A sensitive and specific microchimerism detection method using custom designed genotyping and companion qPCR assays

Since first reports of the presence of a small number of cells from one individual persisting in another, researchers have developed a number of methods to detect microchimerism. Molecular based detection platforms range from gel electrophoresis to quantitative PCR to Next-Gen Sequencing. Central to all approaches is the need for informative polymorphic loci to effectively distinguish microchimeric cells from the host. However, we observed in our studies of maternal microchimerism that currently published approaches can limit the number of samples available for assessment due to the inability to identify an informative marker of the donor in the recipient. This was most striking in our studies of populations of African descent in which the use of HLA-based markers, a common approach, prevented the testing of 30-50% of participants. Other potential options were cost prohibitive or lacked sufficient sensitivity. To address this challenge, we developed a novel, simple, and low-cost approach that leverages global population frequency databases for polymorphism selection, reduces cost by amplifying multiple targets in one multiplex assay to complete genotyping, and has high sensitivity and specificity using rigorously designed qPCR assays to quantify microchimerism. Herein, we outline our design process, detailed assay protocol, and assessment of maternal microchimerism using this approach in two different populations of infants from the United States and South Africa.