Autosomal STR Loci: Beyond the CODIS Markers
Participants: Carolyn R. "Becky" Hill, Michael D. Coble (now at AFDIL), Peter M. Vallone, Margaret C. Kline, and John M. Butler
Project Timeframe: January 2004 to present
Purpose: A number of studies have demonstrated that successful analysis of degraded DNA specimens from mass disasters or forensic evidence improves with smaller sized polymerase chain reaction (PCR) products. If DNA is exposed to the elements or to fire for any length of time, degradation can occur due to bacterial, biochemical or oxidative processes. Within the forensic community, a core set of short tandem repeat (STR) markers have been developed for utilization in forensic casework, and large DNA databases such as the Combined DNA Index System (CODIS) have been developed incorporating these markers. An initial effort to reduce the STR amplicon size for CODIS loci resulted in a set of miniplexes to analyze degraded DNA. However, a few of the core CODIS STR loci cannot be made into smaller amplicons due to repeat flanking regions that are not amenable for redesigned primers (e.g. D7S820) or due to the fact that some of the CODIS loci have large allele ranges (e.g. FGA). We have therefore scanned the literature for new STR loci, unlinked from the CODIS markers, which can generate amplicons less than 150 bp in size and would therefore be helpful in testing degraded DNA samples.
Progress: New PCR primers have been designed and tested for more than 30 miniSTR loci from which a final candidate set of 26 loci were selected based on their variability in a set of more than 600 U.S. population samples. The utility of these new loci have been confirmed in comparing the success of the miniSTR assays for typing degraded bone samples and aged blood and saliva stains while partial profiles were observed with the majority of the samples using a commercial STR kit. A portion of the NIST STRBase website is being devoted to information on these new miniSTR loci: http://www.cstl.nist.gov/biotech/strbase/newSTRs.htm. Some of our first miniSTR loci characterized--D2S441, D10S1248, and D22S1045—have been selected by the European community as recommended STRs for adding to their core genetic systems used for human identity testing. Applied Biosystems, a major commercial supplier of DNA testing kits, has developed a new miniSTR kit based in large measure on our pioneering work here at NIST.
Publications or Presentations Resulting From This Project (selected):
Coble, M.D. and Butler, J.M. (2005) Characterization of new miniSTR loci to aid analysis of degraded DNA. J. Forensic Sci. 50: 43-53.
Dixon, L.A., Dobbins, A.E., Pulker, H., Butler, J.M., Vallone, P.M., Coble, M.D., Parson, W., Berger, B., Grubweiser, P., Mogensen, H.S., Morling, N., Nielsen, K., Sanchez, J.J., Petkovski, E., Carracedo, A., Sanchez-Diz, P., Brion, M., Irwin, J.A., Just, R.S., Loreille, O., Parsons, T.J., Syndercombe-Court, D., Schmitter, H., Gill, P. (2006) Analysis of artificially degraded DNA using STRs and SNPs--results of a collaborative European (EDNAP) exercise. Forensic Sci. Int. 164: 33-44.
Becky Hill poster at 17th International Symposium on Human Identification (Nashville, TN), October 10-12, 2006, "Characterization of 26 New miniSTR Loci" [.pdf]
Becky Hill presentation at the Mid-Atlantic Association of Forensic Scientists annual meeting (Washington, DC), May 24, 2007, "An Evaluation of CODIS and non-CODIS miniSTR Loci" [.pdf]
Hill, C.R., Coble, M.D., Butler, J.M. (2007) Characterization of 26 miniSTR loci for improved analysis of degraded DNA samples. J. Forensic Sci., in press.
Last updated: 06/27/2007
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.