Genetic structures of copy number variants revealed by genotyping single sperm..pdf (371.12 kB)
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Genetic structures of copy number variants revealed by genotyping single sperm.

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posted on 24.06.2020, 09:10 by M Luo, X Cui, D Fredman, AJ Brookes, MA Azaro, DM Greenawalt, G Hu, HY Wang, IV Tereshchenko, Y Lin, Y Shentu, R Gao, L Shen, H Li
BACKGROUND: Copy number variants (CNVs) occupy a significant portion of the human genome and may have important roles in meiotic recombination, human genome evolution and gene expression. Many genetic diseases may be underlain by CNVs. However, because of the presence of their multiple copies, variability in copy numbers and the diploidy of the human genome, detailed genetic structure of CNVs cannot be readily studied by available techniques. METHODOLOGY/PRINCIPAL FINDINGS: Single sperm samples were used as the primary subjects for the study so that CNV haplotypes in the sperm donors could be studied individually. Forty-eight CNVs characterized in a previous study were analyzed using a microarray-based high-throughput genotyping method after multiplex amplification. Seventeen single nucleotide polymorphisms (SNPs) were also included as controls. Two single-base variants, either allelic or paralogous, could be discriminated for all markers. Microarray data were used to resolve SNP alleles and CNV haplotypes, to quantitatively assess the numbers and compositions of the paralogous segments in each CNV haplotype. CONCLUSIONS/SIGNIFICANCE: This is the first study of the genetic structure of CNVs on a large scale. Resulting information may help understand evolution of the human genome, gain insight into many genetic processes, and discriminate between CNVs and SNPs. The highly sensitive high-throughput experimental system with haploid sperm samples as subjects may be used to facilitate detailed large-scale CNV analysis.

Funding

This work was supported by grants from the National Human Genome Research Institute (R01 HG02094), and the National Cancer Institute (R01 CA77363 and R33 CA 96309), National Institutes of Health to H.L. DF acknowledges support by the National Programme for Research in Functional Genomics in Norway (FUGE) in the Research Council of Norway.

History

Citation

PLoS One, 2009, 4 (4), e5236

Author affiliation

Department of Genetics

Version

VoR (Version of Record)

Published in

PLoS One

Volume

4

Publisher

Public Library of Science

eissn

1932-6203

Acceptance date

12/03/2009

Available date

22/04/2009

Language

eng

Publisher version

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0005236