DNA Inverted Repeats as an At-risk Motif for Palindromic Gene Amplification

DNA Inverted Repeats as an At-risk Motif for Palindromic Gene Amplification defines oncogene amplification that is configured as a series of inverted duplications (palindromic gene amplification). To study the impact of palindromic gene amplification in cancer genomes, we developed an approach to enrich DNA palindromes from genomic DNA (Genome-wide Analysis of Palindrome Formation, GAPF-seq). This dbGaP site lists the files of GAPF-seq of tumor DNA and plasma DNA from cancer patients. This site also lists other genomic data, such as shallow whole-genome sequencing (WGS) data. WGS data were used to examine the association of DNA palindromes, detected by GAPF-seq, and genomic amplification, detected by WGS.

In the initial study, we show that the ERBB2 oncogene at 17q12 is susceptible to palindromic gene amplification in HER2-positive breast tumors. We investigated eight tumors in this study, of which five tumors were HER2-positive, and three tumors were HER2-negative. HER2 status was determined by clinical FISH tests. We applied three genomic approaches to investigate the amplification mechanism: (1) copy number analysis by array-CGH on the Affymetrix SNP6.0 platform (8 files), (2) sequencing of DNA libraries enriched with tumor-derived palindromic DNA (Genome-wide Analysis of Palindrome Formation, GAPF-seq) (8 files) and (3) unbiased whole-genome sequencing (WGS) (1 file). These molecular data are made available in the dbGaP.

Genomic studies using tumor DNA were approved under the Internal Institutional Review Board at the Cleveland Clinic (IRB07-136: EXEMPT: Chromosome Breakage and DNA Palindrome Formation). Specimens were obtained and methods were carried out under the auspices of IRB 7881 (Evaluation of Genetic and Molecular Markers in Patients with Breast Cancer). All patients consented to allow their cancer specimens to be used by researchers in an anonymized fashion. The consent form indicates that publication will take place without identifiers to protect the identity of any specific individual.

We observed significant enrichment of palindromic DNA within amplified ERBB2 genomic segments in four out of five HER2-positive tumors. None of the three HER2-negative tumors showed such enrichment. Palindromic DNA was particularly enriched at amplification peaks and boundaries between amplified and normal copy-number regions. Thus, palindromic gene amplification shaped the amplified ERBB2 locus. The moderate enrichment of palindromic DNA throughout the amplified segments leads us to propose that the ERBB2 locus is amplified through a mechanism that repeatedly generates palindromic DNA, such as Breakage-Fusion-Bridge cycles. Our results reveal a potential interaction between local genomic environments and gene amplification mechanisms. This study is published under the title "Palindromic amplification of the ERBB2 oncogene in primary HER2-positive breast tumors" (PMID:28211519). In a follow-up, cell-based molecular and cytogenetic study, we defined a nearby genomic block that is fragile and initiates palindromic amplification of ERBB2 (PMID: 33290559).

We expanded the sequencing of DNA libraries enriched with tumor-derived palindromic DNA (Genome-wide Analysis of Palindrome Formation, GAPF-seq) for other breast cancer subtypes, ER-positive and triple-negative breast tumors. In addition to the GAPF-seq data from tumor DNA, we also examine DNA palindromes in cancer patients' plasma DNA in an effort to evaluate GAPF-seq as a sensitive cancer detection test of liquid biopsy. We initiated liquid biopsy studies using breast and prostate cancer patients' plasma DNA. 

• Study Design:
  • Case Set
• Study Type:
  • Case Set
• Total number of consented subjects: 8
• Subject Sample Telemetry Report (SSTR)

• BioProject
• PubMed
• Sequence Read Archive
• BioSample
• MeSH
• Gene
• PMC

Initially, the study included only HER-2 positive breast cancer patients. However, we expanded the study for other breast cancer subtypes and prostate cancer. For breast cancer DNA, we only include females, as the vast majority of breast tumor patients are females. For prostate cancer study, we only include males, as the prostate is a male-specific organ.

• Primary Phenotype: Neoplasms by Site
• Breast Neoplasms
• Prostate Neoplasms

• AR
• CCND1
• ERBB2

• Principal Investigator
  • Hisashi Tanaka, MD, PhD. Cedars-Sinai Medical Center, Los Angeles, CA, USA.
• Funding Source
  • R01 CA149385. National Institutes of Health, Bethesda, MD, USA.
  • W81XWH1810058. USAMRAA.