SourceInference

The SourceInference method implements a bioinformatic workflow that determines the element-of-origin of somatic L1s through the identification of specific SNVs shared between L1 sources and their derived insertions. The method starts by genotyping all germinal full-length L1 loci within each patient’s normal genome to identify the diagnostic SNVs that characterize each L1 source. Then, the algorithm identifies SNVs in the repertoire of L1 somatic copies in the patient’s tumour genome. Finally, the element-of-origin of each individual somatic copy is inferred by comparing the set of SNVs present in each somatic copy with the set of diagnostic SNVs that characterize each source L1.