Y-SNP Variation in U.S. Populations


Participants: Peter M. Vallone and John M. Butler


Project Timeframe: May 2002 to July 2004


Purpose: Single nucleotide polymorphisms (SNPs) located on the Y-chromosome are attractive DNA marker candidates due to their low mutation rate and male specificity.  The fact that the Y-chromosome is only found in males makes genetic markers located upon it useful in mixed male-female sample (as found in sexual assault evidence).  The low mutation rate of the Y-chromosome SNPs implies potential for determining the geographical origin of an individual.  The purpose of our studies were to develop of multiplex assays for the examination of Y-SNPs in a human identification context and to evaluate the variation of common Y-SNP markers in U.S. populations.


Progress: Our work represents some of the first studies performed to evaluate the frequency of known Y chromosome SNPs in U.S. populations.  We ended up examining 50 well-characterized SNP sites in over 200 U.S. population (African American and Caucasian) samples using a commercial DNA typing kit and custom assays developed in-house. The two assay methodologies, hybridization and primer extension, indicated full concordance for typing 8 overlapping SNP sites.  The overall success rate for typing that samples was over 99% for either methodology.  A pie chart summary of the data is illustrated in the figure.  SNP frequency distributions for the 50 genetics markers typed indicated groupings that were unique to each population.  47% and 23% of the Caucasian and African American samples fell into haplogroup R1b respectively.  58% of the African American samples were found to be in the haplogroup E3a. It is of interest to note that none of the Caucasian samples fell into haplogroup E3a (defined by Y-SNP marker M2) making it a population specific grouping in our sample set.   


Publications or Presentations Resulting From This Project:

Butler, J.M. (2003) Recent developments in Y-short tandem repeat and Y-single nucleotide polymorphism analysis. Forensic Sci. Rev. 15:91-111.


Vallone, P.M. and Butler, J.M. (2004) Multiplexed assays for evaluation of Y-SNP markers in U.S. populations. Progress in Forensic Genetics 10, Elsevier Science: Amsterdam, The Netherlands, International Congress Series 1261, 85-87.


Vallone, P.M. and Butler, J.M. (2004) Y-SNP typing of U.S. African American and Caucasian samples using allele-specific hybridization and primer extension. J. Forensic Sci. 49(4): 723-732.


[Return to NIJ Projects page] [Return to STRBase]


Last updated: 06/25/2007


Disclaimer: This project was supported by National Institute of Justice Grant Number 2003-IJ-R-029, which is an interagency agreement between NIJ and the NIST Office of Law Enforcement Standards, awarded by the National Institute of Justice, Office of Justice Programs, US Department of Justice. Points of view in this document are those of the authors and do not necessarily represent the official position or policies of the US Department of Justice. Certain commercial equipment, instruments and materials are identified in order to specify experimental procedures as completely as possible.  In no case does such identification imply a recommendation or endorsement by the National Institute of Standards and Technology nor does it imply that any of the materials, instruments or equipment identified are necessarily the best available for the purpose.