex. Forensic Sci Int 2001;120(3):177-88.
8. Prinz M, Sansone M. Y chromosome-specific short tandem repeats in forensic casework. Croat Med J 2001;42(3):288-91.
9. 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(2-3):106-13.
10. Sinha SK, Budowle B, Arcot SS, Richey SL, Chakrabor R, Jones MD, et al. Development and validation of a multiplexed Y-chromosome STR genotyping system, Y-PLEX 6, for forensic casework. J Forensic Sci 2003;48(1):93-103.
11. 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(2):e8.
12. 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(1):10-24.
13. Iida R, Tsubota E, Sawazaki K, Masuyama M, Matsuki T, Yasuda T, et al. Characterization and haplotype analysis of the polymorphic Y-STRs DYS443, DYS444 and DYS445 in a Japanese population. Int J Legal Med 2002;116(3):191-4.
14. Redd AJ, Agellon AB, Kearney VA, Contreras VA, Karafet T, Park H, et al. Forensic value of 14 novel STRs on the human Y chromosome. Forensic Sci Int 2002;130(2-3):97-111.
15. 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(2-3):107-21.
16. White PS, Tatum OL, Deaven LL, Longmire JL. New, male-specific microsatellite markers from the human Y chromosome. Genomics 1999;57(3):433-7.
17. 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):1-14.
18. Sinha SK, Nasir H, Gross AM, Budowle B, Shewale JG. Development and validation of the Y-PLEX 5, a Y-chromosome STR genotyping system, for forensic casework. J Forensic Sci 2003;48(5):985-1000.
19. SWGDAM. Revised validation guidelines. Forensic Sci Commun 2004;6(3):1-6.
20. Dai HL, Wang XD, Li YB, Wu J, Zhang J, Zhang HJ, et al. Characterization and haplotype analysis of 10 novel Y-STR loci in Chinese Han population. Forensic Sci Int 2004;145(1):47-55.
21. Iida R, Tsubota E, Matsuki T. Identification and characterization of two novel human polymorphic STRs on the Y chromosome. Int J Legal Med 2001;115(1):54-6.
22. Kayser M, Kittler R, Erler A, Hedman M, Lee AC, Mohyuddin A, et al. A comprehensive survey of human Y-chromosomal microsatellites. Am J Hum Genet 2004;74(6):1183-97.
23. Zhang J, Hou Y, Tang J, Li Y, Wu J. Haplotype frequencies for two new Y-STR loci in Chinese population. J Forensic Sci 2002;47(1):232-3.
24. Hanson EK, Ballantyne J. A highly discriminating 21 locus Y-STR "megaplex" system designed to augment the minimal haplotype loci for forensic casework. J Forensic Sci 2004;49(1):40-51.
25. Comey CK, Presely KW, Smerick JB, Sobieralski CA, Stanley DM, Baechtel FS. Extraction strategies for amplified fragment length polymorphism analysis. J Forensic Sci 1994;39:1254-69.
26. Gill P, Jeffreys AJ, Werrrett DJ. Forensic application of DNA 'fingerprints'. Nature 1985;318:577-9.
27. Kline MC, Duewer DL, Redman JW, Butler JM. NIST mixed stain study: DNA quantitation accuracy and its influence on short tandem repeat multiplex signal intensity. Anal Chem 2003;75(10):2463-9.
28. Hanson EK, Ballantyne J. Comprehensive annotated STR physical map of the human Y chromosome: forensic implications. Leg Med (Tokyo) 2006;8(2):110-20.
29. http://www.genome.ucsc.edu
30. Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 2003;423(6942):825-37.
31. Leclair B, Fregeau CJ, Bowen KL, Fourney RM. Systematic analysis of stutter percentages and allele peak height and peak area ratios at heterozygous STR loci for forensic casework and database samples. J Forensic Sci 2004;49(5):968-80.
32. Walsh PS, Fildes NJ, Reynolds R. Sequence analysis and characterization of stutter products at the tetranucleotide repeat locus vWA. Nucleic Acids Res 1996;24(14):2807-12.
33. Fregeau CJ, Aubin RA, Elliott JC, Gill SS, Fourney RM. Characterization of human lymphoid cell lines GM9947 and GM9948 as intra- and interlaboratory reference standards for DNA typing. Genomics 1995;28(2):184-97.
34. Nei M. Molecular evolutionary genetics. Columbia, NY: University Press, 1987.
35. Jobling MA, Samara V, Pandya A, Fretwell N, Bernasconi B, Mitchell RJ, et al. Recurrent duplication and deletion polymorphisms on the long arm of the Y chromosome in normal males. Hum Mol Genet 1996;5(11):1767-75.
36. Thomas MG, Bradman N, Flinn HM. High throughput analysis of 10 microsatellite and 11 diallelic polymorphisms on the human Y-chromosome. Hum Genet 1999;105(6):577-81.
37. Bosch E, Lee AC, Calafell F, Arroyo E, Henneman P, de Knijff P, et al. High resolution Y chromosome typing: 19 STRs amplified in three multiplex reactions. Forensic Sci Int 2002;125(1):42-51.
38. Gusmao L, Alves C, Beleza S, Amorim A Forensic evaluation and population data on the new Y-STRs DYS434, DYS437, DYS438, DYS439 and GATA A10. Int J Legal Med 2002;116(3):139-47.
39. Hammer MF. A recent insertion of an alu element on the Y chromosome is a useful marker for human population studies. Mol Biol Evol 1994;11(5):749-61.
40. http://www.gdb.org
41. Smith RN. Accurate size comparison of short tandem repeat alleles amplified by PCR. Biotechniques 1995;18(1):122-8.
42. Hughes JF, Skaletsky H, Pyntikova T, Minx PJ, Graves T, Rozen S, et al. Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee. Nature 2005;437(7055):100-3.
43. Li WH, Saunders MA News and views: the chimpanzee and us. Nature 2005;437(7055):50-51.
44. Bravi CM, Bailliet G, Martinez-Marignac VL, Bianchi NO. Origin of YAP+ lineages of the human Y-chromosome. Am J Phys Anthropol 2000;112(2):149-58.
45. Forster P, Rohl A, Lunnemann P, Brinkmann C, Zerjal T, Tyler-Smith C, et al. A short tandem repeat-based phylogeny for the human Y chromosome. Am J Hum Genet 2000;67(1):182-96.
46. Jobling MA, Pandya A, Tyler-Smith C. The Y chromosome in forensic analysis and paternity testing. Int J Legal Med 1997;110(3):118-24.
47. Weale ME, Shah T, Jones AL, Greenhalgh J, Wilson JF, Nymadawa P, et al. Rare deep-rooting Y chromosome lineages in humans: lessons for phylogeography. Genetics 2003;165(1):229-34.
48. Y-Chromosome-Consortium. A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res 2002;12(2):339-48.
49. Brion M, Sanchez JJ, Balogh K, Thacker C, Blanco-Verea A, Borsting C, et al. Introduction of an single nucleodite polymorphism-based "Major Y-chromosome haplogroup typing kit" suitable for predicting the geographical origin of male lineages. Electrophoresis 2005;26(23):4411-20.