The Beavis Effect in Next-Generation Mapping Panels in Drosophila melanogaster
A major goal in the analysis of complex traits is to partition the observed genetic variation in a trait into components due to individual loci and perhaps variants within those loci. However, in both QTL mapping and genetic association studies, the estimated percent variation attributable to a QTL...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Oxford University Press
2017-06-01
|
| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.117.041426 |
| _version_ | 1818609835342561280 |
|---|---|
| author | Elizabeth G. King Anthony D. Long |
| author_facet | Elizabeth G. King Anthony D. Long |
| author_sort | Elizabeth G. King |
| collection | DOAJ |
| description | A major goal in the analysis of complex traits is to partition the observed genetic variation in a trait into components due to individual loci and perhaps variants within those loci. However, in both QTL mapping and genetic association studies, the estimated percent variation attributable to a QTL is upwardly biased conditional on it being discovered. This bias was first described in two-way QTL mapping experiments by William Beavis, and has been referred to extensively as “the Beavis effect.” The Beavis effect is likely to occur in multiparent population (MPP) panels as well as collections of sequenced lines used for genome-wide association studies (GWAS). However, the strength of the Beavis effect is unknown—and often implicitly assumed to be negligible—when “hits” are obtained from an association panel consisting of hundreds of inbred lines tested across millions of SNPs, or in multiparent mapping populations where mapping involves fitting a complex statistical model with several d.f. at thousands of genetic intervals. To estimate the size of the effect in more complex panels, we performed simulations of both biallelic and multiallelic QTL in two major Drosophila melanogaster mapping panels, the GWAS-based Drosophila Genetic Reference Panel (DGRP), and the MPP the Drosophila Synthetic Population Resource (DSPR). Our results show that overestimation is determined most strongly by sample size and is only minimally impacted by the mapping design. When < 100, 200, 500, and 1000 lines are employed, the variance attributable to hits is inflated by factors of 6, 3, 1.5, and 1.1, respectively, for a QTL that truly contributes 5% to the variation in the trait. This overestimation indicates that QTL could be difficult to validate in follow-up replication experiments where additional individuals are examined. Further, QTL could be difficult to cross-validate between the two Drosophila resources. We provide guidelines for: (1) the sample sizes necessary to accurately estimate the percent variance to an identified QTL, (2) the conditions under which one is likely to replicate a mapped QTL in a second study using the same mapping population, and (3) the conditions under which a QTL mapped in one mapping panel is likely to replicate in the other (DGRP and DSPR). |
| first_indexed | 2024-12-16T15:04:51Z |
| format | Article |
| id | doaj.art-974342e1471b403493667a8d08ed6713 |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-16T15:04:51Z |
| publishDate | 2017-06-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-974342e1471b403493667a8d08ed67132022-12-21T22:27:11ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362017-06-01761643165210.1534/g3.117.0414265The Beavis Effect in Next-Generation Mapping Panels in Drosophila melanogasterElizabeth G. KingAnthony D. LongA major goal in the analysis of complex traits is to partition the observed genetic variation in a trait into components due to individual loci and perhaps variants within those loci. However, in both QTL mapping and genetic association studies, the estimated percent variation attributable to a QTL is upwardly biased conditional on it being discovered. This bias was first described in two-way QTL mapping experiments by William Beavis, and has been referred to extensively as “the Beavis effect.” The Beavis effect is likely to occur in multiparent population (MPP) panels as well as collections of sequenced lines used for genome-wide association studies (GWAS). However, the strength of the Beavis effect is unknown—and often implicitly assumed to be negligible—when “hits” are obtained from an association panel consisting of hundreds of inbred lines tested across millions of SNPs, or in multiparent mapping populations where mapping involves fitting a complex statistical model with several d.f. at thousands of genetic intervals. To estimate the size of the effect in more complex panels, we performed simulations of both biallelic and multiallelic QTL in two major Drosophila melanogaster mapping panels, the GWAS-based Drosophila Genetic Reference Panel (DGRP), and the MPP the Drosophila Synthetic Population Resource (DSPR). Our results show that overestimation is determined most strongly by sample size and is only minimally impacted by the mapping design. When < 100, 200, 500, and 1000 lines are employed, the variance attributable to hits is inflated by factors of 6, 3, 1.5, and 1.1, respectively, for a QTL that truly contributes 5% to the variation in the trait. This overestimation indicates that QTL could be difficult to validate in follow-up replication experiments where additional individuals are examined. Further, QTL could be difficult to cross-validate between the two Drosophila resources. We provide guidelines for: (1) the sample sizes necessary to accurately estimate the percent variance to an identified QTL, (2) the conditions under which one is likely to replicate a mapped QTL in a second study using the same mapping population, and (3) the conditions under which a QTL mapped in one mapping panel is likely to replicate in the other (DGRP and DSPR).http://g3journal.org/lookup/doi/10.1534/g3.117.041426complex traitsDrosophila melanogasterBeavis effectQTL mappingGWASDSPRDGRPmultiparental populationsMPP |
| spellingShingle | Elizabeth G. King Anthony D. Long The Beavis Effect in Next-Generation Mapping Panels in Drosophila melanogaster G3: Genes, Genomes, Genetics complex traits Drosophila melanogaster Beavis effect QTL mapping GWAS DSPR DGRP multiparental populations MPP |
| title | The Beavis Effect in Next-Generation Mapping Panels in Drosophila melanogaster |
| title_full | The Beavis Effect in Next-Generation Mapping Panels in Drosophila melanogaster |
| title_fullStr | The Beavis Effect in Next-Generation Mapping Panels in Drosophila melanogaster |
| title_full_unstemmed | The Beavis Effect in Next-Generation Mapping Panels in Drosophila melanogaster |
| title_short | The Beavis Effect in Next-Generation Mapping Panels in Drosophila melanogaster |
| title_sort | beavis effect in next generation mapping panels in drosophila melanogaster |
| topic | complex traits Drosophila melanogaster Beavis effect QTL mapping GWAS DSPR DGRP multiparental populations MPP |
| url | http://g3journal.org/lookup/doi/10.1534/g3.117.041426 |
| work_keys_str_mv | AT elizabethgking thebeaviseffectinnextgenerationmappingpanelsindrosophilamelanogaster AT anthonydlong thebeaviseffectinnextgenerationmappingpanelsindrosophilamelanogaster AT elizabethgking beaviseffectinnextgenerationmappingpanelsindrosophilamelanogaster AT anthonydlong beaviseffectinnextgenerationmappingpanelsindrosophilamelanogaster |