MARCH 2015: planarPart: an efficient and robust approach for genetically-based geographic assignment

The EUROTAST fellows will be presenting the findings of their research at the upcoming Genetics/Heritage conference, 23-25 April at the International Slavery Museum in Liverpool. To attend the conference, visit the Genetics/Heritage website.

Title: planarPart: an efficient and robust approach for genetically-based geographic assignment

Author: Hákon Jónsson

Abstract:

The geographic separation between populations explains a significant proportion of the human genetic variation. Patterns of genetic variation can be exploited to provide insights about past population histories, illuminating events such as migrations and admixture. Additionally, the spatial structure within genetic datasets can be used to geographically assign individuals based on their genetic profiles, with wide ranging applications from genetic management to forensics. Here, we devised a scoring system measuring the genetic affinity of individuals to different geographical locations and model the score in a kriging framework. This allows us to interpolate the score across the geographical range and find the spatial position which maximizes the genetic affinity. This approach is implemented in a new tool, planarPart, and appears to outperform current alternatives in terms of accuracy and computational performance both at local and global scales. It can efficiently position individual without restricting assumptions about the shape of the allele frequency surface.

Our approach is therefore tailored to large-scale datasets such as those now generated by high-throughput sequencing platforms. Our scoring scheme is applicable on the haplotypes, allowing for estimating the spatial origin of the haplotypes present in the admixed populations, efficiently tapping into the information about our spatial ancestry and history encapsulated in the nuclear genome. In particular, we have explored the genetic legacy of the slave trade by tracing the geographical origins of the people captured during the trans-Atlantic slave trade (TAST) and by exploring the mosaic ancestry of populations affected by the TAST.