The Philadelphia Neurodevelopmental Cohort: A publicly available resource for the study of normal and abnormal brain development in youth

“GOASSESS was developed from a modified version of the Kiddie-Schedule for Affective Disorders and Schizophrenia (Kaufman et al., 1997).”

“The PNC is a resource that responds to a paradigm shift in the field of psychiatric neuroscience, where major mental illnesses are increasingly conceptualized as disorders of development (Insel, 2010; Insel, 2009; Casey et al., 2014; Paus et al., 2008).”

“As previously emphasized (Biswal et al., 2010; Gorgolewski et al., 2013; Mennes et al., 2012; Milham, 2012; Nooner et al., 2012; Bis et al., 2012; Stein et al., 2012), large publicly available datasets are a prerequisite for the collaboration necessary to gain traction towards understanding complex…”

“Genotyping procedures are not discussed here, but the genotyping pipeline used at CAG has been previously described in detail (14,15) and further information can be accessed at www.”

“…assessment, cognitive testing, and imaging procedures is provided in PNC manuscripts that have used these data types (Satterthwaite et al., 2012a; Satterthwaite et al., 2013a; Satterthwaite et al., in press; Satterthwaite et al., 2014b; Satterthwaite et al., 2014c; Roalf et al., 2014;…”

“The PNC is a resource that responds to a paradigm shift in the field of psychiatric neuroscience, where major mental illnesses are increasingly conceptualized as disorders of development (Insel, 2010; Insel, 2009; Casey et al., 2014; Paus et al., 2008).”

“Genotyping procedures are not discussed here, but the genotyping pipeline used at CAG has been previously described in detail (Pinto et al., 2010; Glessner et al., 2009) and further information can be accessed at www.”

“Further information regarding clinical assessment, cognitive testing, and imaging procedures is provided in PNC manuscripts that have used these data types (Satterthwaite et al., 2012a; Satterthwaite et al., 2013a; Satterthwaite et al., in press; Satterthwaite et al., 2014b; Satterthwaite et al., 2014c; Roalf et al.,…”

“…information regarding clinical assessment, cognitive testing, and imaging procedures is provided in PNC manuscripts that have used these data types (Satterthwaite et al., 2012a; Satterthwaite et al., 2013a; Satterthwaite et al., in press; Satterthwaite et al., 2014b; Satterthwaite et al.,…”

“As described in detail elsewhere (Mailman et al., 2007), dbGaP was created to be a general repository for sharing genetic and phenotypic data from large-scale studies in a secure manner.”

“Individuals with a variety of clinical and subclinical psychiatric symptoms were included in the PNC dataset (57), potentially introducing noise to the relationship between age and differentiation (10-12).”

“Similar improvements were observed across other common performance metrics (e.g., Spearman’s ρ , root mean squared error, coefficient of determination, Supplementary Tables S2 - S4), as well as for prediction of IQ in an independent cohort of youth in the Philadelphia Neurodevelopmental Cohort ( Satterthwaite et al.,…”

“The PNC was designed to characterize the interactions among brain imaging, behavior, and genetics in a diverse sample of adolescents [33].”

“1): HCP-D [31] ( n = 509; 271 females; age 8–21 years), PNC [33, 36] ( n = 1,159; 623 females; age 8–23 years), and HBN [32] ( n = 1,159; 472 females; age 5– 21 years) [31-34 , 36].”

“Recruitment procedures, sample characteristics, clinical, cognitive, and imaging protocols are described in detail by Satterthwaite et al (2016).”

“The PNC is a community-based sample of 8–21 year-olds designed to integrate multimodal neuroimaging, cognitive and clinical phenotypes, and genetics in order to elucidate the relationship be-tween neurodevelopment and psychiatric disorders (Satterthwaite et al. 2016).”

“While we also demonstrated the utility of our approach to predict a small number of additional phenotypes from HCP, and to also predict IQ using data from the Philadelphia Neurodevelopmental Cohort, further testing of the robustness of our approach to other datasets – including those acquired without harmonized acquis…”

“The [12].”

“3 compares the connectivity matrices obtained with Pearson’s r (i.e., correlation matrix) and the concurrence coefficient (i.e., concurrence matrix) on a version of the Philadelphia Neurodevelopmental Cohort dataset [39] that was pre-processed as in prior work [40].”

“The dataset utilized in this investigation originates from the Philadelphia Neurodevelopmental Cohort[13-14], a significant joint endeavor in applied genomics between the Children’s Hospital of Philadelphia and the University of Pennsylvania’s Brain Behavioral Laboratory.”

“…Understanding of Recovery after Trauma (AURORA) study (McLean et al., 2020), the Philadelphia Neurodevelopmental Cohort (PNC) (Calkins et al., 2015, Satterthwaite et al., 2016), the Tulsa 1000 study (Victor et al., 2018), and the Texas Resilience Against Depression (T-RAD) (Trivedi et al., 2020)…”

“We selected 39 summary scores from cognitive tasks from the PNC dataset (Satterthwaite et al., 2016; Gur et al., 2010; Roalf et al., 2014).”

“We conducted standard quality control and 238 imputation, excluding SNPs with call rate <95%, minor allele frequency <5%, Hardy-Weinberg 239 equilibrium p<1*10 (32,39).”

“; https://doi.org/10.1101/2020.10.22.20217596doi: medRxiv preprint 5 (Satterthwaite et al., 2016).”

“Meanwhile, researchers argued that for patients with MDD and PTSD, the cognitive control regions, including DLPFC and inferior frontal gyrus (IFG), presented decreased connectivity with amygdala (Satterthwaite et al., 2016).”

“It is available in the dbGaP database[4], and contains resting-state fMRI for children aged from 8 to 22 years.”

“Raw neuroimaging scans, neuropsychological assessments, genotypes, and demographic information collected by the PNC study were obtained from dbGAP [43].”

“The permutation test is perhaps the most widely used nonparametric test procedure in sciences [8,19,21,24,27].”

“For both datasets, 268 timecourses of fMRI data were extracted using a whole-brain, functional atlas (Shen et al., 2013).”