Ena-DATASET-DUKE-NUS-08-09-2014-07:15:03:235-173 - samples
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ABSTRACT:
PROVIDER: EGAD00001001002 | EGA |
REPOSITORIES: EGA
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Project description:Neisseria gonorrhoeae strain:07/15/03 Genome sequencing and assembly
| PRJNA868293 | ENA
Project description:We performed whole exome sequencing and copy number analysis for 15 triplets, each comprising normal colorectal tissue, primary colorectal carcinoma, and its synchronous matched liver metastasis. We analyzed the similarities and differences between primary colorectal carcinoma and matched liver metastases in regards to somatic mutations and somatic copy number alterationss (SCNAs). The genomic profiling demonstrated mutations in APC(73%), KRAS (33%), ARID1A and PIK3CA (6.7%) genes between primary colorectal and metastatic liver tumors. TP53 mutation was observed in 47% of the primary samples and 67% in liver metastatic samples. The grouped pairs, in hierarchical clustering showed similar SCNA patterns, in contrast to the ungrouped pairs. Many mutations (including those of known key cancer driver genes) were shared in the grouped pairs. The ungrouped pairs exhibited distinct mutation patterns with no shared mutations in key driver genes. Four ungrouped liver metastasis samples had mutations in DNA mismatch repair genes along with hypermutations and a substantial number of copy number of alterations. Genomically, colorectal and metastatic liver tumors were very similar. However, in a subgroup of patients, there were genetic variations in liver metastases in the loss of DNA mismatch repair genes.
2014-03-01 | GSE53799 | GEO
Project description: Not available
| S-EPMC4261147 | biostudies-literature
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| S-EPMC4261148 | biostudies-literature
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| S-EPMC7402390 | biostudies-literature
Project description:Multicentric reticulohistiocytosis (MRH) is a rare cause of destructive inflammatory arthritis involving both small, as well as larger joints. We report the case of a 40-year-old Caucasian female with a family history of neoplasia who was referred to our service witha two-month history of inflammatory joint pain. On examination, the patient had inflammatory arthritis, mainly involving the peripheral joints, sacroiliac joint pain, and numerous papulonodular mucocutaneous lesions, including periungual "coral beads". Imaging tests revealed erosive arthritis with synovitis and tenosynovitis, sacroiliac joint changes, as well as papulonodular mucosal lesions in the nasal vestibule, the oropharyngeal mucosa, and supraglottic larynx. She tested positive for HLA-B*07 (Human Leukocyte Antigen B*07) and HLA-B*08, ANA (antinuclear antibodies), RF (rheumatoid factor), anti-Ro52, anti-SSA/Ro, and anti-SSB/La antibodies. The skin biopsy was suggestive of MRH, showing a histiocyte infiltrate and frequent giant multinucleated cells. The patient exhibited favorable outcomes under Methotrexate, then Leflunomide. However, she displayed worsening clinical symptoms while under Azathioprine. To our knowledge, this is the first case of MRH to exhibit positive HLA-B*07 together with HLA-B*08. The rarity of MRH, its unknown etiology and polymorphic clinical presentation, as well as its potential neoplastic/paraneoplastic, and autoimmune nature demand extensive investigation.
| S-EPMC7560105 | biostudies-literature
Project description:We performed whole exome sequencing and copy number analysis for 15 triplets, each comprising normal colorectal tissue, primary colorectal carcinoma, and its synchronous matched liver metastasis. We analyzed the similarities and differences between primary colorectal carcinoma and matched liver metastases in regards to somatic mutations and somatic copy number alterationss (SCNAs). The genomic profiling demonstrated mutations in APC(73%), KRAS (33%), ARID1A and PIK3CA (6.7%) genes between primary colorectal and metastatic liver tumors. TP53 mutation was observed in 47% of the primary samples and 67% in liver metastatic samples. The grouped pairs, in hierarchical clustering showed similar SCNA patterns, in contrast to the ungrouped pairs. Many mutations (including those of known key cancer driver genes) were shared in the grouped pairs. The ungrouped pairs exhibited distinct mutation patterns with no shared mutations in key driver genes. Four ungrouped liver metastasis samples had mutations in DNA mismatch repair genes along with hypermutations and a substantial number of copy number of alterations. Genomically, colorectal and metastatic liver tumors were very similar. However, in a subgroup of patients, there were genetic variations in liver metastases in the loss of DNA mismatch repair genes. Copy number analysis of Affymetrix CytoScanHD arrays was performed for 15 primary colorectal carcinoma and 15 samples of their matched liver metastases. 15 normal samples prepared from each of the patient was used as the reference for the study. Nexus Copy number 6.1 software was used for somatic copy number alteration analysis.
