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Journal of Computational Biology
Robustness of Inference of Haplotype Block Structure
To cite this article:
Russell Schwartz, Bjarni V. Halldórsson, Vineet Bafna, Andrew G. Clark, Sorin Istrail.
Journal of Computational Biology.
February 2003,
10(1): 13-19.
doi:10.1089/106652703763255642.
Russell Schwartz Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213 Bjarni V. Halldórsson Celera Genomics, Informatics Research, Rockville, MD 20850 Vineet Bafna The Center for Advancement of Genetics, Rockville, MD 20850 Andrew G. Clark Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 Sorin Istrail Celera Genomics, Informatics Research, Rockville, MD 20850 In this report, we examine the validity of the haplotype block concept by comparing block decompositions derived from public data sets by variants of several leading methods of block detection. We first develop a statistical method for assessing the concordance of two block decompositions. We then assess the robustness of inferred haplotype blocks to the specific detection method chosen, to arbitrary choices made in the block-detection algorithms, and to the sample analyzed. Although the block decompositions show levels of concordance that are very unlikely by chance, the absolute magnitude of the concordance may be low enough to limit the utility of the inference. For purposes of SNP selection, it seems likely that methods that do not arbitrarily impose block boundaries among correlated SNPs might perform better than block-based methods.  This paper was cited by:Patterns of Linkage Disequilibrium between SNPs in a Sardinian Population Isolate and the Selection of Markers for Association Studies Andrea Angius, Fiona C.L. Hyland, Ivana Persico, Nicola Pirastu, Trevor Woodage, Mario Pirastu, Francisco M. De La Vega Human Heredity. Feb 2008, Vol. 65, No. 1: 9-22 CrossRef Methods for the selection of tagging SNPs: a comparison of tagging efficiency and performance Keyue Ding, Iftikhar J Kullo European Journal of Human Genetics. Mar 2007, Vol. 15, No. 2: 228-236 CrossRef Identification and functional significance of SNPs underlying conserved haplotype frameworks across ethnic populations Ching Ouyang, Theodore G. Krontiris Pharmacogenetics and Genomics. Oct 2006, Vol. 16, No. 9: 667-682 CrossRef Reconstructing Ancestral Haplotypes with a Dictionary Model Kristin L. Ayers, Chiara Sabatti, Kenneth Lange Journal of Computational Biology. Apr 2006, Vol. 13, No. 3: 767-785 Abstract | Full Text PDF | Reprints & PermissionsBipolar I Disorder and Schizophrenia: A 440–Single-Nucleotide Polymorphism Screen of 64 Candidate Genes among Ashkenazi Jewish Case-Parent Trios M FALLIN, V LASSETER, D AVRAMOPOULOS, K NICODEMUS, P WOLYNIEC, J MCGRATH, G STEEL, G NESTADT, K LIANG, R HUGANIR The American Journal of Human Genetics. Jan 2006, Vol. 77, No. 6: 918-936 CrossRef THE PATTERNS OF NATURAL VARIATION IN HUMAN GENES Dana C. Crawford, Dayna T. Akey, Deborah A. Nickerson Annual Review of Genomics and Human Genetics. Oct 2005, Vol. 6, No. 1: 287-312 CrossRef Linkage Disequilibrium Patterns and tagSNP Transferability among European Populations J MUELLER, E LOHMUSSAAR, R MAGI, M REMM, T BETTECKEN, P LICHTNER, S BISKUP, T ILLIG, A PFEUFER, J LUEDEMANN The American Journal of Human Genetics. Apr 2005, Vol. 76, No. 3: 387-398 CrossRef Definition and Clinical Importance of Haplotypes Dana C. Crawford, Deborah A. Nickerson Annual Review of Medicine. Mar 2005, Vol. 56, No. 1: 303-320 CrossRef Haplotypes and haplotype-tagging single-nucleotide polymorphism: Presentation Group 8 of Genetic Analysis Workshop 14 Lars Beckmann, Andreas Ziegler, Priya Duggal, Joan E. Bailey-Wilson Genetic Epidemiology. Feb 2005, Vol. 29, No. S1: S59-S71 CrossRef The role of haplotypes in candidate gene studies Andrew G. Clark Genetic Epidemiology. Jan 2005, Vol. 27, No. 4: 321-333 CrossRef Model-Based Inference of Haplotype Block Variation Gideon Greenspan, Dan Geiger Journal of Computational Biology. Mar 2004, Vol. 11, No. 2-3: 493-504 Abstract | Full Text PDF | Reprints & PermissionsOptimal Selection of SNP Markers for Disease Association Studies Bjarni V. Halldórsson, Sorin Istrail, Francisco M. De La Vega Human Heredity. Feb 2004, Vol. 58, No. 3-4: 190-202 CrossRef Haplotype Parsing Russell Schwartz Applied Bioinformatics. Feb 2004, Vol. 3, No. 2: 181-191 CrossRef
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