We analyzed whole-exome hybrid capture Illumina sequencing (WES) 36 (link) data from 214 ovarian carcinoma tumor-normal pairs previously analyzed by the TCGA consortium 33 (link). We used the program muTect (K. Cibulskis, et al., in preparation.) We have used a newer version of the program muTect than used in previous analysis of this data 33 (link). The primary improvement in the new version is a reduction in the prior that somatic mutations be at an allelic fraction of 0.5, allowing greater sensitive at low allelic-fraction mutations, such as clonal events in impure samples, or to subclonal mutations. This procedure resulted in 29,268 somatic mutations.
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Ovarian Neoplasm
Ovarian Neoplasm
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Most cited protocols related to «Ovarian Neoplasm»
Alleles
Carcinoma
Clone Cells
Diploid Cell
Hybrids
Mutation
Neoplasms
Ovarian Cancer
Ovarian Neoplasm
The extent to which the ovarian cancer cell lines match genetic characteristics shared by the majority of TCGA high-grade serous ovarian tumours was assessed using an empirical numerical score. This suitability score S, in which selected features of HGSOC are positively weighted and characteristics of other ovarian cancer subtypes are negatively weighted is given by
where A is the correlation with the mean CNA of HGSOC tumours, B is 1 for cell lines harbouring a TP53 mutation and 0 otherwise, C is 1 for hypermutated cell lines and 0 otherwise, and D is the number of genes mutated among the seven ‘non-HGSOC’ genes recurrently altered only in the other ovarian cancer subtypes (ARID1A, BRAF, CTNNB1, ERBB2, KRAS, PIK3CA and PTEN). This score serves to distinguish better and poorer cell line models of HGSOC, but is not considered a finely graduated ranking (Supplementary Data S1 ).
where A is the correlation with the mean CNA of HGSOC tumours, B is 1 for cell lines harbouring a TP53 mutation and 0 otherwise, C is 1 for hypermutated cell lines and 0 otherwise, and D is the number of genes mutated among the seven ‘non-HGSOC’ genes recurrently altered only in the other ovarian cancer subtypes (ARID1A, BRAF, CTNNB1, ERBB2, KRAS, PIK3CA and PTEN). This score serves to distinguish better and poorer cell line models of HGSOC, but is not considered a finely graduated ranking (
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ARID1A protein, human
Be1 Cells
BRAF protein, human
Cell Lines
CTNNB1 protein, human
ERBB2 protein, human
Genes
K-ras Genes
Mutation
Neoplasms
Ovarian Cancer
Ovarian Neoplasm
PIK3CA protein, human
PTEN protein, human
Reproduction
Serum
TP53 protein, human
Breast Neoplasm
Cell Lines
Colonic Neoplasms
Gene Expression
Gene Products, Protein
Genes
Ovarian Neoplasm
Transcription, Genetic
Microarray gene expression data from frozen tissue samples obtained at the time of primary cytoreductive surgery from two previously-published human ovarian cancer cohorts were also used for the development and independent evaluation of our molecular predictors. The first cohort of 185 primary ovarian tumors treated with adjuvant chemotherapy was originally obtained for identifying prognostic molecular signatures of survival [15] (link). We used the subset of 167 patients with platinum-based chemotherapeutic response information for our predictor development. These patients comprised 112 (67%) complete response (CR), 41 (25%) partial response (PR), and 14 (8%) progress of disease (PD). The second set (Dressman-119) of 119 ovarian cancer patients from the Duke University and H. Lee Moffitt Cancer Center also received platinum-based adjuvant chemotherapy [9] (link). Of 119, 85 (71%) patients had a complete response whereas 34 (29%) patients showed an incomplete response (IR) to the chemotherapy. Expression profiling data of the frozen-tissue tumor samples from both sets were available with Affymetrix HG-U133A GeneChip® arrays.
