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Targeted genome sequencing data of young women breast cancer patients in Cipto Mangunkusumo national hospital, Jakarta.

ABSTRACT: Breast cancer is the most common cancer in women, accounting for approximately 25% of all cancer cases worldwide. Some breast cancer patients are genetically predisposed to genes involved in genomic stability. We report the targeted genome sequencing data of 24 young women (aged below 45 years) breast cancer patients admitted to Cipto Mangunkusumo National Hospital, Jakarta, Indonesia. These data will be useful in detecting the genome markers of breast cancer and in deciding the diagnostics and therapies. DNA sequences were obtained using the Illumina NextSeq 500 platform. FASTQ raw files are available under BioProject accession number PRJNA606794 and Sequence Read Archive accession numbers SRR11774092-SRR11774115.

SUBMITTER: Panigoro SS

PROVIDER: S-EPMC7452687 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Targeted genome sequencing data of young women breast cancer patients in Cipto Mangunkusumo national hospital, Jakarta.

Panigoro Sonar Soni SS Siswiandari Kristina Maria KM Paramita Rafika Indah RI Fadilah Fadilah F Erlina Linda L

Data in brief 20200806

Breast cancer is the most common cancer in women, accounting for approximately 25% of all cancer cases worldwide. Some breast cancer patients are genetically predisposed to genes involved in genomic stability. We report the targeted genome sequencing data of 24 young women (aged below 45 years) breast cancer patients admitted to Cipto Mangunkusumo National Hospital, Jakarta, Indonesia. These data will be useful in detecting the genome markers of breast cancer and in deciding the diagnostics and ...[more]

PMID: 32904294

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Project description:IntroductionSpondylitis tuberculosis can cause changes in spinopelvic parameters including pelvic incidence, pelvic tilt, and sacral slope due to biomechanical changes of the spine. Posterior instrumentation is one of the modality for the treatment of spondylitis tuberculosis. However, in Indonesia, clinical and radiological outcomes after posterior instrumentation in tuberculosis of lumbar vertebrae are still rare. This study aims to investigate the clinical and radiological outcomes of patients with spondylitis tuberculosis of the lumbar vertebrae after posterior instrumentation.MethodThis study was a cross-sectional study in patients with spondylitis tuberculosis of the lumbar vertebrae who underwent posterior instrumentation in Cipto Mangunsukumo and Fatmawati Hospital. Subjects were collected through consecutive sampling. 23 subjects were collected and analyzed. Clinical and radiological outcomes before and after posterior instrumentation were compared. The clinical outcome included the Visual Analog Scale (VAS) and Oswestry Disability Index (ODI). The radiological outcome included sacral slope, pelvic tilt, pelvic incidence, and lumbar lordosis.ResultsThe median age of the subjects was 31 (9-57) years with a female-majority (60,9%). The median of the total vertebral infected was 2 (1-4). Median of VAS score before surgery, 6 months after surgery, and 12 months after surgery were 9 (4-10), 4 (1-7), dan 2 (1-6) (p < 0,001) consecutively. Median of ODI score before surgery, 6 months after surgery, and 12 months after surgery were 70 (40-86), 34 (10-74), dan 12 (2-74) (p < 0,001) consecutively. There was no significant difference in spinopelvic parameters before and after the surgery. The difference of ODI score before and after the surgery inversely correlated with the difference of lumbar lordotic and sacral slope.ConclusionPosterior instrumentation could improve clinical outcomes in patients with spondylitis tuberculosis of the lumbar. Change of lumbar lordotic and sacral slope after posterior instrumentation led to an improvement of quality of life marked by the reduction of the ODI score.

