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Power Estimates for Voxel-Based Genetic Association Studies Using Diffusion Imaging [chapter]

Neda Jahanshad, Peter Kochunov, David C. Glahn, John Blangero, Thomas E. Nichols, Katie L. McMahon, Greig I. de Zubicaray, Nicholas G. Martin, Margaret J. Wright, Clifford R. Jack, Matt A. Bernstein, Michael W. Weiner (+2 others)
2013 Mathematics and Visualization  
We computed voxel-wise heritability estimates for fractional anisotropy in over 1100 DTI scans, and used the results to threshold FA images from new studies.  ...  Here, we developed a method to compute and boost power to detect genetic associations in brain images.  ...  Here, we show that meta-analyzed heritability estimates are useful for genetic studies on the entire image space.  ... 
doi:10.1007/978-3-319-02475-2_21 fatcat:4enknzpfizddxi5q7cwbn3uxxa

Multi-site study of additive genetic effects on fractional anisotropy of cerebral white matter: Comparing meta and megaanalytical approaches for data pooling

Peter Kochunov, Neda Jahanshad, Emma Sprooten, Thomas E. Nichols, René C. Mandl, Laura Almasy, Tom Booth, Rachel M. Brouwer, Joanne E. Curran, Greig I. de Zubicaray, Rali Dimitrova, Ravi Duggirala (+29 others)
2014 NeuroImage  
This is especially important for genetic studies where a large number of observations are required to obtain sufficient power to detect and replicate genetic effects.  ...  There is a need to develop and evaluate methods for joint-analytical analyses of rich datasets collected in imaging genetics studies.  ...  Data collection for the Bipolar Family Study was supported by an Academy of Medical Sciences/Health Foundation Clinician Scientist Fellowship to AMM.  ... 
doi:10.1016/j.neuroimage.2014.03.033 pmid:24657781 pmcid:PMC4043878 fatcat:mxe7lkp2hfdyrdmcgzzhdbh3zm

Multi-site genetic analysis of diffusion images and voxelwise heritability analysis: A pilot project of the ENIGMA–DTI working group

Neda Jahanshad, Peter V. Kochunov, Emma Sprooten, René C. Mandl, Thomas E. Nichols, Laura Almasy, John Blangero, Rachel M. Brouwer, Joanne E. Curran, Greig I. de Zubicaray, Ravi Duggirala, Peter T. Fox (+19 others)
2013 NeuroImage  
DTI measures, such as the fractional anisotropy (FA) of water diffusion, may be useful for identifying genetic variants that influence brain microstructure.  ...  Diffusion tensor imaging (DTI) yields quantitative measures sensitive to brain development and degeneration, and some common genetic variants may be associated with white matter integrity or connectivity  ...  large genome-wide association studies (GWAS)especially metaanalyses of multiple studiesto uncover genetic loci associated with MRI-based phenotypes including hippocampal volumes Stein et al., 2012) ,  ... 
doi:10.1016/j.neuroimage.2013.04.061 pmid:23629049 pmcid:PMC3729717 fatcat:j4q3mc76wzbazexgmsz7xybx3a

Extending Genetic Linkage Analysis to Diffusion Tensor Images to Map Single Gene Effects on Brain Fiber Architecture [chapter]

Ming-Chang Chiang, Christina Avedissian, Marina Barysheva, Arthur W. Toga, Katie L. McMahon, Greig I. de Zubicaray, Margaret J. Wright, Paul M. Thompson
2009 Lecture Notes in Computer Science  
We extended genetic linkage analysis -an analysis widely used in quantitati ve genetics -to 3D images to analyze single gene effects on brain fiber architecture.  ...  After highdimensional fluid registration, at each voxel we estimated the genetic linkage between the single nucleotide polymorphism (SNP), Val66Met (dbSNP number rs6265), of the BDNF gene (brain-derived  ...  We used the FMRIB software library (FSL, http://www.fmrib.ox. ac.uk/fsl/) for initial pre-processing of the diffusion images.  ... 
doi:10.1007/978-3-642-04271-3_62 fatcat:xycyxdhakjao7mjdybywwm6ryu

Heritability of brain network topology in 853 twins and siblings

L. Zhan, N. Jahanshad, J. Faskowitz, D. Zhu, G. Prasad, N. G. Martin, G. I. de Zubicaray, K. L. McMahon, M. J. Wright, P. M. Thompson
2015 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI)  
Some global network measures (probtrackx-derived GLOB and ST) showed significant genetic effects, making them attractive targets for genome-wide association studies.  ...  Genetic analysis of these networks may help identify processes giving rise to heritable brain disorders, but we do not yet know which network measures are promising for genetic analyses.  ...  Bedpostx stands for Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques [15] . In our study, up to 3 fibers were modeled per voxel.  ... 
doi:10.1109/isbi.2015.7163908 pmid:26413204 pmcid:PMC4578220 dblp:conf/isbi/ZhanJFZPMZMWT15 fatcat:4jmwwba7svbn3fz5mx7hhi6zya

