Methods
The African Kinship Reunion (TAKiR) project employs advanced genetic analysis and social science research methods to uncover ancestral connections and facilitate family reunifications between Africans and their historic diaspora.
DNA Sample Collection and Processing
Participants provide DNA samples using saliva collection kits, which are processed at the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign. DNA is extracted from the saliva samples and genotyped using the Illumina Global Diversity Array and high-quality, array-based methods. This array is specifically designed to capture genetic diversity across global populations, making it well-suited for studying African ancestry and the African diaspora. The resulting genotype data is then subjected to rigorous quality control measures, including the removal of duplicate entries, filtering for SNPs, and setting minor allele frequency thresholds to ensure data integrity and accuracy.
Haplotype Phasing and Reference Panel Selection
To enhance the resolution and accuracy of the genetic analysis, the genotype data is phased using Beagle 5.4, a powerful statistical phasing tool. Beagle 5.4 employs an iterative algorithm and hidden Markov models to estimate haplotypes, which are the specific combinations of alleles inherited from each parent. This phasing process is crucial for identifying shared segments of DNA and inferring genetic relatedness. The phased data is then merged with a carefully selected reference panel, which includes populations from the 1000 Genomes Project, such as African Ancestry SW (ASW), Gambian Mandinka (GWD), Mende (MSL), Yoruba (YRI), and CEPH (CEU). By incorporating this diverse reference panel, the project can obtain valuable relatedness information and contextualize the genetic ancestry of participants within the broader landscape of African genetic diversity.
Identity-by-Descent (IBD) Analysis
To identify shared genetic segments and infer relatedness among participants and between participants and individuals in the reference panel, TAKiR utilizes IBIS, an advanced IBD segment detection method. IBIS is specifically designed to detect IBD segments in populations with complex ancestry, such as African Americans and other members of the African diaspora. By leveraging the power of IBIS, the project can detect genetic relatedness between Africans and members of the historic diaspora, even for distant relationships dating back to the era of the Transatlantic Slave Trade. This approach allows TAKiR to uncover previously unknown connections and shed light on the genetic legacy of this historical event.
Genetic Family Tree Inference
Building upon the IBD analysis, TAKiR employs the Bonsai method to reconstruct multigenerational genetic family trees. Bonsai is a sophisticated algorithm that infers large, sparse pedigrees from genotype data in three main stages. First, it constructs small pedigrees of close relatives using pairwise genetic data and age information. Next, these small pedigrees are combined into larger pedigrees using specialized tools, including a generalized degree estimator, ancestral lineage checks, and background IBD detection. These tools enable Bonsai to accurately infer relationships and construct comprehensive family trees spanning multiple generations. Finally, the algorithm re-infers portions of the pedigree when implied relationships conflict with initial predictions, ensuring the consistency and reliability of the inferred family trees.
Social Science Research
Recognizing the profound social, emotional, and cultural significance of family reunification, TAKiR conducts concurrent social science research to explore the lived experiences and perspectives of participants. Through surveys, interviews, and focus group discussions, participants are invited to share their motivations for joining the project, their reactions to discovering their genetic heritage, and the impact of reconnecting with long-lost relatives. This qualitative data provides valuable insights into the personal and collective journeys of identity, belonging, and healing that unfold through the process of family reunification. By integrating genetic analysis with social science research, TAKiR aims to create a holistic understanding of the African diaspora experience and the enduring legacy of the Transatlantic Slave Trade.