Massively expedited genome-wide heritability analysis (MEGHA)
The discovery and prioritization of heritable phenotypes is a computational challenge in a variety of settings, including neuroimaging genetics and analyses of the vast phenotypic repositories in electronic health record systems and population-based biobanks. Classical estimates of heritability requ...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | en_US |
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National Academy of Sciences (U.S.)
2015
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| Online Access: | http://hdl.handle.net/1721.1/98025 https://orcid.org/0000-0002-5002-1227 |
| _version_ | 1826207841660174336 |
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| author | Ge, Tian Nichols, Thomas E. Lee, Phil H. Holmes, Avram J. Roffman, Joshua L. Buckner, Randy L. Sabuncu, Mert R. Smoller, Jordan W. |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Ge, Tian Nichols, Thomas E. Lee, Phil H. Holmes, Avram J. Roffman, Joshua L. Buckner, Randy L. Sabuncu, Mert R. Smoller, Jordan W. |
| author_sort | Ge, Tian |
| collection | MIT |
| description | The discovery and prioritization of heritable phenotypes is a computational challenge in a variety of settings, including neuroimaging genetics and analyses of the vast phenotypic repositories in electronic health record systems and population-based biobanks. Classical estimates of heritability require twin or pedigree data, which can be costly and difficult to acquire. Genome-wide complex trait analysis is an alternative tool to compute heritability estimates from unrelated individuals, using genome-wide data that are increasingly ubiquitous, but is computationally demanding and becomes difficult to apply in evaluating very large numbers of phenotypes. Here we present a fast and accurate statistical method for high-dimensional heritability analysis using genome-wide SNP data from unrelated individuals, termed massively expedited genome-wide heritability analysis (MEGHA) and accompanying nonparametric sampling techniques that enable flexible inferences for arbitrary statistics of interest. MEGHA produces estimates and significance measures of heritability with several orders of magnitude less computational time than existing methods, making heritability-based prioritization of millions of phenotypes based on data from unrelated individuals tractable for the first time to our knowledge. As a demonstration of application, we conducted heritability analyses on global and local morphometric measurements derived from brain structural MRI scans, using genome-wide SNP data from 1,320 unrelated young healthy adults of non-Hispanic European ancestry. We also computed surface maps of heritability for cortical thickness measures and empirically localized cortical regions where thickness measures were significantly heritable. Our analyses demonstrate the unique capability of MEGHA for large-scale heritability-based screening and high-dimensional heritability profile construction. |
| first_indexed | 2024-09-23T13:55:48Z |
| format | Article |
| id | mit-1721.1/98025 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T13:55:48Z |
| publishDate | 2015 |
| publisher | National Academy of Sciences (U.S.) |
| record_format | dspace |
| spelling | mit-1721.1/980252022-09-28T17:09:00Z Massively expedited genome-wide heritability analysis (MEGHA) Ge, Tian Nichols, Thomas E. Lee, Phil H. Holmes, Avram J. Roffman, Joshua L. Buckner, Randy L. Sabuncu, Mert R. Smoller, Jordan W. Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Sabuncu, Mert R. The discovery and prioritization of heritable phenotypes is a computational challenge in a variety of settings, including neuroimaging genetics and analyses of the vast phenotypic repositories in electronic health record systems and population-based biobanks. Classical estimates of heritability require twin or pedigree data, which can be costly and difficult to acquire. Genome-wide complex trait analysis is an alternative tool to compute heritability estimates from unrelated individuals, using genome-wide data that are increasingly ubiquitous, but is computationally demanding and becomes difficult to apply in evaluating very large numbers of phenotypes. Here we present a fast and accurate statistical method for high-dimensional heritability analysis using genome-wide SNP data from unrelated individuals, termed massively expedited genome-wide heritability analysis (MEGHA) and accompanying nonparametric sampling techniques that enable flexible inferences for arbitrary statistics of interest. MEGHA produces estimates and significance measures of heritability with several orders of magnitude less computational time than existing methods, making heritability-based prioritization of millions of phenotypes based on data from unrelated individuals tractable for the first time to our knowledge. As a demonstration of application, we conducted heritability analyses on global and local morphometric measurements derived from brain structural MRI scans, using genome-wide SNP data from 1,320 unrelated young healthy adults of non-Hispanic European ancestry. We also computed surface maps of heritability for cortical thickness measures and empirically localized cortical regions where thickness measures were significantly heritable. Our analyses demonstrate the unique capability of MEGHA for large-scale heritability-based screening and high-dimensional heritability profile construction. National Institutes of Health (U.S.) (Grant R01 NS083534) National Institutes of Health (U.S.) (Grant R01 NS070963) National Institute for Biomedical Imaging and Bioengineering (U.S.) (Grant 1K25EB013649-01) BrightFocus Foundation (Grant AHAF-A2012333) 2015-08-05T14:25:16Z 2015-08-05T14:25:16Z 2015-02 2014-08 Article http://purl.org/eprint/type/JournalArticle 0027-8424 1091-6490 http://hdl.handle.net/1721.1/98025 Ge, Tian, Thomas E. Nichols, Phil H. Lee, Avram J. Holmes, Joshua L. Roffman, Randy L. Buckner, Mert R. Sabuncu, and Jordan W. Smoller. “Massively Expedited Genome-Wide Heritability Analysis (MEGHA).” Proc Natl Acad Sci USA 112, no. 8 (February 9, 2015): 2479–2484. https://orcid.org/0000-0002-5002-1227 en_US http://dx.doi.org/10.1073/pnas.1415603112 Proceedings of the National Academy of Sciences Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf National Academy of Sciences (U.S.) National Academy of Sciences (U.S.) |
| spellingShingle | Ge, Tian Nichols, Thomas E. Lee, Phil H. Holmes, Avram J. Roffman, Joshua L. Buckner, Randy L. Sabuncu, Mert R. Smoller, Jordan W. Massively expedited genome-wide heritability analysis (MEGHA) |
| title | Massively expedited genome-wide heritability analysis (MEGHA) |
| title_full | Massively expedited genome-wide heritability analysis (MEGHA) |
| title_fullStr | Massively expedited genome-wide heritability analysis (MEGHA) |
| title_full_unstemmed | Massively expedited genome-wide heritability analysis (MEGHA) |
| title_short | Massively expedited genome-wide heritability analysis (MEGHA) |
| title_sort | massively expedited genome wide heritability analysis megha |
| url | http://hdl.handle.net/1721.1/98025 https://orcid.org/0000-0002-5002-1227 |
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