Granisetron

The effect of different background correction methods on reproducibility was assessed using data from 20 pairs of duplicate samples that were part of a previously published study of methylation in 891 infant whole blood samples (12 (link)). As part of this study, duplicate samples were located on separate 96 well plates that underwent independent bisulfite conversion, hybridization and array scanning. One sample was excluded due to poor data quality, leaving 19 duplicate pairs (38 samples) for evaluation.
The effect of different background correction methods on measurement accuracy was assessed using data from methylation control mixture samples for this same study (12 (link)), where purified human 100% methylated and unmethylated DNA (Zymo Research, Irving CA) were mixed together in different proportions to create laboratory control samples with specific methylation levels: 0%, 5%, 10%, 20%, 40%, 50%, 60%, 80% and 100% methylated Replicates for each methylation level (n = 10, 3, 2, 3, 3, 2, 3, 3 and 10, respectively) were independently assayed on different arrays.
To avoid possible impact on evaluations, we excluded 69 075 probes, which include non-specific bind probes, common (MAF > 0.05) SNPs at CpG target regions, probes on sex chromosomes and probes with multimodal methylation distributions identified using ENmix R package. We also excluded probes with low quality methylation values where the number of beads was less than 3 or detection P-value greater than 0.05.
To demonstrate the effect of ENmix background correction method on epigenome-wide association studies (EWAS), we re-analyzed raw blood DNA methylation data from 889 infants in relation to maternal smoking (12 (link)). We preprocessed the data with different methods or combinations of methods: raw data, Q5 background correction, ENmix_oob background correction, ENmix and dye bias correction (ENmixD), ENmix+dye bias correction+quantile normalization (ENmixDQ) and ENmix+dye bias correction+quantile normalization+BMIQ (ENmixDQB). We used a robust linear regression model to test for association between maternal smoking and infant DNA methylation level adjusting for the following variables: cell type proportion (CD8T, CD4T, NK, Bcell, Mono and Gran) estimated using the Houseman method (13 (link)) from minfi R package, gestational age in weeks, sex, education in two categories, birth weight, maternal age, maternal BMI, parity, experimental batch, cleft phenotype and baby birth year.

The Gervin reference was obtained from UCB samples (n = 11, 5 males and 6 females) from full-term births at the Alternative Birth Care unit at Oslo University Hospital in Norway. The Gervin reference consisted of all native Norwegians. All samples were successfully fractionated into six cell types (Gran, Mono, Bcell, CD4T, CD8T, and NK) using FACS. Notably, nRBCs were not included in this reference dataset. 450 K DNAm data was retrieved from the R package FlowSorted.CordBloodNorway.450 K in Bioconductor. For full details, refer to Gervin et al. [21 (link)].

We analyzed the mean expression of multiple previously published gene signatures [7 (link),15 (link)-19 (link)]. Briefly, these signatures include leukocyte-related signatures from Palmer et al. [17 (link)]: CD8 (n = 10 genes), B_Cell (n = 286), T_Cell (n = 178), and GRANS (n = 353). Stromal-related signatures were obtained from West et al. [16 (link)] (n = 402; DTF and SFT signatures combined) and Beck et al. [19 (link)] (n = 174). Genes enriched more than twofold in mammosphere-derived cells compared with differentiated cells were obtained from Dontu et al. [15 (link)] (n = 58). From Shipitsin et al. [18 (link)], we calculated the mean expression of the upregulated (n = 357) and downregulated (n = 353) genes from CD44⁺ versus CD24⁺ breast cancer cells from metastatic pleural effusions. From Creighton et al. [7 (link)], we calculated the mean expression of the CD44⁺/CD24^-/low/mammosphere signature reported (n = 119 upregulated genes; n = 279 downregulated genes). Finally, the proliferation and luminal gene cluster signatures were hand-picked (node correlation > 0.75) from the unsupervised intrinsic hierarchical clustering of the UNC337 using the intrinsic list of Parker et al. [9 (link)] and average linkage clustering using Cluster v2.12 (M. Eisen) [20 (link)] as shown in Figure S1 in Additional file 1. Gene lists from all genomic signatures are displayed in Supplemental Data in Additional file 2.

We recruited patients with MyD88 or IRAK-4 deficiency who had suffered COVID-19 between the start of the pandemic and January 2022. Data were collected through an anonymized survey sent to specialists in immunology or pediatrics with reported or unreported patients with these IEIs, and through clinicians caring for patients with IEIs identified from the European Society for Immunodeficiencies (ESID) Registry. Samples were obtained from the probands, parents and relatives with written informed consent. The study was approved by the French Ethics Committee “Comité de Protection des Personnes,” the French National Agency for Medicine and Health Product Safety, the “Institut National de la Santé et de la Recherche Médicale,” in Paris, France (protocol no. C10-13), the Rockefeller University Institutional Review Board in New York, NY, USA (protocol no. JCA-0700), the Committees for Ethical Research of the University Hospital of Gran Canaria Dr. Negrínn (protocol no. 2020-200-1 COVID-19) and Hospital San Joan de Deu (protocol no. PIC-173-21), and the Office of Research & Innovation at Drexel University, Philadelphia, PA, USA (protocol no. 2112008918).

Nursing Home Gran Residencia, is a public nursing home located in Madrid, Spain. Medication of residents is centrally controlled at Hospital Clínico San Carlos, in Madrid. Starting January 2021, Gran Residencia offered the BNT162b2 mRNA-based vaccine to all its residents. All of them were invited to participate in the study, finally including all those who accepted and signed the informed consent. Initially, a total of 196 NHR with or without documented pre-existing SARSCoV-2 infection were enrolled. Previous infection status was based on a positive PCR test or presence of anti-N IgG antibodies in the past or at pre-vaccination testing. The evolution of anti-RBD titer was monitoring over six months in 166 individuals out of the initially recruited. Twenty-four of these also provided paired samples for assessment of SARS-CoV-2 T-cell response. In order to investigate the influence of age and environment on IgG levels, humoral response of the residents was compared with that obtained with two different volunteer groups: nursing home staff (n = 44) and members of the association of retired health workers of the Hospital Clínico San Carlos over 65 years of age who live outside of Gran Residencia (n = 36). The two control groups were recruited similarly to residents. All of them were invited to participate in the study and all those who accepted were included. Enrolled participants completed a questionnaire, indicating age, gender, underlying conditions and usual medication (if any). A phone number was also added for future contacts. The age of all the staff was less than 65 years. The booster effect was determined only in 115 of the initially recruited individuals. The residents dropped out of the study for several reasons (own decision or that of their relatives, deterioration of their health, exitus).

Descriptive analyses of the study population characteristics were conducted. The study population was defined as residents who lived in Gran Residencia. Due to the characteristics of the study, the required sample size was not calculated and it was considered equal to the total number of residents who agreed to participate in the study and signed the informed consent. Data for vaccine double dose evaluation were represented as mean (standard deviation) and the median and Interquartile Range (IQR) with 95% confidence interval (95% CI). Categorical variables were represented as number and percentage. IgGs anti-RBD evolution over time and effect of the third dose were represented as log₁₀ of BAU/mL. The log₁₀ transformation of antibody levels was performed to simplify the construction of figures, due to the wide range of values obtained in the analysis. A Kolmogorov-Smirnov test was performed to verify normal distribution. Since there were no-normal distribution, the non-parametric Mann Whitney U test was used for comparison. Statistical significance was defined as p < 0.05. All statistical analyses were performed in IBM SPSS Statistic (version 26.0).