Related Experiment Video
Updated: Jun 3, 2026

Large-Scale Multi-Omics Genome-Wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization
Published on: July 27, 2021
The extent of linkage disequilibrium and computational challenges of single nucleotide polymorphisms in genome-wide
Yao-Ting Huang1, Chia-Jung Chang, Kun-Mao Chao
1Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan. ythuang@cs.ccu.edu.tw
Abstract:
Single Nucleotide Polymorphisms (SNPs) are the most abundant form of genetic variations observed in the human genome. With the advent of high-throughput genotyping arrays and next-generation sequencing (NGS) platforms, tens of millions of SNPs have been uncovered in several human populations. However, the huge amount of SNPs bring new challenges in subsequent analysis. In reality, a number of SNPs may not be genotyped, and non-mutant bases may be falsely reported as SNPs in the microarray and NGS platforms. Furthermore, the identification of disease susceptibility genes are often confounded by numerous SNPs correlated by chance. In this paper, we review existing approaches for calling SNPs using microarrays and next-generation sequencing (NGS) platforms. Methods for measuring linkage disequilibrium (LD) and applications of the LD structure are discussed. Finally, we compare methods for inferring haplotypes from genotypes using microarray and NGS platforms and present the challenges of using SNPs in large-scale association studies.
Related Concept Videos
Genome-wide Association Studies-GWAS
GWAS does not require the identification of the target gene involved in...
Comparing Copy Number Variations and SNPs
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%...
Single Nucleotide Polymorphisms-SNPs
Principles of Pharmacogenetics: Types of Genetic Variants
Pharmacogenomics: Identification of New Drug Targets
Modern Molecular Taxonomy
