Haplotype Block Partition with Limited Resources and Applications to Human Chromosome 21 Haplotype Data Kui Zhang, Fengzhu Sun, Michael S. Waterman,

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Haplotype Block Partition with Limited Resources and Applications to Human Chromosome 21 Haplotype Data Kui Zhang, Fengzhu Sun, Michael S. Waterman, Ting Chen The American Journal of Human Genetics Volume 73, Issue 1, Pages 63-73 (July 2003) DOI: 10.1086/376437 Copyright © 2003 The American Society of Human Genetics Terms and Conditions

Figure 1 Results of the 2D dynamic programming for block partitioning. A, Relationship between the number of tag SNPs and the percentage of the total number of SNPs being included. B, Relationship between the number of tag SNPs and the percentage of the actual genomic length being included. The American Journal of Human Genetics 2003 73, 63-73DOI: (10.1086/376437) Copyright © 2003 The American Society of Human Genetics Terms and Conditions

Figure 2 Relationship between the deletion parameter (λ) and the corresponding coverage of the total number of SNPs at the intersection points of piecewise-linear segments of the score function S(n,λ), using the parametric dynamic programming algorithm. The penalty for a set of excluded consecutive SNPs is chosen as the product of the deletion parameter λ and the number of SNPs. The American Journal of Human Genetics 2003 73, 63-73DOI: (10.1086/376437) Copyright © 2003 The American Society of Human Genetics Terms and Conditions

Figure 3 Relationship between the number of tag SNPs and the corresponding percentage of the total number of SNPs being included at the intersection points of piecewise-linear segments of the score function S(n,λ), using the parametric dynamic programming algorithm. The penalty for a set of excluded consecutive SNPs is chosen as the product of deletion parameter λ and the number of SNPs. The American Journal of Human Genetics 2003 73, 63-73DOI: (10.1086/376437) Copyright © 2003 The American Society of Human Genetics Terms and Conditions

Figure 4 Scoring function S(n,λ) with respect to the deletion parameter λ. The penalty for a set of excluded consecutive SNPs is chosen as the product of deletion parameter λ and the number of SNPs. The American Journal of Human Genetics 2003 73, 63-73DOI: (10.1086/376437) Copyright © 2003 The American Society of Human Genetics Terms and Conditions

Figure 5 The histograms for the number of genes according to the number of SNPs in genes (a), the number of SNPs in exons (b), the number of SNPs in coding regions (c), and the number of non-synonymous SNPs (d). The American Journal of Human Genetics 2003 73, 63-73DOI: (10.1086/376437) Copyright © 2003 The American Society of Human Genetics Terms and Conditions

Figure 6 Histogram for the number of blocks according to the number of distinct haplotypes in a block. The blocks are obtained on the basis of a data set of human chromosome 21 from Patil et al. 2001, using the dynamic programming algorithm (Zhang et al. 2002b). The number of tag SNPs in each block, measured by f(·), is defined as the minimum number of SNPs that can distinguish at least 80% of unambiguous haplotypes. The American Journal of Human Genetics 2003 73, 63-73DOI: (10.1086/376437) Copyright © 2003 The American Society of Human Genetics Terms and Conditions