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• Nuclease deficiencies alter plasma cell-free DNA methylation profiles (Human samples)

  The dataset contains 2x75bp paired-end sequencing data in DNASE1L3-deficient human subjects. We performed bisulfite sequencing of plasma samples from three DNASE1L3-deficient subjects and one heterozygous parent to investigate how nuclease deficiencies alter plasma cell-free DNA methylation profiles.

  Dataset EGAD00001007750

• RNA-seq from PDAC samples

  Bam and fastq files from RNA-seq of PDAC samples used in the PCSI mismatch repair study

  Dataset EGAD00001006261

• ECCO-GEN Valve Methylation Dataset (non-diseased)

  The valve methylation dataset consists of 12 bam files of human non-diseased valve tissue samples that are free from calcification (6 aortic and 6 mitral valves - matched; 10 males: 2 females; age range 42 – 64 years, mean age 52.2 years, SD 9.9682). Donor hearts are free from cardiovascular and valvular complications.

  Dataset EGAD00001006303

• Characterization of four subtypes in morphologically normal tissue excised proximal and distal to breast cancer

  RNA sequencing data from breast cancers (n=18) and their matched HN tissues (n=36), healthy breast from cosmetic reduction mammoplasty (RM; n=5), and risk reducing mastectomies (RR, n=5), with peritumoral samples excised proximal to (TP, less than 2 cm) and distal from (TD, 5-10 cm) the primary tumor.

  Dataset EGAD00001006291

• Alopecia and Vitiligo

  exome sequencing data captured with agilent v4 (71k) and sequenced on illumina technology. data from a total of 40 samples, of which 14 are vitiligo cases with familial history of vitiligo or immune disease, and the remaining are alopecia areata cases.

  Dataset EGAD00001005289

• Capture Hi-C on Hodgkin lymphoma

  In situ promoter capture Hi-C on Hodgkin lymphoma cell line L-428 in experimental triplicates. Hi-C libraries were prepared as previously described (Orlando et al., 2018, https://currentprotocols.onlinelibrary.wiley.com/doi/pdf/10.1002/cphg.63). Promoter capture was based on 32,313 biotinylated 120-mer RNA baits (Agilent). Hi-C libraries were sequenced using Illumina HiSeq 2000 technology. The files are in FASTQ format.

  Dataset EGAD00001004321

• Spectrum and significance of MYC and BCL2 mutations in DLBCL

  We analyzed the spectrum and clinical significance of MYC and BCL2 mutations in 347 DLBCL cases from population-based cohort of BC, Canada.

  Dataset EGAD00001003140

• Genome and transcriptome sequence data from a leiomyosarcoma patient

  Genome and transcriptome sequence data from a leiomyosarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002891

• PIK3R4 (VPS15)

  WES of human: A mutation in VPS15 (PIK3R4) causes a ciliopathy and affects IFT20 release from the cis-Golgi WES (Agilent SureSelect All Exon XT2 50 Mb kit) has been realized on three affected siblings (II.1, II.3, II.5) and one healthy sister (II.4). Raw data (BAM files) are provided: - II.1.aligned.sorted.dedup.realign.recal.bam - II.3.aligned.sorted.dedup.realign.recal.bam - II.5.aligned.sorted.dedup.realign.recal.bam - II.4.aligned.sorted.dedup.realign.recal.bam

  Dataset EGAD00001002736

• Integrative Analysis of Lung Adenocarcinoma in EAGLE (Version 2)

  We performed a comprehensive analysis of intratumor heterogeneity of somatic mutations in cancer driver genes, copy number aberrations and DNA methylation in 292 tumor samples from 84 lung adenocarcinoma (LUAD) patients from the Environment And Genetics in Lung cancer Etiology (EAGLE) study. SNVs of 37 established lung cancer driver genes were profiled by deep target sequencing in 180 tumor samples and 55 blood samples and 1 buccal sample from 56 subjects. Somatic copy number alterations were profiled using SNP arrays in 268 tumor samples from 80 subjects. DNA methylation levels were profiled with methylation arrays in 205 tumor samples and 74 normal tissue samples from 68 subjects.

  Study phs001169