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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

17.7K
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%...
17.7K
Single Nucleotide Polymorphisms-SNPs01:05

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Related Experiment Video

Updated: Jul 18, 2025

Detection of Copy Number Alterations Using Single Cell Sequencing
09:45

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

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Single-cell somatic copy number variants in brain using different amplification methods and reference genomes.

Ester Kalef-Ezra1,2, Zeliha Gozde Turan1,2, Diego Perez-Rodriguez1

  • 1Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.

Biorxiv : the Preprint Server for Biology
|August 23, 2023
PubMed
Summary
This summary is machine-generated.

Somatic copy number variants (CNVs) exist in human brain cells. Choosing the right whole genome amplification method and reference genome is crucial for accurate CNV detection in neurological research.

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Area of Science:

  • Neuroscience
  • Genetics
  • Genomics

Background:

  • Somatic mutations, including copy number variants (CNVs), are present in the brain.
  • Studying these requires single-cell whole genome amplification before sequencing.

Approach:

  • Compared PicoPLEX, primary template-directed amplification (PTA), and droplet multiple displacement amplification (MDA) on 93 human brain cortical nuclei.
  • Evaluated amplification breadth, evenness, and chimeric profiles of each method.
  • Performed copy number variant (CNV) calling on two multiple system atrophy brains and one control brain using different reference genomes.

Key Points:

  • PTA showed the broadest amplification, PicoPLEX the most even, with distinct chimeric profiles.
  • 38% of brain cells analyzed had at least one megabase-scale CNV.
  • CNV calls varied based on the whole genome amplification method and reference genome used.

Conclusions:

  • The choice of whole genome amplification method and reference genome significantly impacts CNV calling accuracy.
  • Somatic CNVs are present in both healthy and diseased human brain cells.
  • This research underscores the importance of methodological selection for robust brain somatic CNV detection.