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Biological Markers
Chemotherapy, Adjuvant
Cytoreductive Surgery
Freezing
Gene Chips
Gene Expression
Homo sapiens
Malignant Neoplasms
Microarray Analysis
Neoplasms
Ovarian Cancer
Ovarian Neoplasm
Patients
Pharmacotherapy
Platinum
Tissues
We benchmarked SpeedSeq’s processing time using the NA12878 genome from the Illumina Platinum Genomes dataset (European Nucleotide Archive: ERP001960), which comprises 50× WGS datasets for each of the 17 members of the three-generation CEPH 1463 pedigree (Supplementary Fig. 4 ).
Whole-genome sequencing data from five matched tumor-normal pairs and their orthogonally validated somatic mutations were obtained from The Cancer Genome Atlas (TCGA). These included three colorectal tumors (TCGA-A6-6141, TCGA-CA-6718, TCGA-D5-6540), one ovarian tumor (TCGA-13-0751), and one breast tumor (TCGA-B6-A0I6). Raw FASTQ reads were down-sampled to 50× coverage in the tumor and 30× coverage in the normal sample. Samples were processed with SpeedSeq for alignment, somatic mutations, and structural variants using default parameters and then loaded into GEMINI for variant interpretation. We also analyzed WGS data from a tumor-normal pair (63× tumor, 49× normal coverage) of a patient with an invasive breast carcinoma (TCGA-E2-A14P) containing a previously reported gene fusion between TBL1XR1 and PIK3CA20 .
Whole-genome sequencing data from five matched tumor-normal pairs and their orthogonally validated somatic mutations were obtained from The Cancer Genome Atlas (TCGA). These included three colorectal tumors (TCGA-A6-6141, TCGA-CA-6718, TCGA-D5-6540), one ovarian tumor (TCGA-13-0751), and one breast tumor (TCGA-B6-A0I6). Raw FASTQ reads were down-sampled to 50× coverage in the tumor and 30× coverage in the normal sample. Samples were processed with SpeedSeq for alignment, somatic mutations, and structural variants using default parameters and then loaded into GEMINI for variant interpretation. We also analyzed WGS data from a tumor-normal pair (63× tumor, 49× normal coverage) of a patient with an invasive breast carcinoma (TCGA-E2-A14P) containing a previously reported gene fusion between TBL1XR1 and PIK3CA20 .
Breast Carcinoma
Breast Neoplasm
Colorectal Neoplasms
Diploid Cell
Europeans
Gene Fusion
Genome
Malignant Neoplasms
Mutation
Neoplasms
Nucleotides
Ovarian Neoplasm
Patients
Platinum
TBLR1 protein, human
Most recents protocols related to «Ovarian Neoplasm»
Example 4
Synthesis of Peptides
All peptides were synthesized using standard and well-established solid phase peptide synthesis using the Fmoc-strategy. Identity and purity of each individual peptide have been determined by mass spectrometry and analytical RP-HPLC. The peptides were obtained as white to off-white lyophilizes (trifluoro acetate salt) in purities of >50%. All TUMAPs are preferably administered as trifluoro-acetate salts or acetate salts, other salt-forms are also possible.
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Acetate
High-Performance Liquid Chromatographies
Immunotherapy
Malignant Neoplasms
Mass Spectrometry
Ovarian Neoplasm
Peptide Biosynthesis
Peptides
Salts
Sodium Chloride
The study cohort included 35 patients with GI cancer with KTs who underwent mass resection in the Gastrointestinal Surgery Department of Guangxi Medical University Cancer Hospital from June 2014 to June 2020.
Inclusion criteria included (1): the primary lesion was located in the stomach or colorectum and was diagnosed as KTs following differentiation from primary malignant or benign ovarian tumor, as revealed by pathological examination and (2) clinical data were complete, pathological wax blocks were well-preserved, and long-term follow-up data were obtained.
Exclusion criteria included (1): other tumors or intestinal diseases (2); primary foci originating from other sites, such as breast, appendix, and cervix; and (3) patients who simply received medical treatment, out-of-hospital surgery, or just received pathological consultation in our hospital.
Inclusion criteria included (1): the primary lesion was located in the stomach or colorectum and was diagnosed as KTs following differentiation from primary malignant or benign ovarian tumor, as revealed by pathological examination and (2) clinical data were complete, pathological wax blocks were well-preserved, and long-term follow-up data were obtained.
