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- Publisher Website: 10.1017/S0016672320000026
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- PMID: 32234109
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Article: A robust test for X-chromosome genetic association accounting for X-chromosome inactivation and imprinting
Title | A robust test for X-chromosome genetic association accounting for X-chromosome inactivation and imprinting |
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Authors | |
Keywords | association test imprinting effects inactivation X chromosome |
Issue Date | 2020 |
Publisher | Cambridge University Press. The Journal's web site is located at https://www.cambridge.org/core/journals/genetics-research |
Citation | Genetics Research, 2020, v. 102, p. article no. e2 How to Cite? |
Abstract | The X chromosome is known to play an important role in many sex-specific diseases. However, only a few single-nucleotide polymorphisms on the X chromosome have been found to be associated with diseases. Compared to the autosomes, conducting association tests on the X chromosome is more intractable due to the difference in the number of X chromosomes between females and males. On the other hand, X-chromosome inactivation takes place in female mammals, which is a phenomenon in which the expression of one copy of two X chromosomes in females is silenced in order to achieve the same gene expression level as that in males. In addition, imprinting effects may be related to certain diseases. Currently, there are some existing approaches taking X-chromosome inactivation into account when testing for associations on the X chromosome. However, none of them allows for imprinting effects. Therefore, in this paper, we propose a robust test, ZXCII, which accounts for both X-chromosome inactivation and imprinting effects without requiring specifying the genetic models in advance. Simulation studies are conducted in order to investigate the validity and performance of ZXCII under various scenarios of different parameter values. The simulation results show that ZXCII controls the type I error rate well when there is no association. Furthermore, with regards to power, ZXCII is robust in all of the situations considered and generally outperforms most of the existing methods in the presence of imprinting effects, especially under complete imprinting effects. |
Persistent Identifier | http://hdl.handle.net/10722/288168 |
ISSN | 2023 Impact Factor: 1.4 2023 SCImago Journal Rankings: 0.265 |
PubMed Central ID | |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Yu, Z | - |
dc.contributor.author | XU, S | - |
dc.contributor.author | Wei, L | - |
dc.contributor.author | Fung, TWK | - |
dc.contributor.author | Zhou, JY | - |
dc.date.accessioned | 2020-10-05T12:08:52Z | - |
dc.date.available | 2020-10-05T12:08:52Z | - |
dc.date.issued | 2020 | - |
dc.identifier.citation | Genetics Research, 2020, v. 102, p. article no. e2 | - |
dc.identifier.issn | 0016-6723 | - |
dc.identifier.uri | http://hdl.handle.net/10722/288168 | - |
dc.description.abstract | The X chromosome is known to play an important role in many sex-specific diseases. However, only a few single-nucleotide polymorphisms on the X chromosome have been found to be associated with diseases. Compared to the autosomes, conducting association tests on the X chromosome is more intractable due to the difference in the number of X chromosomes between females and males. On the other hand, X-chromosome inactivation takes place in female mammals, which is a phenomenon in which the expression of one copy of two X chromosomes in females is silenced in order to achieve the same gene expression level as that in males. In addition, imprinting effects may be related to certain diseases. Currently, there are some existing approaches taking X-chromosome inactivation into account when testing for associations on the X chromosome. However, none of them allows for imprinting effects. Therefore, in this paper, we propose a robust test, ZXCII, which accounts for both X-chromosome inactivation and imprinting effects without requiring specifying the genetic models in advance. Simulation studies are conducted in order to investigate the validity and performance of ZXCII under various scenarios of different parameter values. The simulation results show that ZXCII controls the type I error rate well when there is no association. Furthermore, with regards to power, ZXCII is robust in all of the situations considered and generally outperforms most of the existing methods in the presence of imprinting effects, especially under complete imprinting effects. | - |
dc.language | eng | - |
dc.publisher | Cambridge University Press. The Journal's web site is located at https://www.cambridge.org/core/journals/genetics-research | - |
dc.relation.ispartof | Genetics Research | - |
dc.rights | Genetics Research. Copyright © Cambridge University Press. | - |
dc.rights | This article has been published in a revised form in [Genetics Research] [http://doi.org/10.1017/S0016672320000026]. This version is free to view and download for private research and study only. Not for re-distribution, re-sale or use in derivative works. © copyright holder. | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject | association test | - |
dc.subject | imprinting effects | - |
dc.subject | inactivation | - |
dc.subject | X chromosome | - |
dc.title | A robust test for X-chromosome genetic association accounting for X-chromosome inactivation and imprinting | - |
dc.type | Article | - |
dc.identifier.email | Fung, TWK: wingfung@hkucc.hku.hk | - |
dc.identifier.authority | Fung, TWK=rp00696 | - |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1017/S0016672320000026 | - |
dc.identifier.pmid | 32234109 | - |
dc.identifier.pmcid | PMC7132553 | - |
dc.identifier.scopus | eid_2-s2.0-85082655598 | - |
dc.identifier.hkuros | 315176 | - |
dc.identifier.volume | 102 | - |
dc.identifier.spage | article no. e2 | - |
dc.identifier.epage | article no. e2 | - |
dc.identifier.isi | WOS:000524943200001 | - |
dc.publisher.place | United Kingdom | - |
dc.identifier.issnl | 0016-6723 | - |