Volume measures for linkage disequilibrium

doi:10.1186/1471-2156-7-54

BMC Genetics
Volume 7

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Volume measures for linkage disequilibrium

Yuguo Chen¹ , Chia-Ho Lin² and Chiara Sabatti²^,3

¹Department of Statistics, University of Illinois at Urbana-Champaign, Champaign IL 61820, USA

²Department of Statistics, UCLA, Los Angeles CA 90095-1554, USA

³Department of Human Genetics, UCLA, Los Angeles CA 90095-7088, USA

author email corresponding author email

BMC Genetics 2006, 7:54doi:10.1186/1471-2156-7-54


Published:	17 November 2006

Abstract

Background

Defining measures of linkage disequilibrium (LD) that have good small sample properties and are applicable to multiallelic markers poses some challenges. The potential of volume measures in this context has been noted before, but their use has been hampered by computational challenges.

Results

We design a sequential importance sampling algorithm to evaluate volume measures on I × J tables. The algorithm is implemented in a C routine as a complement to exhaustive enumeration. We make the C code available as open source. We achieve fast and accurate evaluation of volume measures in two dimensional tables.

Conclusion

Applying our code to simulated and real datasets reinforces the belief that volume measures are a very useful tool for LD evaluation: they are not inflated in small samples, their definition encompasses multiallelic markers, and they can be computed with appreciable speed.