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Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Genotype Imputation for Latinos Using the HapMap and 1000 Genomes Project Reference Panels.

Xiaoyi Gao¹, Talin Haritunians, Paul Marjoram

¹Department of Ophthalmology, Keck School of Medicine, University of Southern California Los Angeles, CA, USA.

Frontiers in Genetics

|July 4, 2012

Summary

The 1000 Genomes Project reference panel, specifically AMR+CEU+YRI, offers the highest genotype imputation accuracy for Latino populations in genome-wide association studies. Including Asian samples may decrease accuracy.

Keywords:

1000 Genomes Project HapMap Project Latino genotype imputation

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Area of Science:

Genetics
Genomics
Population Genetics

Background:

Genotype imputation is crucial for genome-wide association studies (GWAS) and meta-analyses, enhancing genomic coverage and data pooling across different genotyping platforms.
Current genotype imputation resources for Latino populations are limited compared to European ancestry groups due to a lack of adequate reference data.
The 1000 Genomes Project is increasingly used for reference panels, but its utility for Latino imputation requires detailed evaluation.

Purpose of the Study:

To evaluate the accuracy of genotype imputation in Latino populations using public reference panels.
To identify the optimal reference panel for genotype imputation in Latinos for genome-wide association studies.
To provide a guide for future imputation-based analyses in Latino populations.

Main Methods:

Utilized simulation studies with Illumina OmniExpress GWAS data from the Los Angeles Latino Eye Study.
Employed the MACH software package for genotype imputation.
Evaluated imputation accuracy using the 1000 Genomes Project reference panels, including variations with and without Asian samples.

Main Results:

The 1000 Genomes Project reference panel comprising African, European, and Yoruba populations (AMR+CEU+YRI) demonstrated the highest imputation accuracy for Latinos.
Inclusion of Asian samples in the reference panel was found to potentially reduce imputation accuracy for Latino populations.
Imputation accuracy was detailed for each autosomal chromosome using the 1000 Genomes Project panel for Latinos.

Conclusions:

The AMR+CEU+YRI panel from the 1000 Genomes Project is recommended for optimal genotype imputation accuracy in Latino populations.
Researchers should carefully consider the composition of reference panels to maximize imputation accuracy in diverse populations.
This study provides essential data to guide future genome-wide association studies and meta-analyses targeting Latino individuals.