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• Tamoxifen Response at Single Cell Resolution in Estrogen Receptor Positive Primary Human Breast Tumors

  Primary breast tissue, normal and cancerous, was collected immediately after resection. The tissue was dissociated and treated with 10uM tamoxifen or control media for 12 hours in suspension. Single cell libraries were then created using a 10x Genomics gel bead droplet-based kit and sequenced via Illumina sequencing platforms. Differences in cell response to tamoxifen was observed between cell types and distinct responsive and unresponsive cell populations were determined.

  Study phs003186

• Genome Sequencing of Large, Multigenerational CEPH/Utah Families

  Blood-derived DNA samples were collected from 603 members of large, multigenerational families, collected as part of the Centre d'Etude du Polymorphisme Humain (CEPH) consortium. These DNA samples were sequenced (using Illumina HiSeq technology) to a median genome-wide depth of 30X. Sequenced reads from each individual were aligned to the human reference genome (hg19), generating CRAM files for each individual. Variant calls in VCF format were obtained using the Genome Analysis Toolkit (GATK).

  Study phs001872

• Genomic Profiling of Relapsed and Refractory Childhood Cancers

  Through clinical trials focused on molecularly guided therapy in pediatric cancers (NCT01355679, NCT01802567, NCT02162732), the Beat Childhood Cancer Consortium performed paired tumor/normal whole exome sequencing and/or tumor mRNA sequencing for 202 pediatric or adolescent young adult patients with rare, relapsed and refractory cancers (including neuroblastoma, Ewing sarcoma, osteosarcoma, rhabdomyosarcoma, ependymoma, glioma, and other rare solid tumors). A subset of these patients had multiple biopsies sequenced, including longitudinal profiling.

  Study phs002238

• Multiregional Single-Cell Transcriptomic Analysis of Liver Cancer

  In this study, we performed single-cell transcriptomic profiling of human liver tissues collected from hepatocellular carcinoma and intrahepatic cholangiocarcinoma patients. A total of seven primary liver cancer patients enrolled in this study. Samples were collected from multiple regions, including tumor core, tumor border and adjacent non-tumor tissue. The 10x Genomics platform was used to generate single cell 5' libraries. The Illumina NovaSeq 6000 platform was employed for sequencing.

  Study phs003117

• Whole-genome sequences of Korean populations generated by using long- and short-read sequencing technologies.

  We newly sequenced whole-genome of Korean participants by using long- and short-read sequencing platforms (n = 3 and n = 100 for long- and short-read sequencing, respectively). With these data, generated by Sequel II HiFi system (Pacific Bioscience) and DNBSEQ-T7 (MGI) sequencers, we identified a set of structural variations common in Korean population as well as the genetic features distinct from other ethnicities.

  Study EGAS50000000375

• Genomic profiling identified ERCC2 helicase domain mutations respond to platinum-based neoadjuvant therapy in urothelial bladder cancer

  Genomic profiling of tumours enables therapeutic decisions, and identifying drug-matched mutations will prolong survival and prognosis. Here, we generated a custom panel for detecting genetic alterations in 19 patients with urothelial bladder cancer. This panel targeted 71 genes associated with urological cancer. Targeted sequencing was performed on formalin-fixed paraffin-embedded tumour tissues. In this study, we revealed genome profiles and actionable mutations in patients with urothelial bladder cancer.

  Study JGAS000241

• Characterisation of Cyr61-enriched myeloid angiogenic cells

  We previously demonstrated the enrichment of an angiogenic precursor cell population from peripheral blood mononuclear cells by CYR61, a protein of the CCN family. In vivo, CYR61 mediates the binding of leukocytes and particular monocyte populations at sites of vascular inflammation. Here, we present an in vitro enrichment system mimicking (patho)physiology and at the same time representing an effective tool for enrichment of the CYR61-binding blood cells and analyzed this cell population in depth.

  Study EGAS50000000533

• Multi-omics analysis reveals immune programs delineating disease severity in extrapulmonary tuberculosis

  This study investigates the immune response in extrapulmonary tuberculosis (EPTB) using single-cell RNA sequencing. Hierarchical clustering of patient transcriptomes identified three distinct levels of disease severity, uncovering immunological pathways involved in disease progression, including interferon and IL-1β-mediated signaling. The findings also led to the development of a diagnostic gene expression signature for both EPTB and pulmonary TB, offering potential improvements in TB diagnosis and treatment.

  Study EGAS50000000758

• ONGOING CHROMOSOMAL INSTABILITY ACROSS ANEUPLOID SUBTYPES OF CHILDHOOD B-CELL ACUTE LYMPHOBLASTIC LEUKEMIA ASSOCIATES WITH DISEASE PROGRESSION

  Single-cells from primary cB-ALL samples were isolated using an inverted microscope coupled to a micromanipulator equipped with glass capillary for cell collection. A minimum of 20 cells were isolated per sample in microdrops of 2.5 μl of phosphate buffered saline (PBS) with 0.5% polyvinylpyrrolidone. Cell lysis and DNA amplification was performed using the SurePlex DNA Amplification System (Illumina). Genomic DNA was subsequently fragmented and tagged with the VeriSeq PGS transposome and the TruSeq Index adapters by PCR for library preparation (VeriSeq PGS Library Prep Kit, Illumina). Equal volumes of normalized libraries were pooled and sequenced on an Illumina MySeq platform with 1×75-bp single-end sequencing. Reads were subsequently aligned to the human reference genome (GRCh38/hg38) using Bowtie2 (version 2.2.4).

  Dataset EGAD50000000029

• MutWP5__CRUK_Mutographs_of_Cancer__Breast__BRCA_Carriers__Exome_

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastectomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer.

  Study EGAS00001003316