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Family-Based Analysis of Genetic Variation

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Supplementary Online Content van Winkel R; and Genetic Risk and Outcome of Psychosis (GROUP) Investigators. Family-based analysis of genetic variation underlying psychosis-inducing effects of cannabis: sibling analysis and proband follow-up [published online November 1, 2010]. Arch Gen Psychiatry. doi:10.1001/archgenpsychiatry.2010.152. eTable. Quality control of investigated genetic markers. This supplementary material has been provided by the authors to give readers additional information about their work. © 2010 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/26/2021 eTable. Quality control of investigated genetic markers. Gene dbSNP# HWE (p‐value) Call rate* Included COMT rs4680 0.25 98.2 Yes rs737865 0.02 98.4 Yes rs4818 0.21 95.9 Yes rs6269 0.29 97.9 Yes rs4633 0.22 98.1 Yes rs165815 0.06 97.9 Yes rs174696 0.001 97.5 Yes rs2097603 ⎯ No Call No rs165599 ⎯ No Call No ANKK1 rs1800497 0.93 97.2 Yes DRD1 rs4532 0.81 97.4 Yes rs265981 0.32 95.2 Yes rs1799961 No variance 98.7 No DRD2 rs1799732 0.65 97.7 Yes rs1799978 0.90 80.3 No rs1079597 <.0001 72.7 No rs1800498 0.94 97.5 Yes rs6277 0.19 97.5 Yes DRD3 rs6280 0.86 97.3 Yes rs324029 0.87 97.7 Yes rs324030 0.91 98.6 Yes rs2134655 0.63 97.4 Yes rs10934254 0.85 91.5 Yes rs1800828 0.70 97.8 Yes rs10934256 ⎯ No Call No DRD4 rs1800955 <.0001 67.3 No rs747302 ⎯ No Call No SLC6A3 rs3756450 0.49 98.0 Yes rs2652510 0.29 98.3 Yes rs28362317 0.54 95.8 Yes rs2550956 <.0001 96.7 No rs11564752 <.0001 84.1 No rs1316830 0.48 97.4 Yes rs464049 0.45 96.1 Yes rs27027 0.32 97.7 Yes rs403636 0.25 97.4 Yes rs12516948 0.45 98.3 Yes rs6347 0.62 51.2 No rs456082 0.96 98.0 Yes rs463379 0.99 97.5 Yes PPP1R1B rs4795390 0.40 96.7 Yes rs879606 0.23 98.6 Yes rs11651497 0.84 97.9 Yes rs907094 0.82 98.0 Yes rs3764353 0.82 97.5 Yes © 2010 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/26/2021 rs3764352 0.88 98.0 Yes rs3794712 ⎯ No Call No ADRA2C a2CDel322‐325AR ⎯ No Call No GABRA6 rs3219151 0.82 98.0 Yes BDNF rs6265 0.46 98.0 Yes rs988748 0.98 98.3 Yes GAD1 rs12185692 0.71 97.5 Yes rs2241165 0.27 98.0 Yes rs2058725 0.20 98.3 Yes rs769407 0.96 84.5 No rs3791851 0.79 98.2 Yes rs379850 0.83 95.9 Yes P2RX7 rs2230912 0.21 98.3 Yes MTHFR rs1801133 0.07 98.8 Yes rs1801131 0.04 97.9 Yes CNR1 rs2023239 <.0001 97.7 No rs806379 0.04 96.4 Yes rs1535255 0.95 98.2 Yes rs6454674 0.84 97.3 Yes rs806308 0.86 97.7 Yes rs806377 0.004 98.3 Yes rs1049353 0.27 97.8 Yes rs6928499 0.80 97.1 Yes RGS4 rs10917670 0.28 98.4 Yes rs2661319 0.24 97.4 Yes rs1507754 0.10 98.3 Yes rs951436 0.52 97.1 Yes rs951439 0.55 89.4 No NRG1 rs35753505 0.70 91.6 Yes rs6994992 0.31 87.4 No snp8nrg221132 0.42 93.6 Yes snp8nrg241930 0.76 97.9 Yes snp8nrg433e1006 ⎯ No Call No rs4268090 0.11 97.3 Yes rs4298458 0.05 97.3 Yes rs4452759 <.0001 20.2 No rs4733263 0.10 96.8 Yes rs4476964 0.71 97.4 Yes DTNBP1 rs1011313 0.85 97.4 Yes rs909706 0.78 97.9 Yes rs1018381 0.40 98.8 Yes rs2619539 0.58 97.8 Yes rs2619528 0.53 96.4 Yes rs3213207 0.12 97.1 Yes rs760761 0.33 97.8 Yes rs2619522 0.31 96.4 Yes rs2619538 0.44 98.5 Yes PIP5K2A rs10828317 0.41 98.3 Yes © 2010 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/26/2021 G72/DAOA rs2391191 0.47 97.7 Yes rs3918342 0.37 98.0 Yes rs746187 0.97 98.6 Yes rs3916967 0.08 85.1 No rs778293 0.44 97.7 Yes rs1421292 0.30 96.4 Yes DISC1 hCV219779 0.45 97.5 Yes rs821597 0.19 98.3 Yes rs821616 0.81 92.1 Yes rs1572899 0.89 97.8 Yes rs999710 0.15 97.9 Yes HT2A rs6311 0.53 97.7 Yes rs6313 0.60 98.0 Yes rs6314 0.07 96.8 Yes AKT1 rs3803300 0.26 93.2 Yes rs1130214 0.46 96.2 Yes rs3730358 0.86 97.3 Yes rs1130233 0.47 97.7 Yes rs2494732 0.43 98.3 Yes rs2498784 0.41 97.9 Yes rs10149785 0.07 86.4 No LRRTM1 rs673871 0.74 97.0 Yes rs1446109 0.16 97.8 Yes rs1007371 0.43 98.0 Yes rs723524 0.46 98.0 Yes FGF2 rs12506776 0.06 98.3 Yes rs7700205 0.17 98.6 Yes rs308420 0.12 97.9 Yes rs10452197 0.96 97.5 Yes rs308428 0.30 98.7 Yes rs308439 0.81 98.8 Yes rs308379 0.43 97.5 Yes FGFR1 rs3925 0.38 97.5 Yes rs6987534 0.24 97.3 Yes rs6996321 0.72 98.2 Yes rs7012413 0.19 97.7 Yes rs2978073 0.86 97.8 Yes rs4733946 0.17 98.8 Yes rs7825208 0.44 97.8 Yes rs2288696 0.03 98.2 Yes GPM6A rs10520303 0.18 96.2 Yes PRODH rs2008720 0.64 51.1 No rs450046 0.67 97.9 Yes rs372055 0.20 93.7 Yes TBX1 rs5746832 0.40 97.2 Yes rs2269726 0.74 98.3 Yes SLC18A2 rs363393 0.75 98.8 Yes rs363338 0.96 96.9 Yes © 2010 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/26/2021 rs3633343 ⎯ No Call No rs363227 0.24 98.0 Yes rs929493 0.32 97.9 Yes GRM3 rs187993 0.87 97.4 Yes rs917071 0.36 97.9 Yes rs6465084 0.40 97.1 Yes rs2228595 0.65 96.2 Yes rs1468412 0.19 97.9 Yes rs274622 0.08 98.7 Yes FKBP5 rs3800373 0.30 96.2 Yes rs992105 0.41 98.8 Yes rs9296158 0.23 98.5 Yes rs737054 0.24 96.1 Yes rs133894 0.93 98.5 Yes rs9470080 0.35 97.7 Yes rs4713916 0.10 97.2 Yes NPY rs3037354 0.41 98.9 Yes rs17149106 0.39 98.2 Yes rs16139 0.90 97.9 Yes rs16147 ⎯ No Call No rs5573 0.04 97.5 Yes rs5574 0.09 97.7 Yes NOS1 rs2682826 0.04 97.8 Yes NQO1 rs1800566 0.72 98.3 Yes RGS2 rs4606 0.23 98.7 Yes CHRM3 rs3738435 0.20 98.8 Yes ROBO1 rs1455832 0.30 98.0 Yes GST‐1 rs4925 0.32 98.0 Yes GST‐2 rs2297235 ⎯ No Call No MTR rs1805087 0.83 98.1 Yes MTRR rs1801394 0.03 97.9 Yes DNMT3B rs2424913 0.25 97.7 Yes rs406193 0.13 98.5 Yes EHMT1 rs1577103 0.17 98.3 Yes EHMT2 rs535586 0.15 98.2 Yes PRDM2 rs2235515 0.56 96.9 Yes * If a SNP's probe intensity values do not pass the detection filter score (DS) or the Relative Allele Scores (RAS) fall outside the boundaries of the statistical model then the SNP is assigned a "No Call" value HWE: Hardy‐Weinberg Equilibrium © 2010 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/26/2021.
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  • Machine Learning Classification of ADHD and HC by Multimodal Serotonergic Data

