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Cheek CL, Lindner P, Grigorenko EL. Statistical and Machine Learning Analysis in Brain-Imaging Genetics: A Review of Methods. Behav Genet 2024; 54:233-251. [PMID: 38336922 DOI: 10.1007/s10519-024-10177-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/24/2024] [Indexed: 02/12/2024]
Abstract
Brain-imaging-genetic analysis is an emerging field of research that aims at aggregating data from neuroimaging modalities, which characterize brain structure or function, and genetic data, which capture the structure and function of the genome, to explain or predict normal (or abnormal) brain performance. Brain-imaging-genetic studies offer great potential for understanding complex brain-related diseases/disorders of genetic etiology. Still, a combined brain-wide genome-wide analysis is difficult to perform as typical datasets fuse multiple modalities, each with high dimensionality, unique correlational landscapes, and often low statistical signal-to-noise ratios. In this review, we outline the progress in brain-imaging-genetic methodologies starting from early massive univariate to current deep learning approaches, highlighting each approach's strengths and weaknesses and elongating it with the field's development. We conclude by discussing selected remaining challenges and prospects for the field.
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Affiliation(s)
- Connor L Cheek
- Texas Institute for Evaluation, Measurement, and Statistics, University of Houston, Houston, TX, USA.
- Department of Physics, University of Houston, Houston, TX, USA.
| | - Peggy Lindner
- Texas Institute for Evaluation, Measurement, and Statistics, University of Houston, Houston, TX, USA
- Department of Information Science Technology, University of Houston, Houston, TX, USA
| | - Elena L Grigorenko
- Texas Institute for Evaluation, Measurement, and Statistics, University of Houston, Houston, TX, USA
- Department of Psychology, University of Houston, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
- Sirius University of Science and Technology, Sochi, Russia
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Pan W, Shan Y, Li C, Huang S, Li T, Li Y, Zhu H. FPLS-DC: functional partial least squares through distance covariance for imaging genetics. Bioinformatics 2024; 40:btae173. [PMID: 38552322 PMCID: PMC11034987 DOI: 10.1093/bioinformatics/btae173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/28/2024] [Accepted: 03/27/2024] [Indexed: 04/24/2024] Open
Abstract
MOTIVATION Imaging genetics integrates imaging and genetic techniques to examine how genetic variations influence the function and structure of organs like the brain or heart, providing insights into their impact on behavior and disease phenotypes. The use of organ-wide imaging endophenotypes has increasingly been used to identify potential genes associated with complex disorders. However, analyzing organ-wide imaging data alongside genetic data presents two significant challenges: high dimensionality and complex relationships. To address these challenges, we propose a novel, nonlinear inference framework designed to partially mitigate these issues. RESULTS We propose a functional partial least squares through distance covariance (FPLS-DC) framework for efficient genome wide analyses of imaging phenotypes. It consists of two components. The first component utilizes the FPLS-derived base functions to reduce image dimensionality while screening genetic markers. The second component maximizes the distance correlation between genetic markers and projected imaging data, which is a linear combination of the FPLS-basis functions, using simulated annealing algorithm. In addition, we proposed an iterative FPLS-DC method based on FPLS-DC framework, which effectively overcomes the influence of inter-gene correlation on inference analysis. We efficiently approximate the null distribution of test statistics using a gamma approximation. Compared to existing methods, FPLS-DC offers computational and statistical efficiency for handling large-scale imaging genetics. In real-world applications, our method successfully detected genetic variants associated with the hippocampus, demonstrating its value as a statistical toolbox for imaging genetic studies. AVAILABILITY AND IMPLEMENTATION The FPLS-DC method we propose opens up new research avenues and offers valuable insights for analyzing functional and high-dimensional data. In addition, it serves as a useful tool for scientific analysis in practical applications within the field of imaging genetics research. The R package FPLS-DC is available in Github: https://github.com/BIG-S2/FPLSDC.
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Affiliation(s)
- Wenliang Pan
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
| | - Yue Shan
- Departments of Biostatistics, Statistics, Genetics, and Computer Science and Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Chuang Li
- Department of Statistical Science, School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Shuai Huang
- Departments of Biostatistics, Statistics, Genetics, and Computer Science and Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Tengfei Li
- Departments of Radiology and Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yun Li
- Departments of Biostatistics, Statistics, Genetics, and Computer Science and Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Hongtu Zhu
- Departments of Biostatistics, Statistics, Genetics, and Computer Science and Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Departments of Radiology and Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC 27599, USA
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Shi J, He Q, Pan Y, Zhang X, Li M, Chen S. Estimation of Appendicular Skeletal Muscle Mass for Women Aged 60-70 Years Using a Machine Learning Approach. J Am Med Dir Assoc 2022; 23:1985.e1-1985.e7. [PMID: 36216159 DOI: 10.1016/j.jamda.2022.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVES This article aimed to develop and validate an anthropometric equation based on the least absolute shrinkage and selection operator (LASSO) regression, a machine learning approach, to predict appendicular skeletal muscle mass (ASM) in 60-70-year-old women. DESIGN A cross-sectional study. SETTING AND PARTICIPANTS Community-dwelling women aged 60-70 years. METHODS A total of 1296 community-dwelling women aged 60-70 years were randomly divided into the development or the validation group (1:1 ratio). ASM was evaluated by bioelectrical impedance analysis (BIA) as the reference. Variables including weight, height, body mass index (BMI), sitting height, waist-to-hip ratio (WHR), calf circumference (CC), and 5 summary measures of limb length were incorporated as candidate predictors. LASSO regression was used to select predictors with 10-fold cross-validation, and multiple linear regression was applied to develop the BIA-measured ASM prediction equation. Paired t test and Bland-Altman analysis were used to validate agreement. RESULTS Weight, WHR, CC, and sitting height were selected by LASSO regression as independent variables and the equation is ASM = 0.2308 × weight (kg) - 27.5652 × WHR + 8.0179 × CC (m) + 2.3772 × Sitting height (m) + 22.2405 (adjusted R2 = 0.848, standard error of the estimate = 0.661 kg, P < .001). Bland-Altman analysis showed a high agreement between BIA-measured ASM and predicted ASM that the mean difference between the 2 methods was -0.041 kg, with the 95% limits of agreement of -1.441 to 1.359 kg. CONCLUSIONS AND IMPLICATIONS The equation for 60-70-year-old women could provide an available measurement of ASM for communities that cannot equip with BIA, which promotes the early screening of sarcopenia at the community level. Additionally, sitting height could predict ASM effectively, suggesting that maybe it can be used in further studies of muscle mass.
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Affiliation(s)
- Jianan Shi
- School of Nursing and Rehabilitation, Cheeloo College of Medicine, Shandong University, Jinan City, Shandong Province, China
| | - Qiang He
- School of Physical Education, Shandong University, Jinan City, Shandong Province, China
| | - Yang Pan
- School of Physical Education, Shandong University, Jinan City, Shandong Province, China
| | - Xianliang Zhang
- School of Physical Education, Shandong University, Jinan City, Shandong Province, China
| | - Ming Li
- School of Nursing and Rehabilitation, Cheeloo College of Medicine, Shandong University, Jinan City, Shandong Province, China.
| | - Si Chen
- School of Nursing and Rehabilitation, Cheeloo College of Medicine, Shandong University, Jinan City, Shandong Province, China.
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Genç M, Özkale MR. Lasso regression under stochastic restrictions in linear regression: An application to genomic data. COMMUN STAT-THEOR M 2022. [DOI: 10.1080/03610926.2022.2149243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Murat Genç
- Department of Management Information Systems, Faculty of Economics and Administrative Sciences, Tarsus University, Mersin, Turkey
| | - M. Revan Özkale
- Department of Statistics, Faculty of Science and Letters, Çukurova University, Adana, Turkey
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Zu T, Lian H, Green B, Yu Y. Ultra-high Dimensional Quantile Regression for Longitudinal Data: an Application to Blood Pressure Analysis. J Am Stat Assoc 2022. [DOI: 10.1080/01621459.2022.2128806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Tianhai Zu
- Department of Operations, Business Analytics, & Information Systems, University of Cincinnati, Cincinnati, Ohio, USA
| | - Heng Lian
- Department of Mathematics, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong Hong Kong, China
| | - Brittany Green
- Department of Information Systems, Analytics, and Operations, University of Louisville, Louisville, Kentucky, USA
| | - Yan Yu
- Department of Operations, Business Analytics, & Information Systems, University of Cincinnati, Cincinnati, Ohio, USA
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Osterman J, Hammenhag C, Ortiz R, Geleta M. Discovering candidate SNPs for resilience breeding of red clover. FRONTIERS IN PLANT SCIENCE 2022; 13:997860. [PMID: 36247534 PMCID: PMC9554550 DOI: 10.3389/fpls.2022.997860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/07/2022] [Indexed: 06/02/2023]
Abstract
Red clover is a highly valuable crop for the ruminant industry in the temperate regions worldwide. It also provides multiple environmental services, such as contribution to increased soil fertility and reduced soil erosion. This study used 661 single nucleotide polymorphism (SNP) markers via targeted sequencing using seqSNP, to describe genetic diversity and population structure in 382 red clover accessions. The accessions were selected from NordGen representing red clover germplasm from Norway, Sweden, Finland and Denmark as well as from Lantmännen, a Swedish seed company. Each accession was represented by 10 individuals, which was sequenced as a pool. The mean Nei's standard genetic distance between the accessions and genetic variation within accessions were 0.032 and 0.18, respectively. The majority of the accessions had negative Tajima's D, suggesting that they contain significant proportions of rare alleles. A pairwise FST revealed high genetic similarity between the different cultivated types, while the wild populations were divergent. Unlike wild populations, which exhibited genetic differentiation, there was no clear differentiation among all cultivated types. A principal coordinate analysis revealed that the first principal coordinate, distinguished most of the wild populations from the cultivated types, in agreement with the results obtained using a discriminant analysis of principal components and cluster analysis. Accessions of wild populations and landraces collected from southern and central Scandinavia showed a higher genetic similarity to Lantmännen accessios. It is therefore possible to link the diversity of the environments where wild populations were collected to the genetic diversity of the cultivated and wild gene pools. Additionally, least absolute shrinkage and selection operator (LASSO) models revealed associations between variation in temperature and precipitation and SNPs within genes controlling stomatal opening. Temperature was also related to kinase proteins, which are known to regulate plant response to temperature stress. Furthermore, the variation between wild populations and cultivars was correlated with SNPs within genes regulating root development. Overall, this study comprehensively investigated Nordic European red clover germplasm, and the results provide forage breeders with valuable information for further selection and development of red clover cultivars.
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Abstract
AbstractAs basic research, it has also received increasing attention from people that the “curse of dimensionality” will lead to increase the cost of data storage and computing; it also influences the efficiency and accuracy of dealing with problems. Feature dimensionality reduction as a key link in the process of pattern recognition has become one hot and difficulty spot in the field of pattern recognition, machine learning and data mining. It is one of the most challenging research fields, which has been favored by most of the scholars’ attention. How to implement “low loss” in the process of feature dimension reduction, keep the nature of the original data, find out the best mapping and get the optimal low dimensional data are the keys aims of the research. In this paper, two-dimensionality reduction methods, feature selection and feature extraction, are introduced; the current mainstream dimensionality reduction algorithms are analyzed, including the method for small sample and method based on deep learning. For each algorithm, examples of their application are given and the advantages and disadvantages of these methods are evaluated.
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Paiva T, Canas-Simião H. Sleep and violence perpetration: A review of biological and environmental substrates. J Sleep Res 2022; 31:e13547. [PMID: 35037316 DOI: 10.1111/jsr.13547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 11/27/2022]
Abstract
Violence is a worldwide societal burden that negatively impacts individual health, wellbeing and economic development. Evidence suggests a bidirectional relationship between sleep changes and violence. This review details, evaluates and discusses the biological and demographic substrates linking sleep and violence perpetration, and summarizes the overlap of brain areas, functional neuronal systems and genetic features involved, not including violent behaviours during sleep. Knowledge on the biological variables that affect the individual's susceptibility to violent behaviour may have implications for criminology, management of detentions and rehabilitation strategies.
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Affiliation(s)
- Teresa Paiva
- Sleep and Medicine Center (CENC), Comprehensive Health Research Center (CHRC), Instituto de Saúde Ambiental - Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Hugo Canas-Simião
- Psychiatry and Mental Health Department, Centro Hospitalar de Lisboa Ocidental (CHLO); Comprehensive Health Research Center (CHRC); Sleep and Medicine Center (CENC), Lisbon, Portugal
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Cassidy JM, Wodeyar A, Srinivasan R, Cramer SC. Coherent neural oscillations inform early stroke motor recovery. Hum Brain Mapp 2021; 42:5636-5647. [PMID: 34435705 PMCID: PMC8559506 DOI: 10.1002/hbm.25643] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 12/24/2022] Open
Abstract
Neural oscillations may contain important information pertaining to stroke rehabilitation. This study examined the predictive performance of electroencephalography‐derived neural oscillations following stroke using a data‐driven approach. Individuals with stroke admitted to an inpatient rehabilitation facility completed a resting‐state electroencephalography recording and structural neuroimaging around the time of admission and motor testing at admission and discharge. Using a lasso regression model with cross‐validation, we determined the extent of motor recovery (admission to discharge change in Functional Independence Measurement motor subscale score) prediction from electroencephalography, baseline motor status, and corticospinal tract injury. In 27 participants, coherence in a 1–30 Hz band between leads overlying ipsilesional primary motor cortex and 16 leads over bilateral hemispheres predicted 61.8% of the variance in motor recovery. High beta (20–30 Hz) and alpha (8–12 Hz) frequencies contributed most to the model demonstrating both positive and negative associations with motor recovery, including high beta leads in supplementary motor areas and ipsilesional ventral premotor and parietal regions and alpha leads overlying contralesional temporal–parietal and ipsilesional parietal regions. Electroencephalography power, baseline motor status, and corticospinal tract injury did not significantly predict motor recovery during hospitalization (R2 = 0–6.2%). Findings underscore the relevance of oscillatory synchronization in early stroke rehabilitation while highlighting contributions from beta and alpha frequency bands and frontal, parietal, and temporal–parietal regions overlooked by traditional hypothesis‐driven prediction models.