Project description:Background:Carbapenem-nonsusceptible A. baumannii-calcoaceticus complex have emerged worldwide, but the epidemiology in Indonesian hospitals has not been studied. Methods:A prospective observational study was performed on the intensive care units (ICUs) of the national referral hospital in Jakarta-Indonesia, in 2013 and 2014. All consecutive adult patients admitted and hospitalized for >48 h in ICUs were included. Basic and clinical data at admission were recorded. Carbapenem-nonsusceptible A. baumannii-calcoaceticus complex from clinical cultures and standardized screening were included. Environmental niches and healthcare workers (HCWs) were also screened. PCR was used to detect carbapenemase genes, and Raman spectroscopy as well as multilocus sequence typing (MLST) for typing. Results:Of 412 included patients, 69 (16.7%) carried carbapenem-nonsusceptible A. baumannii-calcoaceticus complex on admission, and 89 (25.9%) became positive during ICU stay. The acquisition rate was 43 per 1000 patient-days at risk. Six isolates were cultured from environment and one from a HCW. Acquisition of carbapenem-nonsusceptible A. baumannii-calcoaceticus complex was associated with longer ICU stay (median interquartile range [IQR]: 11 days [5-18], adjusted hazard ratio [aHR]: 2.56 [99% confidence interval (CI):1.76-3.70]), but not with mortality (adjusted odds ratio: 1.59 [99%CI: 0.74-3.40] at the chosen level of significance). The blaOXA-23-like gene was detected in 292/318 (91.8%) isolates, including isolates from the environment and HCW. Typing revealed five major clusters. Sequence types (ST)195, ST208, ST218, ST642 as well as new STs were found. The dominant clone consisted of isolates from patients and environment throughout the study period. Conclusions:Carbapenem-nonsusceptible A. baumannii-calcoaceticus complex are endemic in this setting. Prevention requires source control and limiting transmission of strains. Trial registration:The study was retrospectively registered at www.trialregister.nl (No:5541). Candidate number: 23,527, NTR number: NTR5541, Date registered NTR: 22nd December 2015.

Project description:OBJECTIVE:A prospective observational study was performed to assess the epidemiology and clinical impact of carbapenem-non-susceptible Klebsiella pneumoniae (CNKP) in intensive care units (ICUs) of the national referral hospital in Jakarta, Indonesia. MATERIALS/METHODS:Adult patients consecutively hospitalized for >?48?h in two ICUs of the national referral hospital were included from April until October 2013 and from April until August 2014. K. pneumoniae from clinical cultures and standardized screening of rectum and throat on admission, discharge and weekly if hospitalized >?7?days were collected. Environmental niches and healthcare workers (HCWs) were also screened. Susceptibility was determined phenotypically and the presence of carbapenemase genes by PCR. Raman spectroscopy as well as multiple-locus variable number tandem repeat analysis (MLVA) were used for typing. RESULTS:Twenty-two out of 412 (5.3%) patients carried CNKP on admission and 37/390 (9.5%) acquired CNKP during ICU stay. The acquisition rate was 24.7/1000 patient-days at risk. One out of 31 (3.2%) environmental isolates was a CNKP. None of the HCWs carried CNKP. Acquisition of CNKP was associated with longer ICU stay (adjusted Hazard Ratio: 2.32 [CI99: 1.35-3.68]). ICU survival was lower among patients with CNKP compared to patients with carbapenem-susceptible K. pneumoniae (aHR 2.57, p?=?0.005). Ninety-six of the 100 (96%) CNKP isolates carried a carbapenemase gene, predominantly blaNDM. Raman typing revealed three major clusters among 48 Raman types identified, whereas MLVA distinguished six major clusters among a total of 30 different genotypes. CONCLUSIONS:NDM-producing CNKP are introduced into these ICUs and some strains expand clonally among patients and the environment, resulting in endemic CNKP. CNKP acquisition was associated with prolonged ICU stay and may affect ICU survival. TRIAL REGISTRATION:The study was registered at Netherlands Trial Register http://www.trialregister.nl. Candidate number: 23527, NTR number: NTR5541, NL number: NL5425 (https://www.trialregister.nl/trial/5424), Retrospectively registered: NTR: 22 December 2015.

Dataset Information

Targeted genome sequencing data of young women breast cancer patients in Cipto Mangunkusumo national hospital, Jakarta.

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Targeted genome sequencing data of young women breast cancer patients in Cipto Mangunkusumo national hospital, Jakarta.

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