FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4200563555> ?p ?o ?g. }

• W4200563555 abstract "Abstract In recent work, Wang et al introduced the “Sum of Single Effects” ( SuSiE ) model, and showed that it provides a simple and efficient approach to fine-mapping genetic variants from individual-level data. Here we present new methods for fitting the SuSiE model to summary data, for example to single-SNP z -scores from an association study and linkage disequilibrium (LD) values estimated from a suitable reference panel. To develop these new methods, we first describe a simple, generic strategy for extending any individual-level data method to deal with summary data. The key idea is to replace the usual regression likelihood with an analogous likelihood based on summary data. We show that existing fine-mapping methods such as FINEMAP and CAVIAR also (implicitly) use this strategy, but in different ways, and so this provides a common framework for understanding different methods for fine-mapping. We investigate other common practical issues in fine-mapping with summary data, including problems caused by inconsistencies between the z -scores and LD estimates, and we develop diagnostics to identify these inconsistencies. We also present a new refinement procedure that improves model fits in some data sets, and hence improves overall reliability of the SuSiE fine-mapping results. Detailed evaluations of fine-mapping methods in a range of simulated data sets show that SuSiE applied to summary data is competitive, in both speed and accuracy, with the best available fine-mapping methods for summary data. Author summary The goal of fine-mapping is to identify the genetic variants that causally affect some trait of interest. Fine-mapping is challenging because the genetic variants can be highly correlated, due to a phenomenon called linkage disequilibrium (LD). The most successful current approaches to fine-mapping frame the problem as a variable selection problem , and here we focus on one such approach based on the “Sum of Single Effects” ( SuSiE ) model. The main contribution of this paper is to extend SuSiE to work with summary data, which is often accessible when the full genotype and phenotype data are not. In the process of extending SuSiE , we also developed a new mathematical framework that helps to explain existing fine-mapping methods for summary data, why they work well (or not), and under what circumstances. In simulations, we show that SuSiE applied to summary data is competitive with the best available fine-mapping methods for summary data. We also show how different factors such as accuracy of the LD estimates can affect the quality of the fine-mapping." @default.
• W4200563555 created "2021-12-31" @default.
• W4200563555 creator A5036504609 @default.
• W4200563555 creator A5046051048 @default.
• W4200563555 creator A5054433786 @default.
• W4200563555 creator A5061140470 @default.
• W4200563555 date "2021-11-04" @default.
• W4200563555 modified "2023-10-10" @default.
• W4200563555 title "Fine-mapping from summary data with the “Sum of Single Effects” model" @default.
• W4200563555 cites W1533942137 @default.
• W4200563555 cites W1862369546 @default.
• W4200563555 cites W1981041672 @default.
• W4200563555 cites W2018617521 @default.
• W4200563555 cites W2029892338 @default.
• W4200563555 cites W2039627167 @default.
• W4200563555 cites W2062125287 @default.
• W4200563555 cites W2070659891 @default.
• W4200563555 cites W2073836327 @default.
• W4200563555 cites W2078803352 @default.
• W4200563555 cites W2099085143 @default.
• W4200563555 cites W2101505979 @default.
• W4200563555 cites W2127922938 @default.
• W4200563555 cites W2133520037 @default.
• W4200563555 cites W2136091734 @default.
• W4200563555 cites W2142752948 @default.
• W4200563555 cites W2143992683 @default.
• W4200563555 cites W2147215182 @default.
• W4200563555 cites W2150692563 @default.
• W4200563555 cites W2152325859 @default.
• W4200563555 cites W2152885121 @default.
• W4200563555 cites W2152915426 @default.
• W4200563555 cites W2154439634 @default.
• W4200563555 cites W2297334215 @default.
• W4200563555 cites W2322235902 @default.
• W4200563555 cites W2328393125 @default.
• W4200563555 cites W2400221198 @default.
• W4200563555 cites W2471410861 @default.
• W4200563555 cites W2553123256 @default.
• W4200563555 cites W2613151407 @default.
• W4200563555 cites W2725988230 @default.
• W4200563555 cites W2759790573 @default.
• W4200563555 cites W2767037176 @default.
• W4200563555 cites W2800582290 @default.
• W4200563555 cites W2802104200 @default.
• W4200563555 cites W2806225217 @default.
• W4200563555 cites W2895486342 @default.
• W4200563555 cites W2952008083 @default.
• W4200563555 cites W2999668254 @default.
• W4200563555 cites W3010193979 @default.
• W4200563555 cites W3015746229 @default.
• W4200563555 cites W3042068575 @default.
• W4200563555 cites W3047390881 @default.
• W4200563555 cites W3123589318 @default.
• W4200563555 cites W4220840525 @default.
• W4200563555 cites W4225768109 @default.
• W4200563555 cites W3105826405 @default.
• W4200563555 doi "https://doi.org/10.1101/2021.11.03.467167" @default.
• W4200563555 hasPublicationYear "2021" @default.
• W4200563555 type Work @default.
• W4200563555 citedByCount "14" @default.
• W4200563555 countsByYear W42005635552021 @default.
• W4200563555 countsByYear W42005635552022 @default.
• W4200563555 countsByYear W42005635552023 @default.
• W4200563555 crossrefType "posted-content" @default.
• W4200563555 hasAuthorship W4200563555A5036504609 @default.
• W4200563555 hasAuthorship W4200563555A5046051048 @default.
• W4200563555 hasAuthorship W4200563555A5054433786 @default.
• W4200563555 hasAuthorship W4200563555A5061140470 @default.
• W4200563555 hasBestOaLocation W42005635551 @default.
• W4200563555 hasConcept C104317684 @default.
• W4200563555 hasConcept C111472728 @default.
• W4200563555 hasConcept C121332964 @default.
• W4200563555 hasConcept C124101348 @default.
• W4200563555 hasConcept C137314826 @default.
• W4200563555 hasConcept C138885662 @default.
• W4200563555 hasConcept C159985019 @default.
• W4200563555 hasConcept C163258240 @default.
• W4200563555 hasConcept C185592680 @default.
• W4200563555 hasConcept C192562407 @default.
• W4200563555 hasConcept C204323151 @default.
• W4200563555 hasConcept C2780586882 @default.
• W4200563555 hasConcept C31266012 @default.
• W4200563555 hasConcept C41008148 @default.
• W4200563555 hasConcept C43214815 @default.
• W4200563555 hasConcept C55493867 @default.
• W4200563555 hasConcept C62520636 @default.
• W4200563555 hasConcept C77088390 @default.
• W4200563555 hasConceptScore W4200563555C104317684 @default.
• W4200563555 hasConceptScore W4200563555C111472728 @default.
• W4200563555 hasConceptScore W4200563555C121332964 @default.
• W4200563555 hasConceptScore W4200563555C124101348 @default.
• W4200563555 hasConceptScore W4200563555C137314826 @default.
• W4200563555 hasConceptScore W4200563555C138885662 @default.
• W4200563555 hasConceptScore W4200563555C159985019 @default.
• W4200563555 hasConceptScore W4200563555C163258240 @default.
• W4200563555 hasConceptScore W4200563555C185592680 @default.
• W4200563555 hasConceptScore W4200563555C192562407 @default.
• W4200563555 hasConceptScore W4200563555C204323151 @default.
• W4200563555 hasConceptScore W4200563555C2780586882 @default.
• W4200563555 hasConceptScore W4200563555C31266012 @default.

• next