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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: Jun 1, 2026

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

Parent-specific copy number in paired tumor-normal studies using circular binary segmentation.

Adam B Olshen1, Henrik Bengtsson, Pierre Neuvial

  • 1Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA. olshena@biostat.ucsf.edu

Bioinformatics (Oxford, England)
|June 14, 2011
PubMed
Summary
This summary is machine-generated.

A new method, Paired PSCBS, analyzes parent-specific copy number (PSCN) from high-throughput genomic data. This approach effectively identifies copy-neutral loss of heterozygosity (LOH) in cancer genomes.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • High-throughput techniques enable genome-wide DNA copy number measurement.
  • Single nucleotide polymorphism (SNP) arrays allow quantification of parent-specific copy number (PSCN), unlike older total copy number methods.
  • Unphased, two-dimensional raw data from these experiments require novel analytical approaches.

Purpose of the Study:

  • To develop and enhance an algorithm for analyzing parent-specific copy number (PSCN) from paired genomic samples.
  • To adapt and improve the circular binary segmentation (CBS) algorithm for PSCN analysis.
  • To enable accurate identification of copy-neutral loss of heterozygosity (LOH).

Main Methods:

  • The Paired PSCBS algorithm was developed by enhancing the circular binary segmentation (CBS) method.
  • It identifies regions of equal total copy number and segments them based on PSCN changes.
  • The method performs copy number calls for parental contributions and LOH, computing PSCN estimates before and after.

Main Results:

  • Paired PSCBS demonstrated favorable performance compared to existing methods in simulations.
  • The method successfully identified significant genomic regions, including copy-neutral LOH, in glioblastoma data.
  • The PSCBS R package is available as open-source software.

Conclusions:

  • The Paired PSCBS method provides a robust approach for analyzing parent-specific copy number data.
  • It is effective in identifying copy-neutral LOH, a relevant finding in cancer genomics.
  • The open-source implementation facilitates its application in research.