Texas population substructure and its impact on estimating the rarity of y STR haplotypes from DNA evidence

Journal of Forensic Sciences

Volumn 54, Issue 5, 2009, Pages 1016-1021

  Budowle, Bruce ^a   Ge, Jianye ^b,c   Aranda, Xavier G ^a   Planz, John V ^a   Eisenberg, Arthur J ^a   Chakraborty, Ranajit ^c  

^a UNIVERSITY OF NORTH TEXAS   (United States)

^b University of Cincinnati   (United States)

^c UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

Author keywords

Autosomal STR loci; DNA typing; FST; Forensic science; Independence; Joint match probability and theta correction; Partial profile; Population substructure; Statistics; Y chromosome; Y STR

Indexed keywords

AFRICAN AMERICAN; ARTICLE; AUTOSOME; CAUCASIAN; DNA DETERMINATION; DNA FINGERPRINTING; FORENSIC GENETICS; GENE LOCUS; HISPANIC; HUMAN; MALE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SHORT TANDEM REPEAT; UNITED STATES; Y CHROMOSOME;

CHROMOSOMES, HUMAN, Y; CONTINENTAL POPULATION GROUPS; DNA FINGERPRINTING; GENETIC MARKERS; GENETIC VARIATION; HAPLOTYPES; HUMANS; MALE; POLYMERASE CHAIN REACTION; TANDEM REPEAT SEQUENCES; TEXAS;

EID: 69649093088     PISSN: 00221198     EISSN: 15564029     Source Type: Journal    
DOI: 10.1111/j.1556-4029.2009.01105.x     Document Type: Article

References (27)

1. Budowle B, Sinha SK, Lee HS, Chakraborty R. Utility of Y-chromosome STR haplotypes in forensic applications. Forensic Sci Rev 2003 15 : 153 164.
2. Corach D, Risso LF, Marino F, Penacino G, Sala A. Routine Y-STR typing in forensic casework. Forensic Sci Int 2001 118 : 131 135.
3. Dekairelle AF, Hoste B. Application of Y-STR pentaplex PCR (DYS19, DYS389I and II, DYS390, and DYS393) to sexual assault cases. Forensic Sci Int 2001 118 : 122 125.
4. Honda K, Roewer L, de Knijff P. Male DNA typing from 25-year-old vaginal swabs using Y chromosomal STR polymorphisms in retrial request case. J Forensic Sci 1999 44 : 868 872.
5. Jobling MA, Pandya A, Tyler-Smith C. The Y chromosome in forensic analysis and paternity testing. Int J Legal Med 1997 110 : 118 124.
6. Kayser M, Cagliá 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 : 125 133.
7. ® Y system. Profiles DNA 2003 6 : 6 9.
8. 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.
9. 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 : 177 188.
10. 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 (1 64 75.
11. Budowle B, Adamowicz M, Aranda X, Barna C, Chakraborty R, Eisenberg AJ, et al. Twelve short tandem repeat loci Y chromosome haplotypes: genetic analysis on populations residing in North America. Forensic Sci Int 2005 150 (1 1 15.
12. Budowle B, Ge J, Chakraborty R. Basic principles for estimating the rarity of Y-STR haplotypes derived from forensic evidence. Eighteenth International Symposium on Human Identification, Oct 1-4, 2007; Hollywood, California. Madison, WI : Promega Corporation, 2007. http://www.promega.com/ geneticidproc/ussymp18proc/oralpresentations.htm. Accessed June 16, 2009.
13. Budowle B, Allard MW, Wilson MR, Chakraborty R. Forensics and mitochondrial DNA: applications, debates, and foundations. Ann Rev Genomics Hum Genet 2003 4 : 119 141.
14. Kayser M, Krawczak M, Excoffier L, Dieltjes P, Corach D, Pascali V, et al. An extensive analysis of Y-chromosomal microsatellite haplotypes in globally dispersed human populations. Am J Hum Genet 2001 68 : 990 1018.
15. Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution 1984 38 : 1358 1370.
16. Weir BS Genetic data analysis II. Sunderland, MA : Sinauer Associates, 1996 170 176.
17. Rogers AR, Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 1992 9 : 552 569.
18. Pereira L, Prata MJ, Amorim A. Mismatch distribution analysis of Y-STR haplotypes as a tool for the evaluation of identity-by-state proportions and significance of matches - the European picture. Forensic Sci Int 2002 130 : 147 155.
19. 2 and the problem of small populations. Mol Biol Evol 1989 6 : 539 545.
20. Sinha SK, Budowle B, Chakraborty R, Paunovic A, Guidry RD, Larsen C, et al. Utility of the Y-STR typing systems Y-PLEX 6 and Y-PLEX 5 in forensic casework and 11 Y-STR haplotype database for three major population groups in the United States. J Forensic Sci 2004 49 : 691 700.
21. Walsh B, Redd A, Hammer M. Joint match probabilities for Y chromosomal and autosomal markers. Forensic Sci Int 2008 174 : 234 238.
22. Beleza S, Alves C, Gonzalez-Neira A, Lareu M, Amorim A, Carracedo A, et al. Extending STR markers in Y chromosome haplotypes. Int J Legal Med 2003 117 : 27 33.
23. Jin L, Chakraborty R. Population substructure, stepwise mutations, heterozygote deficiency and their implications in DNA forensics. Heredity 1995 74 : 274 285.
24. National Research Council. The evaluation of forensic DNA evidence. Washington, DC : National Academy Press, 1996.
25. Balding DJ, Nichols RA. DNA profile match probability calculation: how to allow for population stratification, relatedness, database selection and single bands. Forensic Sci Int 1994 64 : 125 140.
26. Budowle B, Shea B, Niezgoda S, Chakraborty R. CODIS STR loci data from 41 sample populations. J Forensic Sci 2001 46 (3 453 489. (Pubitemid 32520569)
27. Gross AM, Berdos P, Ballantyne J. Y-STR concordance study between Y-Plex5, Y-Plex6, Y-Plex12, PowerplexY, Y-Filer, MPI, and MPII. J Forensic Sci 2007 51 (6 1423 1428.