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Affiliation(s)
- Jessica M Cassidy
- Department of Allied Health Sciences, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Anirudh Wodeyar
- Department of Cognitive Sciences, University of California Irvine, Irvine, California, USA
| | - Ramesh Srinivasan
- Department of Cognitive Sciences, University of California Irvine, Irvine, California, USA.,Department of Biomedical Engineering, University of California Irvine, Irvine, California, USA
| | - Steven C Cramer
- Department of Neurology, University of California, Los Angeles, Los Angeles, California, USA.,California Rehabilitation Institute, Los Angeles, California, USA
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Wang S, Celebi ME, Zhang YD, Yu X, Lu S, Yao X, Zhou Q, Miguel MG, Tian Y, Gorriz JM, Tyukin I. Advances in Data Preprocessing for Biomedical Data Fusion: An Overview of the Methods, Challenges, and Prospects. INFORMATION FUSION 2021; 76:376-421. [DOI: 10.1016/j.inffus.2021.07.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Oppenheimer CW, Bertocci M, Greenberg T, Chase HW, Stiffler R, Aslam HA, Lockovich J, Graur S, Bebko G, Phillips ML. Informing the study of suicidal thoughts and behaviors in distressed young adults: The use of a machine learning approach to identify neuroimaging, psychiatric, behavioral, and demographic correlates. Psychiatry Res Neuroimaging 2021; 317:111386. [PMID: 34537601 PMCID: PMC8548992 DOI: 10.1016/j.pscychresns.2021.111386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 08/14/2021] [Accepted: 08/31/2021] [Indexed: 11/25/2022]
Abstract
Young adults are at high risk for suicide, yet there is limited ability to predict suicidal thoughts and behaviors. Machine learning approaches are better able to examine a large number of variables simultaneously to identify combinations of factors associated with suicidal thoughts and behaviors. The current study used LASSO regression to investigate extent to which a number of demographic, psychiatric, behavioral, and functional neuroimaging variables are associated with suicidal thoughts and behaviors during young adulthood. 78 treatment seeking young adults (ages 18-25) completed demographic, psychiatric, behavioral, and suicidality measures. Participants also completed an implicit emotion regulation functional neuroimaging paradigm. Report of recent suicidal thoughts and behaviors served as the dependent variable. Five variables were identified by the LASSO regression: Two were demographic variables (age and level of education), two were psychiatric variables (depression and general psychiatric distress), and one was a neuroimaging variable (left amygdala activity during sad faces). Amygdala function was significantly associated with suicidal thoughts and behaviors above and beyond the other factors. Findings inform the study of suicidal thoughts and behaviors among treatment seeking young adults, and also highlight the importance of investigating neurobiological markers.
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Affiliation(s)
- Caroline W Oppenheimer
- University of Pittsburgh, School of Medicine, 3811 O'Hara St., Pittsburgh, PA 15213, United States.
| | - Michele Bertocci
- University of Pittsburgh, School of Medicine, 3811 O'Hara St., Pittsburgh, PA 15213, United States
| | - Tsafrir Greenberg
- University of Pittsburgh, School of Medicine, 3811 O'Hara St., Pittsburgh, PA 15213, United States
| | - Henry W Chase
- University of Pittsburgh, School of Medicine, 3811 O'Hara St., Pittsburgh, PA 15213, United States
| | - Richelle Stiffler
- University of Pittsburgh, School of Medicine, 3811 O'Hara St., Pittsburgh, PA 15213, United States
| | - Haris A Aslam
- University of Pittsburgh, School of Medicine, 3811 O'Hara St., Pittsburgh, PA 15213, United States
| | - Jeanette Lockovich
- University of Pittsburgh, School of Medicine, 3811 O'Hara St., Pittsburgh, PA 15213, United States
| | - Simona Graur
- University of Pittsburgh, School of Medicine, 3811 O'Hara St., Pittsburgh, PA 15213, United States
| | - Genna Bebko
- University of Pittsburgh, School of Medicine, 3811 O'Hara St., Pittsburgh, PA 15213, United States
| | - Mary L Phillips
- University of Pittsburgh, School of Medicine, 3811 O'Hara St., Pittsburgh, PA 15213, United States
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Li Y, Nan B, Zhu J. A Structured Brain-wide and Genome-wide Association Study Using ADNI PET Images. CAN J STAT 2021; 49:182-202. [PMID: 34566241 DOI: 10.1002/cjs.11605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A multi-stage variable selection method is introduced for detecting association signals in structured brain-wide and genome-wide association studies (brain-GWAS). Compared to conventional single-voxel-to-single-SNP approaches, our approach is more efficient and powerful in selecting the important signals by integrating anatomic and gene grouping structures in the brain and the genome, respectively. It avoids large number of multiple comparisons while effectively controls the false discoveries. Validity of the proposed approach is demonstrated by both theoretical investigation and numerical simulations. We apply the proposed method to a brain-GWAS using ADNI PET imaging and genomic data. We confirm previously reported association signals and also find several novel SNPs and genes that either are associated with brain glucose metabolism or have their association significantly modified by Alzheimer's disease status.
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Affiliation(s)
- Yanming Li
- Department of Biotatistics & Data Science, University of Kansas Medical Center Kansas City, KS 66160
| | - Bin Nan
- Department of Statistics, University of California at Irvine Irvine, CA 92697
| | - Ji Zhu
- Department of Statistics, University of Michigan Ann Arbor, MI 48109
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Li X, Lin Y, Meng X, Qiu Y, Hu B. An L 0 Regularization Method for Imaging Genetics and Whole Genome Association Analysis on Alzheimer's Disease. IEEE J Biomed Health Inform 2021; 25:3677-3684. [PMID: 34181562 DOI: 10.1109/jbhi.2021.3093027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although the neuroimaging measures build a bridge between genetic variants and disease phenotypes, an assessment of single nucleotide variants changes in brain structure and their clinically influence on the progression of Alzheimer's disease remain largely preliminary. Note that each variant has very weak correlation signal to neuroimaging measures or Alzheimer's disease phenotypes. Therefore, traditional sparse regression-based image genetics approaches confront with unresolvable features, relative high regression error or inapplicability of high-dimensional data. Adopting an [Formula: see text] regularization method, we significantly elevate the regression accuracy of imaging genetics compared with group-sparse multitask regression method. With further analysis on the simulation results, we conclude that multiple regression tasks model may be unsuitable for image genetics. In addition, we carried out a whole genome association analysis between genetic variants (about 388 million loci) and phenotypes (cognition normal, mild cognitive impairment and Alzheimer's disease) with using the [Formula: see text] regularization method. After annotating the effect of all variants by Ensembl Variant Effect Predictor (VEP), our method locates 33 missense variants which can explain 40% phenotype variance. Then, we mapped each missense variant to the nearest gene and carried out pathway enrichment analysis. The Notch signaling pathway and Apoptosis pathway have been reported to be related to the formation of Alzheimer's disease.
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Alnak A, Kuşcu Özücer İ, Okay Çağlayan A, Coşkun M. Peripheral Expression of MACROD2 Gene Is Reduced Among a Sample of Turkish Children with Autism Spectrum Disorder. PSYCHIAT CLIN PSYCH 2021; 31:261-268. [PMID: 38765943 PMCID: PMC11079661 DOI: 10.5152/pcp.2021.21144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 08/18/2021] [Indexed: 05/22/2024] Open
Abstract
Background Genomic variations in mono-ADP ribosylhydrolase 2 (MACROD2) have been associated with autism spectrum disorder (ASD) in recent genome-wide studies and case reports. In this study, we aimed to evaluate the MACROD2 expression profile in patients with ASD. Methods The study group included 100 children with a DSM-5 diagnosis of ASD, and the control group consisted of 105 healthy controls. Blood samples were obtained from all participants in this study, and the gene expression level was determined using quantitative reverse transcription PCR (RT-qPCR). Statistical analysis was performed with R 3.4.0 and Statistical Program for Social Sciences (SPSS for Windows, 21.0). Results The mean ages of the participants in the study and control groups were 9.22 ± 3.62 and 9.27 ± 3.86 years, respectively. There was no significant difference concerning gender (P = .944) and age (P = .914) between the 2 groups. MACROD2 gene expression was found to be decreased in the study group compared to the control group (study group = 5.73, control group = 89.56; fold change =-3.967; P < .001). While the level of MACROD2 expression was not correlated with the ASD severity, it was associated with the severity of the hyperactivity/impulsivity symptoms (P = .008). Conclusions This is the first study in the literature investigating the peripheral expression of the MACROD2 gene. We showed that the expression level of MACROD2 was decreased in patients with ASD when compared to the control group. As the relationship between the MACROD2 gene expression profile and ASD remains to be further investigated, this study may provide an insight for further studies.
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Affiliation(s)
- Alper Alnak
- Department of Child and Adolescent Psychiatry, Istanbul University School of Medicine, Istanbul, Turkey
| | - İpek Kuşcu Özücer
- Department of Child and Adolescent Psychiatry, Istanbul University School of Medicine, Istanbul, Turkey
| | - Ahmet Okay Çağlayan
- Department of Medical Genetics, Dokuz Eylul University School of Medicine, Izmir, Turkey
| | - Murat Coşkun
- Department of Child and Adolescent Psychiatry, Istanbul University School of Medicine, Istanbul, Turkey
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Huang M, Lai H, Yu Y, Chen X, Wang T, Feng Q. Deep-gated recurrent unit and diet network-based genome-wide association analysis for detecting the biomarkers of Alzheimer's disease. Med Image Anal 2021; 73:102189. [PMID: 34343841 DOI: 10.1016/j.media.2021.102189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/30/2021] [Accepted: 07/16/2021] [Indexed: 01/01/2023]
Abstract
Genome-wide association analysis (GWAS) is a commonly used method to detect the potential biomarkers of Alzheimer's disease (AD). Most existing GWAS methods entail a high computational cost, disregard correlations among imaging data and correlations among genetic data, and ignore various associations between longitudinal imaging and genetic data. A novel GWAS method was proposed to identify potential AD biomarkers and address these problems. A network based on a gated recurrent unit was applied without imputing incomplete longitudinal imaging data to integrate the longitudinal data of variable lengths and extract an image representation. In this study, a modified diet network that can considerably reduce the number of parameters in the genetic network was proposed to perform GWAS between image representation and genetic data. Genetic representation can be extracted in this way. A link between genetic representation and AD was established to detect potential AD biomarkers. The proposed method was tested on a set of simulated data and a real AD dataset. Results of the simulated data showed that the proposed method can accurately detect relevant biomarkers. Moreover, the results of real AD dataset showed that the proposed method can detect some new risk-related genes of AD. Based on previous reports, no research has incorporated a deep-learning model into a GWAS framework to investigate the potential information on super-high-dimensional genetic data and longitudinal imaging data and create a link between imaging genetics and AD for detecting potential AD biomarkers. Therefore, the proposed method may provide new insights into the underlying pathological mechanism of AD.
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Affiliation(s)
- Meiyan Huang
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou 510515, China; Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou 510515, China.
| | - Haoran Lai
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Yuwei Yu
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Xiumei Chen
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Tao Wang
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Qianjin Feng
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou 510515, China; Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou 510515, China.
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Lemercier P, Vergallo A, Lista S, Zetterberg H, Blennow K, Potier MC, Habert MO, Lejeune FX, Dubois B, Teipel S, Hampel H. Association of plasma Aβ40/Aβ42 ratio and brain Aβ accumulation: testing a whole-brain PLS-VIP approach in individuals at risk of Alzheimer's disease. Neurobiol Aging 2021; 107:57-69. [PMID: 34388400 DOI: 10.1016/j.neurobiolaging.2021.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/25/2021] [Accepted: 07/07/2021] [Indexed: 11/29/2022]
Abstract
Molecular and brain regional/network-wise pathophysiological changes at preclinical stages of Alzheimer's disease (AD) have primarily been found through knowledge-based studies conducted in late-stage mild cognitive impairment/dementia populations. However, such an approach may compromise the objective of identifying the earliest spatial-temporal pathophysiological processes. We investigated 261 individuals with subjective memory complaints, a condition at increased risk of AD, to test a whole-brain, non-a-priori method based on partial least squares in unraveling the association between plasma Aβ42/Aβ40 ratio and an extensive set of brain regions characterized through molecular imaging of Aβ accumulation and cortical metabolism. Significant associations were mapped onto large-scale networks, identified through an atlas and by knowledge, to elaborate on the reliability of the results. Plasma Aβ42/40 ratio was associated with Aβ-PET uptake (but not FDG-PET) in regions generally investigated in preclinical AD such as those belonging to the default mode network, but also in regions/networks normally not accounted - including the central executive and salience networks - which likely have a selective vulnerability to incipient Aβ accumulation. The present whole-brain approach is promising to investigate early pathophysiological changes of AD to fully capture the complexity of the disease, which is essential to develop timely screening, detection, diagnostic, and therapeutic interventions.
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Affiliation(s)
- Pablo Lemercier
- Sorbonne University, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Boulevard de l'hôpital, Paris, France.
| | - Andrea Vergallo
- Sorbonne University, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Boulevard de l'hôpital, Paris, France
| | - Simone Lista
- Sorbonne University, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Boulevard de l'hôpital, Paris, France
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden; Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK; UK Dementia Research Institute at UCL, London, UK
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Marie-Claude Potier
- ICM Institut du Cerveau et de la Moelle épinière, CNRS UMR7225, INSERM U1127, UPMC, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Marie-Odile Habert
- Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, Paris, France; Centre pour l'Acquisition et le Traitement des Images (www.cati-neuroimaging.com), Paris, France; Department of Psychosomatic Medicine, University Medicine Rostock, Rostock, Germany; AP-HP, Hôpital Pitié-Salpêtrière, Département de Médecine Nucléaire, Paris, France
| | - François-Xavier Lejeune
- Bioinformatics and Biostatistics Core Facility iCONICS, Sorbonne Université UMR S 1127, Institut du Cerveau et de La Moelle Épinière, Paris, France
| | - Bruno Dubois
- Sorbonne University, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Boulevard de l'hôpital, Paris, France
| | - Stefan Teipel
- Clinical Dementia Research Section, German Center for Neurodegenerative Diseases (DZNE), Rostock, Germany
| | - Harald Hampel
- Sorbonne University, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Boulevard de l'hôpital, Paris, France.