Hierarchical clustering of the genetic connectivity matrix reveals the network topology of gene action on brain microstructure: An N=531 twin study

Ming-Chang Chiang, Marina Barysheva, Katie L. McMahon, Greig I. de Zubicaray, Kori Johnson, Nicholas G. Martin, Arthur W. Toga, Margaret J. Wright, Paul M. Thompson
2011 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro  
In an analysis of 4 Tesla diffusion tensor images (DTI) from 531 healthy young adult twins and their siblings, we generalized the concept of genetic correlation to determine common genetic influences on  ...  We applied genome-wide association (GWA) to assess associations between 529,497 SNPs and FA in clusters defined by hubs of the clustered genetic correlation matrix.  ...  Recently, voxel-based searches have been performed, for genetic markers that correlate with image-derived measures at each voxel in the brain (e.g., vGWAS [1] ).  ... 
doi:10.1109/isbi.2011.5872533 dblp:conf/isbi/ChiangBMZJMTWT11 fatcat:76ocferydza6hgozvhl6ewvria

Scalar connectivity measures from fast-marching tractography reveal heritability of white matter architecture

Vishal Patel, Ming-Chang Chiang, Paul M. Thompson, Katie L. McMahon, Greig I. de Zubicaray, Nicholas G. Martin, Margaret J. Wright, Arthur W. Toga
2010 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro  
Recent advances in diffusion-weighted MRI (DWI) have enabled studies of complex white matter tissue architecture in vivo.  ...  We then calculate connectivity maps for a DTI dataset from 92 healthy adult twins and decompose the genetic and environmental contributions to the variance in these metrics using structural equation models  ...  The diffusion tensor (DT) model estimates a single Gaussian diffusion profile at each voxel [1] .  ... 
doi:10.1109/isbi.2010.5490187 dblp:conf/isbi/PatelCTMZMWT10 fatcat:urz2yvtlenhuroxes7i7rxtk2u

Genetics of Path Lengths in Brain Connectivity Networks: HARDI-Based Maps in 457 Adults [chapter]

Neda Jahanshad, Gautam Prasad, Arthur W. Toga, Katie L. McMahon, Greig I. de Zubicaray, Nicholas G. Martin, Margaret J. Wright, Paul M. Thompson
2012 Lecture Notes in Computer Science  
We defined a new measure, based on Dijkstra's algorithm, to compute path lengths for tracts connecting pairs of cortical regions.  ...  Brain connectivity analyses are increasingly popular for investigating organization.  ...  Additional support for algorithm development was provided by NIH R01 grants EB008432, EB008281, and EB007813.  ... 
doi:10.1007/978-3-642-33530-3_3 pmid:25584366 pmcid:PMC4288784 fatcat:tk4hg5uzjzh2zf46jprizdsxfm

Voxelwise gene-wide association study (vGeneWAS): Multivariate gene-based association testing in 731 elderly subjects

Derrek P. Hibar, Jason L. Stein, Omid Kohannim, Neda Jahanshad, Andrew J. Saykin, Li Shen, Sungeun Kim, Nathan Pankratz, Tatiana Foroud, Matthew J. Huentelman, Steven G. Potkin, Clifford R. Jack (+3 others)
2011 NeuroImage  
Imaging traits provide a powerful and biologically relevant substrate to examine the influence of genetics on the brain.  ...  This multivariate, gene-based voxelwise association study offers a novel framework to detect genetic influences on the brain.  ...  Acknowledgments Data collection and sharing for this project was funded by the Alzheimer's Disease Neuroimaging Initiative (ADNI) (National Institutes of Health Grant U01 AG024904, 3U01AG024904-03S5).  ... 
doi:10.1016/j.neuroimage.2011.03.077 pmid:21497199 pmcid:PMC3366726 fatcat:plqqxysutvgbjn3ue3prfgk7gi

Whole-genome analyses of whole-brain data: working within an expanded search space

Sarah E Medland, Neda Jahanshad, Benjamin M Neale, Paul M Thompson
2014 Nature Neuroscience  
With the advent of global neuroimaging consortia, imaging studies are now well powered to discover genetic variants that reliably affect the brain.  ...  Meanwhile, brain imaging studies are increasing in size and scope, revealing disease and genetic effects on brain structure and function, and implicating neural pathways and causal mechanisms.  ...  The power to identify a given genetic effect, at a given voxel, can be determined if we can estimate the proportion of variance in the signal at that voxel due to the variant.  ... 
doi:10.1038/nn.3718 pmid:24866045 pmcid:PMC4300949 fatcat:ililaltty5d2rmtzgxsnlryuzi

