1000 Genomes: A rich profile of genetic diversity

September 30, 2015
Written By:
Laurel Thomas

ANN ARBOR—A project to survey genetic information from across the world has completed its final phase, after analyzing the genomes of 2,504 individuals from 26 populations across five continents and 18 countries.

In the end, scientists from around the world catalogued 88 million variants, which mark genetic differences within and among populations.

One of the top researchers in the multiyear study is Gonçalo Abecasis, chair of the U-M School of Public Health’s Department of Biostatistics and co-lead author of a cover article featured in the latest issue of Nature.

“We now have a public repository that describes the range and diversity of genetic variation around the world,” Abeçasis said. “We now know which genes rarely change and which are altered in different populations.”

The latest phase of the project mapped individuals sampled from Africa, East Asia, Europe, South Asia and the Americas.

The researchers said the typical genome differs from a reference human genome at 4-5 million sites along the DNA strand. They found that 12 million of the 88 million variants were common across all continents, while 24 million were unique to a geographic area or population.

The majority of the variants, 64 million, were considered rare in frequency, occurring in only 1 percent or less of the population.

The group with the most variants was African, which the researchers said reflects the outmigration of that population to other parts of the world.

“Over the course of the 1000 Genomes Project, we have dramatically improved our knowledge of variation in the human genome. Now, the key challenge for the community is to understand how this variation influences disease,” said lead author Adam Auton, who conducted the research while at the Albert Einstein College of Medicine in New York, and recently moved to the private genetic mapping company 23andMe.

The ultimate goal of the project was to have detailed genetic information on at least 1,000 people, leading a better understanding of the history and evolution of genetic variation. This catalog of genetic diversity was created to support further study by scientists seeking to understand disease origins and behaviors, and looking for treatments and cures.

The first human genome was mapped some 15 years ago at a cost of $3 billion, Abeçasis said.

“When a goal was set to map the genes of 1,000 people across the world and work was started in 2008, the genomes of six or seven individuals had been sequenced,” he said.

Over the course of the project, much work went into perfecting the equipment and methods used, increasing the speed of discovery and lowering costs for the research.

One statistic the authors point to that demonstrates this improvement is that when the team announced the first 180 genomes in 2010, scientists were missing approximately 15-20 percent of each genome. In the most recent analysis, the number was down to 4 percent, reflecting increased improvements in DNA analysis tools and computational methods.

In fact, so much has advanced in the field since the project started that larger genome studies have been using methods developed by the project to study diseases like Alzheimer’s, autism and diabetes, Abecasis said. Yet the majority of those projects have looked at one population, most often Europeans, and no research to date reflects the breadth of 1000 Genomes in terms of the various populations studied.

“Another thing that distinguishes 1000 Genomes is that the donors agreed that their data would be open and available to researchers around the world,” Abeçasis said. “This, and the diversity of variants we have discovered, make the outcome of this work relevant for the long haul.”


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