DNA palindromes are a type of chromosomal aberration that appears frequently during tumorigenesis. They are characterized by sequences of nucleotides that are identical to their reverse complements and often arise due to illegitimate repair of DNA double-strand breaks, fusion of telomeres, or stalled replication forks, all of which are common adverse early events in cancer. Here, we describe the protocol for enriching palindromes from genomic DNA sources with low-input DNA amounts and detail a bioinformatics tool for assessing the enrichment and location of de novo palindrome formation from low-coverage whole-genome sequencing data.
Keywords: Bioinformatics; Breakage–fusion–bridge (BFB) cycles; DNA palindromes; Fold-back inversions; Genomic amplification; Genomic instability; Inverted repeats; Large chromosomal aberrations; Next-generation sequencing.
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.