Challenges in Detecting Somatic Recombination of Repeat Elements: Insights from Short and Long Read Datasets

Non-allelic copies of the two major families of repeat elements in the human genome, Alu and L1, recombine somatically at high frequency. Tissue-specific recombination profiles are dynamic in cell differentiation and are altered in neurodegeneration, suggesting that somatic recombination of repeat elements can contribute to functional heterogeneity of cells in health and disease. The study of these genomic variants, however, presents several technical challenges related to their extremely low copy number and their sequence content. Here, we address key issues regarding detecting and annotating structural variants derived from recombining repeat elements in NGS data. We show that PCR introduces significant changes of recombination profiles in sequencing libraries and that recombination profiles are affected by the choice of sequencing platform. We refine previous estimates of recombination in single cells by analyzing recombination profiles in PCR-free HG002 datasets sequenced by Oxford Nanopore Technologies and PacBio sequencers while describing several platform-specific differences. We additionally provide evidence that recombination events annotated in state-of-the-art single-cell HG002 whole-genome sequencing datasets are likely molecular artifacts generated by PCR. By exploring the limits of current technologies, this work establishes essential requirements for future developments to enhance the reliability of detecting somatic recombination of repeat elements in genomic datasets.