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Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan
Jason C Ting1, Ying Ye, George H Thomas
1Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA. ting@kennedykrieger.org
BMC Bioinformatics
|January 20, 2006
Summary
SNPscan is a new tool that analyzes high-density single nucleotide polymorphism (SNP) array data to detect chromosomal abnormalities. It successfully identified previously unrecognized genetic anomalies in normal individuals, aiding disease research.
Area of Science:
- Genomics
- Bioinformatics
- Medical Genetics
Background:
- Chromosomal abnormalities like aneuploidies, microdeletions, and uniparental disomy cause various diseases.
- High-density single nucleotide polymorphism (SNP) microarrays generate complex data for analyzing copy number and genotype.
- Identifying diverse anomalies within SNP data presents a significant challenge.
Purpose of the Study:
- To develop and validate SNPscan, a web-accessible tool for analyzing and visualizing high-density SNP data.
- To enable researchers to detect chromosomal copy number anomalies and uniparental isodisomy.
- To facilitate the comparison of paired samples and visualization of SNP data in genome browsers.
Main Methods:
- Developed SNPscan, a web-accessible tool accepting data from Affymetrix Copy Number Analysis Tool.
- Utilized SNP intensity and allelic call data for anomaly detection.
- Validated the tool with known deletion, duplication, and uniparental disomy cases, and analyzed data from 90 normal individuals.
Main Results:
- SNPscan successfully identified chromosomal copy number anomalies and uniparental isodisomy.
- Analysis of 90 normal individuals revealed previously unrecognized abnormalities, including uniparental isodisomy, mosaic X chromosome, mislabeled datasets, and a microdeletion.
- Independent confirmation of a microdeletion and uniparental disomy region by FISH and sequencing, respectively.
Conclusions:
- SNPscan is effective for identifying chromosomal abnormalities using SNP intensity and heterozygosity data.
- The tool aids in detecting copy number changes, loss of heterozygosity (LOH), and uniparental disomy (UPD).
- SNPscan and its source code are publicly available for research use.
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,...