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1.  Altered Structural Brain Connectivity in Healthy Carriers of the Autism Risk Gene, CNTNAP2 
Brain connectivity  2011;1(6):447-459.
Recently, carriers of a common variant in the autism risk gene, CNTNAP2, were found to have altered functional brain connectivity using functional MRI. Here we scanned 328 young adults with high-field (4-Tesla) diffusion imaging, to test the hypothesis that carriers of this gene variant would have altered structural brain connectivity. All participants (209 females, 119 males, age: 23.4 +/−2.17 SD years) were scanned with 105-gradient high angular diffusion imaging (HARDI) at 4 Tesla. After performing a whole-brain fiber tractography using the full angular resolution of the diffusion scans, 70 cortical surface-based regions of interest were created from each individual’s co-registered anatomical data to compute graph metrics for all pairs of cortical regions. In graph theory analyses, subjects homozygous for the risk allele (CC) had lower characteristic path length, greater small-worldness and global efficiency in whole brain analyses, as well as greater eccentricity (maximum path length) in 60 of 70 nodes in regional analyses. These results were not reducible to differences in more commonly studied traits such as fiber density or fractional anisotropy. This is the first study to link graph theory metrics of brain structural connectivity to a common genetic variant linked with autism and will help us understand the neurobiology of circuits implicated in risk for autism.
doi:10.1089/brain.2011.0064
PMCID: PMC3420970  PMID: 22500773
structural connectivity; HARDI; autism; CNTNAP2; graph theory; twins
2.  lop-DWI: A Novel Scheme for Pre-Processing of Diffusion-Weighted Images in the Gradient Direction Domain 
We describe and evaluate a pre-processing method based on a periodic spiral sampling of diffusion-gradient directions for high angular resolution diffusion magnetic resonance imaging. Our pre-processing method incorporates prior knowledge about the acquired diffusion-weighted signal, facilitating noise reduction. Periodic spiral sampling of gradient direction encodings results in an acquired signal in each voxel that is pseudo-periodic with characteristics that allow separation of low-frequency signal from high frequency noise. Consequently, it enhances local reconstruction of the orientation distribution function used to define fiber tracks in the brain. Denoising with periodic spiral sampling was tested using synthetic data and in vivo human brain images. The level of improvement in signal-to-noise ratio and in the accuracy of local reconstruction of fiber tracks was significantly improved using our method.
doi:10.3389/fneur.2014.00290
PMCID: PMC4290594  PMID: 25628600
spiral sampling; gradient direction domain; diffusion-weighted imaging; pre-processing; HARDI; local reconstruction
3.  Genetics of Path Lengths in Brain Connectivity Networks: HARDI-Based Maps in 457 Adults 
Brain connectivity analyses are increasingly popular for investigating organization. Many connectivity measures including path lengths are generally defined as the number of nodes traversed to connect a node in a graph to the others. Despite its name, path length is purely topological, and does not take into account the physical length of the connections. The distance of the trajectory may also be highly relevant, but is typically overlooked in connectivity analyses. Here we combined genotyping, anatomical MRI and HARDI to understand how our genes influence the cortical connections, using whole-brain tractography. We defined a new measure, based on Dijkstra’s algorithm, to compute path lengths for tracts connecting pairs of cortical regions. We compiled these measures into matrices where elements represent the physical distance traveled along tracts. We then analyzed a large cohort of healthy twins and show that our path length measure is reliable, heritable, and influenced even in young adults by the Alzheimer’s risk gene, CLU.
doi:10.1007/978-3-642-33530-3_3
PMCID: PMC4288784  PMID: 25584366
Structural connectivity; neuroimaging genetics; Dijkstra’s algorithm; HARDI tractography; path length
4.  LABELING WHITE MATTER TRACTS IN HARDI BY FUSING MULTIPLE TRACT ATLASES WITH APPLICATIONS TO GENETICS 
Accurate identification of white matter structures and segmentation of fibers into tracts is important in neuroimaging and has many potential applications. Even so, it is not trivial because whole brain tractography generates hundreds of thousands of streamlines that include many false positive fibers. We developed and tested an automatic tract labeling algorithm to segment anatomically meaningful tracts from diffusion weighted images. Our multi-atlas method incorporates information from multiple hand-labeled fiber tract atlases. In validations, we showed that the method outperformed the standard ROI-based labeling using a deformable, parcellated atlas. Finally, we show a high-throughput application of the method to genetic population studies. We use the sub-voxel diffusion information from fibers in the clustered tracts based on 105-gradient HARDI scans of 86 young normal twins. The whole workflow shows promise for larger population studies in the future.
doi:10.1109/ISBI.2013.6556524
PMCID: PMC4236723  PMID: 25419442
HARDI; Tractography; Fiber Clustering; Label Fusion; Genetic Heritability
5.  Relation between variants in the neurotrophin receptor gene, NTRK3, and white matter integrity in healthy young adults 
NeuroImage  2013;82:146-153.
The NTRK3 gene (also known as TRKC) encodes a high affinity receptor for the neurotrophin 3′-nucleotidase (NT3), which is implicated in oligodendrocyte and myelin development. We previously found that white matter integrity in young adults related to genetic variants in genes encoding neurotrophins and their receptors. This underscores the importance of neurotrophins for white matter development. NTRK3 variants are putative risk factors for schizophrenia, bipolar disorder, and obsessive-compulsive disorder hoarding, suggesting that some NTRK3 variants may affect the brain.
To test this, we scanned 392 healthy adult twins and their siblings (mean age, 23.6 ± 2.2 years; range: 20-29 years) with 105-gradient 4-Tesla diffusion tensor imaging (DTI). We identified 18 single nucleotide polymorphisms (SNPs) in the NTRK3 gene that have been associated with neuropsychiatric disorders. We used a multi-SNP model, adjusting for family relatedness, age, and sex, to relate these variants to voxelwise fractional anisotropy (FA) – a DTI measure of white matter integrity.
