Linkage and Association Studies

There are two primary strategies for mapping genes that cause or increase susceptibility to human disease:
(1) classic linkage can be performed based on a known genetic model or, when the model is unknown, by studying pairs of affected relatives.
(2) disease genes can be mapped using allelic association studies.

Genetic Linkage


Genetic linkage refers to the fact that genes are physically connected, or linked, to one another along the chromosomes.

Two fundamental principles are essential for understanding the concept of linkage:

(1) when two genes are close together on a chromosome, they are usually transmitted together, unless a recombination event separates them.
(2) the odds of a crossover, or recombination event, between two linked genes is proportional to the distance that separates them. Thus, genes that are further apart are more likely to undergo a recombination event than genes that are very close together.

The detection of chromosomal loci that segregate with a disease by linkage can be used to identify the gene responsible for the disease (positional cloning) and to predict the odds of disease gene transmission in genetic counseling.

Polymorphisms are essential for linkage studies because they provide a means to distinguish the maternal and paternal chromosomes in an individual. On average, 1 out of every 1000 bp varies from one person to the next. Although this degree of variation seems low (99.9% identical), it means that >3 million sequence differences exist between any two unrelated individuals and the probability that the sequence at such loci will differ on the two homologous chromosomes is high (often >70–90%). These sequence variations include VNTRs, short tandem repeats (STRs), and SNPs. Most STRs, also called polymorphic microsatellite markers, consist of di-, tri-, or tetranucleotide repeats that can be measured readily using PCR. Characterization of SNPs, using DNA chips, provides an important new tool for comprehensive analyses of genetic variation, linkage, and association studies. Although these sequence variations usually have no apparent functional consequences, they provide much of the basis for variation in genetic traits.

In order to identify a chromosomal locus that segregates with a disease, it is necessary to characterize polymorphic DNA markers from affected and unaffected individuals of one or several pedigrees. One can then assess whether certain marker alleles cosegregate with the disease.

Markers that are closest to the disease gene are less likely to undergo recombination events and therefore receive a higher linkage score.
Linkage is expressed as a lod (logarithm of odds) score—the ratio of the probability that the disease and marker loci are linked rather than unlinked. Lod scores of +3 (1000:1) are generally accepted as supporting linkage, whereas a score of –2 is consistent with the absence of linkage.


Allelic association refers to a situation in which the frequency of an allele is significantly increased or decreased in individuals affected by a particular disease in comparison to controls.

Linkage and association differ in several aspects. Genetic linkage is demonstrable in families or sibships. Association studies, on the other hand, compare a population of affected individuals with a control population. Association studies can be performed as case-control studies that include unrelated affected individuals and matched controls, or as family-based studies that compare the frequencies of alleles transmitted or not transmitted to affected children. Allelic association studies are particularly useful for identifying susceptibility genes in complex diseases.

When alleles at two loci occur more frequently in combination than would be predicted (based on known allele frequencies and recombination fractions), they are said to be in linkage disequilibrium .