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Curtis D. Multiple Linear Regression Allows Weighted Burden Analysis of Rare Coding Variants in an Ethnically Heterogeneous Population. Hum Hered 2021; 85:1-10. [PMID: 33412546 DOI: 10.1159/000512576] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/20/2020] [Indexed: 11/19/2022] Open
Abstract
Weighted burden analysis has been used in exome-sequenced case-control studies to identify genes in which there is an excess of rare and/or functional variants associated with phenotype. Implementation in a ridge regression framework allows simultaneous analysis of all variants along with relevant covariates, such as population principal components. In order to apply the approach to a quantitative phenotype, a weighted burden score is derived for each subject and included in a linear regression analysis. The weighting scheme is adjusted in order to apply differential weights to rare and very rare variants and a score is derived based on both the frequency and predicted effect of each variant. When applied to an ethnically heterogeneous dataset consisting of 49,790 exome-sequenced UK Biobank subjects and using body mass index as the phenotype, the method produces a very inflated test statistic. However, this is almost completely corrected by including 20 population principal components as covariates. When this is done, the top 30 genes include a few which are quite plausibly associated with the phenotype, including LYPLAL1 and NSDHL. This approach offers a way to carry out gene-based analyses of rare variants identified by exome sequencing in heterogeneous datasets without requiring that data from ethnic minority subjects be discarded. This research has been conducted using the UK Biobank Resource.
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Affiliation(s)
- David Curtis
- UCL Genetics Institute, University College London, London, United Kingdom, .,Centre for Psychiatry, Queen Mary University of London, London, United Kingdom,
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Helliwell SB, Karkare S, Bergdoll M, Rahier A, Leighton-Davis JR, Fioretto C, Aust T, Filipuzzi I, Frederiksen M, Gounarides J, Hoepfner D, Hofmann A, Imbert PE, Jeker R, Knochenmuss R, Krastel P, Margerit A, Memmert K, Miault CV, Rao Movva N, Muller A, Naegeli HU, Oberer L, Prindle V, Riedl R, Schuierer S, Sexton JA, Tao J, Wagner T, Yin H, Zhang J, Roggo S, Reinker S, Parker CN. FR171456 is a specific inhibitor of mammalian NSDHL and yeast Erg26p. Nat Commun 2015; 6:8613. [PMID: 26456460 PMCID: PMC4633953 DOI: 10.1038/ncomms9613] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 09/10/2015] [Indexed: 01/07/2023] Open
Abstract
FR171456 is a natural product with cholesterol-lowering properties in animal models, but its molecular target is unknown, which hinders further drug development. Here we show that FR171456 specifically targets the sterol-4-alpha-carboxylate-3-dehydrogenase (Saccharomyces cerevisiae—Erg26p, Homo sapiens—NSDHL (NAD(P) dependent steroid dehydrogenase-like)), an essential enzyme in the ergosterol/cholesterol biosynthesis pathway. FR171456 significantly alters the levels of cholesterol pathway intermediates in human and yeast cells. Genome-wide yeast haploinsufficiency profiling experiments highlight the erg26/ERG26 strain, and multiple mutations in ERG26 confer resistance to FR171456 in growth and enzyme assays. Some of these ERG26 mutations likely alter Erg26 binding to FR171456, based on a model of Erg26. Finally, we show that FR171456 inhibits an artificial Hepatitis C viral replicon, and has broad antifungal activity, suggesting potential additional utility as an anti-infective. The discovery of the target and binding site of FR171456 within the target will aid further development of this compound. FR171456 is a bioactive chemical produced by some microorganisms. Here, the authors identify the enzyme NSDHL of the sterol synthesis pathway as the molecular target of FR171456, rendering it the first compound to specifically target this class of enzyme in yeast and mammalian cells.
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Affiliation(s)
- Stephen B Helliwell
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Shantanu Karkare
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Marc Bergdoll
- Institut de Biologie Moléculaire des Plantes, CNRS, Unité Propre de Recherche 2357, Strasbourg cedex 67083, France
| | - Alain Rahier
- Institut de Biologie Moléculaire des Plantes, CNRS, Unité Propre de Recherche 2357, Strasbourg cedex 67083, France
| | | | - Celine Fioretto
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Thomas Aust
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Ireos Filipuzzi
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Mathias Frederiksen
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - John Gounarides
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
| | - Dominic Hoepfner
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Andreas Hofmann
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Pierre-Eloi Imbert
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Rolf Jeker
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Richard Knochenmuss
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Philipp Krastel
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Anais Margerit
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Klaus Memmert
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Charlotte V Miault
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - N Rao Movva
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Alban Muller
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Hans-Ulrich Naegeli
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Lukas Oberer
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | | | - Ralph Riedl
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Jessica A Sexton
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
| | | | - Trixie Wagner
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Hong Yin
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
| | - Juan Zhang
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Silvio Roggo
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Stefan Reinker
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
| | - Christian N Parker
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, CH-4056, Switzerland
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