Journal article
Accurate and adaptive imputation of summary statistics in mixed-ethnicity cohorts.
- Togninalli M Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- Roqueiro D Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- Borgwardt KM
- 2018-11-14
Published in:
- Bioinformatics (Oxford, England). - 2018
English
Motivation
Methods based on summary statistics obtained from genome-wide association studies have gained considerable interest in genetics due to the computational cost and privacy advantages they present. Imputing missing summary statistics has therefore become a key procedure in many bioinformatics pipelines, but available solutions may rely on additional knowledge about the populations used in the original study and, as a result, may not always ensure feasibility or high accuracy of the imputation procedure.
Results
We present ARDISS, a method to impute missing summary statistics in mixed-ethnicity cohorts through Gaussian Process Regression and automatic relevance determination. ARDISS is trained on an external reference panel and does not require information about allele frequencies of genotypes from the original study. Our method approximates the original GWAS population by a combination of samples from a reference panel relying exclusively on the summary statistics and without any external information. ARDISS successfully reconstructs the original composition of mixed-ethnicity cohorts and outperforms alternative solutions in terms of speed and imputation accuracy both for heterogeneous and homogeneous datasets.
Availability and implementation
The proposed method is available at https://github.com/BorgwardtLab/ARDISS.
Supplementary information
Supplementary data are available at Bioinformatics online.
Methods based on summary statistics obtained from genome-wide association studies have gained considerable interest in genetics due to the computational cost and privacy advantages they present. Imputing missing summary statistics has therefore become a key procedure in many bioinformatics pipelines, but available solutions may rely on additional knowledge about the populations used in the original study and, as a result, may not always ensure feasibility or high accuracy of the imputation procedure.
Results
We present ARDISS, a method to impute missing summary statistics in mixed-ethnicity cohorts through Gaussian Process Regression and automatic relevance determination. ARDISS is trained on an external reference panel and does not require information about allele frequencies of genotypes from the original study. Our method approximates the original GWAS population by a combination of samples from a reference panel relying exclusively on the summary statistics and without any external information. ARDISS successfully reconstructs the original composition of mixed-ethnicity cohorts and outperforms alternative solutions in terms of speed and imputation accuracy both for heterogeneous and homogeneous datasets.
Availability and implementation
The proposed method is available at https://github.com/BorgwardtLab/ARDISS.
Supplementary information
Supplementary data are available at Bioinformatics online.
- Language
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- English
- Open access status
- hybrid
- Identifiers
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- DOI 10.1093/bioinformatics/bty596
- PMID 30423082
- Persistent URL
- https://sonar.ch/global/documents/50947
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