FA was optimally predicted (based on the highest false discovery rate critical p), by five SNPs (rs1017412, rs2114252, rs16941261, rs3784406, and rs7176429; overall FDR critical p = 0.028). Gene effects were widespread and included the corpus callosum genu and inferior longitudinal fasciculus - regions implicated in several neuropsychiatric disorders and previously associated with other neurotrophin-related genetic variants in an overlapping sample of subjects. NTRK3 genetic variants, and neurotrophins more generally, may influence white matter integrity in brain regions implicated in neuropsychiatric disorders.
doi:10.1016/j.neuroimage.2013.05.095
PMCID: PMC3948328  PMID: 23727532
Fractional anisotropy; diffusion tensor imaging; single nucleotide polymorphism; schizophrenia; obsessive compulsive disorder; bipolar disorder
6.  LEFT VERSUS RIGHT HEMISPHERE DIFFERENCES IN BRAIN CONNECTIVITY: 4-TESLA HARDI TRACTOGRAPHY IN 569 TWINS 
Diffusion imaging can map anatomical connectivity in the living brain, offering new insights into fundamental questions such as how the left and right brain hemispheres differ. Anatomical brain asymmetries are related to speech and language abilities, but less is known about left/right hemisphere differences in brain wiring. To assess this, we scanned 457 young adults (age 23.4±2.0 SD years) and 112 adolescents (age 12-16) with 4-Tesla 105-gradient high-angular resolution diffusion imaging. We extracted fiber tracts throughout the brain with a Hough transform method. A 70×70 connectivity matrix was created, for each subject, based on the proportion of fibers intersecting 70 cortical regions. We identified significant differences in the proportions of fibers intersecting left and right hemisphere cortical regions. The degree of asymmetry in the connectivity matrices varied with age, as did the asymmetry in network topology measures such as the small-world effect.
doi:10.1109/ISBI.2012.6235601
PMCID: PMC4232939  PMID: 25404993
tractography; high angular resolution diffusion imaging (HARDI); small-world effect; connectome; laterality
7.  Multi-site genetic analysis of diffusion images and voxelwise heritability analysis: A pilot project of the ENIGMA–DTI working group 
NeuroImage  2013;81:455-469.
The ENIGMA (Enhancing NeuroImaging Genetics through Meta-Analysis) Consortium was set up to analyze brain measures and genotypes from multiple sites across the world to improve the power to detect genetic variants that influence the brain. 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. DTI measures, such as the fractional anisotropy (FA) of water diffusion, may be useful for identifying genetic variants that influence brain microstructure. However, genome-wide association studies (GWAS) require large populations to obtain sufficient power to detect and replicate significant effects, motivating a multi-site consortium effort. As part of an ENIGMA–DTI working group, we analyzed high-resolution FA images from multiple imaging sites across North America, Australia, and Europe, to address the challenge of harmonizing imaging data collected at multiple sites. Four hundred images of healthy adults aged 18–85 from four sites were used to create a template and corresponding skeletonized FA image as a common reference space. Using twin and pedigree samples of different ethnicities, we used our common template to evaluate the heritability of tract-derived FA measures. We show that our template is reliable for integrating multiple datasets by combining results through meta-analysis and unifying the data through exploratory mega-analyses. Our results may help prioritize regions of the FA map that are consistently influenced by additive genetic factors for future genetic discovery studies. Protocols and templates are publicly available at (http://enigma.loni.ucla.edu/ongoing/dti-working-group/).
doi:10.1016/j.neuroimage.2013.04.061
PMCID: PMC3729717  PMID: 23629049
Diffusion Tensor Imaging (DTI); Imaging genetics; Heritability; Meta-analysis; Multi-site; Reliability
8.  Heritability of White Matter Fiber Tract Shapes: A HARDI Study of 198 Twins* 
Genetic analysis of diffusion tensor images (DTI) shows great promise in revealing specific genetic variants that affect brain integrity and connectivity. Most genetic studies of DTI analyze voxel-based diffusivity indices in the image space (such as 3D maps of fractional anisotropy) and overlook tract geometry. Here we propose an automated workflow to cluster fibers using a white matter probabilistic atlas and perform genetic analysis on the shape characteristics of fiber tracts. We apply our approach to large study of 4-Tesla high angular resolution diffusion imaging (HARDI) data from 198 healthy, young adult twins (age: 20–30). Illustrative results show heritability for the shapes of several major tracts, as color-coded maps.
PMCID: PMC4205954  PMID: 25346947
HARDI; Tractography; Image Registration; White Matter Probabilistic Atlas; Fiber Alignment; Clustering; Curve Matching; Heritability
9.  The roles of shared vs. distinctive conceptual features in lexical access 
Frontiers in Psychology  2014;5:1014.
Contemporary models of spoken word production assume conceptual feature sharing determines the speed with which objects are named in categorically-related contexts. However, statistical models of concept representation have also identified a role for feature distinctiveness, i.e., features that identify a single concept and serve to distinguish it quickly from other similar concepts. In three experiments we investigated whether distinctive features might explain reports of counter-intuitive semantic facilitation effects in the picture word interference (PWI) paradigm. In Experiment 1, categorically-related distractors matched in terms of semantic similarity ratings (e.g., zebra and pony) and manipulated with respect to feature distinctiveness (e.g., a zebra has stripes unlike other equine species) elicited interference effects of comparable magnitude. Experiments 2 and 3 investigated the role of feature distinctiveness with respect to reports of facilitated naming with part-whole distractor-target relations (e.g., a hump is a distinguishing part of a CAMEL, whereas knee is not, vs. an unrelated part such as plug). Related part distractors did not influence target picture naming latencies significantly when the part denoted by the related distractor was not visible in the target picture (whether distinctive or not; Experiment 2). When the part denoted by the related distractor was visible in the target picture, non-distinctive part distractors slowed target naming significantly at SOA of −150 ms (Experiment 3). Thus, our results show that semantic interference does occur for part-whole distractor-target relations in PWI, but only when distractors denote features shared with the target and other category exemplars. We discuss the implications of these results for some recently developed, novel accounts of lexical access in spoken word production.
