Synonyms: Gametic phase disequilibrium
LD is the non-random occurrence of genetic variants in the population, produced due to the chromosomal sections of genetic material inherited, such that alleles for genetic variants close together are always co-inherited unless randomly segregated by recombination. This induces correlation between genetic variants because the allele of one locus is disproportionately co-inherited with an allele at another locus. LD is typically high amongst variants close together on the same chromosome, but long-range LD including across multiple chromosome can be induced due to various population processes. The term LD describes a state that represents a departure from the hypothetical situation in which all loci exhibit complete independence (linkage equilibrium, LE).
In MR, the use of multiple IVs is akin to aggregating information from multiple independent trials. Therefore, ideally independent genetic IVs are used as to not ‘double-count’ the contribution of any particular variants, which would lead to under-estimation of the standard error of the estimate. This is done by either 1) clumping, whereby only a SNP is retained per locus based on LD within that population (or by using a representative reference panel); or 2) the estimation procedure is performed conditional on the LD matrix between genetic variants.