Wikipedia
Haplotype-relative-risk (HRR) is a family based method for determining gene allele association to a disease. Nuclear families with one affected child are sampled using the parental haplotypes not transmitted as a control. While similar to genotype relative risk (RR), HRR provides a solution to the problem of population stratification by only sampling within family trios. HRR method was first proposed by Rubinstein in 1981 then detailed in 1987 by Rubinstein and Falk and is an important tool in genetic association studies.
The original method proposed by Falk and Rubinstien fell under scrutiny in 1989, when Ott showed the equivalence of HRR to the classical RR method demonstrating the HRR holds only when there is zero chance of recombination between disease locus and its markers. This led to the adoption of the transmission disequilibrium test as the more commonly used method for association linkage; Yet, when the recombination factor for a gene marker and its locus are >0 there is no tendency for false positives seen.
While HRR method has been shown as an effective means of avoiding population stratification another family based associations test known as the transmission disequilibrium test or, TDT is more commonly used because of its more simplified algorithms. Some research uses both HRR and TDT for their ability to complement each other since one result my give no association while the other will. A positive association result from both TDT and HRR means there is strong evidence that a link exists and vice versa. For example, both HRR and TDT methods were used in a study looking for polymorphism in D2 and D3 dopamine receptor in association with schizophrenia and found no linkage in both tests; showing absolutely no possible association.