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| PMID |
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| TITLE |
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| Homogenizing Estimates of Heritability Among SOLAR-Eclipse, OpenMx, APACE, and FPHI Software Packages in Neuroimaging Data. |
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| ABSTRACT |
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| Imaging genetic analyses use heritability calculations to measure the fraction of phenotypic variance attributable to additive genetic factors. We tested the agreement between heritability estimates provided by four methods that are used for heritability estimates in neuroimaging traits. SOLAR-Eclipse and OpenMx use iterative maximum likelihood estimation (MLE) methods. Accelerated Permutation inference for ACE (APACE) and fast permutation heritability inference (FPHI), employ fast, non-iterative approximation-based methods. We performed this evaluation in a simulated twin-sibling pedigree and phenotypes and in diffusion tensor imaging (DTI) data from three twin-sibling cohorts, the human connectome project (HCP), netherlands twin register (NTR) and BrainSCALE projects provided as a part of the enhancing neuro imaging genetics analysis (ENIGMA) consortium. We observed that heritability estimate may differ depending on the underlying method and dataset. The heritability estimates from the two MLE approaches provided excellent agreement in both simulated and imaging data. The heritability estimates for two approximation approaches showed reduced heritability estimates in datasets with deviations from data normality. We propose a data homogenization approach (implemented in solar-eclipse; www.solar-eclipse-genetics.org) to improve the convergence of heritability estimates across different methods. The homogenization steps include consistent regression of any nuisance covariates and enforcing normality on the trait data using inverse Gaussian transformation. Under these conditions, the heritability estimates for simulated and DTI phenotypes produced converging heritability estimates regardless of the method. Thus, using these simple suggestions may help new heritability studies to provide outcomes that are comparable regardless of software package. |
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| DATE PUBLISHED |
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| HISTORY |
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| PUBSTATUS |
PUBSTATUSDATE |
| received |
2017/07/05 |
| accepted |
2019/02/25 |
| entrez |
2019/03/28 06:00 |
| pubmed |
2019/03/28 06:00 |
| medline |
2019/03/28 06:01 |
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| AUTHORS |
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| NAME |
COLLECTIVENAME |
LASTNAME |
FORENAME |
INITIALS |
AFFILIATION |
AFFILIATIONINFO |
| Kochunov P |
|
Kochunov |
Peter |
P |
|
Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, United States. |
| Patel B |
|
Patel |
Binish |
B |
|
Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, United States. |
| Ganjgahi H |
|
Ganjgahi |
Habib |
H |
|
Department of Statistics, University of Oxford, Oxford, United Kingdom. |
| Donohue B |
|
Donohue |
Brian |
B |
|
Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, United States. |
| Ryan M |
|
Ryan |
Meghann |
M |
|
Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, United States. |
| Hong EL |
|
Hong |
Elliot L |
EL |
|
Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, United States. |
| Chen X |
|
Chen |
Xu |
X |
|
Department of Cognitive Neuroscience, Maastricht University, Maastricht, Netherlands. |
| Adhikari B |
|
Adhikari |
Bhim |
B |
|
Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, United States. |
| Jahanshad N |
|
Jahanshad |
Neda |
N |
|
Imaging Genetics Center, Keck School of Medicine of USC, Marina del Rey, CA, United States. |
| Thompson PM |
|
Thompson |
Paul M |
PM |
|
Imaging Genetics Center, Keck School of Medicine of USC, Marina del Rey, CA, United States. |
| Van't Ent D |
|
Van't Ent |
Dennis |
D |
|
Department of Biological Psychology, VU University, Amsterdam, Netherlands. |
| den Braber A |
|
den Braber |
Anouk |
A |
|
Department of Biological Psychology, VU University, Amsterdam, Netherlands. |
| de Geus EJC |
|
de Geus |
Eco J C |
EJC |
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Department of Biological Psychology, VU University, Amsterdam, Netherlands. |
| Brouwer RM |
|
Brouwer |
Rachel M |
RM |
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Department of Biological Psychology, VU University, Amsterdam, Netherlands. |
| Boomsma DI |
|
Boomsma |
Dorret I |
DI |
|
Department of Biological Psychology, VU University, Amsterdam, Netherlands. |
| Hulshoff Pol HE |
|
Hulshoff Pol |
Hilleke E |
HE |
|
Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, Netherlands. |
| de Zubicaray GI |
|
de Zubicaray |
Greig I |
GI |
|
Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Brisbane, QLD, Australia. |
| McMahon KL |
|
McMahon |
Katie L |
KL |
|
Centre for Advanced Imaging, University of Queensland, Brisbane, QLD, Australia. |
| Martin NG |
|
Martin |
Nicholas G |
NG |
|
QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia. |
| Wright MJ |
|
Wright |
Margaret J |
MJ |
|
Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia. |
| Nichols TE |
|
Nichols |
Thomas E |
TE |
|
Big Data Institute, University of Oxford, Oxford, United Kingdom. |
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| INVESTIGATORS |
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| JOURNAL |
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| VOLUME: 13 |
| ISSUE: |
| TITLE: Frontiers in neuroinformatics |
| ISOABBREVIATION: Front Neuroinform |
| YEAR: 2019 |
| MONTH: |
| DAY: |
| MEDLINEDATE: |
| SEASON: |
| CITEDMEDIUM: Print |
| ISSN: 1662-5196 |
| ISSNTYPE: Print |
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| MEDLINE JOURNAL |
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| MEDLINETA: Front Neuroinform |
| COUNTRY: Switzerland |
| ISSNLINKING: 1662-5196 |
| NLMUNIQUEID: 101477957 |
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| PUBLICATION TYPE |
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| PUBLICATIONTYPE TEXT |
| Journal Article |
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| COMMENTS AND CORRECTIONS |
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| GRANTS |
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| GRANTID |
AGENCY |
COUNTRY |
| R01 EB015611 |
NIBIB NIH HHS |
United States |
| S10 OD023696 |
NIH HHS |
United States |
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| GENERAL NOTE |
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| KEYWORDS |
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| KEYWORD |
| DTI |
| computational methods |
| genetics |
| heritability |
| imaging genetics |
| population |
| reproducability |
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| MESH HEADINGS |
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| SUPPLEMENTARY MESH |
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| GENE SYMBOLS |
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| CHEMICALS |
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| OTHER ID's |
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