Comparison of fractional and geodesic anisotropy in diffusion tensor images of 90 monozygotic and dizygotic twins

Agatha D. Lee, Natasha Lepore, Marina Barysheva, Yi-Yu Chou, Caroline Brun, Sarah K. Madsen, Katie L. McMahon, Greig I. de Zubicaray, Matthew Meredith, Margaret J. Wright, Arthur W. Toga, Paul M. Thompson
2008 2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro  
We used diffusion tensor magnetic resonance imaging (DTI) to reveal the extent of genetic effects on brain fiber microstructure, based on tensor-derived measures, in 22 pairs of monozygotic (MZ) twins  ...  While maps were relatively noisy, the CDFs showed promise for detecting genetic influences on brain fiber integrity as the current sample expands.  ...  Figure 4 4 shows non-parametric permutation based p-values at each voxel, based on r values for tGA and FA for MZ and DZ groups.  ... 
doi:10.1109/isbi.2008.4541153 pmid:30546820 pmcid:PMC6289524 fatcat:h2oxnppaxnguhk3snfkddyswg4

Genetics of the connectome

Paul M. Thompson, Tian Ge, David C. Glahn, Neda Jahanshad, Thomas E. Nichols
2013 NeuroImage  
Here we review a variety of genetic analysis methods--such as genome-wide association studies (GWAS), linkage and candidate gene studies--that have been fruitfully adapted to imaging data to implicate  ...  We also review some consortium efforts, such as ENIGMA, that offer the power to detect robust common genetic associations using phenotypic harmonization procedures and meta-analysis.  ...  By grouping SNPs based on gene membership, a voxel-wise gene-wide association study (vGeneWAS) was carried out, using the same imaging and genetic data as in vGWAS Stein et al., 2010a) showed increased  ... 
doi:10.1016/j.neuroimage.2013.05.013 pmid:23707675 pmcid:PMC3905600 fatcat:dv26qigaovc4vdpm6jkealvoly

A multivariate to multivariate approach for voxel-wise genome-wide association analysis [article]

Qiong Wu, Yuan Zhang, Xiaoqi Huang, Tianzhou Ma, L. Elliot Hong, Peter Kochunov, Shuo Chen
2021 bioRxiv   pre-print
., a set of SNPs highly correlated with a cluster of voxels) for the systematic association pattern.  ...  We attempt to identify underlying organized association patterns of SNP-voxel pairs and understand the polygenic and pleiotropic networks on brain imaging traits.  ...  We tested the imaging-genetic associations between SNPs across 22 chromosomes and voxel-level imaging traits using our proposed method.  ... 
doi:10.1101/2021.11.02.467021 fatcat:nj232szeq5cfvbvh3oylkutare

Heritability of fractional anisotropy in human white matter: A comparison of Human Connectome Project and ENIGMA-DTI data

Peter Kochunov, Neda Jahanshad, Daniel Marcus, Anderson Winkler, Emma Sprooten, Thomas E. Nichols, Susan N. Wright, L. Elliot Hong, Binish Patel, Timothy Behrens, Saad Jbabdi, Jesper Andersson (+41 others)
2015 NeuroImage  
FA measurements were derived using (Enhancing NeuroImaging Genetics through Meta-Analysis) ENIGMA DTI protocols and heritability estimates were calculated using the SOLAR-Eclipse imaging genetic analysis  ...  We compared heritability estimates derived from HCP data to those publicly available through the ENIGMA-DTI consortium, which were pooled together from five-family based studies across the US, Europe,  ...  The HCP diffusion imaging data differs from those used in previous ENIGMA-DTI studies in several important ways, including higher spatial resolution (1.25 mm isotropic voxels vs. 2-3 mm for ENIGMA-DTI  ... 
doi:10.1016/j.neuroimage.2015.02.050 pmid:25747917 pmcid:PMC4387079 fatcat:s4lpvm3wozd27fdqjc36aewfoe

Homogenizing Estimates of Heritability Among SOLAR-Eclipse, OpenMx, APACE, and FPHI Software Packages in Neuroimaging Data

Peter Kochunov, Binish Patel, Habib Ganjgahi, Brian Donohue, Meghann Ryan, Elliot L. Hong, Xu Chen, Bhim Adhikari, Neda Jahanshad, Paul M. Thompson, Dennis Van't Ent, Anouk den Braber (+9 others)
2019 Frontiers in Neuroinformatics  
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.  ...  Imaging genetic studies combine methods from both imaging and genetic disciplines.  ... 
doi:10.3389/fninf.2019.00016 pmid:30914942 pmcid:PMC6422938 fatcat:zo5ci45nwra7jcwcvthim5xury
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