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17
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Wen C, Yang Y, Xiao Q, Huang M, Pan W. Genome-wide association studies of brain imaging data via weighted distance correlation. Bioinformatics 2021; 36:4942-4950. [PMID: 32619001 DOI: 10.1093/bioinformatics/btaa612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 06/17/2020] [Accepted: 06/26/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Imaging genetics is mainly used to reveal the pathogenesis of neuropsychiatric risk genes and understand the relationship between human brain structure, functional and individual differences. Increasingly, the brain-wide imaging phenotypes in voxels are available to test the association with genetic markers. A challenge with analyzing such data is their high dimensionality and complex relationships. RESULTS To tackle this challenge, we introduce a weighed distance correlation (wdCor) that can assess the association between genetic markers and voxel-based imaging data. Importantly, the wdCor test takes the voxel-based data as a whole multivariate phenotype, which preserves the spatial continuity and might enhance the power. Besides, an adaptive permutation procedure is introduced to determine the P-values of the wdCor test and also alleviate the computational burden in GWAS. In extensive simulation studies, wdCor achieves much better performances compared to the original distance correlation. We also successfully apply wdCor to conduct a large-scale analysis on data from the Alzheimer's disease neuroimaging project (ADNI). AVAILABILITY AND IMPLEMENTATION Our wdCor method provides new research directions and ideas for multivariate analysis of high-dimensional data, it can also be used as a tool for scientific analysis of imaging genetics research in practical applications. The R package wdcor, and the code for reproducing all results in this article is available in Github: https://github.com/yangyuhui0129/wdcor. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Canhong Wen
- Department of Statistics and Finance, School of Management, University of Science and Technology of China, Hefei 230026, China
| | - Yuhui Yang
- Department of Statistics and Finance, School of Management, University of Science and Technology of China, Hefei 230026, China
| | - Quan Xiao
- Department of Statistics and Finance, School of Management, University of Science and Technology of China, Hefei 230026, China
| | - Meiyan Huang
- Guangdong Provincial Key Laboratory of Medical Image Processing, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China
| | - Wenliang Pan
- Department of Statistical Science, School of Mathematics, Sun Yat-Sen University, Guangzhou 510275, China
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18
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Kim M, Kim JS, Youn J, Park H, Cho JW. GraphNet-based imaging biomarker model to explain levodopa-induced dyskinesia in Parkinson's disease. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 196:105713. [PMID: 32846317 DOI: 10.1016/j.cmpb.2020.105713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND OBJECTIVE Levodopa-induced dyskinesia (LID) is a disabling complication of Parkinson's disease (PD). Imaging-based measurements, especially those related to the surface shape of the basal ganglia, have shown potential for explaining the severity of LID in PD. Here, we aimed to explore a novel application of the methodology to find biomarkers of LID severity in PD using regularization. METHODS We proposed an application of graph-constrained elastic net (GraphNet) regularization to detect surface-based shape biomarkers explaining the severity of LID and compared the approach with other conventional regularization methods. To examine the methods, we used two independent datasets, one as a training dataset to build the model, and the other dataset was used to validate the constructed model. RESULTS We found that the left striatum (putamen was the greatest and the caudate was second) was the most significant surface-based biomarker related to the severity of LID. Our results improved the interpretability of identified surface-based biomarkers compared to competing methods. We also found that GraphNet regularization improved prediction of the severity of LID better than the conventional regularization methods. Our model performed better in terms of root-mean-squared error and correlation coefficient between predicted and actual clinical scores. CONCLUSION The proposed algorithm offers an advantage of interpretable anatomical variations related to the deformation of the cortical surface. The experimental results showed that GraphNet regularization was robust to identify surface-based shape biomarkers related to both hypokinetic and hyperkinetic movement disorders.
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Affiliation(s)
- Mansu Kim
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, USA; Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon, Korea; Center for Neuroscience Imaging Research (CNIR), Institute for Basic Science, Korea
| | - Ji Sun Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; Neuroscience Center, Samsung Medical Center, Seoul, Korea
| | - Jinyoung Youn
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; Neuroscience Center, Samsung Medical Center, Seoul, Korea
| | - Hyunjin Park
- Center for Neuroscience Imaging Research (CNIR), Institute for Basic Science, Korea; School of Electronic and Electrical Engineering, Sungkyunkwan University, Suwon, Korea.
| | - Jin Whan Cho
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; Neuroscience Center, Samsung Medical Center, Seoul, Korea
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Zhou J, Qiu Y, Chen S, Liu L, Liao H, Chen H, Lv S, Li X. A Novel Three-Stage Framework for Association Analysis Between SNPs and Brain Regions. Front Genet 2020; 11:572350. [PMID: 33193677 PMCID: PMC7542238 DOI: 10.3389/fgene.2020.572350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/17/2020] [Indexed: 12/17/2022] Open
Abstract
Motivation: At present, a number of correlation analysis methods between SNPs and ROIs have been devised to explore the pathogenic mechanism of Alzheimer's disease. However, some of the deficiencies inherent in these methods, including lack of statistical efficacy and biological meaning. This study aims at addressing issues: insufficient correlation by previous methods (relative high regression error) and the lack of biological meaning in association analysis. Results: In this paper, a novel three-stage SNPs and ROIs correlation analysis framework is proposed. Firstly, clustering algorithm is applied to remove the potential linkage unbalanced structure of two SNPs. Then, the group sparse model is used to introduce prior information such as gene structure and linkage unbalanced structure to select feature SNPs. After the above steps, each SNP has a weight vector corresponding to each ROI, and the importance of SNPs can be judged according to the weights in the feature vector, and then the feature SNPs can be selected. Finally, for the selected feature SNPS, a support vector machine regression model is used to implement the prediction of the ROIs phenotype values. The experimental results under multiple performance measures show that the proposed method has better accuracy than other methods.
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Affiliation(s)
- Juan Zhou
- School of Software, East China Jiaotong University, Nanchang, China
| | - Yangping Qiu
- School of Software, East China Jiaotong University, Nanchang, China
| | - Shuo Chen
- School of Software, East China Jiaotong University, Nanchang, China
| | - Liyue Liu
- School of Software, East China Jiaotong University, Nanchang, China
| | - Huifa Liao
- School of Software, East China Jiaotong University, Nanchang, China
| | - Hongli Chen
- School of Software, East China Jiaotong University, Nanchang, China
| | - Shanguo Lv
- School of Software, East China Jiaotong University, Nanchang, China
| | - Xiong Li
- School of Software, East China Jiaotong University, Nanchang, China
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20
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Ruisch IH, Dietrich A, Klein M, Faraone SV, Oosterlaan J, Buitelaar JK, Hoekstra PJ. Aggression based genome-wide, glutamatergic, dopaminergic and neuroendocrine polygenic risk scores predict callous-unemotional traits. Neuropsychopharmacology 2020; 45:761-769. [PMID: 31918432 PMCID: PMC7075955 DOI: 10.1038/s41386-020-0608-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 12/03/2019] [Accepted: 12/30/2019] [Indexed: 12/17/2022]
Abstract
Aggression and callous, uncaring, and unemotional (CU) traits are clinically related behavioral constructs caused by genetic and environmental factors. We performed polygenic risk score (PRS) analyses to investigate shared genetic etiology between aggression and these three CU-traits. Furthermore, we studied interactions of PRS with smoking during pregnancy and childhood life events in relation to CU-traits. Summary statistics for the base phenotype were derived from the EAGLE-consortium genome-wide association study of children's aggressive behavior and were used to calculate individual-level genome-wide and gene-set PRS in the NeuroIMAGE target-sample. Target phenotypes were 'callousness', 'uncaring', and 'unemotional' sumscores of the Inventory of Callous-Unemotional traits. A total of 779 subjects and 1,192,414 single-nucleotide polymorphisms were available for PRS-analyses. Gene-sets comprised serotonergic, dopaminergic, glutamatergic, and neuroendocrine signaling pathways. Genome-wide PRS showed evidence of association with uncaring scores (explaining up to 1.59% of variance; self-contained Q = 0.0306, competitive-P = 0.0015). Dopaminergic, glutamatergic, and neuroendocrine PRS showed evidence of association with unemotional scores (explaining up to 1.33, 2.00, and 1.20% of variance respectively; self-contained Q-values 0.037, 0.0115, and 0.0473 respectively, competitive-P-values 0.0029, 0.0002, and 0.0045 respectively). Smoking during pregnancy related to callousness scores while childhood life events related to both callousness and unemotionality. Moreover, dopaminergic PRS appeared to interact with childhood life events in relation to unemotional scores. Our study provides evidence suggesting shared genetic etiology between aggressive behavior and uncaring, and unemotional CU-traits in children. Gene-set PRS confirmed involvement of shared glutamatergic, dopaminergic, and neuroendocrine genetic variation in aggression and CU-traits. Replication of current findings is needed.
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Affiliation(s)
- I Hyun Ruisch
- Department of Child and Adolescent Psychiatry, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713GZ, Groningen, The Netherlands.
| | - Andrea Dietrich
- Department of Child and Adolescent Psychiatry, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713GZ, Groningen, The Netherlands
| | - Marieke Klein
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA, Nijmegen, The Netherlands
- Department of Psychiatry, University Medical Center Utrecht, Brain Center Rudolf Magnus, Utrecht, The Netherlands
| | - Stephen V Faraone
- Department of Psychiatry and of Neuroscience and Physiology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
- K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - Jaap Oosterlaan
- Department of Clinical Neuropsychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jan K Buitelaar
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525GA, Nijmegen, The Netherlands
- Karakter Child and Adolescent Psychiatry University Centre, Reinier Postlaan 12, 6525GC, Nijmegen, The Netherlands
| | - Pieter J Hoekstra
- Department of Child and Adolescent Psychiatry, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713GZ, Groningen, The Netherlands
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21
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Fernàndez-Castillo N, Gan G, van Donkelaar MMJ, Vaht M, Weber H, Retz W, Meyer-Lindenberg A, Franke B, Harro J, Reif A, Faraone SV, Cormand B. RBFOX1, encoding a splicing regulator, is a candidate gene for aggressive behavior. Eur Neuropsychopharmacol 2020; 30:44-55. [PMID: 29174947 PMCID: PMC10975801 DOI: 10.1016/j.euroneuro.2017.11.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/27/2017] [Accepted: 11/08/2017] [Indexed: 12/11/2022]
Abstract
The RBFOX1 gene (or A2BP1) encodes a splicing factor important for neuronal development that has been related to autism spectrum disorder and other neurodevelopmental phenotypes. Evidence from complementary sources suggests that this gene contributes to aggressive behavior. Suggestive associations with RBFOX1 have been identified in genome-wide association studies (GWAS) of anger, conduct disorder, and aggressive behavior. Nominal association signals in RBFOX1 were also found in an epigenome-wide association study (EWAS) of aggressive behavior. Also, variants in this gene affect temporal lobe volume, a brain area that is altered in several aggression-related phenotypes. In animals, this gene has been shown to modulate aggressive behavior in Drosophila. RBFOX1 has also been associated with canine aggression and is upregulated in mice that show increased aggression after frustration of an expected reward. Associated common genetic variants as well as rare duplications and deletions affecting RBFOX1 have been identified in several psychiatric and neurodevelopmental disorders that are often comorbid with aggressive behaviors. In this paper, we comprehensively review the cumulative evidence linking RBFOX1 to aggression behavior and provide new results implicating RBFOX1 in this phenotype. Most of these studies (genetic and epigenetic analyses in humans, neuroimaging genetics, gene expression and animal models) are hypothesis-free, which strengthens the validity of the findings, although all the evidence is nominal and should therefore be taken with caution. Further studies are required to clarify in detail the role of this gene in this complex phenotype.
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Affiliation(s)
- Noèlia Fernàndez-Castillo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain.
| | - Gabriela Gan
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Marjolein M J van Donkelaar
- Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Department of Human Genetics, Nijmegen, The Netherlands
| | - Mariliis Vaht
- Division of Neuropsychopharmacology, Department of Psychology, University of Tartu, Tartu, Estonia
| | - Heike Weber
- Deptartment of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt - Goethe University, Frankfurt am Main, Germany; Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital of Würzburg, Würzburg, Germany
| | - Wolfgang Retz
- Department of Psychiatry and Psychotherapy, University Medical Center Mainz, Mainz, Germany
| | - Andreas Meyer-Lindenberg
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Barbara Franke
- Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Department of Human Genetics, Nijmegen, The Netherlands; Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Department of Psychiatry, Nijmegen, The Netherlands
| | - Jaanus Harro
- Division of Neuropsychopharmacology, Department of Psychology, University of Tartu, Tartu, Estonia
| | - Andreas Reif
- Deptartment of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt - Goethe University, Frankfurt am Main, Germany
| | - Stephen V Faraone
- Departments of Psychiatry and of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA; K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain.
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22
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Hao X, Yao X, Risacher SL, Saykin AJ, Yu J, Wang H, Tan L, Shen L, Zhang D. Identifying Candidate Genetic Associations with MRI-Derived AD-Related ROI via Tree-Guided Sparse Learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1986-1996. [PMID: 29993890 PMCID: PMC7144227 DOI: 10.1109/tcbb.2018.2833487] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Imaging genetics has attracted significant interests in recent studies. Traditional work has focused on mass-univariate statistical approaches that identify important single nucleotide polymorphisms (SNPs) associated with quantitative traits (QTs) of brain structure or function. More recently, to address the problem of multiple comparison and weak detection, multivariate analysis methods such as the least absolute shrinkage and selection operator (Lasso) are often used to select the most relevant SNPs associated with QTs. However, one problem of Lasso, as well as many other feature selection methods for imaging genetics, is that some useful prior information, e.g., the hierarchical structure among SNPs, are rarely used for designing a more powerful model. In this paper, we propose to identify the associations between candidate genetic features (i.e., SNPs) and magnetic resonance imaging (MRI)-derived measures using a tree-guided sparse learning (TGSL) method. The advantage of our method is that it explicitly models the complex hierarchical structure among the SNPs in the objective function for feature selection. Specifically, motivated by the biological knowledge, the hierarchical structures involving gene groups and linkage disequilibrium (LD) blocks as well as individual SNPs are imposed as a tree-guided regularization term in our TGSL model. Experimental studies on simulation data and the Alzheimer's Disease Neuroimaging Initiative (ADNI) data show that our method not only achieves better predictions than competing methods on the MRI-derived measures of AD-related region of interests (ROIs) (i.e., hippocampus, parahippocampal gyrus, and precuneus), but also identifies sparse SNP patterns at the block level to better guide the biological interpretation.
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23
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Ong ML, Tuan TA, Poh J, Teh AL, Chen L, Pan H, MacIsaac JL, Kobor MS, Chong YS, Kwek K, Saw SM, Godfrey KM, Gluckman PD, Fortier MV, Karnani N, Meaney MJ, Qiu A, Holbrook JD. Neonatal amygdalae and hippocampi are influenced by genotype and prenatal environment, and reflected in the neonatal DNA methylome. GENES BRAIN AND BEHAVIOR 2019; 18:e12576. [PMID: 31020763 DOI: 10.1111/gbb.12576] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/01/2019] [Accepted: 04/13/2019] [Indexed: 12/28/2022]
Abstract
The amygdala and hippocampus undergo rapid development in early life. The relative contribution of genetic and environmental factors to the establishment of their developmental trajectories has yet to be examined. We performed imaging on neonates and examined how the observed variation in volume and microstructure of the amygdala and hippocampus varied by genotype, and compared with prenatal maternal mental health and socioeconomic status. Gene × Environment models outcompeted models containing genotype or environment only to best explain the majority of measures but some, especially of the amygdaloid microstructure, were best explained by genotype only. Models including DNA methylation measured in the neonate umbilical cords outcompeted the Gene and Gene × Environment models for the majority of amygdaloid measures and minority of hippocampal measures. This study identified brain region-specific gene networks associated with individual differences in fetal brain development. In particular, genetic and epigenetic variation within CUX1 was highlighted.