    Machine Learning Classification of ADHD and HC by Multimodal Serotonergic Data

    Kautzky et al. Translational Psychiatry (2020) 10:104 https://doi.org/10.1038/s41398-020-0781-2 Translational Psychiatry ARTICLE Open Access Machine learning classification of ADHD and HC by multimodal serotonergic data A. Kautzky1,T.Vanicek1,C.Philippe2,G.S.Kranz 1,3,W.Wadsak 2,4,M.Mitterhauser2,5, A. Hartmann6,A.Hahn 1, M. Hacker2,D.Rujescu6,S.Kasper1 and R. Lanzenberger 1 Abstract Serotonin neurotransmission may impact the etiology and pathology of attention-deficit and hyperactivity disorder (ADHD), partly mediated through single nucleotide polymorphisms (SNPs). We propose a multivariate, genetic and positron emission tomography (PET) imaging classification model for ADHD and healthy controls (HC). Sixteen patients with ADHD and 22 HC were scanned by PET to measure serotonin transporter (SERT‘) binding potential with [11C] DASB. All subjects were genotyped for thirty SNPs within the HTR1A, HTR1B, HTR2A and TPH2 genes. Cortical and subcortical regions of interest (ROI) were defined and random forest (RF) machine learning was used for feature selection and classification in a five-fold cross-validation model with ten repeats. Variable selection highlighted the ROI posterior cingulate gyrus, cuneus, precuneus, pre-, para- and postcentral gyri as well as the SNPs HTR2A rs1328684 and rs6311 and HTR1B rs130058 as most discriminative between ADHD and HC status. The mean accuracy for the validation sets across repeats was 0.82 (±0.09) with balanced sensitivity and specificity of 0.75 and 0.86, respectively. With a prediction accuracy above 0.8, the findings underlying the proposed model advocate the relevance of the SERT as well as the HTR1B and HTR2A genes in ADHD and hint towards disease-specific effects.