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• RNA-Seq data on multiple myeloma CD138positive bone marrow plasma cells

  RNA-Seq data on multiple myeloma CD138positive bone marrow plasma cells, 11 samples, sequenced on HiSeq 4000 and HiSeq X-Ten, using mostly the TruSeq stranded mRNA Kit.

  Dataset EGAD00001008619

• sWGS data of Pap test smears and tumor tissues

  Shallow whole-genome sequencing data divided into three groups: - sWGS data from Pap smears of patients with confirmed high grade serous ovarian cancer - sWGS data from matched tumor tissue (at diagnosis) from the same patients - sWGS data from Pap tests smears of healthy women

  Dataset EGAD00001010141

• High-throughput transcriptome data of paediatric ETV6-RUNX1 acute lymphoblastic leukemia

  High-throughput transcriptome sequencing data from paediatric (<18-y) ETV6-RUNX1 fusion positive acute lymphoblastic leukemias. Dataset includes fastq and BAM files from diagnostic samples of 33 patients.

  Dataset EGAD00001010164

• Colonbiome shot-gun metagenomics

  156 samples of shot-gun gut metagenomics, corresponding to 51 patients with CRCm 54 patients with adenoma, and 51 healthy controls

  Dataset EGAD00001010068

• WGS

  Purified DNA from PDX samples were subjected to WGS. Libraries were performed using the TruSeq DNA PCR-Free kit (Illumina) starting with 1μg of input DNA and performed following manufacturer's instructions. Libraries were sequenced on a NovaSeq 6000 (2x151 bp) instrument (Illumina). A mean coverage of 30.4x was obtained.

  Dataset EGAD00001010309

• Single-cell RNA-sequencing of nivolumab-treated glioblastoma

  Single-cell RNA-sequencing of 8 patients, from primary and relapse tumour (total of 16 samples). Patients were treated with nivolumab prior to relapse surgery.

  Dataset EGAD00001010843

• Longitudinal breast cancer cohort in SMC

  Whole transcriptome sequencing (WTS) of a longitudinal breast cancer (BC) cohort consisting of 146 cases (281 tumors, 109 pairs), including 52 (38%) that achieved pathologic complete responses (pCR) and 85 (62%) that harbored residual diseases at time of surgery.

  Dataset EGAD00001004487

• Whole genome sequence data from Illumina HiSeqX instruments

  This dataset includes bam files from 120 samples. These samples were sequenced using 2x150bp reads on an Illumina HiSeqX sequencer and aligned using the Isaac aligner. All samples were processed with TruSeq DNA PCR-free sample preparation.

  Dataset EGAD00001003562

• Genome-wide data of Erasmus Rucphen Family (ERF) Study

  The data consists of 678189 genome-wide polymorphic variants of 3658 individuals from ERF/GRIP region in a variant call format (vcf) file. ERF has been genotyped with different genotyping platform: Illumina 318 k, 350 k, 610 k and Affymetrics 200 k.

  Dataset EGAD00001003571

• Oxford Nanopore whole genome sequencing of two patients with congenital disease

  BAM files with sequencing reads derived from Oxford Nanopore MinION whole genome sequencing of two DNA samples from lymphoblastoid cell lines from two patients with congenital disease. Samples were prepared using 1D and 2D library preps.

  Dataset EGAD00001003511

• Whole Exome Sequencing of a Melanoma Patient with Acquired Resistance to MEK plus CDK4/6 Inhibition

  Longitudinal biopsies from a melanoma patient who initially responded to MEK plus CDK4/6 inhibitor therapy were whole exome sequenced to identify potential resistance mutations. The biopsies included normal tissue, pre-treatment, on-treatment, and several post-resistance timepoints.

  Dataset EGAD00001003989

• Somatic mutation analysis based on Whole exome Sequencing (WES) of multiple tumor biopsies, patient-derived spheroids and leukocyte DNA from colorectal cancer patients (vcf files)

  Somatic mutations were called using whole exome Sequencing (WES) data from colorectal cancer samples (dataset EGAD00001003821) using MuTect2, with matched constitutional WES-data obtained from leukocytes samples as reference.

  Dataset EGAD00001003823

• TRACERx esophageal adenocarcinoma multi-region NGS

  This dataset contains whole exome data from 8 esophageal adenocarcinoma tumors, that has been subjected to multiregion sequencing, ranging from 3-8 regions per tumor. In total, 40 tumor samples and 8 normal blood samples have been sequenced on Illumina HiSeq 2500 at a median dept of 90x.

  Dataset EGAD00001001364

• Papuan Genomes: high depth (30x) whole genome sequence data

  This dataset includes the whole genomes, sequenced to high depth (30x) of 25 individuals from Papua New Guinea. The individuals were chosen from several geographically distinct Papuan groups, focusing on the highland regions: Bundi, Kundiawa, Mendi, Marawaka and Tari.

