Ena-DATASET-DUKE-NUS-08-09-2014-07:15:03:235-173 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001001002 | EGA |
REPOSITORIES: EGA
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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
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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.
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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:BackgroundIn Canada, increasing numbers of women, especially First Nations women, are affected by diabetes during pregnancy, which is a major risk factor for adverse maternal and neonatal outcomes. The aim of this study was to examine temporal trends in pregnancy outcomes and use of health care services in a population-based cohort of First Nations women compared to other women in Ontario according to diabetes status during pregnancy.MethodsUsing health administrative databases, we created annual cohorts of pregnant women from 2002/03 to 2014/15 and identified those with preexisting diabetes and gestational diabetes. We used the Indian Register to identify First Nations women. We estimated rates of adverse maternal and infant outcomes, and measures of use of health care services in each population.ResultsThere were 1 671 337 deliveries among 1 065 950 women during the study period; of these deliveries, 31 417 (1.9%) were in First Nations women, and 1 639 920 (98.1%) were in other women. First Nations women had a higher prevalence of preexisting diabetes and gestational diabetes than other women in Ontario. First Nations women with preexisting diabetes had higher rates of preeclampsia (3.2%-5.6%), labour induction (33.4%-42.9%) and cesarean delivery (47.8%-53.7%) than other women in Ontario, as did First Nations women with gestational diabetes (3.2%-4.7%, 38.5%-46.9% and 41.4%-43.4%, respectively). The rate of preterm birth was similar between First Nations women and other women in Ontario. Although First Nations women had a higher rate of babies who were large for gestational age than other women, regardless of diabetes status, obstructed labour rates were similar for the 2 cohorts. Almost all First Nations women, regardless of diabetes status, were seen by a primary care provider during their pregnancy, but rates of use of specialty care were lower for First Nations women than for other women. Fifteen percent of all pregnant women with preexisting diabetes visited an ophthalmologist during their pregnancy.InterpretationOur results confirm disparities in maternal and neonatal outcomes between First Nations women and other women in Ontario. Access to primary care for pregnant women seemed adequate, but access to specialized care, especially for women with preexisting diabetes, needs to improve.
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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.
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