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The haplotype refers to the combination of alleles or variants found on the same chromosome. With the exception of the sex chromosomes in males, every individual has two copies of each gene/chromosome and two haplotypes although in general many more haplotypes exist within the population.

Use in clinical context

Haplotypes can be directly inherited from parents i.e. they share a haplotype. Alternatively, recombination can disrupt the parental haplotype and therefore it is not seen in their offspring.

While some variants individually can be clinically informative, in other situations knowing a person’s haplotype is more beneficial. In these situations, the context of the variant within the copy of the gene or chromosome is important to understand disease risk.

Hypothetical example:

An individual can be ‘A’ or ‘C’ at position 1 in a gene and ‘T’ or ‘G’ at position 2 in the same gene.

This results in four possible haplotypes:

A – T

A – G

C – T

C – G

In this example, none of the variants or genotypes at either position give an increased risk of disease but, when in combination, the A – T haplotype is associated with a greatly increased risk of disease:

Position 1 Position 2 Risk of disease
A T 60%
A G 10%
C T 12%
C G 9%

In this case knowing the individual’s haplotype is more important than knowing genotypes at each position.

Last updated on 31st May, 2019