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• WES of der(1;7)(q10;p10)

  This dataset contains the BAM files of WES of 26 myeloid neoplasm patients with der(1;7)(q10;p10)(+) cases. The dataset was used to identify key driver genes in patients with der(1;7)(q10;p10). Already known drivers along with novel driver genes were identified through the use of this WES.

  Dataset EGAD50000000986

• Short-read (RNA-seq)

  The goal of this project was to perform long-read RNA sequencing (LR-seq, PacBio) in combination with short-read RNA-seq for systematic characterization of the isoform diversity in primary breast tumor samples. We sequenced the full-length transcriptomes of 26 breast tumors and 4 normal breast samples.

  Dataset EGAD00001006596

• BLUEPRINT: RNA-seq of progenitor cells

  Data supporting the paper Transcriptional diversity during lineage commitment of human blood progenitors

  Dataset EGAD00001000745

• Cancerous Adaptive Dosing Melanoma WGS Dataset

  Illumina NovaSeq 6000 30x WGS of 26 samples, each with up to 5 matched timepoints. Timepoints A,B,C,D,and E correspond to Pretreatment, Week 3, Week 6, Week 9, and Week 12 after treatment, respectively. Additional sample metadata (sample recurrence, treatment course, age, sex, comorbidities, etc.) are present in sample description.

  Dataset EGAD00001010926

• WGS data of plasma cell free DNA

  Raw paired-end whole-genome sequencing data of plasma cell free DNA on the NovaSeq 6000.

  Dataset EGAD50000000257

• Whole genome sequencing of circulating cell-free DNA on Illumina and Ultima platforms

  The dataset includes Illumina (n=1) and Ultima (n=92) sequencing of circulating cell-free DNA. The dataset was generated through standard whole genome sequencing (Illumina n=1 & Ultima n = 15) and using a duplex unique molecular identifier whole genome sequencing workflow (Ultima, n=77). This dataset includes cancer samples and cancer-free control samples.

  Dataset EGAD50000001234

• Cell-free DNA sequencing using newly developed single-strand DNA library preparation

  We performed whole genome sequencing of cell-free DNA that was collected from human plasma using an improved cfDNA purification protocol and DNA library prepared with newly developped protocol of our own.

  Study JGAS000257

• An Ultrasensitive Method for Detection of Cell-Free RNA

  Our study describes the development of a novel method for cell free RNA (cfRNA) analysis called RARE-Seq (Random priming & Affinity capture of cell-free RNA fragments for Enrichment analysis by Sequencing). We find RARE-Seq improves the limit of detection for tumor-naïve cancer detection while maintaining high specificity. We explore the potential utility of RARE-Seq in diverse clinical applications, including non-invasive ctRNA genotyping, treatment resistance monitoring, and molecular characterization of non-malignant conditions.

  Study phs004091

• Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection

  Deregulation of transcription factors (TFs) is an important driver of tumorigenesis, but non-invasive assays for assessing transcription factor activity are lacking. We Here we developed and validated a minimally invasive method for assessing TF activity based on cell-free DNA sequencing and nucleosome footprint analysis. We analyzed whole genome sequencing data for >1,000 cell-free DNA samples from cancer patients and healthy controls using a newly developed bioinformatics pipeline developed by us that infers accessibility of TF binding sites from cell-free DNA fragmentation patterns. We observe patient-specific as well as tumor-specific patterns, including accurate prediction of tumor subtypes in prostate cancer, with important clinical implications for the management of patients. Furthermore, we show that cell-free DNA TF profiling is capable of detection of early-stage colorectal carcinomas. Our approach for mapping tumor-specific transcription factor binding in vivo based on blood samples makes a key part of the noncoding genome amenable to clinical analysis.

  Study EGAS00001003206

• Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring

  Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring

  Dataset EGAD00001006237