doi:10.3389/fpsyg.2014.01014
PMCID: PMC4165322  PMID: 25278914
lexical access; competition; semantic interference; picture naming; shared features; distinctive features
10.  Exhaustive search of the SNP-SNP interactome identifies epistatic effects on brain volume in two cohorts 
The SNP-SNP interactome has rarely been explored in the context of neuroimaging genetics mainly due to the complexity of conducting ∼1011 pairwise statistical tests. However, recent advances in machine learning, specifically the iterative sure independence screening (SIS) method, have enabled the analysis of datasets where the number of predictors is much larger than the number of observations. Using an implementation of the SIS algorithm (called EPISIS), we used exhaustive search of the genome-wide, SNP-SNP interactome to identify and prioritize SNPs for interaction analysis. We identified a significant SNP pair, rs1345203 and rs1213205, associated with temporal lobe volume. We further examined the full-brain, voxelwise effects of the interaction in the ADNI dataset and separately in an independent dataset of healthy twins (QTIM). We found that each additional loading in the epistatic effect was associated with ∼5% greater brain regional brain volume (a protective effect) in both the ADNI and QTIM samples.
PMCID: PMC4109883  PMID: 24505811
epistasis; interaction; genome; sure independence; tensor-based morphometry
11.  A Commonly Carried Genetic Variant in the Delta Opioid Receptor Gene, OPRD1, is Associated with Smaller Regional Brain Volumes: Replication in Elderly and Young Populations 
Human brain mapping  2013;35(4):1226-1236.
Delta opioid receptors are implicated in a variety of psychiatric and neurological disorders. These receptors play a key role in the reinforcing properties of drugs of abuse, and polymorphisms in OPRD1 (the gene encoding delta opioid receptors) are associated with drug addiction. Delta opioid receptors are also involved in protecting neurons against hypoxic and ischemic stress. Here, we first examined a large sample of 738 elderly participants with neuroimaging and genetic data from the Alzheimer’s Disease Neuroimaging Initiative. We hypothesized that common variants in OPRD1 would be associated with differences in brain structure, particularly in regions relevant to addictive and neurodegenerative disorders. One very common variant (rs678849) predicted differences in regional brain volumes. We replicated the association of this single-nucleotide polymorphism with regional tissue volumes in a large sample of young participants in the Queensland Twin Imaging study. Although the same allele was associated with reduced volumes in both cohorts, the brain regions affected differed between the two samples. In healthy elderly, exploratory analyses suggested that the genotype associated with reduced brain volumes in both cohorts may also predict cerebrospinal fluid levels of neurodegenerative biomarkers, but this requires confirmation. If opiate receptor genetic variants are related to individual differences in brain structure, genotyping of these variants may be helpful when designing clinical trials targeting delta opioid receptors to treat neurological disorders.
doi:10.1002/hbm.22247
PMCID: PMC4046708  PMID: 23427138
neuroimaging; genetics; neurodegeneration; drug addiction; opiates
12.  Genome-wide association identifies genetic variants associated with lentiform nucleus volume in N=1345 young and elderly subjects 
Brain imaging and behavior  2013;7(2):102-115.
Deficits in lentiform nucleus volume and morphometry are implicated in a number of genetically influenced disorders, including Parkinson’s disease, schizophrenia, and ADHD. Here we performed genome-wide searches to discover common genetic variants associated with differences in lentiform nucleus volume in human populations. We assessed structural MRI scans of the brain in two large genotyped samples: the Alzheimer’s Disease Neuroimaging Initiative (ADNI; N=706) and the Queensland Twin Imaging Study (QTIM; N=639). Statistics of association from each cohort were combined meta-analytically using a fixed-effects model to boost power and to reduce the prevalence of false positive findings. We identified a number of associations in and around the flavin-containing monooxygenase (FMO) gene cluster. The most highly associated SNP, rs1795240, was located in the FMO3 gene; after meta-analysis, it showed genome-wide significant evidence of association with lentiform nucleus volume (PMA=4.79×10−8). This commonly-carried genetic variant accounted for 2.68 % and 0.84 % of the trait variability in the ADNI and QTIM samples, respectively, even though the QTIM sample was on average 50 years younger. Pathway enrichment analysis revealed significant contributions of this gene to the cytochrome P450 pathway, which is involved in metabolizing numerous therapeutic drugs for pain, seizures, mania, depression, anxiety, and psychosis. The genetic variants we identified provide replicated, genome-wide significant evidence for the FMO gene cluster’s involvement in lentiform nucleus volume differences in human populations.
doi:10.1007/s11682-012-9199-7
PMCID: PMC3779070  PMID: 22903471
Basal ganglia; Genome-wide association study (GWAS); MRI; Replication; Morphometry; Drug metabolism
13.  Test-Retest Reliability of Graph Theory Measures of Structural Brain Connectivity 
The human connectome has recently become a popular research topic in neuroscience, and many new algorithms have been applied to analyze brain networks. In particular, network topology measures from graph theory have been adapted to analyze network efficiency and ‘small-world’ properties. While there has been a surge in the number of papers examining connectivity through graph theory, questions remain about its test-retest reliability (TRT). In particular, the reproducibility of structural connectivity measures has not been assessed. We examined the TRT of global connectivity measures generated from graph theory analyses of 17 young adults who underwent two high-angular resolution diffusion (HARDI) scans approximately 3 months apart. Of the measures assessed, modularity had the highest TRT, and it was stable across a range of sparsities (a thresholding parameter used to define which network edges are retained). These reliability measures underline the need to develop network descriptors that are robust to acquisition parameters.
