K. Technical Literature on Genotyping, including OmniPop and Forensic Literature

1. Allard, M.W. et al. (2002). Characterization of the Caucasian haplogroups present in the SWGDAM forensic mtDNA dataset for 1771 human control region sequences. Scientific Working Group on DNA Analysis Methods. J. Forensic Sci. 47: 1215-1223.

2. Anderson, S. et al. (1981) Sequence and organization of the human mitchondrial genome. Nature 290: 457-465.

3. Andrews, R.M. et al. (1999) Reanalysis and revision of the Cambridge Reference Sequence for human mitochondrial DNA. Nature Genetics 23: 147.

4. Aris-Brosou, S., and Excoffier, L. (1996) The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism. Mol. Biol. Evol. 13: 494-504.

5. Balding, DJ and Nichols, RA (1994) DNA profile match probability calculations: how to allow for population stratification, relatedness, database selection and single bands. Forensic Science International 64:125-140

6. Balding, DJ (1995) Estimating products in forensic identification. J. Am. Stat. Assoc. 90:839-844

7. Balding, D.J. et al., eds. (2001). Handbook of Statistical Genetics. New York: Wiley.

8. Bamshad, M., Wooding, S., Salisbury, B. A. & Stephens, J. C. (2004) Deconstructing the relationship between genetics and race. Nature Rev. Genet. 5:598-609. Validates use of sets of markers to deduce population of origin from Y-STR match.

9. Barbujani, G., Magagni, A., Minch, E. & Cavalli-Sforza, L.L. (1997). An apportionment of human DNA diversity. Proc. Natl Acad. Sci. USA 94:4516-4519.| Finds ~85% of human variation within populations, not between populations.

10. Butler, J.M. (2001). Forensic DNA Typing: Biology and Technology behind STR Markers. Academic Press, London.

11. Butler, John M. (2006). Genetics and Genomics of Core Short Tandem Repeat Loci Used in Human Identity Testing. J Forensic Sci. 51/2:253-65.

12. Cann, R.L., M. Stoneking & A.C. Wilson (1987). Mitochondrial DNA and Human Evolution. Nature 325:31-36.

13. Carvalho-Silva, D.R. et al. (1999). Divergent Human Y-chromosome Microsatellite Evolution Rates. J Mol Evol 49:204-14.

14. CODIS STR Loci Data from 41 Sample Populations, J Forensic Sci, 2001, 46(3), 453-489.

15. Elliott, Carl and Paul Brodwin (2002). “Identity and Genetic Ancestry Tracing” in BMJ 325(7378):1469-1471.

16. DNA-Interactive (web site). http://www.dnai.org/index.html Easy to explore video modules on the many applications of DNA in the words of the founders and practitioners of genetics today.

17. ENFSI: European Network of Forensic Science Institutes. ENFSI DNA WG STR Population Database, available http://www.str-base.org/index.php. Population frequency database for cities in European countries. 24 populations, 5,700 profiles. Uses Balding & Nichols Fst correction formula.

18. Foreman LA, Lambert JA, Evett IW (1998). Regional genetic variation in Caucasians. Forensic Science International 95:27-37.

19. Forster, P. et al. (2000). A Short Tandem Repeat-based Phylogeny for the Human Y Chromosome. Am J Hum Genet 66:182-96.

20. Fu, Y.X. (1994) A phylogenetic estimator of effective population size or mutation rate. Genetics 136: 685-92.

21. Gill, P, Foreman L, Buckelton, JS, Triggs, CM, Allen, H (2003) Analysis of DNA databases across Europe compiled by the ENFSI group; Forensic Science International 131:184-196.

22. Handt, O. et al. (1996). The Retrieval of Ancient Human DNA Sequences. Am J Hum Genet 59:368-76.

23. Herrmann B. and S. Hummel (1994). Ancient DNA. Berlin: Springer.
24. Heyer E, Puymirat J, Dieltjes P, Bakker E, & de Knijff P.(1997). "Estimating Y chromosome specific microsatellite mutation frequencies using deep rooting pedigrees," Hum Mol Genet 6(5):799-803.

25. Holland, M.M. (1999) Mitochondrial DNA sequence analysis - validation and use for forensic casework. Forensic Sc. Rev. 11: 21-50.

