A gift to support research in biomolecular engineer David Haussler’s laboratory at the University of California, Santa Cruz, has made possible the Edward Schulak Fellowship in Genomics.
The fellowship is to support groundbreaking research in genomics.
Schulak, an international business leader, architect, entrepreneur, real estate developer, and inventor said, “Genomics is answering the questions that had never been thought possible to answer, even questions we did not know to pose.”
Graduate student Adam Novak received the Schulak fellowship. He will use it to develop a computational method that can resolve ambiguities in disease-related gene sequences.
With this fellowship, Novak will develop a new way to map highly repetitive regions of the genome—regions that frustrate current mapping methods because of their variability.
“This is a way to represent both little changes and massive structural variations in the genome,” Novak said.
Novak explained that when a genome sequence is looked at as simply a line of DNA bases, each time you update the genome with new information—such as adding another genome base or group of bases to the genome—the linear coordinates change, making it hard to locate specific features.
Novak’s new method sets up a graph that condenses related areas of the genome together. “It’s essentially the same process of pinning the DNA segments to a map, but it’s easier to figure out where every segment maps, because highly similar sequences are merged together.”
“This makes the problem smaller and more tractable,” Novak said, “and it allows us to reason more completely about the information in DNA reads that are otherwise ambiguously mapped.”
The new system involves creating a new set of terminology to name locations in the genome, defining them in a manner not related to distance from the start of a chromosome. All the instances of a particular repeated segment can be in one location on the graph. The system will also name common deletions—another type of copy-number variation.
Novak cited a genomic region critical to immune response, the major histocompatibility complex, as a situation for which graphic mapping will provide simpler visualization and analysis. The major histocompatibility complex contains variations associated with a large proportion of known human diseases, and it features alternative ordering and arrangement of genes. “These can be complex series of genes whose variations can lead to a variety of outcomes.”
“Because the major histocompatibility complex is so variable, I would like to be able to show a general situation and then what else can occur.” Novak said, “It would be convenient to assign base names rather than linear location coordinates to the bases involved.”