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Affiliation(s)
- Mei-Lyn Ong
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore
| | - Ta A Tuan
- Department of Biomedical Engineering, Clinical Imaging research Centre, National University of Singapore, Singapore
| | - Joann Poh
- Department of Biomedical Engineering, Clinical Imaging research Centre, National University of Singapore, Singapore
| | - Ai L Teh
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore
| | - Li Chen
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore
| | - Hong Pan
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore.,School of Computer Engineering, Nanyang Technological University (NTU), Singapore
| | - Julia L MacIsaac
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yap S Chong
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore
| | - Kenneth Kwek
- KK Women's and Children's Hospital, Duke National University of Singapore, Singapore
| | - Seang M Saw
- Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology Unit and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Peter D Gluckman
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore.,Centre for Human Evolution, Adaptation and disease, Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Marielle V Fortier
- KK Women's and Children's Hospital, Duke National University of Singapore, Singapore
| | - Neerja Karnani
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore
| | - Michael J Meaney
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore.,Ludmer Centre for Neuroinformatics and Mental Health, Sackler Program for Epigenetics & Psychobiology at McGill University, Douglas University Mental Health Institute, McGill University, Montreal, Canada
| | - Anqi Qiu
- Department of Biomedical Engineering, Clinical Imaging research Centre, National University of Singapore, Singapore.,Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore
| | - Joanna D Holbrook
- Singapore Institute of Clinical sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore
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24
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Lombardo B, Esposito D, Iossa S, Vitale A, Verdesca F, Perrotta C, Di Leo L, Costa V, Pastore L, Franzé A. Intragenic Deletion in MACROD2: A Family with Complex Phenotypes Including Microcephaly, Intellectual Disability, Polydactyly, Renal and Pancreatic Malformations. Cytogenet Genome Res 2019; 158:25-31. [DOI: 10.1159/000499886] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2018] [Indexed: 12/15/2022] Open
Abstract
Diagnosing a complex genetic syndrome and correctly assigning the concomitant phenotypic traits to a well-defined clinical form is often a medical challenge. In this work, we report the analysis of a family with complex phenotypes, including microcephaly, intellectual disability, dysmorphic features, and polydactyly in the proband, with the aim of adding new aspects for obtaining a clear diagnosis. We performed array-comparative genomic hybridization and quantitative reverse transcriptase PCR (qRT-PCR) analyses. We identified a deletion of chromosome 20p12.1 involving the macrodomain containing 2/mono-ADP ribosylhydrolase 2 gene (MACROD2) in several members of the family. This gene is actually not associated with a specific syndrome but with congenital anomalies of multiple organs. qRT-PCR showed higher levels of a MACROD2 mRNA isoform in the individuals carrying the deletion. Our results, together with other data reported in the literature, support the hypothesis that the deletion in MACROD2 can affect correct embryonic development and that the presence of another associated event, such as epigenetic modifications at the MACROD2 locus, can influence the level of severity of the pathology.
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Everson TM, Marsit CJ, Michael O'Shea T, Burt A, Hermetz K, Carter BS, Helderman J, Hofheimer JA, McGowan EC, Neal CR, Pastyrnak SL, Smith LM, Soliman A, DellaGrotta SA, Dansereau LM, Padbury JF, Lester BM. Epigenome-wide Analysis Identifies Genes and Pathways Linked to Neurobehavioral Variation in Preterm Infants. Sci Rep 2019; 9:6322. [PMID: 31004082 PMCID: PMC6474865 DOI: 10.1038/s41598-019-42654-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 04/03/2019] [Indexed: 02/07/2023] Open
Abstract
Neonatal molecular biomarkers of neurobehavioral responses (measures of brain-behavior relationships), when combined with neurobehavioral performance measures, could lead to better predictions of long-term developmental outcomes. To this end, we examined whether variability in buccal cell DNA methylation (DNAm) associated with neurobehavioral profiles in a cohort of infants born less than 30 weeks postmenstrual age (PMA) and participating in the Neonatal Neurobehavior and Outcomes in Very Preterm Infants (NOVI) Study (N = 536). We tested whether epigenetic age, age acceleration, or DNAm levels at individual loci differed between infants based on their NICU Network Neurobehavioral Scale (NNNS) profile classifications. We adjusted for recruitment site, infant sex, PMA, and tissue heterogeneity. Infants with an optimally well-regulated NNNS profile had older epigenetic age compared to other NOVI infants (β1 = 0.201, p-value = 0.026), but no significant difference in age acceleration. In contrast, infants with an atypical NNNS profile had differential methylation at 29 CpG sites (FDR < 10%). Some of the genes annotated to these CpGs included PLA2G4E, TRIM9, GRIK3, and MACROD2, which have previously been associated with neurological structure and function, or with neurobehavioral disorders. These findings contribute to the existing evidence that neonatal epigenetic variations may be informative for infant neurobehavior.
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Affiliation(s)
- Todd M Everson
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, United States.
| | - Carmen J Marsit
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, United States
| | - T Michael O'Shea
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Amber Burt
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, United States
| | - Karen Hermetz
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, United States
| | - Brian S Carter
- Department of Pediatrics-Neonatology, Children's Mercy Hospital, Kansas City, MO, United States
| | - Jennifer Helderman
- Department of Pediatrics, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Julie A Hofheimer
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Elisabeth C McGowan
- Department of Pediatrics, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, United States
| | - Charles R Neal
- Department of Pediatrics, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, United States
| | - Steven L Pastyrnak
- Department of Pediatrics, Spectrum Health-Helen Devos Hospital, Grand Rapids, MI, United States
| | - Lynne M Smith
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Antoine Soliman
- Department of Pediatrics, Miller Children's and Women's Hospital Long Beach, Long Beach, CA, United States
| | - Sheri A DellaGrotta
- Brown Center for the Study of Children at Risk, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, United States
| | - Lynne M Dansereau
- Brown Center for the Study of Children at Risk, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, United States
| | - James F Padbury
- Department of Pediatrics, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, United States
| | - Barry M Lester
- Department of Pediatrics, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, United States
- Brown Center for the Study of Children at Risk, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, United States
- Department of Psychiatry and Human Behavior, Brown Alpert Medical School, Providence, RI, United States
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Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers. G3-GENES GENOMES GENETICS 2019; 9:463-471. [PMID: 30622122 PMCID: PMC6385974 DOI: 10.1534/g3.118.200516] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Post-traumatic stress disorder is a concerning psychobehavioral disorder thought to emerge from the complex interaction between genetic and environmental factors. For soldiers exposed to combat, the risk of developing this disorder is twofold and diagnosis is often late, when much sequela has set in. To be able to identify and diagnose in advance those at “risk” of developing post-traumatic stress disorder, would greatly taper the gap between late sequelae and treatment. Therefore, this study sought to determine whether the transcriptome can be used to track the development of post-traumatic stress disorder in this unique and susceptible cohort of individuals. Gene expression levels in peripheral blood samples from 85 Canadian infantry soldiers (n = 58 participants negative for symptoms of post-traumatic stress disorder and n = 27 participants with symptoms of post-traumatic stress disorder) following return from deployment to Afghanistan were determined using RNA sequencing technology. Count-based gene expression quantification, normalization and differential analysis (with thorough correction for confounders) revealed genes associated to PTSD; LRP8 and GOLM1. These preliminary results provide a proof-of-principle for the diagnostic utility of blood-based gene expression profiles for tracking symptoms of post-traumatic stress disorder in soldiers returning from tour. It is also the first to report transcriptome-wide expression profiles alongside a post-traumatic symptom checklist.
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Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity. Nat Genet 2018; 51:106-116. [PMID: 30559488 PMCID: PMC6309590 DOI: 10.1038/s41588-018-0288-4] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/23/2018] [Indexed: 12/11/2022]
Abstract
We combined de novo mutation (DNM) data from 10,927 individuals with developmental delay and autism to identify 253 candidate neurodevelopmental disease genes with an excess of missense and/or likely gene-disruptive (LGD) mutations. Of these genes, 124 reach exome-wide significance (P < 5 × 10-7) for DNM. Intersecting these results with copy number variation (CNV) morbidity data shows an enrichment for genomic disorder regions (30/253, likelihood ratio (LR) +1.85, P = 0.0017). We identify genes with an excess of missense DNMs overlapping deletion syndromes (for example, KIF1A and the 2q37 deletion) as well as duplication syndromes, such as recurrent MAPK3 missense mutations within the chromosome 16p11.2 duplication, recurrent CHD4 missense DNMs in the 12p13 duplication region, and recurrent WDFY4 missense DNMs in the 10q11.23 duplication region. Network analyses of genes showing an excess of DNMs highlights functional networks, including cell-specific enrichments in the D1+ and D2+ spiny neurons of the striatum.
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Smith AH, Ovesen PL, Skeldal S, Yeo S, Jensen KP, Olsen D, Diazgranados N, Zhao H, Farrer LA, Goldman D, Glerup S, Kranzler HR, Nykjær A, Gelernter J. Risk Locus Identification Ties Alcohol Withdrawal Symptoms to SORCS2. Alcohol Clin Exp Res 2018; 42:2337-2348. [PMID: 30252935 PMCID: PMC6317871 DOI: 10.1111/acer.13890] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/06/2018] [Indexed: 01/11/2023]
Abstract
BACKGROUND Efforts to promote the cessation of harmful alcohol use are hindered by the affective and physiological components of alcohol withdrawal (AW), which can include life-threatening seizures. Although previous studies of AW and relapse have highlighted the detrimental role of stress, little is known about genetic risk factors. METHODS We conducted a genome-wide association study of AW symptom count in uniformly assessed subjects with histories of serious AW, followed by additional genotyping in independent AW subjects. RESULTS The top association signal for AW severity was in sortilin family neurotrophin receptor gene SORCS2 on chromosome 4 (European American meta-analysis n = 1,478, p = 4.3 × 10-9 ). There were no genome-wide significant findings in African Americans (n = 1,231). Bioinformatic analyses were conducted using publicly available high-throughput transcriptomic and epigenomic data sets, showing that in humans SORCS2 is most highly expressed in the nervous system. The identified SORCS2 risk haplotype is predicted to disrupt a stress hormone-modulated regulatory element that has tissue-specific activity in human hippocampus. We used human neural lineage cells to demonstrate in vitro a causal relationship between stress hormone levels and SORCS2 expression, and show that SORCS2 levels in culture are increased upon ethanol exposure and withdrawal. CONCLUSIONS Taken together, these findings indicate that the pathophysiology of withdrawal may involve the effects of stress hormones on neurotrophic factor signaling. Further investigation of these pathways could produce new approaches to managing the aversive consequences of abrupt alcohol cessation.
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Affiliation(s)
- Andrew H. Smith
- Interdepartmental Neuroscience Program and Medical Scientist Training Program, Yale School of Medicine
- Division of Human Genetics, Department of Psychiatry, VA CT Healthcare Center and Yale School of Medicine
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Peter L. Ovesen
- The Lundbeck Foundation Research Center MIND, Danish Research Institute of Translational Neuroscience DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Sune Skeldal
- The Lundbeck Foundation Research Center MIND, Danish Research Institute of Translational Neuroscience DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Seungeun Yeo
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism
| | - Kevin P. Jensen
- Division of Human Genetics, Department of Psychiatry, VA CT Healthcare Center and Yale School of Medicine
| | - Ditte Olsen
- The Lundbeck Foundation Research Center MIND, Danish Research Institute of Translational Neuroscience DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Nancy Diazgranados
- Office of the Clinical Director, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health
| | - Lindsay A. Farrer
- Departments of Medicine (Biomedical Genetics), Neurology, and Ophthalmology, School of Medicine, and Departments of Biostatistics and Epidemiology, School of Public Health, Boston University, Boston, MA 02118, USA
| | - David Goldman
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism
- Office of the Clinical Director, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892, USA
| | - Simon Glerup
- The Lundbeck Foundation Research Center MIND, Danish Research Institute of Translational Neuroscience DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Henry R. Kranzler
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania and Corporal Michael J. Crescenz VAMC, Philadelphia, Pennsylvania 19104, USA
| | - Anders Nykjær
- The Lundbeck Foundation Research Center MIND, Danish Research Institute of Translational Neuroscience DANDRITE - Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark
- Department of Neuroscience, Mayo Clinic, Jacksonville 32224, Florida, USA
| | - Joel Gelernter
- Division of Human Genetics, Department of Psychiatry, VA CT Healthcare Center and Yale School of Medicine
- Departments of Genetics and Neuroscience, Yale School of Medicine, Yale University, New Haven, Connecticut 06510, USA
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29
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Zhang F, Tapera TM, Gou J. Application of a new dietary pattern analysis method in nutritional epidemiology. BMC Med Res Methodol 2018; 18:119. [PMID: 30373530 PMCID: PMC6206725 DOI: 10.1186/s12874-018-0585-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/19/2018] [Indexed: 11/29/2022] Open
Abstract
Background Diet plays an important role in chronic disease, and the use of dietary pattern analysis has grown rapidly as a way of deconstructing the complexity of nutritional intake and its relation to health. Pattern analysis methods, such as principal component analysis (PCA), have been used to investigate various dimensions of diet. Existing analytic methods, however, do not fully utilize the predictive potential of dietary assessment data. In particular, these methods are often suboptimal at predicting clinically important variables. Methods We propose a new dietary pattern analysis method using the advanced LASSO (Least Absolute Shrinkage and Selection Operator) model to improve the prediction of disease-related risk factors. Despite the potential advantages of LASSO, this is the first time that the model has been adapted for dietary pattern analysis. Hence, the systematic evaluation of the LASSO model as applied to dietary data and health outcomes is highly innovative and novel. Using Food Frequency Questionnaire data from NHANES 2005–2006, we apply PCA and LASSO to identify dietary patterns related to cardiovascular disease risk factors in healthy US adults (n = 2609) after controlling for confounding variables (e.g., age and BMI). Both analyses account for the sampling weights. Model performance in terms of prediction accuracy is evaluated using an independent test set. Results PCA yields 10 principal components (PCs) that together account for 65% of the variation in the data set and represent distinct dietary patterns. These PCs are then used as predictors in a regression model to predict cardiovascular disease risk factors. We find that LASSO better predicts levels of triglycerides, LDL cholesterol, HDL cholesterol, and total cholesterol (adjusted R2 = 0.861, 0.899, 0.890, and 0.935 respectively) than does the traditional, linear-regression-based, dietary pattern analysis method (adjusted R2 = 0.163, 0.005, 0.235, and 0.024 respectively) when the latter is applied to components derived from PCA. Conclusions The proposed method is shown to be an appropriate and promising statistical means of deriving dietary patterns predictive of cardiovascular disease risk. Future studies, involving different diseases and risk factors, will be necessary before LASSO’s broader usefulness in nutritional epidemiology can be established.
