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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

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Related Experiment Video

Updated: May 12, 2026

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors
09:22

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Published on: February 28, 2021

Clinical variant interpretation comparing two saturation genome editing-based functional studies for BRCA2.

Ju Hyeon Shin1,2, Kyung Sun Park3, Young-Gon Kim1

  • 1Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.

Frontiers in Genetics
|May 11, 2026
PubMed
Summary

Saturation genome editing (SGE) studies for BRCA2 variants showed conflicting results. Concordant findings aided variant reclassification, while discordant results highlighted the HAP1-SGE dataset

Keywords:
BRCA2MAVEfunctional evidencesaturation genome editingvariant interpretation

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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

Published on: October 6, 2014

Area of Science:

  • Genomic Medicine
  • Molecular Biology
  • Clinical Genetics

Background:

  • Saturation genome editing (SGE) studies for BRCA2 variants yield contradictory functional results.
  • Discrepancies observed in 16.9% of variants between HAP1 and mouse embryonic stem cell studies.
  • Need for clinical variant interpretation to reconcile conflicting SGE data with clinicopathological information.

Purpose of the Study:

  • To address discordance in SGE functional results for BRCA2 variants.
  • To compare SGE findings with clinical data and reclassify variants.
  • To evaluate the utility of SGE in clinical variant interpretation.

Main Methods:

  • Retrospective collection of patient data with BRCA2 variants from SGE studies.
  • Reassessment of variants using ClinGen BRCA1/2 guidelines and multifactorial likelihood analysis.
  • Assignment of PS3 or BS3 for concordant SGE results and comparison of error rates for discordant results.

Main Results:

  • 13 of 88 variants (14.8%) showed discordant SGE results.
  • HAP1-SGE dataset showed lower major error rates, but not statistically significant.
  • 28 variants assigned PS3 and 47 assigned BS3 based on concordant results.
  • 93.1% of variants of uncertain significance were reclassified (3 likely pathogenic, 24 likely benign).

Conclusions:

  • Concordant SGE results are valuable for clinical variant reclassification.
  • Functional evidence should not be assigned for discordant SGE results.
  • The HAP1-SGE dataset appears more consistent with patient-specific data.
  • Further studies are required to resolve discordant SGE findings.