2014-03-01 | E-GEOD-53799 | biostudies-arrayexpress
Project description:BackgroundNorovirus (NoV) is a major cause of gastroenteritis during the autumn and winter seasons in Japan as well as in other temperate climate regions. Most outbreaks are thought to occur by secondary attacks through person-to-person infection by fecal-oral route. Severe cases are found in young children or patients with chronic diseases. Clarifying the patterns of epidemic diffusion is important for considering effective monitoring and surveillance as well as possible prevention.MethodsWe considered the predominant viral genotype from the laboratory result obtained from Infectious Agents Surveillance Report (IASR) of National Institute of Infectious Diseases (NIID). We investigated the increase of NoV cases nationwide for the 2006-07 to 2008-09 seasons using sentinel gastroenteritis data collected from about 3000 pediatric clinics on National Epidemiological Surveillance of Infectious Diseases (NESID) acquired from the kriging method in the geographic information system (GIS).ResultsDuring these three seasons, the majority of the detected virus was GII.4, which ranged from 60.4 to 88.9%. The number of cases (per sentinel site) at the peak week was 22.81 in the 2006-07 season and it decreased in the following seasons. NoV cases began to increase earlier in the southern areas and gradually extended into the northern areas, similarly, over the seasons. The average period from when the increase of cases was detected in the southern area to when it reached the northern area was 12.7 weeks.ConclusionThe decrease of the number of sentinel cases at the peak week may suggest the development of herd immunity after a period of high prevalence. Although the NoV epidemic is thought to be associated with cold weather, its cases first increased in the southern area with relatively warm temperature, indicating there are other climate factors involved. Geographic study using the sentinel data could enhance the monitoring and surveillance of and preparedness against epidemics.
| S-EPMC3747177 | biostudies-literature
Project description:RNA timecourse data for Streptomyces fradiae wildtype (ATCC19609) and overproducing strain KOS155-3C(RUS). Strains were grown at 30 C in shake flask cultures in R5 medium with no glucose. RNA samples were harvested over 5 days as tylosin was produced. 12 h RNA samples of each strain were used as the reference sample(green) within their respective timecourses. The WT gDNA vs. 12 h RNA control displays relative gene expression at the beginning of the timecourse. The 12 h RNA control compares initial RNA levels between the WT and overproducer. Groups of assays that are related as part of a time series. Keywords: time_series_design
2005-07-26 | GSE2995 | GEO
Project description:Strong associations between HLA alleles and infectious and autoimmune diseases are well established. Although obesity is also associated with these diseases, the relationship between HLA and obesity has not been systematically investigated in a large cohort. In the current study, we analyzed the association of HLA alleles with BMI using data from 1.3 million healthy adult donors from the Chinese Marrow Donor Program (CMDP). We found 23 HLA alleles, including 12 low-resolution and 11 high-resolution alleles, were significantly associated with BMI after correction for multiple testing. Alleles associated with high BMI were enriched in haplotypes that were common in both Chinese and European populations, whereas the alleles associated with low BMI were enriched in haplotypes common only in Asians. Alleles B*07, DRB1*07, DRB1*12, and C*03:02 provided the strongest associations with BMI (P = 6.89 × 10-10, 1.32 × 10-9, 1.52 × 10-9, and 4.45 × 10-8, respectively), where B*07 and DRB1*07 also had evidence for sex-specific effects (Pheterogeneity = 0.0067 and 0.00058, respectively). These results, which identify associations between alleles of HLA-B, DRB1, and C with BMI in Chinese young adults, implicate a novel biological connection between HLA alleles and obesity.
| S-EPMC6463754 | biostudies-literature