Abstract
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.
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Acknowledgments
This work is supported by the National Cancer Institute (2 R01 CA149385), Department of Defense (W81XWH-18-1-0058), Cedars-Sinai Medical Center (to H.T.), and the Margie and Robert E. Petersen Foundation (to A.E.G.).
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Murata, M.M., Giuliano, A.E., Tanaka, H. (2023). Genome-Wide Analysis of Palindrome Formation with Next-Generation Sequencing (GAPF-Seq) and a Bioinformatics Pipeline for Assessing De Novo Palindromes in Cancer Genomes. In: Kasid, U.N., Clarke, R. (eds) Cancer Systems and Integrative Biology. Methods in Molecular Biology, vol 2660. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3163-8_2
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DOI: https://doi.org/10.1007/978-1-0716-3163-8_2
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