Humanht 12 v3

Expression, genotypes, and clinical phenotypes were acquired via dbGaP Project #5358 (dbGaP accession phs000703). Expression levels had been determined using Illumina HumanHT-12-v3 in RNA from whole blood. We considered variables recorded in pht003672: age (phv00197199), gender (phv00197207), hypercholesterolemia (phv00197204), smoking (phv00197208), number of diseased vessels (phv00197295), CAD Index (phv00197202) and history of myocardial infarction (phv00197212). Approximating the definition of CAD used in the CARDIoGRAMplusC4D Consortium GWAS by Nikpay et al., we defined CAD as history of myocardial infarction and/or vessel occlusion >50% (CAD Index). We restricted analysis to Caucasians (race (phv00197206)) for sample size considerations (862 Caucasians; 259 African Americans). The approach developed here can be extended to other ethnic groups as these datasets become available. Data access was approved by the Ohio State University IRB (Protocol #2013H0096).

Gene expression of abdominal fat samples in 825 individuals were analyzed with the Illumina Human HT-12 V3 (Illumina, Inc., San Diego, CA, USA) for the Muther study, as described previously.^{29 (link)} In all, 586 individuals were analyzed for expression association with the top metabolite using a random intercept linear regression including age, BMI, metabolite batch, expression batch and family relatedness.

Expression data, genotypes, and clinical phenotypes were acquired from CATHeritization GENetics (CATHGEN) via dbGaP Project #5358 (dbGaP accession number phs0000703 on 25 March 2015). Expression levels had been determined using Illumina HumanHT-12 v3 in RNA from whole blood at the time of catheterization and recruitment to the study. We considered age (phv00197199), gender (phv00197207), and race (phv00197206) as additional covariates in our models recorded in pht003672. Myocardial infarction (MI), defined by a previous recorded history of MI (phv00197212) or a non-zero CAD index (phv00197202) recorded in pht003672, was used as a phenotype/outcome variable. CAD index was used in addition to previous history of MI to define cases because of a large number of missing values regarding MI history. Based on work by both Kitsios et al. and Nikpay et al., we anticipate similar results for cases defined solely by MI status and those defined by CAD index [37 (link)–39 (link)]. Hypercholesterolemia (phv00197204) recorded in pht003672 was also used as a phenotype/outcome variable. Our access of this study was approved by the Ohio State University IRB (Protocol #2013H0096).

We obtained postmortem cortex transcriptome data from Jaffe et al. [28 (link)] (GSE60190) and compared the gene expression of the ED and OCD patients to that of a healthy control. GSE60190 contains normalized Illumina HumanHT-12 v3 (San Diego, CA, USA) microarray data collected on postmortem dorsolateral prefrontal cortexes. The acquisition and process of data from the case and control were performed similarly. We applied limma [33 (link)] on this transcriptome data to identify the genes that were significantly dysregulated in the cortex of patients with ED or OCD. We first fit a linear model with the following design, which controlled all the provided covariates and compared the ED and OCD groups to the control:
Then, we computed empirical Bayesian statistics for comparison between the ED and control groups as well as between the OCD and control groups. We extracted all the genes with a Benjamini–Hochberg adjusted p-value < 0.05 as the Differentially Expressed Genes (DEGs).

Whole genome-wide expression profiling was done using HumanWG-6 v3.0 and HumanHT-12 v3 direct hybridization assay (Illumina, San Diego, CA) in 2 batches. The HumanWG-6 Bead Chip contains >48,000 probes, while HumanHT-12 chip contains the same panel of probes targeting more than 25,000 (human) genes from Reference Sequence (RefSeq) and UniGene database, from the National Center for Biotechnology Information (NCBI); but the later chip provides higher throughput processing of 12 samples per chip. In the present study a total of 29 tumour samples, including 12 Early-onset tumours (ET), from patients having age ≤40 years, and 17 Late-onset tumours (LT), from patients having age ≥55 years, along with 9 distant normal specimens as controls were used for gene expression profiling. Five hundred nanograms of total RNA was converted to complementary DNA (cDNA), followed by an in vitro transcription step to generate labeled complementary RNA(cRNA) using the ‘Ambion Illumina Total Prep RNA Amplification Kit’ (Ambion, Austin, TX) as per manufacturer’s instructions. The labeled cRNA was hybridized to bead chip array and washed following manufacturer’s protocols, which was scanned by ‘Illumina Bead Array Reader, to obtain the raw data. The expression profiles of 29 cases and 9 controls have been deposited in NCBI’s Gene Expression Omnibus (GEO) with GSE accession number GSE 89116.