Haplotypes at ATM Identify Coding-Sequence Variation and Indicate a Region of Extensive Linkage Disequilibrium Penelope E. Bonnen, Michael D. Story,

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Haplotypes at ATM Identify Coding-Sequence Variation and Indicate a Region of Extensive Linkage Disequilibrium Penelope E. Bonnen, Michael D. Story, Cheryl L. Ashorn, Thomas A. Buchholz, Michael M. Weil, David L. Nelson The American Journal of Human Genetics Volume 67, Issue 6, Pages 1437-1451 (December 2000) DOI: 10.1086/316908 Copyright © 2000 The American Society of Human Genetics Terms and Conditions

Figure 1 Schematic of ATM. The 184 kb of the ATM locus is illustrated, with the 64 exons represented by black boxes. Twenty-nine ∼500-bp regions were amplified by PCR in five unrelated individuals. These regions were sequenced and found to contain 17 SNPs. The American Journal of Human Genetics 2000 67, 1437-1451DOI: (10.1086/316908) Copyright © 2000 The American Society of Human Genetics Terms and Conditions

Figure 2 ATM SNP allele frequencies for 14 ATM SNPs in each of four ethnic groups. A total of 260 individuals (71 African American, 39 Asian American, 77 white European American, and 73 Hispanic) were genotyped by ASO hybridization. The American Journal of Human Genetics 2000 67, 1437-1451DOI: (10.1086/316908) Copyright © 2000 The American Society of Human Genetics Terms and Conditions

Figure 3 Four-gamete test for recombination in ATM. White boxes denote site pairs having four gametic types, which implies that recombination has occurred between these two sites. Also shown is the Hudson and Kaplan recombination statistic R, which is an estimate of the number and sites of recombination events needed to explain the results of the four-gamete matrix. A white box containing an “×” denotes a potential site of recombination. The asterisk (*) denotes an SNP that is not polymorphic in the sample population. The American Journal of Human Genetics 2000 67, 1437-1451DOI: (10.1086/316908) Copyright © 2000 The American Society of Human Genetics Terms and Conditions

Figure 4 Fisher's exact test for LD in ATM. White boxes denote site pairs that do not have a significant value by Fisher’s exact test, indicating linkage equilibrium. Gray columns and rows denote SNPs that have a minor-allele frequency ≤.05. The asterisk (*) denotes an SNP that is not polymorphic in the sample population. The American Journal of Human Genetics 2000 67, 1437-1451DOI: (10.1086/316908) Copyright © 2000 The American Society of Human Genetics Terms and Conditions

Figure 5 D′, measured as D′=D/|D|max in a pairwise fashion across 14 SNP loci. A score of either 1 or −1 is considered perfect disequilibrium. Black boxes denote site pairs with perfect disequilibrium; white boxes denote site pairs with |D′|<1. The asterisk (*) pair denotes an SNP that is not polymorphic in the sample population. The American Journal of Human Genetics 2000 67, 1437-1451DOI: (10.1086/316908) Copyright © 2000 The American Society of Human Genetics Terms and Conditions