Locus-Specific Brackets (LSBs) for Y-STR Typing

Participants: John M. Butler, Jill E. Appleby, and David Duewer

Project Timeframe: October 2003 to July 2004

Purpose: Short tandem repeat (STR) loci, widely used as genetic markers in disease diagnostic studies and human identity applications, are traditionally genotyped through comparison of allele sizes to a sequenced allelic ladder.  Allelic ladders permit a floating bin allele calling method to be utilized that enables reliable allele calling across laboratories, instrument platforms, and electrophoretic conditions.  Precise sizing methods for STR allele calling involving fixed bins can also be used when a high degree of precision has been demonstrated within an instrument platform and set of electrophoretic conditions.  An alternative method for reliable genotyping of STR markers involves locus-specific brackets (LSBs), which are artificial alleles created through molecular biology manipulations to be shorter or longer than alleles commonly seen in populations under investigation.  The size and repeat number of measured alleles are interpolated between the two LSB products that are mixed with the PCR-amplified STR alleles. 

Progress:  This project was initiated at the request of NIJ in order to complete the work started by a previous grantee OligoTrail, LLC and publish the results. Materials were supplied by Debang Liu of OligoTrail. A concordance study was performed between the LSB typing approach and conventional STR typing methods involving allelic ladders.  Complete agreement was observed with 162 samples studied at 5 Y-chromosome loci.  The project was completed in the summer of 2004 and the results were published in the journal Electrophoresis.

Publications or Presentations Resulting From This Project:

Butler, J.M., Appleby, J.E., Duewer, D.L. (2005) Locus-specific brackets for reliable typing of Y-chromosome short tandem repeat markers. Electrophoresis, 26: 2583-2590.

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Last updated: 06/18/2007

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.