Failing the four-gamete test enables exact phasing: the Corners' Algorithm.

ABSTRACT:

Background

Failing the four-gamete test for two polymorphic DNA markers is an indication that two or three rather than four haplotypes segregate in the population. The objective of this paper is to show that when just three haplotypes are segregating, all three haplotypes can be fully and unambiguously phase-resolved.

Theory and methods

The Corners' Algorithm tests the four corners in a 3 × 3 table of two-locus genotypes. If one of the four corners is filled with zeroes, then the missing haplotype is identified and the phases of all three haplotypes can be unambiguously resolved for all individuals. Three applications of this method are proposed when the four-gamete test fails: (1) direct estimation of linkage disequilibrium (LD), (2) haplotype-based genome-wide association

SUBMITTER: Gomez-Raya L 

PROVIDER: S-EPMC9661815 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature