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Updated: Jun 26, 2026
08:27
Large-Scale Multi-Omics Genome-Wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization
Published on: July 27, 2021
Genome-wide linkage analysis with clustered SNP markers.
Kaja K Selmer1, Kristin Brandal, Ole K Olstad
1Institute of Medical Genetics, University of Oslo, Oslo, Norway. k.k.selmer@medisin.uio.no
Journal of Biomolecular Screening
|January 28, 2009
Summary
Single nucleotide polymorphisms (SNPs) offer advantages over microsatellites for genetic linkage analysis. The Applied Biosystems Human LMS 4K set and GeneMapper 4.0 software performed well but were less automated than Affymetrix 10K 2.0.
Area of Science:
- Genetics
- Genomics
- Bioinformatics
Background:
- Single nucleotide polymorphisms (SNPs) are increasingly preferred over microsatellites for genetic linkage analysis due to higher abundance and automated genotyping capabilities.
- The Applied Biosystems Human Linkage Mapping Set (LMS) 4K utilizes SNPlex technology with clustered SNPs for genome-wide analysis.
Purpose of the Study:
- To evaluate the performance of the Applied Biosystems Human LMS 4K set and GeneMapper 4.0 software for linkage analysis in families with monogenic diseases.
- To compare the Applied Biosystems method with the Affymetrix GeneChip Human Mapping 10K 2.0 array for genome-wide linkage analysis.
Main Methods:
- Genome-wide linkage analysis was conducted on 17 families with assumed monogenic diseases using the Applied Biosystems Human LMS 4K set and GeneMapper 4.0 software.
- A comparative genome-wide linkage analysis was performed on one family using the Affymetrix GeneChip Human Mapping 10K 2.0 array.
Main Results:
- Both the Applied Biosystems and Affymetrix methods demonstrated strong technical performance, characterized by high genotype call rates.
- Comparable and low rates of Mendelian inconsistencies were observed between the two genotyping platforms.
- Genotyping with GeneMapper 4.0 was found to be less automated and more time-consuming compared to the Affymetrix software.
Conclusions:
- The Applied Biosystems Human LMS 4K set and GeneMapper 4.0 software are effective tools for genetic linkage analysis.
- While technically sound, the genotyping workflow using GeneMapper 4.0 requires further automation to match the efficiency of alternative platforms like Affymetrix.
Related Concept Videos
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,...
02:26Comparing 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%...