Exclusion criteria included (1): other tumors or intestinal diseases (2); primary foci originating from other sites, such as breast, appendix, and cervix; and (3) patients who simply received medical treatment, out-of-hospital surgery, or just received pathological consultation in our hospital.
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Breast
Cervix Uteri
Gastrointestinal Cancer
Intestinal Diseases
Malignant Neoplasms
Neoplasms
Operative Surgical Procedures
Ovarian Neoplasm
Patients
Stomach
We retrospectively collected information from 273 patients who underwent IVF/ICSI with fresh embryo transfer following an endometrial curettage in the proliferative-phase from January 2020 to May 2022 in the Reproductive Hospital of Jiangxi University of Traditional Chinese Medicine. These patients had no or only 1 previously failed cycle. Patients with uterine abnormalities, endometriosis, intrauterine adhesions (moderate-severe), adenomyosis, uterine mediastina and ovarian tumors, untreated hydrosalpinx, or abnormal uterine bleeding were excluded. All data of patients on demographics, baseline values, and pregnancy outcomes were available. We obtained ethical approval from the Medical Ethics Committee of Nanchang Reproductive Hospital (the Reproductive Hospital of Jiangxi University of Traditional Chinese Medicine) (approval number 2022.005).
Adenomyosis
Curettage
Endometriosis
Endometrium
Ethics Committees, Clinical
Mediastinum
Menstrual Cycle, Proliferative Phase
Ovarian Neoplasm
Patients
Reproduction
Sperm Injections, Intracytoplasmic
Tissue Adhesions
Transfers, Embryo
Uterine Anomalies
Uterus
Ovarian tumor samples were fixed in 4% paraformaldehyde. The tissue was dehydrated, embedded in paraffin, and sectioned for immunohistochemistry. The stained samples were observed and photographed under a microscope. A positive reaction was scored by the appearance of brownish yellow or tan particles, and the intensity of the staining was scored. Positive scoring was divided into weak positive, medium positive, and strong positive. A negative result was scored as “0 points”, weak positive was light yellow and scored as “+ or 1 point”, medium positive was brown and scored “++ or 2 points”, and strong positive was tan and scored “+++ or 3 points”. The average score of three independent investigators was used to define the target protein level.
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Debility
Immunohistochemistry
Light
Microscopy
Ovarian Neoplasm
Paraffin Embedding
paraform
Proteins
Tissues
This study was divided into three steps: (i) preparation and characterization of ORN; (ii) assessment of the ORN-PDT efficacy using tumor models in fragments of ovarian tissue; and (iii) assessment of the PDT specificity using ovarian biopsies of young patients (Fig. 1 ). In the first step, the ORN was prepared by our previously optimized method (Moghassemi et al., 2022d ), and its characteristics, including size, polydispersity index, and zeta potential were studied. Then, in the following step, the efficiency of the best OR/ORN-PDT purging protocol was analyzed on TIMs created by HL-60 cells microinjected into ovarian tissue. Finally, the third step aimed to evaluate the effect of the PDT approach on the follicle population and ovarian tissue quality to ensure that such treatment is not harmful to follicle survival and development for it to be deemed a potential fertility restoration alternative.
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Biopsy
Fertility
HAVCR1 protein, human
HL-60 Cells
Ovarian Follicle
Ovarian Neoplasm
Ovary
Patients
Tissues
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Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
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SKOV3 is a cell line derived from a human ovarian adenocarcinoma. It is commonly used in scientific research as a model for the study of ovarian cancer.
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Penicillin is a type of antibiotic used in laboratory settings. It is a broad-spectrum antimicrobial agent effective against a variety of bacteria. Penicillin functions by disrupting the bacterial cell wall, leading to cell death.
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Streptomycin is a broad-spectrum antibiotic used in laboratory settings. It functions as a protein synthesis inhibitor, targeting the 30S subunit of bacterial ribosomes, which plays a crucial role in the translation of genetic information into proteins. Streptomycin is commonly used in microbiological research and applications that require selective inhibition of bacterial growth.
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RPMI 1640 medium is a commonly used cell culture medium developed at Roswell Park Memorial Institute. It is a balanced salt solution that provides essential nutrients, vitamins, and amino acids to support the growth and maintenance of a variety of cell types in vitro.
