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• McGill Cord Blood Methylome Capture Sequencing Data

  The study includes methylC-capture sequencing (MCC-Seq) on 73 cord blood DNA samples from the result of natural pregnancies (control) and through the assisted reproductive technologies for infertile couples (ART/infertile). Samples were collected as a part of the Quebec-based 3D (Design, Develop, Discover) longitudinal pregnancy cohort study. All the data were generated with 100bp paired-end reads using the Illumina NovaSeq 6000 systems.

  Dataset EGAD00001009495

• Bulk ATAC-Seq HiSeq2500 v4 reagents (100M reads)

  Human data for chromatin accessibility (ATAC-Seq) in eight B-cell precursors: HSC, CLP, pro-B, pre-B, Immature B, Transitional B, Naive B CD5-, Naive B CD5+ cells

  Dataset EGAD00001010909

• ChIP-seq bulk

  This dataset gather ChIP-seq data produced by immunoprecipitating CTCF factor in own laboratory in MM.1S cell line in EtOH and Dex conditions. It also gather ChIP-seq dataset produced by external laboratory (Active Motif) for H3K27ac mark and GR transcription factor in same cell line and conditions ( MM.1S ETOH/Dex)

  Dataset EGAD00001011136

• Sequencing data for oesophageal and related samples - Black et al (WGS)

  Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WGS OACs/BOs/normals)

  Dataset EGAD00001011187

• scRNAseq of aplastic anemia and healthy immune cells co-cultured with autologous HSPCs

  This dataset contains 8 batches of bone marrow or peripheral blood cells of patients with aplastic anemia and bone marrow cells of healthy controls. The samples from different experimental conditions have been multiplexed with Totalseq-C antibodies (feature barcoding). To demultiplex the samples, see instructions in 10.5281/zenodo.2590196 and https://github.com/janihuuh/aa_manu. Each sample is analysed with Chromium V(D)J and 5' Gene Expression Platform v2 (10X Genomics). The raw data includes fastq files for Gene expression, feature barcodes and V(D)J Expression. The processed data have been deposited in the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress).

  Dataset EGAD00001012120

• PD-L1 blockade immunotherapy rewires cancer-induced emergency myelopoiesis

  HSPCs were sorted as CD34+ cells from bone marrow of patients with Hodgkin Lymphoma (HL). Control samples were isolated before initiating treatment.These were compared to samples from two additional HL patients who had relapsed and were being treated with nivolumab. Nivolumab was administered at a dose of 240 mg every two weeks, with BM samples collected the day before the scheduled dose. The patients receiving nivolumab were in remission at the time of BM collection. RNA was extracted using Arcturus™ PicoPure™ RNA Isolation Kit (Thermo Fisher Scientific, #12204-01) ` instructions. Paired-end sequencing was reads were generated for each sample in the Illumina Novaseq 6000 system.

  Dataset EGAD00001015403

• Acral Melanoma PDXs from the admixed Brazilian Population - Tumour and unfiltered PDX sample CRAM files - RNAseq

  Patient Derived Xenograft RNAseq sample CRAM files mapped to build GRCh38. Acral melanoma (AM) is an aggressive melanoma subtype with limited therapeutic options and poor outcomes. In non-European descent and admixed populations, like in Latin America, it can account for a significant proportion of cutaneous melanoma cases. Here, we performed comprehensive genomic and functional profiling of AM from a uniquely diverse Brazilian cohort. Whole-exome and transcriptome sequencing was performed on both tumours and patient-derived xenograft (PDX) samples. The PDX were obtained from a comprehensive collection of patient-derived xenograft (AM-PDX) models that we established which faithfully retained the histopathological and genomic features of the original tumours.

  Dataset EGAD00001015742

• Chinese Alternating Hemiplegia of Childhood (AHC) Disease Study

  AHC is a rare and severe neurological disorder, and characterized by episodic hemiplegia or quadriplegia attacks, accompanied by other paroxysmal symptoms of oculomotor abnormalities, dystonia, seizures and autonomic disturbances; the age of onset usually occurrs before 18 months of life. Sodium-potassium ATPase alpha3 subunit (ATP1A3) has recently been identified as a causal gene for sporadic AHC by three groups. However, there has not been any large genetic study on a Chinese cohort. In the submitted data, whole-exome sequencing of three trios and three sporadic cases in a Chinese cohort produced an average of 18.8 gigabases of raw sequence. Through our analysis pipeline including BWA mapping, GATK recalibration, variant calling and filtering, all six patients contained missense mutations in ATP1A3 which were further confirmed as de novo mutations. Along with validation in additional patients, this study confirmed ATP1A3 as a causal gene in Chinese AHC patients, and reported six novel mutations.

  Study phs000660

• Exploiting New Patterns of Genome Damage in Triple Negative Breast Cancer

  Genomic instability, a feature of triple negative breast cancers (TNBC), represents an opportunity for discovery of biologic and clinically relevant subgroups of patients. Owing to TP53 mutation in the majority of cases, DNA repair deficiency through loss of BRCA1 and BRCA2, and by expression features patterning a basal cell of origin, TNBC represents a molecularly and clinically distinct group of breast cancer patients. Unfortunately, targetable molecular features of TNBC remain elusive and TNBC patients suffer the poorest outcomes amongst clinical subgroups. Within TNBC patients, responses to treatment vary and although gene expression patterns within TNBC have been identified, little progress has been made in developing biomarkers; effective stratification as a route to directing patients to more targeted therapy is lacking. In this study, we exploit mutational processes in TNBC as a new opportunity to stratify patients and to understand the evolutionary progression of TNBC cells harboring specific DNA repair properties.

  Study phs003038

• Scalable Whole-Exome Sequencing of Cell-Free DNA Reveals High Concordance with Metastatic Tumors

  We performed whole genome sequencing and whole-exome sequencing of cell-free DNA (cfDNA) and whole-exome sequencing of matched tumor biopsies and germline DNA from patients with metastatic cancer. Using ichorCNA, a software tool that quantifies tumor content in ultra-low pass whole genome sequencing (~0.1x) of cfDNA without prior genomic characterization of the tumor, we show genome-wide concordance between cfDNA and tumor biopsies and detectability of high tumor fractions (>0.1) in the cfDNA of many patients with metastatic cancer. We then established that whole-exome sequencing of cfDNA can enable comprehensive profiling of tumors from blood, with high tumor-content cfDNA samples demonstrating concordance of clonal somatic mutations, copy number alterations, mutational signatures, and neoantigens with matched tumor biopsies. This study introduces a new method to identify patients that could be eligible for tumor profiling from cfDNA and sheds light on the concordance between metastatic tissue and blood biopsies.

  Study phs001417