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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

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%...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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,...
Karyotyping01:17

Karyotyping

Describing the number and physical features of chromosomes can reveal abnormalities that underlie genetic diseases. This description is facilitated by special staining techniques that produce a particular banding pattern on each chromosome. State-of-the-art techniques make this approach even more powerful, enabling the detection of individual genes that cause disease.A Simple Chromosome Staining Technique Provides Valuable Scientific InsightSome genetic diseases can be detected by looking at...
Gene Duplication and Divergence02:37

Gene 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.
Genome Copying Errors02:46

Genome 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.
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

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Human copy number polymorphic genes.

J A Bailey1, J M Kidd, E E Eichler

  • 1Department of Pathology, Case Western University School of Medicine and University Hospitals of Cleveland, Cleveland, OH, USA. jab@case.edu

Cytogenetic and Genome Research
|March 17, 2009
PubMed
Summary
This summary is machine-generated.

This study developed a precise exon-targeted microarray to identify copy number variants (CNVs) in human genes. Results show segmental duplications drive most CNV genes, offering insights into genetic variation and disease association.

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Area of Science:

  • Genomics
  • Human Genetics
  • Molecular Biology

Background:

  • Large-scale genomic studies identify copy number variants (CNVs) in human populations.
  • CNVs often overlap coding regions, generating candidate genes for disease association.
  • Existing microarray technologies lack precision for exon-level CNV detection.

Purpose of the Study:

  • To develop a high-precision exon-targeted oligonucleotide microarray for CNV detection.
  • To assess 2,790 candidate CNV genes in nine HapMap individuals.
  • To identify true CNVs and their association with genomic features.

Main Methods:

  • Designed a customized exon-targeted oligonucleotide microarray.
  • Utilized exon array comparative genomic hybridization (aCGH) for CNV assessment.
  • Confirmed findings using fosmid end sequence pair (ESP) maps and modified mapping strategies.

Main Results:

  • Detected 255 (9%) true CNVs among 2,790 candidates, with 134 varying across the entire gene.
  • Found strong associations between CNVs and segmental duplications (55-71%) and regions of positive selection.
  • Identified segmental duplications as the primary source of full-length copy number polymorphic genes.

Conclusions:

  • Segmental duplications are the main drivers of copy number polymorphic genes, often organized as tandem duplications.
  • A significant fraction of these variant genes are paralogs with high sequence diversity.
  • Provides a targeted set of CNV genes for studying human phenotypic differences and a resource for association studies.