PMCID: PMC4039303  PMID: 23286144
14.  Genetic clustering on the hippocampal surface for genome-wide association studies 
Imaging genetics aims to discover how variants in the human genome influence brain measures derived from images. Genome-wide association scans (GWAS) can screen the genome for common differences in our DNA that relate to brain measures. In small samples, GWAS has low power as individual gene effects are weak and one must also correct for multiple comparisons across the genome and the image. Here we extend recent work on genetic clustering of images, to analyze surface-based models of anatomy using GWAS. We performed spherical harmonic analysis of hippocampal surfaces, automatically extracted from brain MRI scans of 1254 subjects. We clustered hippocampal surface regions with common genetic influences by examining genetic correlations (rg) between the normalized deformation values at all pairs of surface points. Using genetic correlations to cluster surface measures, we were able to boost effect sizes for genetic associations, compared to clustering with traditional phenotypic correlations using Pearson's r.
PMCID: PMC4024454  PMID: 24579201
heritability; GWAS; clustering; hippocampus; 3D surfaces; imaging genetics
15.  Development of Insula Connectivity Between Ages 12 and 30 Revealed by High Angular Resolution Diffusion Imaging 
Human brain mapping  2013;35(4):1790-1800.
The insula, hidden deep within the Sylvian fissures, has proven difficult to study from a connectivity perspective. Most of our current information on the anatomical connectivity of the insula comes from studies of nonhuman primates and post mortem human dissections. To date, only two neuroimaging studies have successfully examined the connectivity of the insula. Here we examine how the connectivity of the insula develops between ages 12 and 30, in 307 young adolescent and adult subjects scanned with 4-Tesla high angular resolution diffusion imaging (HARDI). The density of fiber connections between the insula and the frontal and parietal cortex decreased with age, but the connection density between the insula and the temporal cortex generally increased with age. This trajectory is in line with well-known patterns of cortical development in these regions. In addition, males and females showed different developmental trajectories for the connection between the left insula and the left precentral gyrus. The insula plays many different roles, some of them affected in neuropsychiatric disorders; this information on the insula's connectivity may help efforts to elucidate mechanisms of brain disorders in which it is implicated.
doi:10.1002/hbm.22292
PMCID: PMC4017914  PMID: 23836455
insula; development; tractography; HARDI; structural connectivity
16.  DEVELOPMENT OF THE “RICH CLUB” IN BRAIN CONNECTIVITY NETWORKS FROM 438 ADOLESCENTS & ADULTS AGED 12 TO 30 
The ‘rich club’ coefficient describes a phenomenon where a network's hubs (high-degree nodes) are on average more intensely interconnected than lower-degree nodes. Networks with rich clubs often have an efficient, higher-order organization, but we do not yet know how the rich club emerges in the living brain, or how it changes as our brain networks develop. Here we chart the developmental trajectory of the rich club in anatomical brain networks from 438 subjects aged 12-30. Cortical networks were constructed from 68×68 connectivity matrices of fiber density, using whole-brain tractography in 4-Tesla 105-gradient high angular resolution diffusion images (HARDI). The adult and younger cohorts had rich clubs that included different nodes; the rich club effect intensified with age. Rich-club organization is a sign of a network's efficiency and robustness. These concepts and findings may be advantageous for studying brain maturation and abnormal brain development.
doi:10.1109/ISBI.2013.6556552
PMCID: PMC4017916  PMID: 24827471
rich club coefficient; high angular resolution diffusion imaging (HARDI); tractography; network analyses; development; structural connectivity
17.  Genetic effects on the cerebellar role in working memory: Same brain, different genes? 
NeuroImage  2013;86:392-403.
Over the past several years, evidence has accumulated showing that the cerebellum plays a significant role in cognitive function. Here we show, in a large genetically informative twin sample (n = 430; aged 16–30 years), that the cerebellum is strongly, and reliably (n = 30 rescans), activated during an n-back working memory task, particularly lobules I–IV, VIIa Crus I and II, IX and the vermis. Monozygotic twin correlations for cerebellar activation were generally much larger than dizygotic twin correlations, consistent with genetic influences. Structural equation models showed that up to 65% of the variance in cerebellar activation during working memory is genetic (averaging 34% across significant voxels), most prominently in the lobules VI, and VIIa Crus I, with the remaining variance explained by unique/unshared environmental factors. Heritability estimates for brain activation in the cerebellum agree with those found for working memory activation in the cerebral cortex, even though cerebellar cyto-architecture differs substantially. Phenotypic correlations between BOLD percent signal change in cerebrum and cerebellum were low, and bivariate modeling indicated that genetic influences on the cerebellum are at least partly specific to the cerebellum. Activation on the voxel-level correlated very weakly with cerebellar gray matter volume, suggesting specific genetic influences on the BOLD signal. Heritable signals identified here should facilitate discovery of genetic polymorphisms influencing cerebellar function through genome-wide association studies, to elucidate the genetic liability to brain disorders affecting the cerebellum.
