Advantage of Using Allele-Specific Copy Numbers When Testing for Association in Regions with Common Copy Number Variants
Author
Abstract
Suggested Citation
DOI: 10.1371/journal.pone.0075350
Download full text from publisher
References listed on IDEAS
- Donald F. Conrad & Dalila Pinto & Richard Redon & Lars Feuk & Omer Gokcumen & Yujun Zhang & Jan Aerts & T. Daniel Andrews & Chris Barnes & Peter Campbell & Tomas Fitzgerald & Min Hu & Chun Hwa Ihm & K, 2010. "Origins and functional impact of copy number variation in the human genome," Nature, Nature, vol. 464(7289), pages 704-712, April.
- Teri A. Manolio & Francis S. Collins & Nancy J. Cox & David B. Goldstein & Lucia A. Hindorff & David J. Hunter & Mark I. McCarthy & Erin M. Ramos & Lon R. Cardon & Aravinda Chakravarti & Judy H. Cho &, 2009. "Finding the missing heritability of complex diseases," Nature, Nature, vol. 461(7265), pages 747-753, October.
- Richard Redon & Shumpei Ishikawa & Karen R. Fitch & Lars Feuk & George H. Perry & T. Daniel Andrews & Heike Fiegler & Michael H. Shapero & Andrew R. Carson & Wenwei Chen & Eun Kyung Cho & Stephanie Da, 2006. "Global variation in copy number in the human genome," Nature, Nature, vol. 444(7118), pages 444-454, November.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Andrew K MacLeod & Gail Davies & Antony Payton & Albert Tenesa & Sarah E Harris & David Liewald & Xiayi Ke & Michelle Luciano & Lorna M Lopez & Alan J Gow & Janie Corley & Paul Redmond & Geraldine McN, 2012. "Genetic Copy Number Variation and General Cognitive Ability," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-9, December.
- Zhuoran Xu & Quan Li & Luigi Marchionni & Kai Wang, 2023. "PhenoSV: interpretable phenotype-aware model for the prioritization of genes affected by structural variants," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
- Leonid Iakoubov & Malgorzata Mossakowska & Malgorzata Szwed & Zhibing Duan & Federico Sesti & Monika Puzianowska-Kuznicka, 2013. "A Common Copy Number Variation (CNV) Polymorphism in the CNTNAP4 Gene: Association with Aging in Females," PLOS ONE, Public Library of Science, vol. 8(11), pages 1-1, November.
- Yichen Henry Liu & Can Luo & Staunton G. Golding & Jacob B. Ioffe & Xin Maizie Zhou, 2024. "Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
- Kevin R Thornton & Andrew J Foran & Anthony D Long, 2013. "Properties and Modeling of GWAS when Complex Disease Risk Is Due to Non-Complementing, Deleterious Mutations in Genes of Large Effect," PLOS Genetics, Public Library of Science, vol. 9(2), pages 1-14, February.
- Ilias Georgakopoulos-Soares & Chengyu Deng & Vikram Agarwal & Candace S. Y. Chan & Jingjing Zhao & Fumitaka Inoue & Nadav Ahituv, 2023. "Transcription factor binding site orientation and order are major drivers of gene regulatory activity," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
- Albertas Dvirnas & Callum Stewart & Vilhelm Müller & Santosh Kumar Bikkarolla & Karolin Frykholm & Linus Sandegren & Erik Kristiansson & Fredrik Westerlund & Tobias Ambjörnsson, 2021. "Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach," PLOS ONE, Public Library of Science, vol. 16(11), pages 1-15, November.
- Ruixue Fan & Shaw-Hwa Lo, 2013. "A Robust Model-free Approach for Rare Variants Association Studies Incorporating Gene-Gene and Gene-Environmental Interactions," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-14, December.
- Patrick Breheny & Prabhakar Chalise & Anthony Batzler & Liewei Wang & Brooke L Fridley, 2012. "Genetic Association Studies of Copy-Number Variation: Should Assignment of Copy Number States Precede Testing?," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-9, April.
- Zhongshang Yuan & Hong Liu & Xiaoshuai Zhang & Fangyu Li & Jinghua Zhao & Furen Zhang & Fuzhong Xue, 2013. "From Interaction to Co-Association —A Fisher r-To-z Transformation-Based Simple Statistic for Real World Genome-Wide Association Study," PLOS ONE, Public Library of Science, vol. 8(7), pages 1-8, July.
- Yu Chen & Amy Y. Wang & Courtney A. Barkley & Yixin Zhang & Xinyang Zhao & Min Gao & Mick D. Edmonds & Zechen Chong, 2023. "Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
- Lucia Ruojia Wu & Peng Dai & Michael Xiangjiang Wang & Sherry Xi Chen & Evan N. Cohen & Gitanjali Jayachandran & Jinny Xuemeng Zhang & Angela V. Serrano & Nina Guanyi Xie & Naoto T. Ueno & James M. Re, 2022. "Ensemble of nucleic acid absolute quantitation modules for copy number variation detection and RNA profiling," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
- Lin Yuan & Chang-An Yuan & De-Shuang Huang, 2017. "FAACOSE: A Fast Adaptive Ant Colony Optimization Algorithm for Detecting SNP Epistasis," Complexity, Hindawi, vol. 2017, pages 1-10, September.
- Jae Eun Lee & Jung Hye Sung & Daniel Sarpong & Jimmy T. Efird & Paul B. Tchounwou & Elizabeth Ofili & Keith Norris, 2018. "Knowledge Management for Fostering Biostatistical Collaboration within a Research Network: The RTRN Case Study," IJERPH, MDPI, vol. 15(11), pages 1-13, November.
- Chang Lu & Jan Zaucha & Rihab Gam & Hai Fang & Smithers & Matt E. Oates & Miguel Bernabe-Rubio & James Williams & Natalie Zelenka & Arun Prasad Pandurangan & Himani Tandon & Hashem Shihab & Raju Kalai, 2023. "Hypothesis-free phenotype prediction within a genetics-first framework," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
- Ian Barnett & Rajarshi Mukherjee & Xihong Lin, 2017. "The Generalized Higher Criticism for Testing SNP-Set Effects in Genetic Association Studies," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 112(517), pages 64-76, January.
- Colin D Steer & Patrick Bolton & Jean Golding, 2015. "Preconception and Prenatal Environmental Factors Associated with Communication Impairments in 9 Year Old Children Using an Exposome-Wide Approach," PLOS ONE, Public Library of Science, vol. 10(3), pages 1-26, March.
- Nur Zarina Ali Hassan & Norfilza Mohd Mokhtar & Teow Kok Sin & Isa Mohamed Rose & Ismail Sagap & Roslan Harun & Rahman Jamal, 2014. "Integrated Analysis of Copy Number Variation and Genome-Wide Expression Profiling in Colorectal Cancer Tissues," PLOS ONE, Public Library of Science, vol. 9(4), pages 1-11, April.
- Bingxin Zhao & Fei Zou, 2022. "On polygenic risk scores for complex traits prediction," Biometrics, The International Biometric Society, vol. 78(2), pages 499-511, June.
- von Stumm, Sophie & Kandaswamy, Radhika & Maxwell, Jessye, 2023. "Gene-environment interplay in early life cognitive development," Intelligence, Elsevier, vol. 98(C).
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0075350. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.