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DMEM (Dulbecco's Modified Eagle's Medium) is a cell culture medium formulated to support the growth and maintenance of a variety of cell types, including mammalian cells. It provides essential nutrients, amino acids, vitamins, and other components necessary for cell proliferation and survival in an in vitro environment.
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OVCAR3 is a cell line derived from a human ovarian adenocarcinoma. It is commonly used in research for the study of ovarian cancer.
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RPMI 1640 is a common cell culture medium used for the in vitro cultivation of a variety of cells, including human and animal cells. It provides a balanced salt solution and a source of essential nutrients and growth factors to support cell growth and proliferation.
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The A2780 is a cell line derived from human ovarian carcinoma. It is a commonly used in vitro model for studying ovarian cancer.
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SKOV3 is a type of human ovarian cancer cell line commonly used in laboratory research. The SKOV3 cell line is derived from the ascites of a patient with ovarian adenocarcinoma. These cells are routinely used to study various aspects of ovarian cancer, including proliferation, migration, and drug response.
More about "Ovarian Neoplasm"
Ovarian Cancer, Ovarian Carcinoma, Ovarian Tumors, Ovarian Neoplasms, Ovarian Malignancies, Ovarian Adenocarcinoma, Ovarian Epithelial Carcinoma, Ovarian Germ Cell Tumors, Ovarian Sex Cord-Stromal Tumors, Ovarian Serous Carcinoma, Ovarian Mucinous Carcinoma, Ovarian Clear Cell Carcinoma, Ovarian Endometrioid Carcinoma.
Ovarian cancer is a type of gynecological cancer that originates in the ovaries, the female reproductive organs responsible for producing eggs and female hormones.
It is one of the most common and deadly gynecological cancers, often diagnosed at advanced stages due to a lack of early symptoms.
The etiology of ovarian cancer is multifactorial, involving genetic, hormonal, and environmental factors.
Certain risk factors include family history, genetic mutations (e.g., BRCA1/BRCA2), reproductive history, and age.
Subtypes of ovarian cancer include epithelial (the most common), germ cell, and sex cord-stromal tumors, each with distinct characteristics and treatment approaches.
In vitro models used to study ovarian cancer include cell lines such as FBS, SKOV3, OVCAR3, and A2780, which are often cultured in RPMI 1640 or DMEM media supplemented with fetal bovine serum (FBS) and antibiotics like penicillin and streptomycin.
These models help researchers investigate the biology, pathogenesis, and potential therapies for this complex disease.
Advances in genomics, proteomics, and imaging technologies have led to a better understanding of the molecular mechanisms underlying ovarian cancer, paving the way for the development of targeted therapies and personalized treatment approaches.
Ongoing research aims to improve early detection, optimize treatment strategies, and enhance the quality of life for patients with ovarian neoplasms.
Ovarian cancer is a type of gynecological cancer that originates in the ovaries, the female reproductive organs responsible for producing eggs and female hormones.
It is one of the most common and deadly gynecological cancers, often diagnosed at advanced stages due to a lack of early symptoms.
The etiology of ovarian cancer is multifactorial, involving genetic, hormonal, and environmental factors.
Certain risk factors include family history, genetic mutations (e.g., BRCA1/BRCA2), reproductive history, and age.
Subtypes of ovarian cancer include epithelial (the most common), germ cell, and sex cord-stromal tumors, each with distinct characteristics and treatment approaches.
In vitro models used to study ovarian cancer include cell lines such as FBS, SKOV3, OVCAR3, and A2780, which are often cultured in RPMI 1640 or DMEM media supplemented with fetal bovine serum (FBS) and antibiotics like penicillin and streptomycin.
These models help researchers investigate the biology, pathogenesis, and potential therapies for this complex disease.
Advances in genomics, proteomics, and imaging technologies have led to a better understanding of the molecular mechanisms underlying ovarian cancer, paving the way for the development of targeted therapies and personalized treatment approaches.
Ongoing research aims to improve early detection, optimize treatment strategies, and enhance the quality of life for patients with ovarian neoplasms.