Ontology highlight
ABSTRACT:
PROVIDER: PRJNA638698 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: The uncommonness of gallbladder cancer in the developed world has contributed to the generally poor understanding of the disease. The development of new and effective treatment has been and continues to be a major public health imperative. Methods: We report mutational and copy number analysis of 44 predominantly early-staged gallbladder tumors and 5-gallbladder cancer cell lines by a combination of directed and whole exome sequencing at an average coverage of 100X and above. Using gallbladder cancer cell lines and xenograft mouse models we performed phospho-proteome array profiling, followed by an in-depth functional characterization. Results: We describe recurrent activating ERBB2 somatic mutation in 6 of 44 gallbladder primary tumors with an overall mutation frequency of 13%, along with KRAS activating mutations in 3 of 44 samples. Consistent with whole exome findings, a phospho-proteomic array profile of 49-tyrosine kinase revealed constitutive phosphorylation of ERBB2 and EGFR that were found to heterodimerize. We demonstrate that treatment with ERBB2-specific, EGFR-specific shRNA or with covalent EGFR family inhibitor BIBW-2992 inhibits transformation, survival, migration, invasion, and tumor forming characteristics of gallbladder cancer cells harboring wild type or KRAS (G13D) but not KRAS (G12V) mutation. Furthermore, we show in vivo reduction in tumor size is paralleled by a reduction in the amounts of phospho-ERK in KRAS (G13D) but not in KRAS (G12V) xenografts, validating the in vitro findings Conclusion: Findings from this study implicate ERBB2 as an important therapeutic target in early stage gallbladder cancer. We also present the first evidence that the presence of KRAS (G12V), but not KRAS (G13D) mutation, may preclude gallbladder cancer patients to respond to anti-EGFR treatment, similar to the clinical algorithm commonly practiced to opt for anti-EGFR treatment in colorectal cancer.
2018-12-29 | E-MTAB-6619 | biostudies-arrayexpress
Project description:Cancer is predominantly a somatic disease. A mutant allele found in cancer cell genome is considered somatic when it is absent in paired normal genome and dbSNP, the most comprehensive public SNP database. However, dbSNP inadequately represents several non-Caucasian populations including that from the Indian subcontinent, posing a limitation in cancer genomic analyses of data from these populations. We present TMC-SNPdb, as the first open source freely accessible (through ANNOVAR), flexible and upgradable SNP database from whole exome data of 62 normal samples derived from cancer patients of Indian origin, representing 114,309 unique germline variants. TMC-SNPdb is presented with a companion subtraction tool that can be executed with command line option or an easy-to-use graphical user interface (GUI) with the ability to deplete additional Indian population specific SNPs over and above that possible with dbSNP and 1000 Genomes databases. Using an institutional generated whole exome data set of 132 samples of Indian origin, we demonstrate that TMC-SNPdb reduced 42%, 33% and 28% false positive somatic events post dbSNP depletion in Indian origin tongue, gallbladder, and cervical cancer samples, respectively. Beyond cancer somatic analyses, we anticipate utility of TMC-SNPdb in several Mendelian germline diseases.
2018-06-06 | E-MTAB-4618 | biostudies-arrayexpress
Project description:Whole exome sequencing of 5 MDS/MPN patients to identify the target of chromosome 22 acquired uniparental disomy (22aUPD). For samples E4051 and E6523, peripheral blood leucocytes (tumour) and cultured T-cells (germline) were prepared for exome sequencing using the Agilent SureSelect kit (Agilent Technologies, Palo Alto, CA, USA) (Human All Exon 50 Mb) and then sequenced on an Illumina HiSeq 2000 (Illumina, Great Abington, UK) at the Wellcome Trust Centre for Human Genetics, Oxford, UK. For samples ULSAM1182, ULSAM1242 and ULSAM1356, peripheral blood leukocyte DNA only were exome sequenced by SciLifeLab (Stockholm, Sweden).
2019-01-22 | E-MTAB-7491 | biostudies-arrayexpress
Project description:RNA sequencing and whole-exome sequencing data were obtained from 30 platinum-resistant recurrent ovarian cancer samples.
2023-05-01 | GSE230541 | GEO
Project description:Agilent whole exome hybridisation capture was performed on genomic DNA derived from Chondrosarcoma cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products.
2016-05-17 | E-ERAD-37 | biostudies-arrayexpress
Project description:Formalin-fixed paraffin-embedded (FFPE) tissues are a vast resource of annotated clinical samples. As such, they represent highly desirable and informative materials for the application of high-definition genomics for improved patient management and to advance the development of personalized therapeutics. However, a limitation of FFPE tissues is the variable quality of DNA extracted for analyses. Furthermore, admixtures of non-tumor and polyclonal neoplastic cell populations limit the number of biopsies that can be studied and make it difficult to define cancer genomes in patient samples. To exploit these valuable tissues, we applied flow cytometry-based methods to isolate pure populations of tumor cell nuclei from FFPE tissues and developed a methodology compatible with oligonucleotide array CGH and whole exome sequencing analyses. These were used to profile a variety of tumors (breast, brain, bladder, ovarian and pancreas), including the genomes and exomes of matching fresh frozen and FFPE pancreatic adenocarcinoma samples.
2012-12-31 | GSE40299 | GEO
Project description:Purpose: There are three goals of this study: 1. To compare the genomic, exome and chromatin accessiblity profiles of the specific engineered fallopian tube cells of high-grade serous tubo-ovarian cancer (HGSC) models (this study) using whole-exome, whole-genome and ATAC-seq sequencing. Methods: For whole-exome analysis, genomic DNA was extracted from the cell lines mentioned below. Conclusions: We conclude that whole-exome, whole-genome and ATAC-seq characterization would expedite genetic network analyses and permit the dissection of complex biological functions.
2020-11-17 | GSE159253 | GEO
Project description:Whole exome sequencing identification of putative founder mutations in non-BRCA1/2 breast cancer patients
2013-08-08 | E-MTAB-1172 | biostudies-arrayexpress
Project description:For many years, immortalized cell lines have been used as model systems for cancer research. Cell line panels were established for basic research and drug development, but did not cover the full spectrum of leukemia and lymphoma. Therefore, we now developed a novel panel (LL-100), 100 cell lines covering 22 entities of human leukemia and lymphoma including T-cell, B-cell and myeloid malignancies. Importantly, all cell lines are unequivocally authenticated and assigned to the correct tissue. Cell line samples were proven to be free of mycoplasma and virus contamination. Whole exome sequencing (WES) and RNA sequencing (RNA-seq) of the hundred authenticated leukemia-lymphoma cell lines were conducted with a uniform methodology to complement existing data on these publicly available cell lines. This part captures WES. This data set will be useful for understanding the function of oncogenes and tumor suppressor genes and to develop targeted therapies.
2019-05-28 | E-MTAB-7722 | biostudies-arrayexpress