It’s no secret that genetics is hot right now, especially in the brain realm. The biggest story of 2014 was Ted Stanley’s stunning $650 million gift to mental health research at the Broad Institute, a research center that grew out of the Human Genome Project. But it's actually only the biggest of a wave of ambitious, multi-million-dollar gifts tackling the genetic foundations of everything from cancer to autism. There have been big gifts to develop technologies related to genomic engineering, too, as in the case of Li Ka-Shing’s $10 million gift to Berkeley.
The Simons Foundation seems to be kicking off 2015 in fine fashion, announcing a new $1 million grant to the Genomics Institute at UC Santa Cruz. Its goal? To develop a comprehensive map of human genetic variation.
Lost? Don’t be. Simply put, the current way we understand human genomic data relies on a single reference sequence for the human genome onto which all novel sequencing data is mapped to identify variants—a process that leads to biases and mapping ambiguities.
In an earlier Simons Foundation-funded project at the Broad Institute of MIT and Harvard, researchers David Reich and Nick Patterson amassed more than three hundred complete human genome sequences representing a range of ethnicities. In the UC Santa Cruz project, a team led by Genomics Institute director David Haussler and co-investigator Benedict Paten will use the Reich-Patterson set of genome sequences, which they say is deeper and more completely organized than any other data set, to build a new graph-based human reference genome structure called the Human Genome Variation Map, to replace isolated, incompatible databases around the world with a single fundamental representation formalized as a very large mathematical graph. In one fell swoop, it will take the guesswork out of human genome research.
To that end, the UC Santa Cruz team will collaborate with leading genomics researchers at other institutions to develop algorithms and formulate the best mathematical approach for constructing the new map. Initial work on developing a standard data model for the map is already under way in the context of the Global Alliance for Genomics & Health's Reference Variation Task Team, which is co-chaired by Paten.
"One exemplary human genome cannot represent humanity as a whole, and the scientific community has not been able to agree on a single precise method to refer to and represent human genome variants," said Haussler. "There is a great deal we still don't know about human genetic variation because of these problems."