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Comparing Copy Number Variations and SNPs

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%...

Cell Lines

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A cell line is a population of cells grown in vitro that can be subcultured over several generations. Normal cells cease to divide after a certain number of cell divisions, a process known as replicative senescence. This number, called the Hayflick limit, was conceptualized by Leonard Hayflick in 1961 when he observed that fetal cells grown in culture could only divide 40-60 times. This limit is due to the shortening of the telomeres during each round of cell division, preventing cell division...

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Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3 variants are also...

Single Nucleotide Polymorphisms-SNPs

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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,...

Lampbrush Chromosomes

Lampbrush Chromosomes

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Updated: May 24, 2026

Chromosome Preparation From Cultured Cells

Chromosome Preparation From Cultured Cells

Published on: January 28, 2014

Chromosomal variation in lymphoblastoid cell lines.

Matthew D Shirley¹, Joseph D Baugher, Eric L Stevens

¹Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.

|March 1, 2012

Summary

Lymphoblastoid cell lines (LCLs) generally reflect primary blood cell genotypes, but a significant percentage exhibit large mosaic chromosomal changes not found in original samples.

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Last Updated: May 24, 2026

Chromosome Preparation From Cultured Cells

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A Simple Red Blood Cell Lysis Method for the Establishment of B Lymphoblastoid Cell Lines

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Area of Science:

Genomics
Cell Biology
Population Genetics

Background:

Lymphoblastoid cell lines (LCLs) are widely used in research for population genomics, disease mechanisms, and pharmacogenomics.
Ensuring the genetic integrity of LCLs is crucial for reliable research outcomes.
Understanding chromosomal variation in LCLs is fundamental for their accurate interpretation.

Purpose of the Study:

To assess chromosomal variation, specifically genotype and copy number, in LCLs compared to their primary source material (PBMCs) and other cell types.
To identify and characterize LCL-specific chromosomal changes.
To provide a community resource of LCL-specific genetic alterations.

Main Methods:

Comparison of genotype and copy number variation in LCLs derived from single individuals' PBMCs.
Analysis of LCLs against differentiated cell lines (DCLs) and HapMap samples.
Validation using data from a large study of blood and LCL samples.

Main Results:

High concordance was observed between LCL genotypes and PBMC genotypes.
13.7% of immortalized LCLs showed mosaic chromosomal regions (>20 Mb) absent in PBMCs, DCLs, or HapMap samples.
Putative LCL-specific changes, including those at immunoglobulin loci, were identified.

Conclusions:

While LCLs largely maintain genomic integrity, a notable proportion harbor significant mosaic alterations.
These LCL-specific changes may impact research findings and need careful consideration.
A curated list of LCL-specific changes is provided as a valuable resource for the research community.