9295 results for "cancer rna-seq"

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• Genome and transcriptome sequence data from a embryonal rhabdomyosarcoma tumor patient

  Genome and transcriptome sequence data from a embryonal rhabdomyosarcoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015330

• Genome and transcriptome sequence data from a pIlomyxoid astrocytoma tumor patient

  Genome and transcriptome sequence data from a pIlomyxoid astrocytoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015333

• Genome and transcriptome sequence data from a wilms tumor tumor patient

  Genome and transcriptome sequence data from a wilms tumor patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015334

• Genome and transcriptome sequence data from a rhabdomyosarcoma, alveolar tumor patient

  Genome and transcriptome sequence data from a rhabdomyosarcoma, alveolar patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015335

• Orphan_Tumour_Study___RNAseq

  The aim of this study is to study the genomes of ultra rare childhood tumours

  Study EGAS00001002534

• CZ_END-2-END_final

  CZ FINAL END-2-END demo dataset with one sample of a synthetic variants from fake brest cancer patient.

  Dataset EGAD50000000475

• Cell_lines_with_telomere_fusion_induced_rearrangements

  Whole-genome somatic rearrangement and point mutation analysis in cell lines with induced telomere fusions.

  Study EGAS00001001059

• Origins and functional consequence of somatic mitochondrial DNA mutations

  Recent sequencing studies have extensively explored the somatic alterations present in the nuclear genomes of cancers. Although mitochondria control energy metabolism and apoptosis, the origins and impact of cancer-associated mutations in mitochondrial DNA (mtDNA) are unclear. Here, we analysed somatic alterations in mtDNA from 1,675 tumors across 31 histologies. We identified 1,907 somatic substitutions, which exhibited dramatic replicative strand bias, predominantly C>T and A>G on the mitochondrial heavy strand. This strand-asymmetric signature differs from those found in nuclear cancer genomes but matches the inferred germline process shaping primate mtDNA sequence content. Numbers of mtDNA mutations showed considerable heterogeneity across tumor types. Missense mutations were selectively neutral and often gradually drifted towards homoplasmy over time. In contrast, mutations resulting in protein truncation undergo negative selection and were almost exclusively heteroplasmic. Our findings indicate that the endogenous mutational mechanism has far greater impact than any other external mutagens in mitochondria, and is fundamentally linked to mtDNA replication.

  Study EGAS00001000968

• Whole-exome sequencing reveals the origin and evolution of Hepato-Cholangiocarcinoma

  Hepatocellular-cholangiocarcinoma (H-ChC) is a rare subtype of liver cancer with clinicopathological features of both hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA). To date, molecular mechanisms underlying the co-existence of HCC and iCCA components in a single tumor remain elusive. Here we show that H-ChC samples contain substantial private mutations from WES analyses, ranging from 33.1% to 86.4%, indicative of substantive intratumor heterogeneity (ITH). However, on the other hand, numerous ubiquitous mutations shared by HCC and iCCA suggest the monoclonal origin of H-ChC. Mutated genes identify herein e.g. VCAN, ACVR2A and FCGBP are speculated to contribute to distinct differentiation of HCC and iCCA within H-ChC. Moreover, immunohistochemistry demonstrate that EpCAM is highly expressed in 80% of H-ChC implying the stemness of such liver cancer. In summary, our data highlight the monoclonal origin and stemness of H-ChC, as well as substantial intratumoral heterogeneity.

  Study EGAS00001002783

• Comparing nodal versus bony metastatic spread using tumour phylogenies

  The role of lymph node metastases in distant prostate cancer dissemination and lethality is ill defined. Patients with metastases restricted to lymph nodes have a better prognosis than those with distant metastatic spread, suggesting the possibility of distinct aetiologies. To explore this, we traced patterns of cancer dissemination using tumour phylogenies inferred from genome-wide copy-number profiling of 48 samples across 3 patients with lymph node metastatic disease and 3 patients with osseous metastatic disease. Our results show that metastatic cells in regional lymph nodes originate from evolutionary advanced extra-prostatic tumour cells rather than less advanced central tumour cell populations. In contrast, osseous metastases do not exhibit such a constrained developmental lineage, arising from either intra or extra-prostatic tumour cell populations, at early and late stages in the evolution of the primary. Collectively, this comparison suggests that lymph node metastases may not be an intermediate developmental step for distant osseous metastases, but rather represent a distinct metastatic lineage.

  Study EGAS00001001801