8433 results for "canc*"

in 21.08 milliseconds.

• Whole-Exome Sequencing of Tumor Biopsies from a Colorectal Cancer Patient with Two Distinct Primary Tumors and Matched Metastases

  Colorectal cancer (CRC) is a heterogeneous disease in which rare genetic alterations, such as neurotrophic receptor tyrosine kinase (NTRK) fusions, have emerged as clinically relevant therapeutic targets. Here, we report the case of a 69-year-old man with an advanced colorectal carcinoma comprising two intermixed but histologically distinct components: a predominant (>90%) poorly differentiated solid carcinoma and a conventional adenocarcinoma with mucinous features. Whole-exome sequencing (WES) of microdissected tumor regions (two primary tumors and two matched metastases) along with germline DNA analysis revealed profound genetic divergence between the two tumor components. This case illustrates the coexistence of two genetically independent yet spatially inseparable CRCs following distinct evolutionary trajectories—one driven by an NTRK1 fusion and microsatellite instability (MSI), and the other by canonical KRAS and SMAD4 alterations.

  Study EGAS50000001385

• Genomic correlates with survival after treatment of oesophageal adenocarcinoma by surgery alone

  A 451 cancer-associated gene panel, described in McCabe et al. 2019, was used to assess genomic alterations associated with survival in a Swedish cohort of 65 oesophageal adenocarcinoma (OAC) patients who underwent surgical resection without perioperative treatment. This DAC controls access to sequencing data.

  Dac EGAC50000001177

• Bladder Cancer Genomics Data Access Committee – Erlangen–Bonn Collaboration

  The Bladder Cancer Genomics Data Access Committee (DAC) represents the collaborative bladder cancer research program between the Institute of Pathology, Universitätsklinikum Erlangen; the Department of Urology and the Institute of Experimental Oncology, Universitätsklinikum Bonn. The DAC comprises representatives from each participating institution, including Prof. Markus Eckstein (Universitätsklinikum Erlangen) and Prof. Niklas Klümper (Universitätsklinikum Bonn). The committee is responsible for reviewing and approving requests for access to controlled-access bladder cancer genomic and associated clinical datasets generated through this collaboration deposited in the European Genome-phenome Archive (EGA). The committee reviews requests from qualified researchers to determine whether the proposed use of the data is consistent with the participants' informed consent, applicable ethical approvals, institutional data access policies, and relevant data protection regulations before granting access.

  Dac EGAC50000001118

• Aligned BAM files from targeted amplicon sequencing

  This dataset contains aligned BAM files generated from targeted amplicon sequencing, using Oncomine Focus assay (Thermo Fisher Scientific). The dataset includes 120 samples from 60 patients of Thyroid cancer. Reads were aligned to the reference genome and are provided as BAM files for downstream analysis. No processed variant calls are included. We uploaded 60 BAM from DNA samples and the 60 BAM of the RNA samples of these patients

  Dataset EGAD50000002861

• Multiomic Analysis of Treatment Naive MYD88 Mutated Patients with Waldenstrom’s Macroglobulinemia

  This study consists of RNASeq with additional whole exome sequencing and enhanced reduced representational bisulfite sequencing for a subset of study participants. Samples were derived from CD19 selected bone marrow biopsies. Deidentified clinical annotation of these samples is also included. Samples range from patients at the earliest stages of disease development to those who are about to initiate therapy. The aim of this study is to look for clinical/molecular subtypes of WM and study the biology of disease evolution/progression.

  Study EGAS50000002182

• Multi-omics analysis revealed clonal evolution of the sarcoma patient-derived xenograft

  We performed whole-exome sequencing and RNA-seq of sarcoma PDXs, along with their matched original tumors when available.

  Study EGAS50000001860

• Genomic sequencing in an oesophageal adenocarcinoma cohort

  Genome sequencing was used to assess genomic alterations associated with survival in a Swedish cohort of 65 oesophageal adenocarcinoma (OAC) patients. Primary tumour tissues and matched normal squamous oesophagus tissues were sequenced using a 451 cancer-associated gene panel. This dataset consists of sequence data in fastq format.

  Dataset EGAD50000003139

• MEDIOLA WOO serial tumor RNA sequencing (raw reads)

  Poly(A)-selected RNA sequencing of 160 fresh-frozen serial tumor biopsies from 54 patients with stage II/III triple-negative or ER-low breast cancer enrolled in the MEDIOLA window-of-opportunity trial (NCT03594396). Biopsies were obtained at baseline (n = 54), on day 14 after olaparib alone and before durvalumab (n = 54), and on day 29 after olaparib plus a single dose of durvalumab (n = 52). Libraries were prepared with the TruSeq Stranded mRNA LT kit and sequenced as paired-end reads on an Illumina NovaSeq 6000. The dataset comprises 320 paired-end FASTQ files (160 runs), encrypted with Crypt4GH.

  Dataset EGAD50000002906

• MEDIOLA WOO baseline tumor and germline whole-exome sequencing (raw reads)

  Whole-exome sequencing of baseline primary breast tumor biopsies and matched peripheral-blood germline DNA from 54 patients with stage II/III triple-negative or ER-low breast cancer enrolled in the MEDIOLA window-of-opportunity trial (NCT03594396), comprising 54 tumor-normal pairs. Exome libraries were prepared with the SureSelect V6 Post Capture Exome Kit and sequenced as 101-bp paired-end reads on an Illumina NovaSeq 6000. The dataset comprises 216 paired-end FASTQ files (108 runs), encrypted with Crypt4GH.

  Dataset EGAD50000002907

• Whole-Exome Sequencing Analysis of Tumor Biopsies from a Colorectal Cancer Patient

  After the sequencing, reads were aligned against the reference human genome GRCh38 using Burrows-Wheeler Aligner (BWA, v0.7.12). SNVs and indels were called using MuTect2 (GATK 4.1.4.1). SNVs or indels with a VAF < 5% or those that were covered by fewer than three reads were discarded., iIf the SNVs were found in both components of one sample, a cut-off of two reads was applied. We further excluded variants identified in at least two of a panel of 210 non-tumor samples, including the non-tumor samples included in the current study. Variant annotation was performed by SnpEff software v.4.1.

  Dataset EGAD50000002011