  Dataset EGAD00001001634

• Somatic genetic basis of Wilms’ tumour

  We investigated the somatic genetic basis of Wilms’ tumour and found complex phylogenetic relations between tumours.

  Dataset EGAD00001004774

• WES, ultra-deep sequencing exome and RNAseq data of diseased liver samples

  1. Utra-deep exome sequencing data, illumina pair-end reads, fastq, 190 samples 2. WES data, illumina pair-end reads, fastq, 120 samples 3. RNA-seq data, illumina, pair-end reads, fastq, 20 samples

  Dataset EGAD00001004792

• Korean Advanced Thyroid Cancer Dataset

  Massively-parallel DNA sequencing of 113 advanced thyroid cancers and Massively-parallel RNA sequencing of 25 advanced thyroid cancers

  Dataset EGAD00001004845

• RNA-seq

  RNA-seq of primary and metastatic sites from highly clinically annotated HGSC samples. Samples were obtained pre-treatment based on a laparoscopic triage algorithm from patients who underwent R0 tumor debulking, or received neoadjuvant chemotherapy (NACT) with excellent (ER) or poor response(PR).

  Dataset EGAD00001005238

• Dnase1l3 deletion causes aberrations in length and end-motif frequencies in plasma DNA

  We showed that mice in which Dnase1l3 had been deleted showed aberrations in the fragmentation of plasma DNA. We also observed a change in the ranked frequencies of end motifs of plasma DNA caused by the Dnase1l3 deletion.

  Dataset EGAD00001005071

• GBM cancer stem cell lines, RNA-seq and WGS data

  This dataset contains 3 GBM stem cell samples profiled by RNA-seq. Two of those samples have been profiled with WGS as well (with matched blood WGS data available)

  Dataset EGAD00001005077

• paired-EXOME (WES) sequencing with SureSelect-V5+UTRs of B-cell lymphoma

  Tumors and control of nodal B-cell lymphoma of one patient. WES sequencing on Illumina HiSeq 4000 with Agilent SureSelect V5+UTRs. Bam files were aligned with bwa mem to hg19.

  Dataset EGAD00001006059

• Single cell RNA sequencing of synovial B cells in early Rheumatoid Arthritis

  This dataset includes 3432 paired single cell sequencing fastq files derived from synovial B cells of 5 early Rheumatoid Arthritis patients. Libraries were prepared using the SmartSeq2 protocol. All wells contained ERCC spike-ins. Libraries were sequenced on an Illumina NovaSeq instrument with 2x100bp paired-end reads yielding a median of 2.5M reads/well. Sample aliases ending on 368 and 384 represent empty control wells. Sample aliases starting with P11417_4 and P13157_1 belong to ACPA- patient A7, sample aliases starting with P11417_5 and P11417_6 belong to ACPA+ patient A1, sample aliases starting with P13157_2 belong to ACPA- patient A3, sample aliases starting with P13157_3 and P13157_6 belong to ACPA+ patient A2, sample aliases starting with P13157_4 and P13157_5 belong to ACPA- patient A4.

  Dataset EGAD00001009076

• Resistance studies in Lung Cancer

  The purpose of the study was to compare gene expression profiles from a cohort of crizotinib-resistant ALK-rearranged lung tumors and a cohort of treatment-naive ALK-rearranged lung tumors. Expression profiles were generated by RNA-seq. In parallel, gene expression profiles were obtained from ALK-rearranged lung cancer cell lines in the presence or absence of the ALK inhibitor TAE684. Gene expression profiles were also obtained from ALK-rearranged cells ectopically expressing genes associated with ALK inhibitor resistance that were identified from a functional genetic study.

  Study phs000855

• CALGB/SWOG 80405 ct DNA Biomarker Evaluation

  To investigate treatment-specific mutations that underlie resistance to treatment with chemotherapy +/- bevacizumab or cetuximab in first line metastatic Colorectal Cancer (mCRC) patients, we performed targeted sequencing of circulating free DNA (cfDNA) from longitudinal plasma samples. These samples were collected at baseline (PRE, n=354), during treatment (OTH, n=254), and/or at progression or end of the protocol treatment (EOT, n=345) from CALGB/SWOG 80405, a randomized phase III trial that evaluated the efficacy of chemotherapy plus bevacizumab or cetuximab treatment in first line colorectal cancer patients (NCT00265850).

  Study phs002941

• IgM heavy chain V(D)J library sequencing using varied PCR parameters

  When amplifying the rearranged V(D)J genes encoding antigen receptors during adaptive immune receptor repertoire sequencing (AIRR-seq), each cycle of the PCR can produce spurious “chimeric” hybrids of two or more different template sequences. To test the effects of PCR protocol variation on chimera formation in AIRR-seq, we produced IgM heavy chain V(D)J repertoire libraries under 8 conditions, varying the number of PCR cycles, indexing PCR template, input RNA, and extension time. Three donors were sequenced using all 8 conditions.

  Study EGAS50000001037