Hearing presentations at the Advances for Genome Biology and Technology conference you don’t know exactly where it may lead. This was the case with Dr. Carlos Bustamonte (Stanford University, California US) and his presentation entitled “PhenoCap: A Targeted Capture Panel for Comprehensive Phenotyping of Forensic DNA Samples”. (Dr. Meredith Carpenter in his group was scheduled to give the presentation but due to an emergency Dr. Bustamonte gave it instead.)
He began his presentation saying that ‘ancient DNA is all the rage’. We’ve written before about using NGS for forensic analysis here and we recorded a video interview of a poster presented at the Society for Human Genetics meeting on decoding ancient bulgarian DNA. His group published an exome-capture method in 2013 that uses biotinylated RNA baits for ancient DNA (aDNA), and using this same approach they developed a forensic genotyping research panel they call ‘PhenoCap’.
This genotyping panel leverages previous work done by the forensic genetics community, such as from Dr. Manfred Keyser who characterized the six SNPs that determine eye color: blue or brown. (We interviewed him here on Behind the Bench.) Hair color can also be determined from genetics. In addition, the determination of gender is straightforward (a presence/absence assay for the Y-chromosome) and determination of maternal lineage via mitochondrial DNA are all available using targeted next-generation sequencing panels.
Bustamonte’s population genetics work covers many aspects of human migration – from the Tyrolian Iceman’s genome (a 5,300-year old mummy) yielding insight into the genetic structure of modern-day Europe, to Native American migration reconstruction using genomic data, to even gorilla demographic history.
In Mauritius and Madagascar, his group is working on the history of the largest long-distance forced movement of people in human history: the trans-Atlantic slave trade. By accessing the remains in graves of slaves over this period in the area, he can use their particular SNP markers to determine from what part of Africa they originated. He showed a photograph of a very high cliff on the island, Le Morne Brabant (556 meters or 1,824 ft from sea level), and shared the brief history of Mauritius as a runaway slave colony in the late 1700’s. In 1835 as an expedition traveled there to inform the population living on the peninsula that the slave trade was abolished, many slaves jumped to their death.
By accessing ancient DNA from these locations, his work traces the slave population from Africa to the Americas and Asia through population genetics. He showed a table of genetic origins of these samples due to waves of admixture with indentured workers and European immigration from 1721 through 1910.
He finished his talk with use of PhenoCap technology for Forensic DNA Phenotyping (called FDP), in particular the ability using Principal Components Analysis and population genetics information to geolocate even admixed samples to specific geographies around Europe. Not a lot of DNA sequencing is required – as few as 3 million reads per sample – illustrating the power of combining this sequencing technology with the remarkable advances in population genetics.