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Affiliation(s)
- Fengqing Zhang
- Department of Psychology, Drexel University, Philadelphia, PA, 19104, USA.
| | - Tinashe M Tapera
- Department of Psychology, Drexel University, Philadelphia, PA, 19104, USA
| | - Jiangtao Gou
- Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, 19111, USA
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30
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Vilor-Tejedor N, Alemany S, Cáceres A, Bustamante M, Pujol J, Sunyer J, González JR. Strategies for integrated analysis in imaging genetics studies. Neurosci Biobehav Rev 2018; 93:57-70. [PMID: 29944960 DOI: 10.1016/j.neubiorev.2018.06.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/30/2018] [Accepted: 06/15/2018] [Indexed: 02/06/2023]
Abstract
Imaging Genetics (IG) integrates neuroimaging and genomic data from the same individual, deepening our knowledge of the biological mechanisms behind neurodevelopmental domains and neurological disorders. Although the literature on IG has exponentially grown over the past years, the majority of studies have mainly analyzed associations between candidate brain regions and individual genetic variants. However, this strategy is not designed to deal with the complexity of neurobiological mechanisms underlying behavioral and neurodevelopmental domains. Moreover, larger sample sizes and increased multidimensionality of this type of data represents a challenge for standardizing modeling procedures in IG research. This review provides a systematic update of the methods and strategies currently used in IG studies, and serves as an analytical framework for researchers working in this field. To complement the functionalities of the Neuroconductor framework, we also describe existing R packages that implement these methodologies. In addition, we present an overview of how these methodological approaches are applied in integrating neuroimaging and genetic data.
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Affiliation(s)
- Natàlia Vilor-Tejedor
- Barcelona Research Institute for Global Health (ISGlobal), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain; Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Barcelona Beta Brain Research Center (BBRC) - Pasqual Maragall Foundation, Barcelona, Spain.
| | - Silvia Alemany
- Barcelona Research Institute for Global Health (ISGlobal), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Alejandro Cáceres
- Barcelona Research Institute for Global Health (ISGlobal), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Mariona Bustamante
- Barcelona Research Institute for Global Health (ISGlobal), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain; Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jesús Pujol
- MRI Research Unit, Hospital del Mar, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM G21, Barcelona, Spain
| | - Jordi Sunyer
- Barcelona Research Institute for Global Health (ISGlobal), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain; IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Juan R González
- Barcelona Research Institute for Global Health (ISGlobal), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.
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Corlier F, Hafzalla G, Faskowitz J, Kuller LH, Becker JT, Lopez OL, Thompson PM, Braskie MN. Systemic inflammation as a predictor of brain aging: Contributions of physical activity, metabolic risk, and genetic risk. Neuroimage 2018; 172:118-129. [PMID: 29357308 PMCID: PMC5954991 DOI: 10.1016/j.neuroimage.2017.12.027] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 12/01/2017] [Accepted: 12/11/2017] [Indexed: 12/17/2022] Open
Abstract
Inflammatory processes may contribute to risk for Alzheimer's disease (AD) and age-related brain degeneration. Metabolic and genetic risk factors, and physical activity may, in turn, influence these inflammatory processes. Some of these risk factors are modifiable, and interact with each other. Understanding how these processes together relate to brain aging will help to inform future interventions to treat or prevent cognitive decline. We used brain magnetic resonance imaging (MRI) to scan 335 older adult humans (mean age 77.3 ± 3.4 years) who remained non-demented for the duration of the 9-year longitudinal study. We used structural equation modeling (SEM) in a subset of 226 adults to evaluate whether measures of baseline peripheral inflammation (serum C-reactive protein levels; CRP), mediated the baseline contributions of genetic and metabolic risk, and physical activity, to regional cortical thickness in AD-relevant brain regions at study year 9. We found that both baseline metabolic risk and AD risk variant apolipoprotein E ε4 (APOE4), modulated baseline serum CRP. Higher baseline CRP levels, in turn, predicted thinner regional cortex at year 9, and mediated an effect between higher metabolic risk and thinner cortex in those regions. A higher polygenic risk score composed of variants in immune-associated AD risk genes (other than APOE) was associated with thinner regional cortex. However, CRP levels did not mediate this effect, suggesting that other mechanisms may be responsible for the elevated AD risk. We found interactions between genetic and environmental factors and structural brain health. Our findings support the role of metabolic risk and peripheral inflammation in age-related brain decline.
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Affiliation(s)
- Fabian Corlier
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA 90292, USA
| | - George Hafzalla
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA 90292, USA
| | - Joshua Faskowitz
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA 90292, USA
| | - Lewis H Kuller
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - James T Becker
- Departments of Neurology, Psychiatry, and Psychology, University of Pittsburgh, Pittsburgh, PA 15139, USA
| | - Oscar L Lopez
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA 90292, USA; Depts. of Neurology, Psychiatry, Engineering, Radiology, & Ophthalmology, Keck/USC School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Meredith N Braskie
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA 90292, USA.
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32
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Hao X, Li C, Yan J, Yao X, Risacher SL, Saykin AJ, Shen L, Zhang D. Identification of associations between genotypes and longitudinal phenotypes via temporally-constrained group sparse canonical correlation analysis. Bioinformatics 2018; 33:i341-i349. [PMID: 28881979 PMCID: PMC5870577 DOI: 10.1093/bioinformatics/btx245] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Motivation Neuroimaging genetics identifies the relationships between genetic variants (i.e., the single nucleotide polymorphisms) and brain imaging data to reveal the associations from genotypes to phenotypes. So far, most existing machine-learning approaches are widely used to detect the effective associations between genetic variants and brain imaging data at one time-point. However, those associations are based on static phenotypes and ignore the temporal dynamics of the phenotypical changes. The phenotypes across multiple time-points may exhibit temporal patterns that can be used to facilitate the understanding of the degenerative process. In this article, we propose a novel temporally constrained group sparse canonical correlation analysis (TGSCCA) framework to identify genetic associations with longitudinal phenotypic markers. Results The proposed TGSCCA method is able to capture the temporal changes in brain from longitudinal phenotypes by incorporating the fused penalty, which requires that the differences between two consecutive canonical weight vectors from adjacent time-points should be small. A new efficient optimization algorithm is designed to solve the objective function. Furthermore, we demonstrate the effectiveness of our algorithm on both synthetic and real data (i.e., the Alzheimer’s Disease Neuroimaging Initiative cohort, including progressive mild cognitive impairment, stable MCI and Normal Control participants). In comparison with conventional SCCA, our proposed method can achieve strong associations and discover phenotypic biomarkers across multiple time-points to guide disease-progressive interpretation. Availability and implementation The Matlab code is available at https://sourceforge.net/projects/ibrain-cn/files/.
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Affiliation(s)
- Xiaoke Hao
- School of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Chanxiu Li
- School of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Jingwen Yan
- Department of Radiology and Imaging Sciences, School of Medicine, Indiana University, Indianapolis, IN, USA.,School of Informatics and Computing, Indiana University, Indianapolis, IN, USA
| | - Xiaohui Yao
- Department of Radiology and Imaging Sciences, School of Medicine, Indiana University, Indianapolis, IN, USA.,School of Informatics and Computing, Indiana University, Indianapolis, IN, USA
| | - Shannon L Risacher
- Department of Radiology and Imaging Sciences, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Li Shen
- Department of Radiology and Imaging Sciences, School of Medicine, Indiana University, Indianapolis, IN, USA.,School of Informatics and Computing, Indiana University, Indianapolis, IN, USA
| | - Daoqiang Zhang
- School of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
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Bertocci MA, Bebko G, Versace A, Iyengar S, Bonar L, Forbes EE, Almeida JRC, Perlman SB, Schirda C, Travis MJ, Gill MK, Diwadkar VA, Sunshine JL, Holland SK, Kowatch RA, Birmaher B, Axelson DA, Frazier TW, Arnold LE, Fristad MA, Youngstrom EA, Horwitz SM, Findling RL, Phillips ML. Reward-related neural activity and structure predict future substance use in dysregulated youth. Psychol Med 2017; 47:1357-1369. [PMID: 27998326 PMCID: PMC5576722 DOI: 10.1017/s0033291716003147] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Identifying youth who may engage in future substance use could facilitate early identification of substance use disorder vulnerability. We aimed to identify biomarkers that predicted future substance use in psychiatrically un-well youth. METHOD LASSO regression for variable selection was used to predict substance use 24.3 months after neuroimaging assessment in 73 behaviorally and emotionally dysregulated youth aged 13.9 (s.d. = 2.0) years, 30 female, from three clinical sites in the Longitudinal Assessment of Manic Symptoms (LAMS) study. Predictor variables included neural activity during a reward task, cortical thickness, and clinical and demographic variables. RESULTS Future substance use was associated with higher left middle prefrontal cortex activity, lower left ventral anterior insula activity, thicker caudal anterior cingulate cortex, higher depression and lower mania scores, not using antipsychotic medication, more parental stress, older age. This combination of variables explained 60.4% of the variance in future substance use, and accurately classified 83.6%. CONCLUSIONS These variables explained a large proportion of the variance, were useful classifiers of future substance use, and showed the value of combining multiple domains to provide a comprehensive understanding of substance use development. This may be a step toward identifying neural measures that can identify future substance use disorder risk, and act as targets for therapeutic interventions.
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Affiliation(s)
- M A Bertocci
- Department of Psychiatry,Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh,Pittsburgh, PA,USA
| | - G Bebko
- Department of Psychiatry,Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh,Pittsburgh, PA,USA
| | - A Versace
- Department of Psychiatry,Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh,Pittsburgh, PA,USA
| | - S Iyengar
- Department of Statistics,University of Pittsburgh,Pittsburgh, PA,USA
| | - L Bonar
- Department of Psychiatry,Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh,Pittsburgh, PA,USA
| | - E E Forbes
- Department of Psychiatry,Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh,Pittsburgh, PA,USA
| | - J R C Almeida
- Department of Psychiatry,Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh,Pittsburgh, PA,USA
| | - S B Perlman
- Department of Psychiatry,Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh,Pittsburgh, PA,USA
| | - C Schirda
- Department of Psychiatry,Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh,Pittsburgh, PA,USA
| | - M J Travis
- Department of Psychiatry,Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh,Pittsburgh, PA,USA
| | - M K Gill
- Department of Psychiatry,Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh,Pittsburgh, PA,USA
| | - V A Diwadkar
- Department of Psychiatry and Behavioral Neuroscience,Wayne State University,Detroit, MI,USA
| | - J L Sunshine
- Department of Radiology,University Hospitals Case Medical Center/Case Western Reserve University,Cleveland, OH,USA
| | - S K Holland
- Cincinnati Children's Hospital Medical Center, University of Cincinnati,Cincinnati, OH,USA
| | - R A Kowatch
- Department of Psychiatry and Behavioral Health,Ohio State University,Columbus, OH,USA
| | - B Birmaher
- Department of Psychiatry,Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh,Pittsburgh, PA,USA
| | - D A Axelson
- Department of Psychiatry and Behavioral Health,Ohio State University,Columbus, OH,USA
| | - T W Frazier
- Pediatric Institute,Cleveland Clinic,Cleveland, OH,USA
| | - L E Arnold
- Department of Psychiatry and Behavioral Health,Ohio State University,Columbus, OH,USA
| | - M A Fristad
- Department of Psychiatry and Behavioral Health,Ohio State University,Columbus, OH,USA
| | - E A Youngstrom
- Department of Psychology,University of North Carolina at Chapel Hill,Chapel Hill, NC,USA
| | - S M Horwitz
- Department of Child and Adolescent Psychiatry,New York University School of Medicine,New York, NY,USA
| | - R L Findling
- Department of Psychiatry,Johns Hopkins University,Baltimore, MD,USA
| | - M L Phillips
- Department of Psychiatry,Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh,Pittsburgh, PA,USA
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Li J, Zhang Q, Chen F, Meng X, Liu W, Chen D, Yan J, Kim S, Wang L, Feng W, Saykin AJ, Liang H, Shen L. Genome-wide association and interaction studies of CSF T-tau/Aβ 42 ratio in ADNI cohort. Neurobiol Aging 2017. [PMID: 28641921 DOI: 10.1016/j.neurobiolaging.2017.05.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The pathogenic relevance in Alzheimer's disease (AD) presents a decrease of cerebrospinal fluid amyloid-ß42 (Aß42) burden and an increase in cerebrospinal fluid total tau (T-tau) levels. In this work, we performed genome-wide association study (GWAS) and genome-wide interaction study of T-tau/Aß42 ratio as an AD imaging quantitative trait on 843 subjects and 563,980 single-nucleotide polymorphisms (SNPs) in ADNI cohort. We aim to identify not only SNPs with significant main effects but also SNPs with interaction effects to help explain "missing heritability". Linear regression method was used to detect SNP-SNP interactions among SNPs with uncorrected p-value ≤0.01 from the GWAS. Age, gender, and diagnosis were considered as covariates in both studies. The GWAS results replicated the previously reported AD-related genes APOE, APOC1, and TOMM40, as well as identified 14 novel genes, which showed genome-wide statistical significance. Genome-wide interaction study revealed 7 pairs of SNPs meeting the cell-size criteria and with bonferroni-corrected p-value ≤0.05. As we expect, these interaction pairs all had marginal main effects but explained a relatively high-level variance of T-tau/Aß42, demonstrating their potential association with AD pathology.
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Affiliation(s)
- Jin Li
- College of Automation, Harbin Engineering University, Harbin, China
| | - Qiushi Zhang
- College of Automation, Harbin Engineering University, Harbin, China; College of Information Engineering, Northeast Dianli University, Jilin, China
| | - Feng Chen
- College of Automation, Harbin Engineering University, Harbin, China
| | - Xianglian Meng
- College of Automation, Harbin Engineering University, Harbin, China
| | - Wenjie Liu
- College of Automation, Harbin Engineering University, Harbin, China
| | - Dandan Chen
- College of Automation, Harbin Engineering University, Harbin, China; College of Information Engineering, Northeast Dianli University, Jilin, China
| | - Jingwen Yan
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN, USA
| | - Sungeun Kim
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Lei Wang
- College of Automation, Harbin Engineering University, Harbin, China
| | - Weixing Feng
- College of Automation, Harbin Engineering University, Harbin, China
| | - Andrew J Saykin
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Hong Liang
- College of Automation, Harbin Engineering University, Harbin, China.
| | - Li Shen
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN, USA.
