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• Analysis of genomic alterations in dedifferentiated liposarcoma

  Multiomics analysis of rare cancers to identify genetic alterations related with pathogenesis and prognosis. To identification of genetics alterations of Dedifferentiated liposarcoma, DNAs and RNAs were extracted from dedifferentiated liposarcoma and paired non-cancer (normal) tissues. NGS libaraies were prepared by using Agilent SureSelect XT Human All Exon V5 + IncRNA kit for whole exome sequencing (WES) and TruSeq Stranded mRNA Prep kit or TruSeq RNA Access Library Prep kit (RNA seq). Sequencing was perfomred by Illumina HiSeq 2500.

  Study JGAS000182

• Paired exome analysis in urothelial carcinoma

  In this study we characterized genomic alterations in two to five metachronous tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth), Ultra deep targeted sequencing (~6,809x mean read depth) and whole transcriptome RNA-seq was performed for all samples. In addition multiregional WES was performed on 8 adjacent regions from a single tumor.

  Study EGAS00001001686

• High-grade serous ovarian cancer refined with single-cell RNA-sequencing

  We performed single-cell RNA-sequencing of 18,403 cells unbiasedly collected from 7 treatment-naive HGSOC tumours. For each phenotypic cluster of tumour or stromal cells, we identified specific transcriptomic markers. Next, we explored which phenotypic clusters correlate with overall survival based on expression of these transcriptomic markers in 1467 bulk RNA-seq tumours. By evaluating molecular subtype signatures in single cells, we assessed to what extent a phenotypic cluster of tumour or stromal cells contributes to each molecular subtype.

  Study EGAS00001004987

• Whole genome analysis of mutation hotspots in gastric cancer

  Tissue-specific driver mutations in non-coding genomic regions remain undefined for most cancer types. In this study, we unbiasedly analysed 212 gastric cancer whole genomes to identify recurrently mutated non-coding regions in gastric cancer. Applying comprehensive statistical approa- ches to accurately model background mutational processes, we observe significant enrich- ment of non-coding indels (insertions/deletions) in three gastric lineage-specific genes. We further identify 34 mutation hotspots, of which 11 overlap CTCF binding sites (CBSs).

  Study EGAS00001002872

• Single Cell Genome Sequence for DLP+ library A118814B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1162B passage 1 on DLP+ library A118814B

  Dataset EGAD00001009443

• Single Cell Genome Sequence for DLP+ library A118808B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1096C passage 1 on DLP+ library A118808B

  Dataset EGAD00001009441

• Single Cell Genome Sequence for DLP+ library A118804A

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1162B passage 1, patient-derived xenograft SA1096B passage 1 on DLP+ library A118804A

  Dataset EGAD00001009439

• Single Cell Genome Sequence for DLP+ library A118797B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1184D passage 1 on DLP+ library A118797B

  Dataset EGAD00001009438

• Single Cell Genome Sequence for DLP+ library A118790A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA610 passage 3, patient-derived xenograft SA1096C passage 1 on DLP+ library A118790A

  Dataset EGAD00001009437

• Single Cell Genome Sequence for DLP+ library A118784A

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1050B passage 1, patient-derived xenograft SA1050E passage 1 on DLP+ library A118784A

  Dataset EGAD00001009436

• Single Cell Genome Sequence for DLP+ library A118425B

  Single Cell Genome Sequence for Immortalized breast epithelium BRCA2+/- Tp53-/- cell line 184-hTert L9 116.66 cell line SA1188 on DLP+ library A118425B

  Dataset EGAD00001009434

• Single Cell Genome Sequence for DLP+ library A118368B

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA605 passage 3 on DLP+ library A118368B

  Dataset EGAD00001009432

• Single Cell Genome Sequence for DLP+ library A118357B

  Single Cell Genome Sequence for Immortalized breast epithelium BRCA2+/- Tp53-/- cell line 184-hTert L9 116.66 cell line SA1188 on DLP+ library A118357B

  Dataset EGAD00001009431

• Single Cell Genome Sequence for DLP+ library A108847B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1182E passage 1 on DLP+ library A108847B

  Dataset EGAD00001009429

• Single Cell Genome Sequence for DLP+ library A95717B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1050D passage 1 on DLP+ library A95717B

  Dataset EGAD00001009489

• Single Cell Genome Sequence for DLP+ library A98243B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient SA1096A, patient-derived xenograft SA1052D passage 1 on DLP+ library A98243B

  Dataset EGAD00001009481

• Single Cell Genome Sequence for DLP+ library A98240A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA530 passage 3 on DLP+ library A98240A

  Dataset EGAD00001009480

• Single Cell Genome Sequence for DLP+ library A96222A

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient SA1105, patient SA1103, patient SA1106, patient SA1104 on DLP+ library A96222A

  Dataset EGAD00001009478

• Single Cell Genome Sequence for DLP+ library A96212B

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA604 passage 7 on DLP+ library A96212B

  Dataset EGAD00001009476

• Single Cell Genome Sequence for DLP+ library A96210B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient SA1047B on DLP+ library A96210B

  Dataset EGAD00001009475

• Single Cell Genome Sequence for DLP+ library A96207B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1052B passage 1 on DLP+ library A96207B

  Dataset EGAD00001009474

• Single Cell Genome Sequence for DLP+ library A96207A

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1051A passage 1 on DLP+ library A96207A

  Dataset EGAD00001009473

• Single Cell Genome Sequence for DLP+ library A96206B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1050F passage 1 on DLP+ library A96206B

  Dataset EGAD00001009472

• Single Cell Genome Sequence for DLP+ library A96205B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1049A passage 1 on DLP+ library A96205B

  Dataset EGAD00001009471

• Single Cell Genome Sequence for DLP+ library A96200B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1052D passage 1 on DLP+ library A96200B

  Dataset EGAD00001009470