Abstract: Systems and methods for predicting a prevalence of loss of heterozygosity (LOH) in a target population of cells are disclosed, wherein the system comprises a memory and a processor configured to receive genetic data for a first reference population of cells. The processor is configured to sequence the genetic data for the first reference population of cells to obtain first reference data; identify and remove heterozygous variant positions having imbalanced allelic expression in the first reference data to generate second reference data; map identifiers for each cell of the target population of cells to the second reference data; and apply the mapped identifiers for each cell of the target population of cells to a supervised machine learning model. The processor is further configured to receive one or more outputs from the model, at least one of the one or more outputs including an LOH for the target population of cells.