Linkage analysis

20/2/09. By Richard Twyman
Finding the rough position of human disease genes relative to known genetic markers.

The human genome is very large and contains many thousands of genes.Therefore, finding the particular gene or genes responsible for anygiven human disease has always been a tricky task, quite literally likefinding a needle in a haystack.
Traditionally, the search for adisease gene begins with linkage analysis. In this approach, the aim isto find out the rough location of the gene relative to another DNAsequence called a genetic marker, which has its position already known.

Principle of linkage analysis. The top diagram shows paternal (blue) and maternal (red) chromosomes aligned in a germ cell, a cell that gives rise to eggs or sperm. Three DNA sequences are shown, labelled A, B and C. The capital letters represent the paternal alleles and the lower case letters represent the maternal alleles. The middle panel shows the physical process of recombination, which involves crossing over of DNA strands between the paired chromosomes. The bottom panel shows what happens when the crossover is resolved. The maternal and paternal alleles are mixed (recombined) and these mixed chromosomes are passed to the sperms or eggs. If A is the disease gene and B and C are genetic markers, recombination is likely to occur much more frequently between A and C than it is between A and B. This allows the disease gene to be mapped relative to the markers B and C.
The principle of linkage analysis is simple. All our chromosomes comein pairs, one inherited from our mother and one from our father. Eachpair of chromosomes contains the same genes in the same order, but thesequences are not identical. This means it should be easy to find outwhether a particular sequence comes from our mother or father. Thesesequence variants are called maternal and paternal alleles.
In the case of the disease gene,the alternative alleles will be the normal allele and the diseaseallele, and they can be distinguished by looking for occurrences of thedisease in a family tree or pedigree. Genetic markers are DNA sequencesthat show polymorphism (variations in size or sequence) in thepopulation. They are present in everyone and they can be typed (theallele can be identified) using techniques such as thepolymerase chain reaction .
This ability to determine the parental origin of a DNA sequence allowsus to show whether recombination has taken place. Recombination occursin germ cells – the cells that make eggs and sperm. In these cells, thematernal and paternal chromosomes pair up and exchange parts. Afterrecombination, the chromosomes contain a mixture of maternal andpaternal alleles. These mixed up chromosomes are placed in our eggs orsperm and passed to our children (see Figure).
As recombination occurs more – orless at random, if there is a large distance between two DNA sequenceson a chromosome, there is a good chance that recombination will occurbetween them and the maternal and paternal alleles will be mixed up(see A and C in the Figure). In contrast, if two DNA sequences are veryclose together, they will recombine only rarely. The maternal andpaternal alleles will tend to stay together (see A and B in theFigure).
Disease genes are mapped bymeasuring recombination against a panel of different markers spreadover the entire genome. In most cases, recombination will occurfrequently, indicating that the disease gene and marker are far apart.Some markers however, due to their proximity, will tend not torecombine with the disease gene and these are said to be linked to it.Ideally, close markers are identified that flank the disease gene anddefine a candidate region of the genome between 1 and 5 million bp inlength. The gene responsible for the disease lies somewhere in thisregion.