Applied Biosystems DNA Analysis Technologies Aiding Genographic Project
News May 07, 2008
As some early humans began to leave their native Africa around 60,000 years ago in a wave of migration that would ultimately populate the planet, they slowly began to accumulate and pass down various random genetic mutations that would ultimately result in the diversity we see in people today.
Analyzing these genetic variations for a better understanding of human diversity and the history of thousands of years of global migration is the goal of the Genographic Project – a five-year research partnership between National Geographic and IBM, with field support from the Waitt Family Foundation, and DNA analysis technology from Applied Biosystems, an Applera Corporation business.
Applied Biosystems, a leading global supplier of life sciences technology, joined the Genographic Project as a supporting sponsor in 2006. Each of the 10 participating global research centres use Applied Biosystems equipment and services in their laboratories.
Since joining the Project, the company has been equipping the regional laboratories with a complete workflow for advanced genetic analysis consisting of instruments, reagents and software, as well as providing training and support, including designing a custom set of genetic assays for the project.
The Genographic researchers utilize Applied Biosystems technology in their ongoing genetic analysis of the field samples. One of a series of planned publications from this field research appeared last month in the American Journal of Human Genetics from the Lebanese American University in Beirut1.
The scientific team for this paper was led by Dr Pierre Zalloua, PhD, and Dr Chris Tyler-Smith, PhD. They used a combination of the company’s genotyping technologies to show that both the Islamic Expansion from the Arabian Peninsula beginning in the 7th century and the Crusades originating out of Western Europe in the 11th-13th centuries, left a genetic footprint on the modern-day Lebanese population.
The Genographic team conducted two types of genotyping analysis to identify the historical markers. Their approach involved studying the non-recombinant region of the Y-chromosome, which does not change with each generation and is directly passed down from father to son. Rare and random mutations provide the only changes to this area of the chromosome.
As a result, scientists can look at polymorphisms resulting from these small and infrequent changes to identify how migrating populations mixed and left recognizable genetic markers in modern populations in different parts of the world.
For the first type of analysis, the team used the Applied Biosystems 7900HT Real-Time PCR System and a set of Custom TaqMan® Genotyping Assays, complemented by the company’s SNaPshot® Multiplex System to assign each of the 926 samples to a haplogroup, which is determined by a common variation that broadly defines the branch of the ancestral tree to which an individual belongs. After showing that both Western European and Arabian markers appeared in the modern-day Lebanese population, the team used a second technological approach to investigate whether these findings could be confirmed and more specific origins suggested.
For the second analysis, the team used the Applied Biosystems 3130xl Genetic Analyzer with the AmpFlSTR® Yfiler® PCR Amplification Kit and a set of custom Y-STR primers to assign each sample to a specific haplotype. This process further refines a person’s ancestry by revealing a detailed lineage that can be family-specific. The result of this analysis suggested that some of the lineages found in the modern-day Lebanese population were in fact the result of historical migrations from Western Europe during the Crusades.
“We found a striking correlation between documented historic events and the genetic signatures identified in the current population of Lebanese men,” said Dr Zalloua. “Applied Biosystems’ lab technologies were chosen and used for this project both for their unprecedented reliability and the tremendous scientific expertise the company brings to our research. I believe the latest study is just the tip of the iceberg of what we can do with the Applied Biosystems technology.”