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Article Dans Une Revue Human Genetics and Genomics Advances Année : 2022

Identifying and correcting for misspecifications in GWAS summary statistics and polygenic scores

Résumé

Publicly available genome-wide association studies (GWAS) summary statistics exhibit uneven quality, which can impact the validity of follow-up analyses. First, we present an overview of possible misspecifications that come with GWAS summary statistics. Then, in both simulations and real-data analyses, we show that additional information such as imputation INFO scores, allele frequencies, and per-variant sample sizes in GWAS summary statistics can be used to detect possible issues and correct for misspecifications in the GWAS summary statistics. One important motivation for us is to improve the predictive performance of polygenic scores built from these summary statistics. Unfortunately, owing to the lack of reporting standards for GWAS summary statistics, this additional information is not systematically reported. We also show that using well-matched linkage disequilibrium (LD) references can improve model fit and translate into more accurate prediction. Finally, we discuss how to make polygenic score methods such as lassosum and LDpred2 more robust to these misspecifications to improve their predictive power.
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Origine : Publication financée par une institution
Licence : CC BY - Paternité

Dates et versions

hal-04144877 , version 1 (29-06-2023)

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Paternité

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Florian Privé, Julyan Arbel, Hugues Aschard, Bjarni Vilhjálmsson. Identifying and correcting for misspecifications in GWAS summary statistics and polygenic scores. Human Genetics and Genomics Advances, 2022, 3 (4), pp.100136. ⟨10.1016/j.xhgg.2022.100136⟩. ⟨hal-04144877⟩
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