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Updated: May 16, 2026
09:16
Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
Published on: February 21, 2015
PAIR: paired allelic log-intensity-ratio-based normalization method for SNP-CGH arrays
Shengping Yang1, Stanley Pounds, Kun Zhang
1Biostatistics Program, School of Public Health, LSU Health Sciences Center, New Orleans, LA, USA. zfang@lsuhsc.edu
Bioinformatics (Oxford, England)
|December 1, 2012
Summary
A new Hidden Markov Model method accurately identifies two-copy probes for DNA copy number analysis normalization in single nucleotide polymorphism arrays. This approach works even when two-copy probes are not dominant, improving reference selection for accurate genomic analysis.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- DNA copy number analysis is crucial for understanding genomic alterations.
- Accurate normalization in single nucleotide polymorphism (SNP) arrays relies on identifying reliable reference probes.
- Existing methods often assume a dominant proportion of two-copy probes, limiting their applicability.
Purpose of the Study:
- To develop a novel method for identifying two-copy probes in the genome for normalization.
- To create a robust normalization strategy for SNP arrays that does not require the dominance of two-copy probes.
- To improve the accuracy of DNA copy number analysis.
Main Methods:
- A two-state Hidden Markov Model (HMM) was developed to identify two-copy probes.
- The HMM-based method was applied to real and simulated SNP array data.
- Performance was compared against existing normalization methods like CGHnormaliter and popLowess.
Main Results:
- The proposed HMM method performs comparably to existing methods when two-copy probes are dominant.
- The new method outperforms existing approaches when two-copy probes are less dominant.
- The algorithm successfully identifies copy-neutral loss of heterozygosity and demonstrates computational efficiency.
Conclusions:
- The proposed Hidden Markov Model offers a flexible and effective approach for identifying two-copy probes for normalization in SNP arrays.
- This method enhances the accuracy of DNA copy number analysis, particularly in scenarios with non-dominant two-copy probe populations.
- The R scripts for the algorithm are publicly available, facilitating broader adoption and 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%...
01:05Single 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,...