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Updated: Jun 29, 2026
09:45
Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
Modeling genetic inheritance of copy number variations
Kai Wang1, Zhen Chen, Mahlet G Tadesse
1Department of Genetics, Division of Human Genetics, Center for Applied Genomics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA. wangk@chop.edu
Nucleic Acids Research
|October 4, 2008
Summary
This study introduces a new statistical framework for detecting copy number variations (CNVs) in families. The method accurately identifies CNVs on homologous chromosomes, improving detection rates and boundary accuracy for genetic studies.
Area of Science:
- Genetics
- Genomics
- Bioinformatics
Background:
- Copy number variations (CNVs) are crucial genetic markers.
- Current CNV detection methods often lack the resolution to distinguish copy numbers on homologous chromosomes.
- This limitation hinders detailed genetic mapping and association studies.
Purpose of the Study:
- To develop a statistical framework for accurate, intensity-based CNV detection using family data.
- To improve the detection of CNVs on individual homologous chromosomes.
- To enable robust CNV calling with Mendelian consistency and detection of de novo CNVs.
Main Methods:
- Developed a statistical framework for simultaneous CNV identification within families.
- Utilized intensity data from genotyping platforms.
- Incorporated Mendelian inheritance principles to infer allele compositions in CNV regions.
Main Results:
- The novel method significantly enhances call rates and boundary inference accuracy compared to existing approaches.
- Demonstrated successful detection of both inherited and de novo CNVs using real family data.
- Showcased the ability to infer SNP allele compositions on homologous chromosomes within CNV regions.
Conclusions:
- The developed framework provides accurate CNV calls and probabilistic estimates of CNV transmission.
- Establishes a foundation for advanced linkage and association analyses incorporating CNVs.
- Offers a significant advancement in high-resolution CNV detection for genetic research.
Related Concept Videos
02:26Comparing 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%...
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%...
01:39Chromosomal Theory of Inheritance
In 1866, Gregor Mendel published the results of his pea plant breeding experiments, providing evidence for predictable patterns in the inheritance of physical characteristics. The significance of his findings was not immediately recognized. In fact, the existence of genes was unknown at the time. Mendel referred to hereditary units as “factors.”
01:25Genetic Variation
Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles, which...
Genes exist in different versions called alleles, which...
02:46Genome Copying Errors
DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their survival. Therefore, the copying errors are checked and repaired at three levels.
02:37Gene Duplication and Divergence
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
01:49Law of Segregation
When crossing pea plants, Mendel noticed that one of the parental traits would sometimes disappear in the first generation of offspring, called the F1 generation, and could reappear in the next generation (F2). He concluded that one of the traits must be dominant over the other, thereby causing masking of one trait in the F1 generation. When he crossed the F1 plants, he found that 75% of the offspring in the F2 generation had the dominant phenotype, while 25% had the recessive phenotype.