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Bertocci MA, Bebko G, Dwojak A, Iyengar S, Ladouceur CD, Fournier JC, Versace A, Perlman SB, Almeida JRC, Travis MJ, Gill MK, Bonar L, Schirda C, Diwadkar VA, Sunshine JL, Holland SK, Kowatch RA, Birmaher B, Axelson D, Horwitz SM, Frazier T, Arnold LE, Fristad MA, Youngstrom EA, Findling RL, Phillips ML. Longitudinal relationships among activity in attention redirection neural circuitry and symptom severity in youth. BIOLOGICAL PSYCHIATRY: COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2017; 2:336-345. [PMID: 28480336 DOI: 10.1016/j.bpsc.2016.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Changes in neural circuitry function may be associated with longitudinal changes in psychiatric symptom severity. Identification of these relationships may aid in elucidating the neural basis of psychiatric symptom evolution over time. We aimed to distinguish these relationships using data from the Longitudinal Assessment of Manic Symptoms (LAMS) cohort. METHODS Forty-one youth completed two study visits (mean=21.3 months). Elastic-net regression (Multiple response Gaussian family) identified emotional regulation neural circuitry that changed in association with changes in depression, mania, anxiety, affect lability, and positive mood and energy dysregulation, accounting for clinical and demographic variables. RESULTS Non-zero coefficients between change in the above symptom measures and change in activity over the inter-scan interval were identified in right amygdala and left ventrolateral prefrontal cortex. Differing patterns of neural activity change were associated with changes in each of the above symptoms over time. Specifically, from Scan1 to Scan2, worsening affective lability and depression severity were associated with increased right amygdala and left ventrolateral prefrontal cortical activity. Worsening anxiety and positive mood and energy dysregulation were associated with decreased right amygdala and increased left ventrolateral prefrontal cortical activity. Worsening mania was associated with increased right amygdala and decreased left ventrolateral prefrontal cortical activity. These changes in neural activity between scans accounted for 13.6% of the variance; that is 25% of the total explained variance (39.6%) in these measures. CONCLUSIONS Distinct neural mechanisms underlie changes in different mood and anxiety symptoms overtime.
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Affiliation(s)
- Michele A Bertocci
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh
| | - Genna Bebko
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh
| | - Amanda Dwojak
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh
| | | | - Cecile D Ladouceur
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh
| | - Jay C Fournier
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh
| | - Amelia Versace
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh
| | - Susan B Perlman
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh
| | | | - Michael J Travis
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh
| | - Mary Kay Gill
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh
| | - Lisa Bonar
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh
| | - Claudiu Schirda
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh
| | - Vaibhav A Diwadkar
- Department of Psychiatry and Behavioral Neuroscience, Wayne State University
| | - Jeffrey L Sunshine
- University Hospitals Case Medical Center/Case Western Reserve University
| | - Scott K Holland
- Cincinnati Children's Hospital Medical Center, University of Cincinnati
| | | | - Boris Birmaher
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh
| | - David Axelson
- The Research Institute at Nationwide Children's Hospital
| | - Sarah M Horwitz
- Department of Child Psychiatry, New York University School of Medicine
| | | | - L Eugene Arnold
- Department of Psychiatry and Behavioral Health, Ohio State University
| | | | - Eric A Youngstrom
- Department of Psychology, University of North Carolina at Chapel Hill
| | - Robert L Findling
- University Hospitals Case Medical Center/Case Western Reserve University.,Department of Psychiatry, Johns Hopkins University
| | - Mary L Phillips
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh Medical Center, University of Pittsburgh
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36
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Salehe BR, Jones CI, Di Fatta G, McGuffin LJ. RAPIDSNPs: A new computational pipeline for rapidly identifying key genetic variants reveals previously unidentified SNPs that are significantly associated with individual platelet responses. PLoS One 2017; 12:e0175957. [PMID: 28441463 PMCID: PMC5404774 DOI: 10.1371/journal.pone.0175957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 04/03/2017] [Indexed: 01/14/2023] Open
Abstract
Advances in omics technologies have led to the discovery of genetic markers, or single nucleotide polymorphisms (SNPs), that are associated with particular diseases or complex traits. Although there have been significant improvements in the approaches used to analyse associations of SNPs with disease, further optimised and rapid techniques are needed to keep up with the rate of SNP discovery, which has exacerbated the 'missing heritability' problem. Here, we have devised a novel, integrated, heuristic-based, hybrid analytical computational pipeline, for rapidly detecting novel or key genetic variants that are associated with diseases or complex traits. Our pipeline is particularly useful in genetic association studies where the genotyped SNP data are highly dimensional, and the complex trait phenotype involved is continuous. In particular, the pipeline is more efficient for investigating small sets of genotyped SNPs defined in high dimensional spaces that may be associated with continuous phenotypes, rather than for the investigation of whole genome variants. The pipeline, which employs a consensus approach based on the random forest, was able to rapidly identify previously unseen key SNPs, that are significantly associated with the platelet response phenotype, which was used as our complex trait case study. Several of these SNPs, such as rs6141803 of COMMD7 and rs41316468 in PKT2B, have independently confirmed associations with cardiovascular diseases (CVDs) according to other unrelated studies, suggesting that our pipeline is robust in identifying key genetic variants. Our new pipeline provides an important step towards addressing the problem of 'missing heritability' through enhanced detection of key genetic variants (SNPs) that are associated with continuous complex traits/disease phenotypes.
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Affiliation(s)
| | - Chris Ian Jones
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Giuseppe Di Fatta
- Department of Computer Science, University of Reading, Reading, United Kingdom
| | - Liam James McGuffin
- School of Biological Sciences, University of Reading, Reading, United Kingdom
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37
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Lee E, Giovanello KS, Saykin AJ, Xie F, Kong D, Wang Y, Yang L, Ibrahim JG, Doraiswamy PM, Zhu H. Single-nucleotide polymorphisms are associated with cognitive decline at Alzheimer's disease conversion within mild cognitive impairment patients. ALZHEIMER'S & DEMENTIA: DIAGNOSIS, ASSESSMENT & DISEASE MONITORING 2017; 8:86-95. [PMID: 28560309 PMCID: PMC5440281 DOI: 10.1016/j.dadm.2017.04.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
INTRODUCTION The growing public threat of Alzheimer's disease (AD) has raised the urgency to quantify the degree of cognitive decline during the conversion process of mild cognitive impairment (MCI) to AD and its underlying genetic pathway. The aim of this article was to test genetic common variants associated with accelerated cognitive decline after the conversion of MCI to AD. METHODS In 583 subjects with MCI enrolled in the Alzheimer's Disease Neuroimaging Initiative (ADNI; ADNI-1, ADNI-Go, and ADNI-2), 245 MCI participants converted to AD at follow-up. We tested the interaction effects between individual single-nucleotide polymorphisms and AD diagnosis trajectory on the longitudinal Alzheimer's Disease Assessment Scale-Cognition scores. RESULTS Our findings reveal six genes, including BDH1, ST6GAL1, RAB20, PDS5B, ADARB2, and SPSB1, which are directly or indirectly related to MCI conversion to AD. DISCUSSION This genome-wide association study sheds light on a genetic mechanism of longitudinal cognitive changes during the transition period from MCI to AD.
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Affiliation(s)
- Eunjee Lee
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Kelly S Giovanello
- Department of Psychology and Neuroscience, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA.,Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Fengchang Xie
- School of Mathematical Sciences, Nanjing Normal University, Nanjing, China
| | - Dehan Kong
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Yue Wang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Liuqing Yang
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joseph G Ibrahim
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - P Murali Doraiswamy
- Department of Psychiatry, Duke University, Durham, NC, USA.,Duke Institute for Brain Sciences, Duke University, Durham, NC, USA
| | - Hongtu Zhu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Mitra I, Lavillaureix A, Yeh E, Traglia M, Tsang K, Bearden CE, Rauen KA, Weiss LA. Reverse Pathway Genetic Approach Identifies Epistasis in Autism Spectrum Disorders. PLoS Genet 2017; 13:e1006516. [PMID: 28076348 PMCID: PMC5226683 DOI: 10.1371/journal.pgen.1006516] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/01/2016] [Indexed: 02/08/2023] Open
Abstract
Although gene-gene interaction, or epistasis, plays a large role in complex traits in model organisms, genome-wide by genome-wide searches for two-way interaction have limited power in human studies. We thus used knowledge of a biological pathway in order to identify a contribution of epistasis to autism spectrum disorders (ASDs) in humans, a reverse-pathway genetic approach. Based on previous observation of increased ASD symptoms in Mendelian disorders of the Ras/MAPK pathway (RASopathies), we showed that common SNPs in RASopathy genes show enrichment for association signal in GWAS (P = 0.02). We then screened genome-wide for interactors with RASopathy gene SNPs and showed strong enrichment in ASD-affected individuals (P < 2.2 x 10-16), with a number of pairwise interactions meeting genome-wide criteria for significance. Finally, we utilized quantitative measures of ASD symptoms in RASopathy-affected individuals to perform modifier mapping via GWAS. One top region overlapped between these independent approaches, and we showed dysregulation of a gene in this region, GPR141, in a RASopathy neural cell line. We thus used orthogonal approaches to provide strong evidence for a contribution of epistasis to ASDs, confirm a role for the Ras/MAPK pathway in idiopathic ASDs, and to identify a convergent candidate gene that may interact with the Ras/MAPK pathway.
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Affiliation(s)
- Ileena Mitra
- Department of Psychiatry, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Alinoë Lavillaureix
- Department of Psychiatry, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Université Paris Descartes, Sorbonne Paris Cité, Faculty of Medicine, Paris, France
| | - Erika Yeh
- Department of Psychiatry, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Michela Traglia
- Department of Psychiatry, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Kathryn Tsang
- Department of Psychiatry, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Carrie E. Bearden
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Psychology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Katherine A. Rauen
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Department of Pediatrics, School of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Lauren A. Weiss
- Department of Psychiatry, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
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Drgonova J, Walther D, Hartstein GL, Bukhari MO, Baumann MH, Katz J, Hall FS, Arnold ER, Flax S, Riley A, Rivero-Martin O, Lesch KP, Troncoso J, Ranscht B, Uhl GR. Cadherin 13: human cis-regulation and selectively-altered addiction phenotypes and cerebral cortical dopamine in knockout mice. Mol Med 2016; 22:537-547. [PMID: 27579475 PMCID: PMC5082297 DOI: 10.2119/molmed.2015.00170] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 07/29/2016] [Indexed: 12/22/2022] Open
Abstract
The cadherin 13 (CDH13) gene encodes a cell adhesion molecule likely to influence development and connections of brain circuits that modulate addiction, locomotion and cognition, including those that involve midbrain dopamine neurons. Human CDH13 mRNA expression differs by more than 80% in postmortem cerebral cortical samples from individuals with different CDH13 genotypes, supporting examination of mice with altered Cdh13 expression as models for common human variation at this locus. Constitutive cdh13 knockout mice display evidence for changed cocaine reward: shifted dose response relationship in tests of cocaine-conditioned place preference using doses that do not alter cocaine conditioned taste aversion. Reduced adult Cdh13 expression in conditional knockouts also alters cocaine reward in ways that correlate with individual differences in cortical Cdh13 mRNA levels. In control and comparison behavioral assessments, knockout mice display modestly-quicker acquisition of rotarod and water maze tasks, with a trend toward faster acquisition of 5 choice serial reaction time tasks that otherwise displayed no genotype-related differences. They display significant differences in locomotion in some settings, with larger effects in males. In assessments of brain changes that might contribute to these behavioral differences, there are selective alterations of dopamine levels, dopamine/metabolite ratios, dopaminergic fiber densities and mRNA encoding the activity dependent transcription factor npas4 in cerebral cortex of knockout mice. These novel data and previously reported human associations of CDH13 variants with addiction, individual differences in responses to stimulant administration and attention deficit hyperactivity disorder (ADHD) phenotypes suggest that levels of CDH13 expression, through mechanisms likely to include effects on mesocortical dopamine, influence stimulant reward and may contribute modestly to cognitive and locomotor phenotypes relevant to ADHD.
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Affiliation(s)
- Jana Drgonova
- Molecular Neurobiology, NIH-IRP, NIDA, Baltimore, Maryland 21224
| | - Donna Walther
- Molecular Neurobiology, NIH-IRP, NIDA, Baltimore, Maryland 21224
| | - G Luke Hartstein
- Molecular Neurobiology, NIH-IRP, NIDA, Baltimore, Maryland 21224
| | | | | | - Jonathan Katz
- Medicinal Chemistry, NIH-IRP, NIDA, Baltimore, Maryland 21224
| | - Frank Scott Hall
- Molecular Neurobiology, NIH-IRP, NIDA, Baltimore, Maryland 21224
| | | | - Shaun Flax
- Dept of Psychology, American Univ, Washington, DC
| | | | - Olga Rivero-Martin
- Translational Neurobiology, Dept Psychiatry, Univ Würzburg, Würzburg Germany
| | - Klaus-Peter Lesch
- Translational Neurobiology, Dept Psychiatry, Univ Würzburg, Würzburg Germany
| | - Juan Troncoso
- Div Neuropathology, Johns Hopkins Sch Med, Baltimore MD 21202
| | | | - George R Uhl
- Molecular Neurobiology, NIH-IRP, NIDA, Baltimore, Maryland 21224
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40
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Hao X, Yao X, Yan J, Risacher SL, Saykin AJ, Zhang D, Shen L. Identifying Multimodal Intermediate Phenotypes Between Genetic Risk Factors and Disease Status in Alzheimer's Disease. Neuroinformatics 2016; 14:439-52. [PMID: 27277494 PMCID: PMC5010986 DOI: 10.1007/s12021-016-9307-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Neuroimaging genetics has attracted growing attention and interest, which is thought to be a powerful strategy to examine the influence of genetic variants (i.e., single nucleotide polymorphisms (SNPs)) on structures or functions of human brain. In recent studies, univariate or multivariate regression analysis methods are typically used to capture the effective associations between genetic variants and quantitative traits (QTs) such as brain imaging phenotypes. The identified imaging QTs, although associated with certain genetic markers, may not be all disease specific. A useful, but underexplored, scenario could be to discover only those QTs associated with both genetic markers and disease status for revealing the chain from genotype to phenotype to symptom. In addition, multimodal brain imaging phenotypes are extracted from different perspectives and imaging markers consistently showing up in multimodalities may provide more insights for mechanistic understanding of diseases (i.e., Alzheimer's disease (AD)). In this work, we propose a general framework to exploit multi-modal brain imaging phenotypes as intermediate traits that bridge genetic risk factors and multi-class disease status. We applied our proposed method to explore the relation between the well-known AD risk SNP APOE rs429358 and three baseline brain imaging modalities (i.e., structural magnetic resonance imaging (MRI), fluorodeoxyglucose positron emission tomography (FDG-PET) and F-18 florbetapir PET scans amyloid imaging (AV45)) from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. The empirical results demonstrate that our proposed method not only helps improve the performances of imaging genetic associations, but also discovers robust and consistent regions of interests (ROIs) across multi-modalities to guide the disease-induced interpretation.
