Genetic Structures of Copy Number Variants Revealed by Genotyping Single Sperm

• Published in: PloS one Vol. 4; no. 4; p. e5236
• Main Authors: Luo, Minjie, Cui, Xiangfeng, Fredman, David, Brookes, Anthony J., Azaro, Marco A., Greenawalt, Danielle M., Hu, Guohong, Wang, Hui-Yun, Tereshchenko, Irina V., Lin, Yong, Shentu, Yue, Gao, Richeng, Shen, Li, Li, Honghua
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 22.04.2009; Public Library of Science (PLoS)
• Subjects: Algorithms; Analysis; Biological evolution; Biotechnology; Cancer; Copy number; Dentistry; Deoxyribonucleic acid; Diploidy; DNA; DNA microarrays; Electrophoresis, Polyacrylamide Gel; Evolution; Evolutionary Biology; Evolutionary Biology/Genomics; Evolutionary Biology/Human Evolution; Gene Dosage; Gene expression; Genes; Genetic Markers; Genetic structure; Genetics; Genetics and Genomics/Genetics of Disease; Genetics and Genomics/Genomics; Genetics and Genomics/Population Genetics; Genomes; Genomics; Genotype; Genotyping; Haplotypes; Humans; Immunology; Male; Medical schools; Medicine; Meiosis; Multiplexing; Oligonucleotide Array Sequence Analysis; Polymerase Chain Reaction; Polymorphism, Single Nucleotide; Recombination; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Sperm; Spermatozoa - metabolism; United States > US; China; New Jersey
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0005236

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. 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. 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.