doi:10.1016/j.neuroimage.2013.10.006
PMCID: PMC3925745  PMID: 24128737
Cerebellum; Heritability; Genetics; Functional MRI; Working memory; Twin study
18.  The ENIGMA Consortium: large-scale collaborative analyses of neuroimaging and genetic data 
Thompson, Paul M. | Stein, Jason L. | Medland, Sarah E. | Hibar, Derrek P. | Vasquez, Alejandro Arias | Renteria, Miguel E. | Toro, Roberto | Jahanshad, Neda | Schumann, Gunter | Franke, Barbara | Wright, Margaret J. | Martin, Nicholas G. | Agartz, Ingrid | Alda, Martin | Alhusaini, Saud | Almasy, Laura | Almeida, Jorge | Alpert, Kathryn | Andreasen, Nancy C. | Andreassen, Ole A. | Apostolova, Liana G. | Appel, Katja | Armstrong, Nicola J. | Aribisala, Benjamin | Bastin, Mark E. | Bauer, Michael | Bearden, Carrie E. | Bergmann, Ørjan | Binder, Elisabeth B. | Blangero, John | Bockholt, Henry J. | Bøen, Erlend | Bois, Catherine | Boomsma, Dorret I. | Booth, Tom | Bowman, Ian J. | Bralten, Janita | Brouwer, Rachel M. | Brunner, Han G. | Brohawn, David G. | Buckner, Randy L. | Buitelaar, Jan | Bulayeva, Kazima | Bustillo, Juan R. | Calhoun, Vince D. | Cannon, Dara M. | Cantor, Rita M. | Carless, Melanie A. | Caseras, Xavier | Cavalleri, Gianpiero L. | Chakravarty, M. Mallar | Chang, Kiki D. | Ching, Christopher R. K. | Christoforou, Andrea | Cichon, Sven | Clark, Vincent P. | Conrod, Patricia | Coppola, Giovanni | Crespo-Facorro, Benedicto | Curran, Joanne E. | Czisch, Michael | Deary, Ian J. | de Geus, Eco J. C. | den Braber, Anouk | Delvecchio, Giuseppe | Depondt, Chantal | de Haan, Lieuwe | de Zubicaray, Greig I. | Dima, Danai | Dimitrova, Rali | Djurovic, Srdjan | Dong, Hongwei | Donohoe, Gary | Duggirala, Ravindranath | Dyer, Thomas D. | Ehrlich, Stefan | Ekman, Carl Johan | Elvsåshagen, Torbjørn | Emsell, Louise | Erk, Susanne | Espeseth, Thomas | Fagerness, Jesen | Fears, Scott | Fedko, Iryna | Fernández, Guillén | Fisher, Simon E. | Foroud, Tatiana | Fox, Peter T. | Francks, Clyde | Frangou, Sophia | Frey, Eva Maria | Frodl, Thomas | Frouin, Vincent | Garavan, Hugh | Giddaluru, Sudheer | Glahn, David C. | Godlewska, Beata | Goldstein, Rita Z. | Gollub, Randy L. | Grabe, Hans J. | Grimm, Oliver | Gruber, Oliver | Guadalupe, Tulio | Gur, Raquel E. | Gur, Ruben C. | Göring, Harald H. H. | Hagenaars, Saskia | Hajek, Tomas | Hall, Geoffrey B. | Hall, Jeremy | Hardy, John | Hartman, Catharina A. | Hass, Johanna | Hatton, Sean N. | Haukvik, Unn K. | Hegenscheid, Katrin | Heinz, Andreas | Hickie, Ian B. | Ho, Beng-Choon | Hoehn, David | Hoekstra, Pieter J. | Hollinshead, Marisa | Holmes, Avram J. | Homuth, Georg | Hoogman, Martine | Hong, L. Elliot | Hosten, Norbert | Hottenga, Jouke-Jan | Hulshoff Pol, Hilleke E. | Hwang, Kristy S. | Jack, Clifford R. | Jenkinson, Mark | Johnston, Caroline | Jönsson, Erik G. | Kahn, René S. | Kasperaviciute, Dalia | Kelly, Sinead | Kim, Sungeun | Kochunov, Peter | Koenders, Laura | Krämer, Bernd | Kwok, John B. J. | Lagopoulos, Jim | Laje, Gonzalo | Landen, Mikael | Landman, Bennett A. | Lauriello, John | Lawrie, Stephen M. | Lee, Phil H. | Le Hellard, Stephanie | Lemaître, Herve | Leonardo, Cassandra D. | Li, Chiang-shan | Liberg, Benny | Liewald, David C. | Liu, Xinmin | Lopez, Lorna M. | Loth, Eva | Lourdusamy, Anbarasu | Luciano, Michelle | Macciardi, Fabio | Machielsen, Marise W. J. | MacQueen, Glenda M. | Malt, Ulrik F. | Mandl, René | Manoach, Dara S. | Martinot, Jean-Luc | Matarin, Mar | Mather, Karen A. | Mattheisen, Manuel | Mattingsdal, Morten | Meyer-Lindenberg, Andreas | McDonald, Colm | McIntosh, Andrew M. | McMahon, Francis J. | McMahon, Katie L. | Meisenzahl, Eva | Melle, Ingrid | Milaneschi, Yuri | Mohnke, Sebastian | Montgomery, Grant W. | Morris, Derek W. | Moses, Eric K. | Mueller, Bryon A. | Muñoz Maniega, Susana | Mühleisen, Thomas W. | Müller-Myhsok, Bertram | Mwangi, Benson | Nauck, Matthias | Nho, Kwangsik | Nichols, Thomas E. | Nilsson, Lars-Göran | Nugent, Allison C. | Nyberg, Lars | Olvera, Rene L. | Oosterlaan, Jaap | Ophoff, Roel A. | Pandolfo, Massimo | Papalampropoulou-Tsiridou, Melina | Papmeyer, Martina | Paus, Tomas | Pausova, Zdenka | Pearlson, Godfrey D. | Penninx, Brenda W. | Peterson, Charles P. | Pfennig, Andrea | Phillips, Mary | Pike, G. Bruce | Poline, Jean-Baptiste | Potkin, Steven G. | Pütz, Benno | Ramasamy, Adaikalavan | Rasmussen, Jerod | Rietschel, Marcella | Rijpkema, Mark | Risacher, Shannon L. | Roffman, Joshua L. | Roiz-Santiañez, Roberto | Romanczuk-Seiferth, Nina | Rose, Emma J. | Royle, Natalie A. | Rujescu, Dan | Ryten, Mina | Sachdev, Perminder S. | Salami, Alireza | Satterthwaite, Theodore D. | Savitz, Jonathan | Saykin, Andrew J. | Scanlon, Cathy | Schmaal, Lianne | Schnack, Hugo G. | Schork, Andrew J. | Schulz, S. Charles | Schür, Remmelt | Seidman, Larry | Shen, Li | Shoemaker, Jody M. | Simmons, Andrew | Sisodiya, Sanjay M. | Smith, Colin | Smoller, Jordan W. | Soares, Jair C. | Sponheim, Scott R. | Sprooten, Emma | Starr, John M. | Steen, Vidar M. | Strakowski, Stephen | Strike, Lachlan | Sussmann, Jessika | Sämann, Philipp G. | Teumer, Alexander | Toga, Arthur W. | Tordesillas-Gutierrez, Diana | Trabzuni, Daniah | Trost, Sarah | Turner, Jessica | Van den Heuvel, Martijn | van der Wee, Nic J. | van Eijk, Kristel | van Erp, Theo G. M. | van Haren, Neeltje E. M. | van ‘t Ent, Dennis | van Tol, Marie-Jose | Valdés Hernández, Maria C. | Veltman, Dick J. | Versace, Amelia | Völzke, Henry | Walker, Robert | Walter, Henrik | Wang, Lei | Wardlaw, Joanna M. | Weale, Michael E. | Weiner, Michael W. | Wen, Wei | Westlye, Lars T. | Whalley, Heather C. | Whelan, Christopher D. | White, Tonya | Winkler, Anderson M. | Wittfeld, Katharina | Woldehawariat, Girma | Wolf, Christiane | Zilles, David | Zwiers, Marcel P. | Thalamuthu, Anbupalam | Schofield, Peter R. | Freimer, Nelson B. | Lawrence, Natalia S. | Drevets, Wayne
Brain Imaging and Behavior  2014;8(2):153-182.
The Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) Consortium is a collaborative network of researchers working together on a range of large-scale studies that integrate data from 70 institutions worldwide. Organized into Working Groups that tackle questions in neuroscience, genetics, and medicine, ENIGMA studies have analyzed neuroimaging data from over 12,826 subjects. In addition, data from 12,171 individuals were provided by the CHARGE consortium for replication of findings, in a total of 24,997 subjects. By meta-analyzing results from many sites, ENIGMA has detected factors that affect the brain that no individual site could detect on its own, and that require larger numbers of subjects than any individual neuroimaging study has currently collected. ENIGMA’s first project was a genome-wide association study identifying common variants in the genome associated with hippocampal volume or intracranial volume. Continuing work is exploring genetic associations with subcortical volumes (ENIGMA2) and white matter microstructure (ENIGMA-DTI). Working groups also focus on understanding how schizophrenia, bipolar illness, major depression and attention deficit/hyperactivity disorder (ADHD) affect the brain. We review the current progress of the ENIGMA Consortium, along with challenges and unexpected discoveries made on the way.
doi:10.1007/s11682-013-9269-5
PMCID: PMC4008818  PMID: 24399358
Genetics; MRI; GWAS; Consortium; Meta-analysis; Multi-site
19.  Development of Brain Structural Connectivity between Ages 12 and 30: A 4-Tesla Diffusion Imaging Study in 439 Adolescents and Adults 
NeuroImage  2012;64:671-684.
Understanding how the brain matures in healthy individuals is critical for evaluating deviations from normal development in psychiatric and neurodevelopmental disorders. The brain’s anatomical networks are profoundly re-modeled between childhood and adulthood, and diffusion tractography offers unprecedented power to reconstruct these networks and neural pathways in vivo. Here we tracked changes in structural connectivity and network efficiency in 439 right-handed individuals aged 12 to 30 (211 female/126 male adults, mean age=23.6, SD=2.19; 31 female/24 male 12 year olds, mean age=12.3, SD=0.18; and 25 female/22 male 16 year olds, mean age=16.2, SD=0.37). All participants were scanned with high angular resolution diffusion imaging (HARDI) at 4 Tesla. After we performed whole brain tractography, 70 cortical gyral-based regions of interest were extracted from each participant’s co-registered anatomical scans. The degree of fiber connections between all pairs of cortical regions, or nodes, were found to create symmetric fiber density matrices, reflecting the structural brain network. From those 70×70 matrices we computed graph theory metrics characterizing structural connectivity. Several key global and nodal metrics changed across development, showing increased network integration, with some connections pruned and others strengthened. The increases and decreases in fiber density, however, were not distributed proportionally across the brain. The frontal cortex had a disproportionate number of decreases in fiber density while the temporal cortex had a disproportionate number of increases in fiber density. This large-scale analysis of the developing structural connectome offers a foundation to develop statistical criteria for aberrant brain connectivity as the human brain matures.
doi:10.1016/j.neuroimage.2012.09.004
PMCID: PMC3603574  PMID: 22982357
HARDI; structural connectivity; graph theory; development
20.  Alzheimer’s Disease Risk Gene, GAB2, is Associated with Regional Brain Volume Differences in 755 Young Healthy Twins 
The development of late-onset Alzheimer’s disease (LOAD) is under strong genetic control and there is great interest in the genetic variants that confer increased risk. The Alzheimer’s disease risk gene, growth factor receptor bound protein 2-associated protein (GAB2), has been shown to provide a 1.27–1.51 increased odds of developing LOAD for rs7101429 major allele carriers, in case-control analysis. GAB2 is expressed across the brain throughout life, and its role in LOAD pathology is well understood. Recent studies have begun to examine the effect of genetic variation in the GAB2 gene on differences in the brain. However, the effect of GAB2 on the young-adult brain has yet to be considered. Here we found a significant association between the GAB2 gene and morphological brain differences in 755 young-adult twins (469 females) (M = 23.1, SD = 3.1 years), using a gene-based test with principal components regression (PCReg). Detectable differences in brain morphology are therefore associated with variation in the GAB2 gene, even in young adults, long before the typical age of onset of Alzheimer’s disease.
doi:10.1017/thg.2012.15
PMCID: PMC3785377  PMID: 22856364
GAB2; imaging genetics; tensor-based morphometry; Alzheimer’s disease
21.  Predicting White Matter Integrity from Multiple Common Genetic Variants 
Neuropsychopharmacology  2012;37(9):2012-2019.
