As explained in the Genetics section, human DNA is made up of thousands of genes. Since there are so many genes, and many have overlapping functions, it’s very difficult to figure out which gene change is responsible for causing a particular disease.
In the past, the most commonly used method of gene discovery was a “linkage study,” which is how we and our collaborators discovered the PANK2 gene. A change or alteration in the PANK2 gene causes PKAN, the most common form of NBIA. A linkage study allows scientists to determine the rough position within the DNA where the gene of interest could be located. In other words, it might be able to tell you the town or neighborhood where the gene lives, but it doesn’t give you the exact address.
We began by identifying and recruiting as many families with NBIA as possible, especially families with more than one affected individual. After getting their consent to be part of the study, we collected their DNA through a blood draw and requested and carefully studied their medical records and brain imaging results. We analyzed and compared all the DNA samples to determine if there was a section of the DNA (a genetic marker) that was present in the individuals with NBIA, but not present in their relatives who were unaffected. By comparing affected relatives to unaffected relatives, we were able to narrow down the number of differences we might find because relatives share much of the same DNA.
Once a genetic marker was identified, we had to start analyzing every gene within that area of the DNA to see if it was the one associated with PKAN. This is similar to knocking door-to-door in the neighborhood where we knew the gene must live. We compiled a list of all the genes in that region and started analyzing them one at a time until we identified PANK2. As you can imagine, this process takes a very long time, but it was the best method we had available back then. The same method was used to discover the PLA2G6 gene, which is associated with PLAN. This time, we narrowed down the region to about 100 genes, and the OHSU team started sequencing genes at one end while our collaborators in the UK started at the other end. We hoped we would get lucky and find the culprit before we met in the middle!
However, things had changed when we recently decided to take another try at finding the BPAN gene. We had tried before using linkage methods, but never found anything. We started the process the same way, by collecting families with NBIA and figuring out which ones had similar symptoms. Since BPAN has some very characteristic findings, including early developmental delay and later onset of movement disorder symptoms, it was easier to group these patients and search for a common thread. This time we used a newer technology called exome sequencing. Exome sequencing allowed us to sequence and compare their entire DNA at once instead of first having to identity an area of interest. This process is much faster, and we ended up finding a change in the same gene (WDR45) in nearly all the individuals with a similar pattern of symptoms.
The linkage methods we used in the past were like trying to find a needle in a haystack. Also, linkage studies get more difficult to do when a condition is rare, like many of the NBIA disorders. Unlike a linkage study, exome sequencing allows us to study rare conditions because fewer samples of DNA are needed, we can compare affected individuals from different families, and we can study conditions caused by a new gene change in the affected individual. Due to exome sequencing, the process of gene discovery has become much faster and easier.
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