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. Author manuscript; available in PMC: 2011 Dec 1.
Published in final edited form as: Genet Epidemiol. 2010 Dec;34(8):803–815. doi: 10.1002/gepi.20527

TABLE I.

Haplotype frequencies for the scenarios used in simulation studies

Haplotype S1: R2 = 0.41, MAF = 0.39
 S2: R2 = 0.59, MAF = 0.28
 S3: R2 = 0.70, MAF = 0.15
UTTTT Frequency TTTUT Frequency TTUTT Frequency
h1 00011 0.0513 00100 0.3171 00000 0.0513
h2 00100 0.0260 00101 0.0988 00100 0.1460
h3 01011 0.0855 00111 0.2027 01000 0.6958
h4 01100 0.3094 01001 0.1518 10011 0.1069
h5 01101 0.1377 10100 0.1059
h6 11011 0.0085 10101 0.0209
h7 11100 0.1775 10111 0.0793
h8 11101 0.0247 11001 0.0235
h9 11111 0.1794
Haplotype S4: R2 = 0.81, MAF = 0.33
 S5: R2 = 0.84, MAF = 0.24
 S6: R2 = 0.93, MAF = 0.15
UTTTT Frequency TTUTT Frequency TTUTT Frequency
h1 00011 0.2846 01101 0.2852 00011 0.0513
h2 00101 0.0128 10100 0.2510 00100 0.0260
h3 00111 0.0342 11000 0.2393 01011 0.0855
h4 10101 0.2374 11100 0.0321 01100 0.3094
h5 10111 0.1917 11101 0.0963 01101 0.1377
h6 11110 0.2393 11110 0.0961 11011 0.0085
h7 11100 0.1775
h8 11101 0.0247
h9 11111 0.1794
Haplotype S7: R2 = 0.95, MAF = 0.09
 S8: R2 = 0.98, MAF = 0.28
 S9: R2 = 0.98, MAF = 0.29
UTTTT Frequency TTUTT Frequency TTTTU Frequency
h1 00111 0.3809 01000 0.4231 01000 0.4231
h2 01110 0.2350 01010 0.1154 01010 0.1154
h3 01111 0.2900 01011 0.0043 01011 0.0043
h4 11001 0.0897 01111 0.2821 01111 0.2821
h5 11111 0.0044 10010 0.1751 10010 0.1751

“U” and “T” indicate the untyped and typed SNP positions, respectively. R2 is the squared correlation between the expected and true allele counts [Stram, 2004]. MAF is the minor allele frequency of the untyped SNP.