Related Experiment Video
Updated: Apr 24, 2026
13:33
Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
41.3K
Evaluating the coverage and potential of imputing the exome microarray with next-generation imputation using the 1000
Erwin Tantoso1, Lai-Ping Wong1, Bowen Li1
1Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.
Plos One
|September 10, 2014
Summary
Exome genotyping arrays poorly represent diverse populations. However, imputation with 1000 Genomes Project data can still provide good coverage, suggesting whole-genome sequencing may be more cost-effective for diverse exonic content discovery.
Area of Science:
- Genomics
- Population Genetics
- Bioinformatics
Background:
- Next-generation genotyping microarrays leverage exome and whole-genome sequencing data.
- Exome arrays aim to genotype functional genomic regions cost-effectively.
- Key questions address exome chip representation and imputation accuracy for underrepresented populations.
Purpose of the Study:
- Evaluate exome chip content representativeness in non-design populations.
- Assess the imputation accuracy of exome chip content using 1000 Genomes Project reference data.
- Compare the cost-effectiveness of exome arrays versus whole-genome sequencing for exonic content imputation.
Main Methods:
- Deep whole-genome sequencing of 96 Southeast Asian Malays and 36 South Asian Indians.
- Genotyping of these samples on Illumina 2.5 M and exome microarrays.
- Imputation analysis using 1000 Genomes Project reference panels.
Main Results:
- Exome chip content showed poor representation of exonic variants in the studied Asian populations.
- Up to 94.1% of polymorphic exome chip variants were confidently imputed using 1000 Genomes Project data.
- Imputation coverage improved with population-specific whole-genome sequencing reference data.
Conclusions:
- Exome arrays offer limited advantages for populations not included in their design.
- Whole-genome sequencing of a small number of samples can enhance exonic content imputation.
- Complementing 1000 Genomes Project data with population-specific WGS is a cost-effective strategy for imputation.
Related Concept Videos
03:00Next-generation Sequencing
87.4K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
87.4K
03:36Genome Annotation and Assembly
16.5K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
16.5K
02:34DNA Microarrays
16.7K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
16.7K
01:11Genome-wide Association Studies-GWAS
12.3K
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...
12.3K
02:02Genomics
35.1K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
35.1K