Figure 1.

Sextet Pedigrees and Representation of Inheritance States

(A) Pedigree A and (B) pedigree B (CEPH 1463). Genomes for only the individuals in generations II and III were used for genetic phasing (nuclear-family sextets). The displayed grandparents in generation I of pedigrees A and B have been sequenced, but the data were not used for haplotyping. Grandparental data were used to confirm the phasing of haplotyping for the nuclear families composed by generations II and III.

(C) Inheritance states are represented by binary vectors indicating the result of Mendel's first law of segregation at a given aligned position of all the genomes in a pedigree. For example, at this hypothetical tetra-allelic position, the first child has received the first allele from the first parent and the first allele from the second parent; these are indicated as “00.” The other children receive the other alleles, indicated as “11.” Combined, the binary inheritance-state vector for this pedigree at this position is “00111111.” Because the labeling of the parental genotypes is arbitrary, the first two bits in a two-generation nuclear-family inheritance-state vector can always be set to 0. Most variant positions in the genome are biallelic, and so inheritance state must be deduced from sets of adjacent variants.