Weighted multiple testing procedures in genome-wide association studies
Multiple testing procedures controlling the false discovery rate (FDR) are increasingly used in the context of genome wide association studies (GWAS), and weighted multiple testing procedures that incorporate covariate information are efficient to improve the power to detect associations. In this wo...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2023-06-01
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| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/15369.pdf |
| _version_ | 1797424055714840576 |
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| author | Ludivine Obry Cyril Dalmasso |
| author_facet | Ludivine Obry Cyril Dalmasso |
| author_sort | Ludivine Obry |
| collection | DOAJ |
| description | Multiple testing procedures controlling the false discovery rate (FDR) are increasingly used in the context of genome wide association studies (GWAS), and weighted multiple testing procedures that incorporate covariate information are efficient to improve the power to detect associations. In this work, we evaluate some recent weighted multiple testing procedures in the specific context of GWAS through a simulation study. We also present a new efficient procedure called wBHa that prioritizes the detection of genetic variants with low minor allele frequencies while maximizing the overall detection power. The results indicate good performance of our procedure compared to other weighted multiple testing procedures. In particular, in all simulated settings, wBHa tends to outperform other procedures in detecting rare variants while maintaining good overall power. The use of the different procedures is illustrated with a real dataset. |
| first_indexed | 2024-03-09T07:56:46Z |
| format | Article |
| id | doaj.art-834c15802b5e47b480c2e0375994a519 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:56:46Z |
| publishDate | 2023-06-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-834c15802b5e47b480c2e0375994a5192023-12-03T00:58:12ZengPeerJ Inc.PeerJ2167-83592023-06-0111e1536910.7717/peerj.15369Weighted multiple testing procedures in genome-wide association studiesLudivine Obry0Cyril Dalmasso1Université Paris-Saclay, CNRS, Univ Evry, Laboratoire de Mathématiques et Modélisation d’Evry, Evry-Courcouronnes, FranceUniversité Paris-Saclay, CNRS, Univ Evry, Laboratoire de Mathématiques et Modélisation d’Evry, Evry-Courcouronnes, FranceMultiple testing procedures controlling the false discovery rate (FDR) are increasingly used in the context of genome wide association studies (GWAS), and weighted multiple testing procedures that incorporate covariate information are efficient to improve the power to detect associations. In this work, we evaluate some recent weighted multiple testing procedures in the specific context of GWAS through a simulation study. We also present a new efficient procedure called wBHa that prioritizes the detection of genetic variants with low minor allele frequencies while maximizing the overall detection power. The results indicate good performance of our procedure compared to other weighted multiple testing procedures. In particular, in all simulated settings, wBHa tends to outperform other procedures in detecting rare variants while maintaining good overall power. The use of the different procedures is illustrated with a real dataset.https://peerj.com/articles/15369.pdfFalse discovery rateGenome wide association studiesWeighted MTP |
| spellingShingle | Ludivine Obry Cyril Dalmasso Weighted multiple testing procedures in genome-wide association studies PeerJ False discovery rate Genome wide association studies Weighted MTP |
| title | Weighted multiple testing procedures in genome-wide association studies |
| title_full | Weighted multiple testing procedures in genome-wide association studies |
| title_fullStr | Weighted multiple testing procedures in genome-wide association studies |
| title_full_unstemmed | Weighted multiple testing procedures in genome-wide association studies |
| title_short | Weighted multiple testing procedures in genome-wide association studies |
| title_sort | weighted multiple testing procedures in genome wide association studies |
| topic | False discovery rate Genome wide association studies Weighted MTP |
| url | https://peerj.com/articles/15369.pdf |
| work_keys_str_mv | AT ludivineobry weightedmultipletestingproceduresingenomewideassociationstudies AT cyrildalmasso weightedmultipletestingproceduresingenomewideassociationstudies |