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Related Concept Videos

Homologous Recombination02:31

Homologous Recombination

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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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Mismatch Repair01:20

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Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
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DNA Distortion and Damage
Cells are regularly exposed to mutagens—factors in the environment that can damage DNA and generate mutations. UV radiation is one of the most common mutagens and is estimated to introduce a significant number of changes in DNA. These include bends or kinks in the structure, which can block DNA replication or transcription. If these errors are not fixed, the damage can cause mutations, which in turn can result in cancer or disease depending on which sequences are...
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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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The Retinoblastoma Gene01:20

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Tumor suppressor genes are normal genes that can slow down cell division, repair DNA mistakes, or program the cells for apoptosis in case of irreparable damage. Hence, they play an essential role in preventing the proliferation of damaged cells.
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Updated: Aug 28, 2025

Identifying the Effects of BRCA1 Mutations on Homologous Recombination using Cells that Express Endogenous Wild-type BRCA1
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RNA-Based Classification of Homologous Recombination Deficiency in Racially Diverse Patients with Breast Cancer.

Andrea Walens1,2, Sarah C Van Alsten2, Linnea T Olsson2

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Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology
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Aberrant DNA repair, specifically homologous recombination deficiency (HRD), impacts breast cancer prognosis. RNA-based HRD indicators predict outcomes in diverse patient groups, highlighting disparities in Black women.

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gDNA Enrichment by a Transposase-based Technology for NGS Analysis of the Whole Sequence of BRCA1, BRCA2, and 9 Genes Involved in DNA Damage Repair
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Area of Science:

  • Genomics
  • Oncology
  • Molecular Biology

Background:

  • Aberrant DNA repair pathways, including homologous recombination (HR), contribute to genomic instability and affect chemotherapy response in breast cancer.
  • DNA repair pathway variations in diverse patient cohorts remain understudied, yet may predict prognosis.

Purpose of the Study:

  • To identify RNA-based expression patterns of DNA repair genes.
  • To develop and validate RNA-based classifiers for homologous recombination deficiency (HRD).
  • To assess the association of these classifiers with patient demographics, tumor characteristics, and clinical outcomes.

Main Methods:

  • Performed unsupervised clustering on 51 DNA repair genes in TCGA BRCA (n=1,094) and CBCS (n=1,461) cohorts.
  • Trained a supervised RNA-based HRD classifier using DNA-based HRD scores from TCGA.
  • Evaluated unsupervised and supervised HRD classifiers against demographics, tumor features, and outcomes.

Main Results:

  • Identified four distinct breast tumor clusters based on DNA repair gene expression, with one showing high HR gene expression.
  • Unsupervised HRD (U-HRD) profiles were found in 39.7% of CBCS and 29.3% of TCGA tumors.
  • Supervised HRD (S-HRD) classifier achieved 84% sensitivity and 73% specificity; S-HRD high tumors showed enrichment for TP53 mutations and basal-like subtype, and were more common in Black patients.
  • S-HRD high was associated with increased recurrence risk (HR: 2.38) in chemotherapy-treated patients.

Conclusions:

  • Homologous recombination deficiency (HRD) is linked to poorer breast cancer prognosis.
  • HRD is disproportionately enriched in the tumors of Black women.
  • RNA-level indicators of HRD are predictive of breast cancer outcomes across diverse populations.