Key words: the ABCD cohort; family relatedness; multi-level block permutation; whole-brain voxel-wise mediation analysis; random intercept cross-lagged panel model (RI-CLPM).
Data and Code of paper:
Shen et al. What is the Link between Attention-Deficit/Hyperactivity Disorder and Sleep Disturbance? A multimodal examination of longitudinal relationships and brain structure using large-scale population-based cohorts. Biological Psychiatry, 2020. https://doi.org/10.1016/j.biopsych.2020.03.010 (in press)
NOTE
- Some codes were adapted from others. Clear copyright and reference was stated in the relevant scripts.
- Per the data accessing policy of the GRIP (http://www.gripinfo.ca/Grip/Public/www/QuoiNeuf/en/faitssaillants.asp?langue=en),
the QLSCD data could be used only after approval. Therefore, the QLSCD data in this folder are not allowed to be shared to anyone else. - Per the data accessing policy of the NDA agreement, the usage of the ABCD data needs the approval by NIMH. The ABCD cohort Release v1.0 (DOI: 10.15154/1460410) was used in this study.
- The GMV file was preprocessed by a PhD student in our group, Mr Jingnan Du using the pipeline descripted in the Method section of the main text.
- If the data and codes are used in your work, please cite the above reference, namely Shen et al. 2020.
SUMMARY （Matlab2018b; MPlus; R3.5.1; PALM:https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM; KING:http://people.virginia.edu/~wc9c/KING/）
Step 1: Cross-lagged Analysis between ADHD symptoms and sleep disturbances.
Step 1.1: the RI-CLPM analysis of the QLSCD sample; (S1_1_RI-CLPM in QLSCD.inp);
Step 1.2: the CLPM analysis of the ABCD sample:
Step 1.2.1: define the multi-level blocks according to the self-reported family relatedness provided by a questionnaire
(acspsw02.txt) in the ABCD data release v1, and generate the block permuted sample by calling the PALM function
(S1_2_1_EBforCLPM_questionnaire.m);
Step 1.2.2: define the multi-level blocks by the genetic kinship estimated using the KING software and generate the permuted
sample ( S1_2_2_EBforCLPM_genetic.m);
Step 1.2.3 CLPM by the questionnaire-defined multi-level block permutation (S1_2_3_CLPM in ABCD_questionnaire.R)
Step 1.2.4 CLPM by the genetic-defined multi-level block permutation (S1_2_4_CLPM in ABCD_gene.R)
Step 1.2.5 meta-analysis of the cross-lagged path coefficients among the data collection sites in ABCD (S1_2_5_Meta-analysis
of CLPM in ABCD.R)
Step 2: Whole-brain voxel-wise association analysis between GMV and sleep/ADHD with multi-level block permutation
(S2_MRI_analysis_with_block_permutation.m)
Step 3: Mediation analysis of GMV-->ADHD-->Sleep; Analysis of ROI; and Exporatory analysis of the whole brain voxels by using the 3M toolboxl (S3_Mediation_overlapping_clusters.m).
Step 4: Transcriptomic analysis
Step 4.1 Preprocessing of the Allen Brain Gene expression (S4_1_AHBA_datapreprocess.m);
Step 4.2 Extracting the t-stats of the mediation for each coordinate as an averaged value within a small volume centered at each
tissue location (S4_2_mediation_t_value_extract.m);
Step 4.3 Identifying gene associations by the partial least squared regression (S4_3_PLSregression.m).
Contact:
Qiang Luo, PhD, Visiting Fellow at the Clare Hall, Cambridge
Associate Principal Investigator
Institute of Science and Technology for Brain-Inspired Intelligence (ISTBI)
Fudan University
Email: [email protected]; [email protected]
Office Phone: 86-21-65648454
https://sites.google.com/site/qluochina/
http://homepage.fudan.edu.cn/qiangluo/
Team Members:
Chun Shen, MSc, [email protected]
Jingnan Du, BA, [email protected]
Xingzhong Zhao, BA, [email protected]
The current version was relesed on 22 Mar 2020.
Citation of this package: Shen et al. What is the Link between Attention-Deficit/Hyperactivity Disorder and Sleep Disturbance? A multimodal examination of longitudinal relationships and brain structure using large-scale population-based cohorts. Biological Psychiatry, 2020. https://doi.org/10.1016/j.biopsych.2020.03.010 (in press)