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Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data.
Yoko Fukuda1, Yasuo Nakahara, Hidetoshi Date
1Department of Neurology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan. yokofukuda-tky@umin.ac.jp
BMC Bioinformatics
|April 28, 2009
Summary
SNP HiTLink enables high-throughput linkage analysis using microarray single nucleotide polymorphism (SNP) data. This system accelerates the identification of disease-associated genes, offering results comparable or superior to traditional methods.
Area of Science:
- Genetics
- Bioinformatics
Background:
- Microarray-based single nucleotide polymorphism (SNP) data are increasingly utilized for linkage analysis in identifying disease-associated genes.
- While SNP analysis reduces genotyping time and cost, processing large datasets for linkage analysis remains time-consuming, requiring efficient platforms.
Purpose of the Study:
- To develop a high-throughput platform for linkage analysis using microarray-based SNP data.
- To streamline the application of large SNP datasets in genetic studies.
Main Methods:
- Developed SNP HiTLink (SNP High Throughput Linkage analysis system).
- Enabled direct import of SNP chip data (Affymetrix 100 k/500 k, Genome-Wide Human SNP 5.0/6.0) into linkage analysis programs (MLINK, Superlink, Merlin, Allegro).
- Incorporated marker-selection functions to manage data quality and select informative markers.
Main Results:
- SNP HiTLink processes SNP chip data directly for parametric and model-free linkage analysis.
- Implemented functions mitigate effects of typing errors and linkage disequilibrium, enhancing data utility.
- Whole-genome analysis completed in under a few hours on standard personal computers.
Conclusions:
- SNP HiTLink provides high-throughput and reliable linkage analysis for microarray SNP data.
- Results using SNP data were comparable or superior to microsatellite markers in LOD scores.
- The system is suitable for widespread application in genetic research, accelerating gene discovery.
Related Concept Videos
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,...
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...
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%...