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Updated: Jun 12, 2026
13:33
Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
Utilizing genotype imputation for the augmentation of sequence data.
Brooke L Fridley1, Gregory Jenkins, Matthew E Deyo-Svendsen
1Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA. fridley.brooke@mayo.edu
Plos One
|June 15, 2010
Summary
Genotype imputation using a subset of sequenced samples is feasible for refining genome-wide association study (GWAS) loci. This approach enables cost-effective cataloging of rare variants for complex traits.
Area of Science:
- Genetics
- Genomics
- Bioinformatics
Background:
- Genome-wide association studies (GWAS) identify numerous single nucleotide polymorphisms (SNPs) associated with complex traits.
- Identified SNPs from GWAS are not always functional variants, necessitating further refinement of associated loci.
- Advancements in genotyping allow for over 1 million SNP markers, increasing the scale of GWAS.
Purpose of the Study:
- To explore cost-effective methods for refining GWAS loci by cataloging rare variants.
- To evaluate genotype imputation strategies using a reference panel from a fraction of study participants.
- To provide guidelines for sequencing study design in the context of advanced imputation methods.
Main Methods:
- Sequencing a portion of study participants to create a reference panel.
- Applying genotype imputation methods to infer genotypes in the remaining individuals.
- Utilizing sequence data from both a candidate gene study and the 1000 Genomes Project for imputation.
Main Results:
- Genotype imputation based on a proportion of sequenced samples is a feasible approach.
- The study explored various imputation strategies using combined reference panels.
- Results inform optimal study design for leveraging imputation in genetic research.
Conclusions:
- Imputation of genetic variation using a fraction of sequenced samples is achievable.
- Selecting a large, diverse reference panel for sequencing is crucial.
- Genotyping numerous "anchor" markers within the reference panel enhances imputation accuracy.
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