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Affiliation(s)
- Xiaoke Hao
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
- Department of Radiology and Imaging Sciences, School of Medicine, Indiana University, Indianapolis, IN, 46202, USA
| | - Xiaohui Yao
- Department of Radiology and Imaging Sciences, School of Medicine, Indiana University, Indianapolis, IN, 46202, USA
| | - Jingwen Yan
- Department of Radiology and Imaging Sciences, School of Medicine, Indiana University, Indianapolis, IN, 46202, USA
| | - Shannon L Risacher
- Department of Radiology and Imaging Sciences, School of Medicine, Indiana University, Indianapolis, IN, 46202, USA
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, School of Medicine, Indiana University, Indianapolis, IN, 46202, USA
| | - Daoqiang Zhang
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China.
| | - Li Shen
- Department of Radiology and Imaging Sciences, School of Medicine, Indiana University, Indianapolis, IN, 46202, USA.
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41
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Predicting clinical outcome from reward circuitry function and white matter structure in behaviorally and emotionally dysregulated youth. Mol Psychiatry 2016; 21:1194-201. [PMID: 26903272 PMCID: PMC4993633 DOI: 10.1038/mp.2016.5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/09/2015] [Accepted: 12/02/2015] [Indexed: 12/20/2022]
Abstract
Behavioral and emotional dysregulation in childhood may be understood as prodromal to adult psychopathology. Additionally, there is a critical need to identify biomarkers reflecting underlying neuropathological processes that predict clinical/behavioral outcomes in youth. We aimed to identify such biomarkers in youth with behavioral and emotional dysregulation in the Longitudinal Assessment of Manic Symptoms (LAMS) study. We examined neuroimaging measures of function and white matter in the whole brain using 80 youth aged 14.0 (s.d.=2.0) from three clinical sites. Linear regression using the LASSO (Least Absolute Shrinkage and Selection Operator) method for variable selection was used to predict severity of future behavioral and emotional dysregulation measured by the Parent General Behavior Inventory-10 Item Mania Scale (PGBI-10M)) at a mean of 14.2 months follow-up after neuroimaging assessment. Neuroimaging measures, together with near-scan PGBI-10M, a score of manic behaviors, depressive behaviors and sex, explained 28% of the variance in follow-up PGBI-10M. Neuroimaging measures alone, after accounting for other identified predictors, explained ~1/3 of the explained variance, in follow-up PGBI-10M. Specifically, greater bilateral cingulum length predicted lower PGBI-10M at follow-up. Greater functional connectivity in parietal-subcortical reward circuitry predicted greater PGBI-10M at follow-up. For the first time, data suggest that multimodal neuroimaging measures of underlying neuropathologic processes account for over a third of the explained variance in clinical outcome in a large sample of behaviorally and emotionally dysregulated youth. This may be an important first step toward identifying neurobiological measures with the potential to act as novel targets for early detection and future therapeutic interventions.
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42
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Gadelha A, Coleman J, Breen G, Mazzoti DR, Yonamine CM, Pellegrino R, Ota VK, Belangero SI, Glessner J, Sleiman P, Hakonarson H, Hayashi MAF, Bressan RA. Genome-wide investigation of schizophrenia associated plasma Ndel1 enzyme activity. Schizophr Res 2016; 172:60-7. [PMID: 26851141 DOI: 10.1016/j.schres.2016.01.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/19/2016] [Accepted: 01/23/2016] [Indexed: 10/22/2022]
Abstract
Ndel1 is a DISC1-interacting oligopeptidase that cleaves in vitro neuropeptides as neurotensin and bradykinin, and which has been associated with both neuronal migration and neurite outgrowth. We previously reported that plasma Ndel1 enzyme activity is lower in patients with schizophrenia (SCZ) compared to healthy controls (HCs). To our knowledge, no previous study has investigated the genetic factors associated with the plasma Ndel1 enzyme activity. In the current analyses, samples from 83 SCZ patients and 92 control subjects that were assayed for plasma Ndel1 enzyme activity were genotyped on Illumina Omni Express arrays. A genetic relationship matrix using genome-wide information was then used for ancestry correction, and association statistics were calculated genome-wide. Ndel1 enzyme activity was significantly lower in patients with SCZ (t=4.9; p<0.001) and was found to be associated with CAMK1D, MAGI2, CCDC25, and GABGR3, at a level of suggestive significance (p<10(-6)), independent of the clinical status. Then, we performed a model to investigate the observed differences for case/control measures. 2 SNPs at region 1p22.2 reached the p<10(-7) level. ZFPM2 and MAD1L1 were the only two genes with more than one hit at 10(-6) order of p value. Therefore, Ndel1 enzyme activity is a complex trait influenced by many different genetic variants that may contribute to SCZ physiopathology.
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Affiliation(s)
- Ary Gadelha
- Department of Psychiatry, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, Brazil.
| | - Jonathan Coleman
- Medical Research Council Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Gerome Breen
- Medical Research Council Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry Psychology and Neuroscience, King's College London, London, United Kingdom; National Institute of Health Research Biomedical Research Centre for Mental Health, Maudsley Hospital and Institute of Psychiatry, Psychology and Neuroscience, King's College London, United Kingdom
| | | | - Camila M Yonamine
- Department of Psychiatry, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, Brazil; Department of Pharmacology, UNIFESP/EPM, São Paulo, Brazil
| | - Renata Pellegrino
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, United States
| | - Vanessa Kiyomi Ota
- Department of Psychiatry, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, Brazil; Department of Morphology and Genetics, UNIFESP/EPM, São Paulo, Brazil
| | - Sintia Iole Belangero
- Department of Psychiatry, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, Brazil; Department of Morphology and Genetics, UNIFESP/EPM, São Paulo, Brazil
| | - Joseph Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, United States
| | - Patrick Sleiman
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, United States; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, United States; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | | | - Rodrigo A Bressan
- Department of Psychiatry, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, Brazil
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Lipina TV, Prasad T, Yokomaku D, Luo L, Connor SA, Kawabe H, Wang YT, Brose N, Roder JC, Craig AM. Cognitive Deficits in Calsyntenin-2-deficient Mice Associated with Reduced GABAergic Transmission. Neuropsychopharmacology 2016; 41:802-10. [PMID: 26171716 PMCID: PMC4707826 DOI: 10.1038/npp.2015.206] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 06/05/2015] [Accepted: 07/01/2015] [Indexed: 11/09/2022]
Abstract
Calsyntenin-2 has an evolutionarily conserved role in cognition. In a human genome-wide screen, the CLSTN2 locus was associated with verbal episodic memory, and expression of human calsyntenin-2 rescues the associative learning defect in orthologous Caenorhabditis elegans mutants. Other calsyntenins promote synapse development, calsyntenin-1 selectively of excitatory synapses and calsyntenin-3 of excitatory and inhibitory synapses. We found that targeted deletion of calsyntenin-2 in mice results in a selective reduction in functional inhibitory synapses. Reduced inhibitory transmission was associated with a selective reduction of parvalbumin interneurons in hippocampus and cortex. Clstn2(-/-) mice showed normal behavior in elevated plus maze, forced swim test, and novel object recognition assays. However, Clstn2(-/-) mice were hyperactive in the open field and showed deficits in spatial learning and memory in the Morris water maze and Barnes maze. These results confirm a function for calsyntenin-2 in cognitive performance and indicate an underlying mechanism that involves parvalbumin interneurons and aberrant inhibitory transmission.
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Affiliation(s)
- Tatiana V Lipina
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada,Federal State Budgetary Scientific Institution, Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia
| | - Tuhina Prasad
- Brain Research Centre and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Daisaku Yokomaku
- Brain Research Centre and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Lin Luo
- Brain Research Centre and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Steven A Connor
- Brain Research Centre and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada,Brain Research Centre and Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Hiroshi Kawabe
- Department of Molecular Neurobiology, Max Planck Institute for Experimental Medicine, Göttingen, Germany
| | - Yu Tian Wang
- Brain Research Centre and Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute for Experimental Medicine, Göttingen, Germany
| | - John C Roder
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Ann Marie Craig
- Brain Research Centre and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada,Brain Research Centre, University of British Columbia, Room F149, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada, Tel: +604 822 7283, Fax: +604 822 7299, E-mail:
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Chan MK, Cooper JD, Bot M, Steiner J, Penninx BWJH, Bahn S. Identification of an Immune-Neuroendocrine Biomarker Panel for Detection of Depression: A Joint Effects Statistical Approach. Neuroendocrinology 2016; 103:693-710. [PMID: 26580065 DOI: 10.1159/000442208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/05/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND/AIMS Less than half of depression patients are correctly diagnosed within the primary care setting. Previous proteomic studies have identified numerous immune and neuroendocrine changes in patients. However, few studies have considered the joint effects of biological molecules and their diagnostic potential. Our aim was to develop and validate a diagnostic serum biomarker panel identified through joint effects analysis of multiplex immunoassay profiling data from 1,007 clinical samples. METHODS In stage 1, we conducted a meta-analysis of two independent cohorts of 78 first-/recent-onset drug-naive/drug-free depression patients and 156 controls and applied the 10-fold cross-validation with least absolute shrinkage and selection operator regression to identify an optimal diagnostic prediction model (biomarker panel). In stage 2, we tested the discriminatory performance of this biomarker panel using the naturalistic Netherlands Study of Depression and Anxiety (NESDA) cohort of 468 depression patients and 305 controls. RESULTS An optimal panel of 33 immune-neuroendocrine biomarkers and gender was selected in the meta-analysis. Testing this biomarker-gender panel using the NESDA cohort resulted in a moderate to good performance to differentiate patients from controls (0.69 < AUC < 0.86), particularly the first-episode patients free of chronic non-psychiatric diseases or medications and following incorporation of sociodemographic covariates (0.76 < AUC < 0.92). CONCLUSION Despite the need for additional validation studies, we demonstrated that a blood-based biomarker-sociodemographic panel can detect depression in naturalistic healthcare settings with good discriminatory power. Further refinements of blood biomarker panels aiding in the diagnosis of depression may provide a cost-effective means to increase accuracy of clinical diagnosis within the primary care setting.
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Affiliation(s)
- Man K Chan
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
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45
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Pearlson GD, Liu J, Calhoun VD. An introductory review of parallel independent component analysis (p-ICA) and a guide to applying p-ICA to genetic data and imaging phenotypes to identify disease-associated biological pathways and systems in common complex disorders. Front Genet 2015; 6:276. [PMID: 26442095 PMCID: PMC4561364 DOI: 10.3389/fgene.2015.00276] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/17/2015] [Indexed: 11/26/2022] Open
Abstract
Complex inherited phenotypes, including those for many common medical and psychiatric diseases, are most likely underpinned by multiple genes contributing to interlocking molecular biological processes, along with environmental factors (Owen et al., 2010). Despite this, genotyping strategies for complex, inherited, disease-related phenotypes mostly employ univariate analyses, e.g., genome wide association. Such procedures most often identify isolated risk-related SNPs or loci, not the underlying biological pathways necessary to help guide the development of novel treatment approaches. This article focuses on the multivariate analysis strategy of parallel (i.e., simultaneous combination of SNP and neuroimage information) independent component analysis (p-ICA), which typically yields large clusters of functionally related SNPs statistically correlated with phenotype components, whose overall molecular biologic relevance is inferred subsequently using annotation software suites. Because this is a novel approach, whose details are relatively new to the field we summarize its underlying principles and address conceptual questions regarding interpretation of resulting data and provide practical illustrations of the method.
