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Updated: May 17, 2026
09:16
Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
Published on: February 21, 2015
Genome-wide copy number variation study in anorectal malformations
Emily H M Wong1, Long Cui, Chun-Laam Ng
1Department of Psychiatry, The University of Hong Kong, Hong Kong SAR, China.
Human Molecular Genetics
|October 31, 2012
Summary
Rare genetic variations called copy number variations (CNVs) are linked to anorectal malformations (ARMs), a common birth defect. These CNVs play a role in both isolated and syndromic ARM cases, offering new insights into the disorder's genetic causes.
Area of Science:
- Genetics
- Developmental Biology
- Pediatric Surgery
Background:
- Anorectal malformations (ARMs) are common congenital defects with significant morbidity.
- The genetic basis of ARMs, particularly isolated cases, remains largely unknown.
- ARMs can occur independently or as part of broader genetic syndromes.
Purpose of the Study:
- To investigate the role of genetic variations, specifically copy number variations (CNVs), in the etiology of anorectal malformations.
- To differentiate the genetic contributions of CNVs in syndromic versus non-syndromic ARM patients.
- To identify potential candidate genes associated with ARM development.
Main Methods:
- Genome-wide analysis of single-nucleotide polymorphisms and CNVs in 363 Han Chinese sporadic ARM patients and 4006 controls.
- Stratification of patients based on the presence or absence of other congenital anomalies.
- Comparison of patient-specific CNVs with large control databases (Database of Genomic Variants).
Main Results:
- A significant 1.3-fold excess of rare CNVs was detected in ARM patients compared to controls.
- Non-syndromic ARM patients showed enrichment for both rare deletions and duplications.
- Twelve chromosomal aberrations and 114 rare CNVs, including a de novo DKK4 duplication, were identified in patients but not in controls.
Conclusions:
- Rare CNVs contribute to the development of both syndromic and isolated anorectal malformations.
- The WNT signaling pathway, influenced by genes like DKK4, is implicated in ARM pathogenesis.
- This study provides a list of candidate genes for further investigation into ARM etiology.
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%...
01:11Genome-wide Association Studies-GWAS
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
01:05Single 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,...
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.