26. Jewish Population Genetic Data in 20 Polymorphic Loci, FSI, 2002, p52-58.

27. Jobling, M.A. (2001) In the name of the father: surnames and genetics. Trends Genet. 17, 353-357.

28. Jobling, M. A. & Tyler-Smith, C. (2003). The human Y chromosome: an evolutionary marker comes of age. Nature Rev. Genet. 4:598-612. | |

29. Kayser, M. et al. (2002). Online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for US populations. J. Forensic Sci. 47:513-519.

30. Kolman, D.J. and N. Tuross (2000). Ancient DNA Analysis of Human Populations. Am J Phys Anthropol 111:5-23.

31. Lao, O. et al. (2006). Proportioning Whole-Genome Single-Nucleotide Polymorphism Diversity for the Identification of Geographic Population Structure and Genetic Ancestry. American Journal of Human Genetics 78:680–690.

32. Levedakou et.al (2000). Allele Frequencies for Fourteen STR Loci of the PowerPlex 1.1 and 2.1 Multiplex Systems and Penta D Locus In Caucasians, African-Americans, Hispanics, and Other Populations of the United States of America and Brazil, JFS 46(3):736-761.

33. Meyer, S. and Von Haeseler, A. (2003) Identifying site-specific substitution rates. Mol. Biol. Evol. 20: 182-89.

34. Nei, M. (1987). Molecular Evolutionary Genetics. New York: Columbia UP.

35. National Research Council. (1996) The evaluation of forensic DNA evidence. National Academy Press, Washington D.C.

36. Perez-Lezaun et al. (2000). “Allele Frequencies of 13 Short Tandem Repeats in Population Samples From the Iberian Peninsula and Northern Africa,” IJLM, 113,:208-214.

37. Population Data on the Thirteen CODIS Core Short Tandem Repeat Loci in Arfican Americans, U.S. Caucasians, Hispanics, Bahamians, Jamaicans, aand Trinidadians, JFS, 1999, 44, 1277-1286.

38. Population studies on three Native Alaska population groups using STR loci, FSI, 2002, p51-57.

39. Population Studies Used for OmniPop available online at http://dnaconsultants.com/Detailed/345.html.

40. Roewer, L. et al. (2001). Online reference database of Y-chromosomal short tandem repeat (STR) haplotypes. Forensic Sci. Int. 118:103-111. Describes the Y-chromosomal DNA reference database that has become indispensable to the analysis of Y-STR DNA profiles.

41. Sigurdardottir, S., et al. (2000). The Mutation Rate in the Human mtDNA Control Region. Am J Hum Genet 66:1599-1609.

42. Sykes, B. & Irven, C. Surnames and the Y chromosome. Am. J. Hum. Genet. 66, 1417-1419 (2000). | |

43. Taylor, R.E. (1994). Radiocarbon Dating of Bone Using Accelerator Mass Spectrometry: Current Discussions and Future Directions. In Bonnichsen, R. and D. Steele, eds., Methods and Theory for Investigating the Peopling of the Americas. Corvallis: Oregon State University.

44. Tills, D., et al. (1983) The Distribution of the Human Blood Groups and Other Polymorphisms. Oxford: Oxford UP.

45. Balding, D.J. et al., eds. (2001). Handbook of Statistical Genetics. New York: Wiley.

46. Willuweit S, Roewer L, on behalf of the International Forensic Y Chromosome User Group, Y chromosome haplotype reference database (YHRD): Update, Forensic Science International: Genetics (2007) 2. Abstract. Release 21 from April 13, 2007. Database consists of 51,253 haplotypes in 447 populations. A subset of 49% has been analyzed for the loci DYS438 and DYS439. Available online at http://www.yhrd.org.

47. Wilson, M.R., et al. (1993). Guidelines for the Use of Mitochondrial DNA Sequencing in Forensic Science. Crime Laboratory Digest 20:68-77.

48. Y Chromosome Consortium (2002). A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups. Genome Research 12:339-48. Establishes the conventional names for male haplogroups according to the mutations they exhibit.

49. Rolf, B. et al. (2001) Paternity testing using Y-STR haplotypes: assigning a probability for paternity in cases of mutations. Int. J. Legal Med. 115:12-15.