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Published on: August 17, 2022
Copy number variation in African Americans
Joseph P McElroy1, Matthew R Nelson, Stacy J Caillier
1Department of Neurology, University of California, San Francisco, CA, USA.
This study created the first copy number variant (CNV) map for African Americans using a high-density SNP platform. It identified population-specific CNV differences and potential DNA artifacts from cell lines.
Area of Science:
- Genomics
- Population Genetics
- Bioinformatics
Background:
- Copy number variants (CNVs) are linked to complex diseases, necessitating understanding their population distribution.
- This research presents the inaugural copy number variant (CNV) map specifically for the African American genome.
Purpose of the Study:
- To generate a comprehensive copy number variant (CNV) map for African Americans.
- To compare CNV frequencies between African Americans and White individuals.
- To identify potential sources of artifact in CNV mapping studies.
Main Methods:
- Utilized a SNP (Single Nucleotide Polymorphism) platform with over 500,000 markers.
- Analyzed DNA from 385 healthy African American individuals and 435 healthy White individuals.
- Compared CNV data derived from both cell lines and whole blood samples.
Main Results:
- A total of 1362 copy number variants (CNVs) were identified in the African American cohort.
- Two specific CNV regions (17q21 and 15q11) showed significant frequency differences between African Americans and Whites.
- A duplication was found in 74% of cell line-derived DNA samples but absent in whole blood samples, indicating a potential artifact.
Conclusions:
- The Affymetrix 500 K array is effective for reliable copy number variant (CNV) mapping.
- Cell line DNA can introduce artifacts, impacting CNV detection accuracy.
- The generated CNV map serves as a crucial resource for identifying disease-associated CNVs in African Americans, highlighting population-specific genetic variations like those at 17q21.
Related Concept Videos
Comparing Copy Number Variations and SNPs
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%...
Principles of Pharmacogenetics: Types of Genetic Variants
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Genetic Variation
Genes exist in different versions called alleles, which...
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