To identify somatic mutations in paediatric diffuse intrinsic pontine gliomas (DIPGs), we performed whole genome sequencing of 7 DIPGs and matched germline DNA, and targeted sequencing of an additional 43 DIPGs and 36 non-brainstem paediatric glioblastomas (non-BS-PGs). 78% of DIPGs and 22% of non-BS-PGs contained K27M mutation in H3F3A, encoding histone H3.3, or the related HIST1H3B, encoding histone H3.1. An additional 14% of non-BS-PGs had somatic G34R H3F3A mutations.
Neuroblastoma is a pediatric tumor of the developing sympathetic nervous system. However, the cellular origin of neuroblastoma remains to be defined. Here, we study single-cell transcriptomes of neuroblastomas and normal human developing adrenal glands at various stages of embryonic and fetal development. We define normal differentiation trajectories during adrenal medullary development and identify the cellular origin of neuroblastoma. Importantly, adrenergic and mesenchymal neuroblastomas with varying clinical phenotypes match different temporal states along normal differentiation trajectories, with the degree of differentiation corresponding to clinical prognosis.
Myocardial ischemia occurs when there is a mismatch between coronary oxygen delivery and metabolic requirements of the myocardium, which may be clinically manifested during angina, coronary angioplasty or cardiopulmonary bypass (CPB). Myocardial ischemia may lead to a spectrum of myocardial stunning, hibernating myocardium, and ultimately cell death if the ischemic insult is severe. In the human heart, irreversible damage begins after approximately 20 to 40 minutes of oxygen deprivation. Observed molecular and cellular changes of myocardial ischemia are characteristic of an inflammatory response, but the exact mechanisms that underlie this pathological process are unclear and may not be full emulated by animal models of ischemia or infarction. Thus, we felt it valuable to investigate a human ischemia model. During cardiac surgery, CPB with aortic cross-clamping (AoXC) and cardioplegic arrest is associated with excellent clinical outcomes and suitable operative conditions. However, despite the use of cardioprotective strategies, AoXc during CPB is accompanied by a variable, yet obligate ischemic period lasting 1 to 3 hours, resulting in hypoxia, metabolic substrate depletion, reperfusion injury, apoptosis, and necrosis. Cardiac specific biomarkers of ischemia and infarction, including troponin, are elevated even after routine coronary artery bypass graft surgery and correlate with the duration of ischemia from AoXc.This process of CPB provides us with the ability to examine the transcriptional profile before and after an expected, consistent, and reproducible human ischemic event, albeit induced by cold cardioplegic arrest and not coronary occlusion. In addition, the absence of reperfusion in this time period allows us to examine the transcriptomic response to intermittent ischemia, without having to account for the perturbations of reperfusion injury. Although various animal models have been used to examine the effects of ischemia on cardiac function, no human data exist which examine the early transcriptomic response to a left ventricular (LV) ischemic insult. We therefore characterized the effect of cold cardioplegia induced acute ischemia on the transcriptional profile of the LV by performing whole transcriptome next-generation RNA-sequencing (RNA-seq) in patients undergoing cardiac surgery by sampling human LV tissue prior to, and after, the obligate ischemia during AoXC. We hypothesized that the cold cardioplegia induced ischemic injury will dramatically alter transcription in the human myocardium, and that we would identify genes and pathways, which will identify interventional targets for pharmacological therapy. Methods:We have collected left ventricle tissue samples and blood sample from patients undergoing heart surgery. We obtained punch biopsies (~3-5μg total RNA content) from the site of a routinely placed surgical vent in the anterolateral apical left ventricular wall of patients undergoing elective aortic valve replacement surgery with cardiopulmonary bypass. After an average of 79 minutes of aortic cross-clamping with intermittent cold blood cardioplegia for myocardial protection every 20 minutes, a second biopsy was obtained in the same manner. Tissue samples were immediately placed in RNAlater® (Ambion, ThermoFisher Scientific, Waltham, MA), and after 48 hours at +4°C were stored at -80°C until RNA extraction. Total RNA was isolated with Trizol and RNA quality was assessed using the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). Libraries were prepared by poly(A) mRNA isolation and reverse transcription Polymerase Chain Reaction (RT-PCR), then sequenced on the Illumina HiSeq2000 or HiSeq2500 (Illumina, San Diego, CA). As samples were analyzed at different times, different read lengths were employed, initially using single-end reads (n=20) and then transitioning to paired end reads (n=216), ranging from 36 - 100 base pairs. Raw sequencing files were processed using Sickle, Skewer, and STAR software, and aligned to GrCh37 or UCSC Hg19. DNA was isolated from whole blood using standard methods. SNP genotyping was performed using the Illumina Omni2.5Exome-8 BeadChip array with additional exome content (Illumina, San Diego, CA) chip, version 1.1. We first phased and imputed 93 subjects using a phasing tool called SHAPEIT and an imputation tool called MINIMAC, with 1000 Genomes phase 1 version 3 for the reference panel. We then phased and imputed 26 more subjects using SHAPEIT, an imputation tool called IMPUTE2, and 1000 Genomes phase 3 version 5.
Raw sequencing data of WES that were obtained from precancerous samples as adenoma and MMR-deficient crypts and paired healthy tissue from MSI CRC patients of which 10 are diagnosed with lynch syndrome and 3 had sporadic cancer. These data were analyzed in order to evaluate microsatellite instability though tumorigenesis and associated to splicing deregulation in MSI tumors RNA.
Investigation of post-zygotic and germline variants using whole exome and ultra-deep duplex sequencing in paired uninvolved margin and primary tumor samples from 126 breast cancer patients with differing survival outcomes, with skin or blood samples as reference. Pairs of uninvolved margin and blood samples were also collected for 15 reduction mammoplasty patients without personal or familial history of cancer, serving as controls.
Low coverage paired end Illumina WGS from cells amplified with Picoplex, PTA, and droplet MDA. Two brains with Multiple System, Atrophy, one control, and non-brain controls (fibroblasts, NA12878)
Targeted sequencing dataset used for the paper entitled "Development of a rapid and comprehensive genomic profiling test supporting diagnosis and research for gliomas". The cohort includes 53 cases of targeted DNA squencing, 15 of them have matched control sequences. The capture panel was made by Agilent SureSelect and the sequence was performed using DNBSEQ or Illumina sequencer.
Bulk-RNAsequencing from human nerve fascicles from patients with polyneuropathies, and human Schwann cell cultures isolated from said nerve fascicles, in comparison to control human Schwann cell cultures and a referential fibroblast culture.
The objective is to generate a comprehensive immunogenomic profiling in thymoma using RNA sequencing and TCR repertoire analysis and to evaluate the potential of immunotherapy in thymoma from multiple perspectives.
Little is known about the genomic and transcriptomic features of hepatocellular carcinoma developing after HCV eradication (SVR-HCC). In this study, we aimed to unveil the genomic and transcriptomic basis of hepatocarcinogenesis after SVR.