Several common genetic variants have recently been discovered that appear to influence white matter microstructure, as measured by diffusion tensor imaging (DTI). Each genetic variant explains only a small proportion of the variance in brain microstructure, so we set out to explore their combined effect on the white matter integrity of the corpus callosum. We measured six common candidate single-nucleotide polymorphisms (SNPs) in the COMT, NTRK1, BDNF, ErbB4, CLU, and HFE genes, and investigated their individual and aggregate effects on white matter structure in 395 healthy adult twins and siblings (age: 20–30 years). All subjects were scanned with 4-tesla 94-direction high angular resolution diffusion imaging. When combined using mixed-effects linear regression, a joint model based on five of the candidate SNPs (COMT, NTRK1, ErbB4, CLU, and HFE) explained ∼6% of the variance in the average fractional anisotropy (FA) of the corpus callosum. This predictive model had detectable effects on FA at 82% of the corpus callosum voxels, including the genu, body, and splenium. Predicting the brain's fiber microstructure from genotypes may ultimately help in early risk assessment, and eventually, in personalized treatment for neuropsychiatric disorders in which brain integrity and connectivity are affected.
doi:10.1038/npp.2012.49
PMCID: PMC3398730  PMID: 22510721
neuroimaging; brain structure; DTI; genetics; genetic profiles; prediction; imaging; clinical or preclinical; neuroanatomy; neurogenetics; pharmacogenetics / pharmacogenomics; neuroimaging; brain structure; DTI; genetics; genetic profiles
22.  Identification of common variants associated with human hippocampal and intracranial volumes 
Stein, Jason L | Medland, Sarah E | Vasquez, Alejandro Arias | Hibar, Derrek P | Senstad, Rudy E | Winkler, Anderson M | Toro, Roberto | Appel, Katja | Bartecek, Richard | Bergmann, Ørjan | Bernard, Manon | Brown, Andrew A | Cannon, Dara M | Chakravarty, M Mallar | Christoforou, Andrea | Domin, Martin | Grimm, Oliver | Hollinshead, Marisa | Holmes, Avram J | Homuth, Georg | Hottenga, Jouke-Jan | Langan, Camilla | Lopez, Lorna M | Hansell, Narelle K | Hwang, Kristy S | Kim, Sungeun | Laje, Gonzalo | Lee, Phil H | Liu, Xinmin | Loth, Eva | Lourdusamy, Anbarasu | Mattingsdal, Morten | Mohnke, Sebastian | Maniega, Susana Muñoz | Nho, Kwangsik | Nugent, Allison C | O’Brien, Carol | Papmeyer, Martina | Pütz, Benno | Ramasamy, Adaikalavan | Rasmussen, Jerod | Rijpkema, Mark | Risacher, Shannon L | Roddey, J Cooper | Rose, Emma J | Ryten, Mina | Shen, Li | Sprooten, Emma | Strengman, Eric | Teumer, Alexander | Trabzuni, Daniah | Turner, Jessica | van Eijk, Kristel | van Erp, Theo G M | van Tol, Marie-Jose | Wittfeld, Katharina | Wolf, Christiane | Woudstra, Saskia | Aleman, Andre | Alhusaini, Saud | Almasy, Laura | Binder, Elisabeth B | Brohawn, David G | Cantor, Rita M | Carless, Melanie A | Corvin, Aiden | Czisch, Michael | Curran, Joanne E | Davies, Gail | de Almeida, Marcio A A | Delanty, Norman | Depondt, Chantal | Duggirala, Ravi | Dyer, Thomas D | Erk, Susanne | Fagerness, Jesen | Fox, Peter T | Freimer, Nelson B | Gill, Michael | Göring, Harald H H | Hagler, Donald J | Hoehn, David | Holsboer, Florian | Hoogman, Martine | Hosten, Norbert | Jahanshad, Neda | Johnson, Matthew P | Kasperaviciute, Dalia | Kent, Jack W | Kochunov, Peter | Lancaster, Jack L | Lawrie, Stephen M | Liewald, David C | Mandl, René | Matarin, Mar | Mattheisen, Manuel | Meisenzahl, Eva | Melle, Ingrid | Moses, Eric K | Mühleisen, Thomas W | Nauck, Matthias | Nöthen, Markus M | Olvera, Rene L | Pandolfo, Massimo | Pike, G Bruce | Puls, Ralf | Reinvang, Ivar | Rentería, Miguel E | Rietschel, Marcella | Roffman, Joshua L | Royle, Natalie A | Rujescu, Dan | Savitz, Jonathan | Schnack, Hugo G | Schnell, Knut | Seiferth, Nina | Smith, Colin | Steen, Vidar M | Valdés Hernández, Maria C | Van den Heuvel, Martijn | van der Wee, Nic J | Van Haren, Neeltje E M | Veltman, Joris A | Völzke, Henry | Walker, Robert | Westlye, Lars T | Whelan, Christopher D | Agartz, Ingrid | Boomsma, Dorret I | Cavalleri, Gianpiero L | Dale, Anders M | Djurovic, Srdjan | Drevets, Wayne C | Hagoort, Peter | Hall, Jeremy | Heinz, Andreas | Jack, Clifford R | Foroud, Tatiana M | Le Hellard, Stephanie | Macciardi, Fabio | Montgomery, Grant W | Poline, Jean Baptiste | Porteous, David J | Sisodiya, Sanjay M | Starr, John M | Sussmann, Jessika | Toga, Arthur W | Veltman, Dick J | Walter, Henrik | Weiner, Michael W | Bis, Joshua C | Ikram, M Arfan | Smith, Albert V | Gudnason, Vilmundur | Tzourio, Christophe | Vernooij, Meike W | Launer, Lenore J | DeCarli, Charles | Seshadri, Sudha | Andreassen, Ole A | Apostolova, Liana G | Bastin, Mark E | Blangero, John | Brunner, Han G | Buckner, Randy L | Cichon, Sven | Coppola, Giovanni | de Zubicaray, Greig I | Deary, Ian J | Donohoe, Gary | de Geus, Eco J C | Espeseth, Thomas | Fernández, Guillén | Glahn, David C | Grabe, Hans J | Hardy, John | Hulshoff Pol, Hilleke E | Jenkinson, Mark | Kahn, René S | McDonald, Colm | McIntosh, Andrew M | McMahon, Francis J | McMahon, Katie L | Meyer-Lindenberg, Andreas | Morris, Derek W | Müller-Myhsok, Bertram | Nichols, Thomas E | Ophoff, Roel A | Paus, Tomas | Pausova, Zdenka | Penninx, Brenda W | Potkin, Steven G | Sämann, Philipp G | Saykin, Andrew J | Schumann, Gunter | Smoller, Jordan W | Wardlaw, Joanna M | Weale, Michael E | Martin, Nicholas G | Franke, Barbara | Wright, Margaret J | Thompson, Paul M
Nature genetics  2012;44(5):552-561.
