ArticleGenome research2012
Assessment of palindromes as platforms for DNA amplification in breast cancer.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 42 citations in OpenAlex.
- A Practical Approach for Targeting Structural Variants Genome-wide in Plasma Cell-free DNA.Research square · 2024Article
- A unifying model that explains the origins of human inverted copy number variants.PLoS genetics · 2024Review
- Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions.Nucleic acids research · 2023Article
- Genome-Wide Analysis of Palindrome Formation with Next-Generation Sequencing (GAPF-Seq) and a Bioinformatics Pipeline for Assessing De Novo Palindromes in Cancer Genomes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Structural parameters of palindromic repeats determine the specificity of nuclease attack of secondary structures.Nucleic acids research · 2021Article
- Palindromes in DNA-A Risk for Genome Stability and Implications in Cancer.International journal of molecular sciences · 2021Review
- PPP2R2B downregulation is associated with immune evasion and predicts poor clinical outcomes in triple-negative breast cancer.Cancer cell international · 2021Article
- A reference catalog of DNA palindromes in the human genome and their variations in 1000 Genomes.Human genome variation · 2020Article
- Mechanisms underlying genome instability mediated by formation of foldback inversions ineLife · 2020Article
- Clonal evolution driven by superdriver mutations.BMC evolutionary biology · 2020Article
- Expression-based analyses indicate a central role for hypoxia in driving tumor plasticity through microenvironment remodeling and chromosomal instability.NPJ systems biology and applications · 2018Article
- Whole Genome Sequence Analysis of Mutations Accumulated inG3 (Bethesda, Md.) · 2017Article
- Palindromic amplification of the ERBB2 oncogene in primary HER2-positive breast tumors.Scientific reports · 2017Article
- A pilot study on the prevalence of DNA palindromes in breast cancer genomes.BMC medical genomics · 2016Article
- Telomere Dysfunction Triggers Palindrome Formation Independently of Double-Strand Break Repair Mechanisms.Genetics · 2016Article
- Cancer evolution: mathematical models and computational inference.Systematic biology · 2015Review
- GAP-Seq: a method for identification of DNA palindromes.BMC genomics · 2014Article
- Large inverted duplications in the human genome form via a fold-back mechanism.PLoS genetics · 2014Article
- Prediction of potential cancer-risk regions based on transcriptome data: towards a comprehensive view.PloS one · 2014Article
- 16p11.2-p12.2 duplication syndrome; a genomic condition differentiated from euchromatic variation of 16p11.2.European journal of human genetics : EJHG · 2013Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
DNA amplification, particularly of chromosomes 8 and 11, occurs frequently in breast cancer and is a key factor in tumorigenesis, often associated with poor prognosis. The mechanisms involved in the amplification of these regions are not fully understood. Studies from model systems have demonstrated that palindrome formation can be an early step in DNA amplification, most notably seen in the breakage-fusion-bridge (BFB) cycle. Therefore, palindromes might be associated with gene amplicons in breast cancer. To address this possibility, we coupled high-resolution palindrome profiling by the Genome-wide Analysis of Palindrome Formation (GAPF) assay with genome-wide copy-number analyses on a set of breast cancer cell lines and primary tumors to spatially associate palindromes and copy-number gains. We identified GAPF-positive regions distributed nonrandomly throughout cell line and tumor genomes, often in clusters, and associated with copy-number gains. Commonly amplified regions in breast cancer, chromosomes 8q and 11q, had GAPF-positive regions flanking and throughout the copy-number gains. We also identified amplification-associated GAPF-positive regions at similar locations in subsets of breast cancers with similar characteristics (e.g., ERBB2 amplification). These shared positive regions offer the potential to evaluate the utility of palindromes as prognostic markers, particularly in premalignant breast lesions. Our results implicate palindrome formation in the amplification of regions with key roles in breast tumorigenesis, particularly in subsets of breast cancers.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.