Figure 1. Haplotype pairs of two individuals for a gene bearing multiple single nucleotide polymorphisms (SNPs). In this case, the phase of the coding SNPs determines the genotype. Even though the two individuals A and B are both heterozygous at the variable site positions 2 and 4, individual B expresses the gene correctly and individual A does not. Typical single SNP scoring methods would fail to distinguish between the two individuals, specifically between the two haplotype pairs. It is important to note that current (mixed diploid) direct sequencing methods allow determination of genotype, but not differentiation of phase, ie, the specific location of each SNP on one of the two chromosomes. Reproduced from reference 55: Hoehe MR, Timmermann B, Lehrach H. Haplotypes and the systematic analysis of genetic variation: disease genes, drug targets and pharmacogenomics [in German], Biospektrum. 2002;8:478-485. Copyright (c) 2002, Elsevier.