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Affiliation(s)
- Godfrey D Pearlson
- The Olin Neuropsychiatry Research Center, Institute of Living, Hartford CT, USA ; Department of Neurobiology, Yale School of Medicine, Yale University, New Haven CT, USA ; Department of Psychiatry, Yale School of Medicine, Yale University, New Haven CT, USA
| | - Jingyu Liu
- Department of Electrical and Computer Engineering, and The Mind Research Network, The University of New Mexico, Albuquerque NM, USA
| | - Vince D Calhoun
- Department of Psychiatry, Yale School of Medicine, Yale University, New Haven CT, USA ; Department of Electrical and Computer Engineering, and The Mind Research Network, The University of New Mexico, Albuquerque NM, USA
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Alemany S, Ribasés M, Vilor-Tejedor N, Bustamante M, Sánchez-Mora C, Bosch R, Richarte V, Cormand B, Casas M, Ramos-Quiroga JA, Sunyer J. New suggestive genetic loci and biological pathways for attention function in adult attention-deficit/hyperactivity disorder. Am J Med Genet B Neuropsychiatr Genet 2015; 168:459-470. [PMID: 26174813 DOI: 10.1002/ajmg.b.32341] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 06/22/2015] [Indexed: 11/09/2022]
Abstract
Attention deficit is one of the core symptoms of the attention-deficit/hyperactivity disorder (ADHD). However, the specific genetic variants that may be associated with attention function in adult ADHD remain largely unknown. The present study aimed to identifying SNPs associated with attention function in adult ADHD and tested whether these associations were enriched for specific biological pathways. Commissions, hit-reaction time (HRT), the standard error of HRT (HRTSE), and intraindividual coefficient variability (ICV) of the Conners Continuous Performance Test (CPT-II) were assessed in 479 unmedicated adult ADHD individuals. A Genome-Wide Association Study (GWAS) was conducted for each outcome and, subsequently, gene set enrichment analyses were performed. Although no SNPs reached genome-wide significance (P < 5E-08), 27 loci showed suggestive evidence of association with the CPT outcomes (P < E-05). The most relevant associated SNP was located in the SORCS2 gene (P = 3.65E-07), previously associated with bipolar disorder (BP), Alzheimer disease (AD), and brain structure in elderly individuals. We detected other genes suggested to be involved in synaptic plasticity, cognitive function, neurological and neuropsychiatric disorders, and smoking behavior such as NUAK1, FGF20, NETO1, BTBD9, DLG2, TOP3B, and CHRNB4. Also, several of the pathways nominally associated with the CPT outcomes are relevant for ADHD such as the ubiquitin proteasome, neurodegenerative disorders, axon guidance, and AD amyloid secretase pathways. To our knowledge, this is the first GWAS and pathway analysis of attention function in patients with persistent ADHD. Overall, our findings reinforce the conceptualization of attention function as a potential endophenotype for studying the molecular basis of adult ADHD. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Silvia Alemany
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Marta Ribasés
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Biomedical Network Research Centre on Mental Health (CIBERSAM), Barcelona, Spain.,Psychiatric Genetics Unit, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Natàlia Vilor-Tejedor
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Mariona Bustamante
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain.,Center for Genomic Regulation (CRG), Barcelona, Spain
| | - Cristina Sánchez-Mora
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Biomedical Network Research Centre on Mental Health (CIBERSAM), Barcelona, Spain.,Psychiatric Genetics Unit, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rosa Bosch
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Biomedical Network Research Centre on Mental Health (CIBERSAM), Barcelona, Spain
| | - Vanesa Richarte
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Biomedical Network Research Centre on Mental Health (CIBERSAM), Barcelona, Spain.,Psychiatric Genetics Unit, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Bru Cormand
- Facultat de Biologia, Departament de Genètica, Universitat de Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Catalonia, Spain
| | - Miguel Casas
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Biomedical Network Research Centre on Mental Health (CIBERSAM), Barcelona, Spain.,Psychiatric Genetics Unit, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep A Ramos-Quiroga
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Biomedical Network Research Centre on Mental Health (CIBERSAM), Barcelona, Spain.,Psychiatric Genetics Unit, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jordi Sunyer
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
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Weiner MW, Veitch DP, Aisen PS, Beckett LA, Cairns NJ, Cedarbaum J, Green RC, Harvey D, Jack CR, Jagust W, Luthman J, Morris JC, Petersen RC, Saykin AJ, Shaw L, Shen L, Schwarz A, Toga AW, Trojanowski JQ. 2014 Update of the Alzheimer's Disease Neuroimaging Initiative: A review of papers published since its inception. Alzheimers Dement 2015; 11:e1-120. [PMID: 26073027 PMCID: PMC5469297 DOI: 10.1016/j.jalz.2014.11.001] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/18/2013] [Indexed: 01/18/2023]
Abstract
The Alzheimer's Disease Neuroimaging Initiative (ADNI) is an ongoing, longitudinal, multicenter study designed to develop clinical, imaging, genetic, and biochemical biomarkers for the early detection and tracking of Alzheimer's disease (AD). The initial study, ADNI-1, enrolled 400 subjects with early mild cognitive impairment (MCI), 200 with early AD, and 200 cognitively normal elderly controls. ADNI-1 was extended by a 2-year Grand Opportunities grant in 2009 and by a competitive renewal, ADNI-2, which enrolled an additional 550 participants and will run until 2015. This article reviews all papers published since the inception of the initiative and summarizes the results to the end of 2013. The major accomplishments of ADNI have been as follows: (1) the development of standardized methods for clinical tests, magnetic resonance imaging (MRI), positron emission tomography (PET), and cerebrospinal fluid (CSF) biomarkers in a multicenter setting; (2) elucidation of the patterns and rates of change of imaging and CSF biomarker measurements in control subjects, MCI patients, and AD patients. CSF biomarkers are largely consistent with disease trajectories predicted by β-amyloid cascade (Hardy, J Alzheimer's Dis 2006;9(Suppl 3):151-3) and tau-mediated neurodegeneration hypotheses for AD, whereas brain atrophy and hypometabolism levels show predicted patterns but exhibit differing rates of change depending on region and disease severity; (3) the assessment of alternative methods of diagnostic categorization. Currently, the best classifiers select and combine optimum features from multiple modalities, including MRI, [(18)F]-fluorodeoxyglucose-PET, amyloid PET, CSF biomarkers, and clinical tests; (4) the development of blood biomarkers for AD as potentially noninvasive and low-cost alternatives to CSF biomarkers for AD diagnosis and the assessment of α-syn as an additional biomarker; (5) the development of methods for the early detection of AD. CSF biomarkers, β-amyloid 42 and tau, as well as amyloid PET may reflect the earliest steps in AD pathology in mildly symptomatic or even nonsymptomatic subjects and are leading candidates for the detection of AD in its preclinical stages; (6) the improvement of clinical trial efficiency through the identification of subjects most likely to undergo imminent future clinical decline and the use of more sensitive outcome measures to reduce sample sizes. Multimodal methods incorporating APOE status and longitudinal MRI proved most highly predictive of future decline. Refinements of clinical tests used as outcome measures such as clinical dementia rating-sum of boxes further reduced sample sizes; (7) the pioneering of genome-wide association studies that leverage quantitative imaging and biomarker phenotypes, including longitudinal data, to confirm recently identified loci, CR1, CLU, and PICALM and to identify novel AD risk loci; (8) worldwide impact through the establishment of ADNI-like programs in Japan, Australia, Argentina, Taiwan, China, Korea, Europe, and Italy; (9) understanding the biology and pathobiology of normal aging, MCI, and AD through integration of ADNI biomarker and clinical data to stimulate research that will resolve controversies about competing hypotheses on the etiopathogenesis of AD, thereby advancing efforts to find disease-modifying drugs for AD; and (10) the establishment of infrastructure to allow sharing of all raw and processed data without embargo to interested scientific investigators throughout the world.
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Affiliation(s)
- Michael W Weiner
- Department of Veterans Affairs Medical Center, Center for Imaging of Neurodegenerative Diseases, San Francisco, CA, USA; Department of Radiology, University of California, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, CA, USA.
| | - Dallas P Veitch
- Department of Veterans Affairs Medical Center, Center for Imaging of Neurodegenerative Diseases, San Francisco, CA, USA
| | - Paul S Aisen
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Laurel A Beckett
- Division of Biostatistics, Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Nigel J Cairns
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, Saint Louis, MO, USA; Department of Neurology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jesse Cedarbaum
- Neurology Early Clinical Development, Biogen Idec, Cambridge, MA, USA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Danielle Harvey
- Division of Biostatistics, Department of Public Health Sciences, University of California, Davis, CA, USA
| | | | - William Jagust
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
| | - Johan Luthman
- Neuroscience Clinical Development, Neuroscience & General Medicine Product Creation Unit, Eisai Inc., Philadelphia, PA, USA
| | - John C Morris
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | | | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Leslie Shaw
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Li Shen
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Adam Schwarz
- Tailored Therapeutics, Eli Lilly and Company, Indianapolis, IN, USA
| | - Arthur W Toga
- Laboratory of Neuroimaging, Institute of Neuroimaging and Informatics, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - John Q Trojanowski
- Institute on Aging, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Alzheimer's Disease Core Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Udall Parkinson's Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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48
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Genetic background of extreme violent behavior. Mol Psychiatry 2015; 20:786-92. [PMID: 25349169 PMCID: PMC4776744 DOI: 10.1038/mp.2014.130] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/25/2014] [Accepted: 08/28/2014] [Indexed: 01/19/2023]
Abstract
In developed countries, the majority of all violent crime is committed by a small group of antisocial recidivistic offenders, but no genes have been shown to contribute to recidivistic violent offending or severe violent behavior, such as homicide. Our results, from two independent cohorts of Finnish prisoners, revealed that a monoamine oxidase A (MAOA) low-activity genotype (contributing to low dopamine turnover rate) as well as the CDH13 gene (coding for neuronal membrane adhesion protein) are associated with extremely violent behavior (at least 10 committed homicides, attempted homicides or batteries). No substantial signal was observed for either MAOA or CDH13 among non-violent offenders, indicating that findings were specific for violent offending, and not largely attributable to substance abuse or antisocial personality disorder. These results indicate both low monoamine metabolism and neuronal membrane dysfunction as plausible factors in the etiology of extreme criminal violent behavior, and imply that at least about 5-10% of all severe violent crime in Finland is attributable to the aforementioned MAOA and CDH13 genotypes.
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49
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Lal D, Ruppert AK, Trucks H, Schulz H, de Kovel CG, Kasteleijn-Nolst Trenité D, Sonsma ACM, Koeleman BP, Lindhout D, Weber YG, Lerche H, Kapser C, Schankin CJ, Kunz WS, Surges R, Elger CE, Gaus V, Schmitz B, Helbig I, Muhle H, Stephani U, Klein KM, Rosenow F, Neubauer BA, Reinthaler EM, Zimprich F, Feucht M, Møller RS, Hjalgrim H, De Jonghe P, Suls A, Lieb W, Franke A, Strauch K, Gieger C, Schurmann C, Schminke U, Nürnberg P, Sander T. Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies. PLoS Genet 2015; 11:e1005226. [PMID: 25950944 PMCID: PMC4423931 DOI: 10.1371/journal.pgen.1005226] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/16/2015] [Indexed: 01/06/2023] Open
Abstract
Genetic generalised epilepsy (GGE) is the most common form of genetic epilepsy, accounting for 20% of all epilepsies. Genomic copy number variations (CNVs) constitute important genetic risk factors of common GGE syndromes. In our present genome-wide burden analysis, large (≥ 400 kb) and rare (< 1%) autosomal microdeletions with high calling confidence (≥ 200 markers) were assessed by the Affymetrix SNP 6.0 array in European case-control cohorts of 1,366 GGE patients and 5,234 ancestry-matched controls. We aimed to: 1) assess the microdeletion burden in common GGE syndromes, 2) estimate the relative contribution of recurrent microdeletions at genomic rearrangement hotspots and non-recurrent microdeletions, and 3) identify potential candidate genes for GGE. We found a significant excess of microdeletions in 7.3% of GGE patients compared to 4.0% in controls (P = 1.8 x 10-7; OR = 1.9). Recurrent microdeletions at seven known genomic hotspots accounted for 36.9% of all microdeletions identified in the GGE cohort and showed a 7.5-fold increased burden (P = 2.6 x 10-17) relative to controls. Microdeletions affecting either a gene previously implicated in neurodevelopmental disorders (P = 8.0 x 10-18, OR = 4.6) or an evolutionarily conserved brain-expressed gene related to autism spectrum disorder (P = 1.3 x 10-12, OR = 4.1) were significantly enriched in the GGE patients. Microdeletions found only in GGE patients harboured a high proportion of genes previously associated with epilepsy and neuropsychiatric disorders (NRXN1, RBFOX1, PCDH7, KCNA2, EPM2A, RORB, PLCB1). Our results demonstrate that the significantly increased burden of large and rare microdeletions in GGE patients is largely confined to recurrent hotspot microdeletions and microdeletions affecting neurodevelopmental genes, suggesting a strong impact of fundamental neurodevelopmental processes in the pathogenesis of common GGE syndromes.
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Affiliation(s)
- Dennis Lal
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany
- EPICURE Consortium
| | - Ann-Kathrin Ruppert
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Holger Trucks
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Herbert Schulz
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Carolien G. de Kovel
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Anja C. M. Sonsma
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bobby P. Koeleman
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dick Lindhout
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
- SEIN Epilepsy Institute in the Netherlands, Hoofddorp, The Netherlands
| | - Yvonne G. Weber
- EPICURE Consortium
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Holger Lerche
- EPICURE Consortium
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Claudia Kapser
- EPICURE Consortium
- Department of Neurology, University of Munich Hospital—Großhadern, Munich, Germany
| | - Christoph J. Schankin
- EPICURE Consortium
- Department of Neurology, University of Munich Hospital—Großhadern, Munich, Germany
| | - Wolfram S. Kunz
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Rainer Surges
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Christian E. Elger
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Verena Gaus
- EPICURE Consortium
- Department of Neurology, Charité University Medicine, Campus Virchow Clinic, Berlin, Germany
| | - Bettina Schmitz
- EPICURE Consortium
- Department of Neurology, Charité University Medicine, Campus Virchow Clinic, Berlin, Germany
- Department of Neurology, Vivantes Humboldt-Klinikum, Berlin, Germany
| | - Ingo Helbig
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Hiltrud Muhle
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Ulrich Stephani
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Karl M. Klein
- EPICURE Consortium
- Epilepsy-Center Hessen, Department of Neurology, Philipps-University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhein-Main, Department of Neurology, Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany
| | - Felix Rosenow
- EPICURE Consortium
- Epilepsy-Center Hessen, Department of Neurology, Philipps-University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhein-Main, Department of Neurology, Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany
| | - Bernd A. Neubauer
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany
| | - Eva M. Reinthaler
- EPICURE Consortium
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Fritz Zimprich
- EPICURE Consortium
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Martha Feucht
- EPICURE Consortium
- Department of Pediatrics and Neonatology, Medical University of Vienna, Vienna, Austria
| | - Rikke S. Møller
- EPICURE Consortium
- Department of Neurology, Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Helle Hjalgrim
- EPICURE Consortium
- Department of Neurology, Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Peter De Jonghe
- EPICURE Consortium
- Neurogenetics Group, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Arvid Suls
- EPICURE Consortium
- Neurogenetics Group, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Christian Albrechts University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, and Chair of Genetic Epidemiology, Ludwig-Maximilians-University, Munich, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Claudia Schurmann
- Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University, Greifswald, Germany
| | - Ulf Schminke
- Department of Neurology, University Medicine Greifswald, Ernst Moritz Arndt University, Greifswald, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- EPICURE Consortium
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | | | - Thomas Sander
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
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Yang T, Wang J, Sun Q, Hibar DP, Jahanshad N, Liu L, Wang Y, Zhan L, Thompson PM, Ye J. Detecting Genetic Risk Factors for Alzheimer's Disease in Whole Genome Sequence Data via Lasso Screening. PROCEEDINGS. IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING 2015; 2015:985-989. [PMID: 26413209 DOI: 10.1109/isbi.2015.7164036] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Genetic factors play a key role in Alzheimer's disease (AD). The Alzheimer's Disease Neuroimaging Initiative (ADNI) whole genome sequence (WGS) data offers new power to investigate mechanisms of AD by combining entire genome sequences with neuroimaging and clinical data. Here we explore the ADNI WGS SNP (single nucleotide polymorphism) data in depth and extract approximately six million valid SNP features. We investigate imaging genetics associations using Lasso regression-a widely used sparse learning technique. To solve the large-scale Lasso problem more efficiently, we employ a highly efficient screening rule for Lasso-called dual polytope projections (DPP)-to remove irrelevant features from the optimization problem. Experiments demonstrate that the DPP can effectively identify irrelevant features and leads to a 400× speedup. This allows us for the first time to run the compute-intensive model selection procedure called stability selection to rank SNPs that may affect the brain and AD risk.
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Affiliation(s)
- Tao Yang
- Dept. of Computer Science and Engineering, Arizona State Univ., Tempe, AZ, USA ; Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State Univ., Tempe, AZ, USA
| | - Jie Wang
- Dept. of Computer Science and Engineering, Arizona State Univ., Tempe, AZ, USA ; Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State Univ., Tempe, AZ, USA
| | - Qian Sun
- Dept. of Computer Science and Engineering, Arizona State Univ., Tempe, AZ, USA ; Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State Univ., Tempe, AZ, USA
| | - Derrek P Hibar
- Imaging Genetics Center, Keck School of Medicine, Univ. of Southern California, Los Angeles, CA, USA
| | - Neda Jahanshad
- Imaging Genetics Center, Keck School of Medicine, Univ. of Southern California, Los Angeles, CA, USA
| | - Li Liu
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State Univ., Tempe, AZ, USA
| | - Yalin Wang
- Dept. of Computer Science and Engineering, Arizona State Univ., Tempe, AZ, USA
| | - Liang Zhan
- Imaging Genetics Center, Keck School of Medicine, Univ. of Southern California, Los Angeles, CA, USA
| | - Paul M Thompson
- Imaging Genetics Center, Keck School of Medicine, Univ. of Southern California, Los Angeles, CA, USA
| | - Jieping Ye
- Dept. of Computational Medicine and Bioinformatics, Univ. of Michigan, Ann Arbor, MI, USA ; Dept. of Electrical Engineering and Computer Science, Univ. of Michigan, Ann Arbor, MI, USA
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