Identifying genetic variants influencing human brain structures may reveal new biological mechanisms underlying cognition and neuropsychiatric illness. The volume of the hippocampus is a biomarker of incipient Alzheimer’s disease1,2 and is reduced in schizophrenia3, major depression4 and mesial temporal lobe epilepsy5. Whereas many brain imaging phenotypes are highly heritable6,7, identifying and replicating genetic influences has been difficult, as small effects and the high costs of magnetic resonance imaging (MRI) have led to underpowered studies. Here we report genome-wide association meta-analyses and replication for mean bilateral hippocampal, total brain and intracranial volumes from a large multinational consortium. The intergenic variant rs7294919 was associated with hippocampal volume (12q24.22; N = 21,151; P = 6.70 × 10−16) and the expression levels of the positional candidate gene TESC in brain tissue. Additionally, rs10784502, located within HMGA2, was associated with intracranial volume (12q14.3; N = 15,782; P = 1.12 × 10−12). We also identified a suggestive association with total brain volume at rs10494373 within DDR2 (1q23.3; N = 6,500; P = 5.81 × 10−7).
doi:10.1038/ng.2250
PMCID: PMC3635491  PMID: 22504417
23.  Hierarchical topological network analysis of anatomical human brain connectivity and differences related to sex and kinship 
NeuroImage  2011;59(4):3784-3804.
Modern non-invasive brain imaging technologies, such as diffusion weighted magnetic resonance imaging (DWI), enable the mapping of neural fiber tracts in the white matter, providing a basis to reconstruct a detailed map of brain structural connectivity networks. Brain connectivity networks differ from random networks in their topology, which can be measured using small worldness, modularity, and high-degree nodes (hubs). Still, little is known about how individual differences in structural brain network properties relate to age, sex, or genetic differences. Recently, some groups have reported brain network biomarkers that enable differentiation among individuals, pairs of individuals, and groups of individuals. In addition to studying new topological features, here we provide a unifying general method to investigate topological brain networks and connectivity differences between individuals, pairs of individuals, and groups of individuals at several levels of the data hierarchy, while appropriately controlling false discovery rate (FDR) errors. We apply our new method to a large dataset of high quality brain connectivity networks obtained from High Angular Resolution Diffusion Imaging (HARDI) tractography in 303 young adult twins, siblings, and unrelated people. Our proposed approach can accurately classify brain connectivity networks based on sex (93% accuracy) and kinship (88.5% accuracy). We find statistically significant differences associated with sex and kinship both in the brain connectivity networks and in derived topological metrics, such as the clustering coefficient and the communicability matrix.
doi:10.1016/j.neuroimage.2011.10.096
PMCID: PMC3551467  PMID: 22108644
Anatomical brain connectivity; Complex networks; Diffusion weighted MRI; Topological analysis; Hierarchical analysis; False discovery rate; Sex and kinship brain network differences
24.  DIFFUSION IMAGING PROTOCOL EFFECTS ON GENETIC ASSOCIATIONS 
Large multi-site image-analysis studies have successfully discovered genetic variants that affect brain structure in tens of thousands of subjects scanned worldwide. Candidate genes have also associated with brain integrity, measured using fractional anisotropy in diffusion tensor images (DTI). To evaluate the heritability and robustness of DTI measures as a target for genetic analysis, we compared 417 twins and siblings scanned on the same day on the same high field scanner (4-Tesla) with two protocols: (1) 94-directions; 2mm-thick slices, (2) 27-directions; 5mm-thickness. Using mean FA in white matter ROIs and FA ‘skeletons’ derived using FSL, we (1) examined differences in voxelwise means, variances, and correlations among the measures; and (2) assessed heritability with structural equation models, using the classical twin design. FA measures from the genu of the corpus callosum were highly heritable, regardless of protocol. Genome-wide analysis of the genu mean FA revealed differences across protocols in the top associations.
doi:10.1109/ISBI.2012.6235712
PMCID: PMC3420973  PMID: 22903274
imaging genetics; DTI protocol stability; corpus callosum; genome-wide association study; multi-site analysis
25.  CHANGES IN ANATOMICAL BRAIN CONNECTIVITY BETWEEN AGES 12 AND 30: A HARDI STUDY OF 467 ADOLESCENTS AND ADULTS 
Graph theory can be applied to matrices that represent the brain’s anatomical connections, to better understand global properties of anatomical networks, such as their clustering, efficiency and “small-world” topology. Network analysis is popular in adult studies of connectivity, but only one study – in just 30 subjects – has examined how network measures change as the brain develops over this period. Here we assessed the developmental trajectory of graph theory metrics of structural brain connectivity in a cross-sectional study of 467 subjects, aged 12 to 30. We computed network measures from 70×70 connectivity matrices of fiber density generated using whole-brain tractography in 4-Tesla 105-gradient high angular resolution diffusion images (HARDI). We assessed global efficiency and modularity, and both age and age2 effects were identified. HARDI-based connectivity maps are sensitive to the remodeling and refinement of structural brain connections as the human brain develops.
doi:10.1109/ISBI.2012.6235695
PMCID: PMC3420974  PMID: 22903354
graph theory; high angular resolution diffusion imaging (HARDI); tractography; network analyses; development; structural connectivity

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