Minimum description length block finder, a method to identify haplotype blocks and to compare the strength of block boundaries

American Journal of Human Genetics
H MannilaE Ukkonen

Abstract

We describe a new probabilistic method for finding haplotype blocks that is based on the use of the minimum description length (MDL) principle. We give a rigorous definition of the quality of a segmentation of a genomic region into blocks and describe a dynamic programming algorithm for finding the optimal segmentation with respect to this measure. We also describe a method for finding the probability of a block boundary for each pair of adjacent markers: this gives a tool for evaluating the significance of each block boundary. We have applied the method to the published data of Daly and colleagues. The results expose some problems that exist in the current methods for the evaluation of the significance of predicted block boundaries. Our method, MDL block finder, can be used to compare block borders in different sample sets, and we demonstrate this by applying the MDL-based method to define the block structure in chromosomes from population isolates.

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Citations

Jul 20, 2007·Journal of Human Genetics·Hironori FujisawaMasaaki Matsuura
Oct 11, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Laxmi ParidaUNKNOWN Genographic Consortium
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May 12, 2007·BMC Bioinformatics·Niels LandwehrHeikki Mannila
Feb 21, 2009·BMC Bioinformatics·Zhaoxia YuDaniel J Schaid
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Dec 18, 2008·BMC Bioinformatics·Olivier DelaneauJean-François Zagury
Dec 19, 2003·American Journal of Human Genetics·Eric C Anderson, Montgomery Slatkin
Jul 15, 2003·American Journal of Human Genetics·Eric C Anderson, John Novembre
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Jan 15, 2014·American Journal of Men's Health·Carole A RobinsonJamie Tomlinson

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