Abstract:
BACKGROUND:Bladder cancer has numerous genomic features that are potentially actionable by targeted agents. Nevertheless, both pre-clinical and clinical research using molecular targeted agents have been very limited in bladder cancer. RESULTS:We created the Genomics of Drug Sensitivity in Bladder Cancer (GDBC) database, an integrated database (DB) to facilitate the genomic understanding of bladder cancer in relation to drug sensitivity, in order to promote potential therapeutic applications of targeted agents in bladder cancer treatment. The GDBC database contains two separate datasets: 1) in-house drug sensitivity data, in which 13 targeted agents were tested against 10 bladder cancer cell lines; 2) data extracted and integrated from public databases, including the Cancer Therapeutics Research Portal, Cancer Cell Line Encyclopedia, Genomics of Drug Sensitivity in Cancer, Kyoto Encyclopedia of Genes and Genomes, and the Cancer Gene Census databases, as well as bladder cancer genomics data and synthetic lethality/synthetic dosage lethality connections. CONCLUSIONS:GDBC is an integrated DB of genomics and drug sensitivity data with a specific focus on bladder cancer. With a user-friendly web-interface, GDBC helps users generate genomics-based hypotheses that can be tested experimentally using drugs and cell lines included in GDBC.
journal_name
BMC Med Genomicsjournal_title
BMC medical genomicsauthors
Ansari AA,Park I,Kim I,Park S,Ahn SM,Lee JLdoi
10.1186/s12920-018-0406-2subject
Has Abstractpub_date
2018-10-03 00:00:00pages
88issue
1issn
1755-8794pii
10.1186/s12920-018-0406-2journal_volume
11pub_type
杂志文章abstract:BACKGROUND:With 15,949 markers, the low-density Infinium QC Array-24 BeadChip enables linkage analysis, HLA haplotyping, fingerprinting, ethnicity determination, mitochondrial genome variations, blood groups and pharmacogenomics. It represents an attractive independent QC option for NGS-based diagnostic laboratories, a...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-017-0297-7
更新日期:2017-10-06 00:00:00
abstract:BACKGROUND:Methotrexate is one of the earliest cytotoxic drugs used in cancer therapy, and despite the isolation of multiple other folate antagonists, methotrexate maintains its significant role as a treatment for different types of cancer and other disorders. The usefulness of treatment with methotrexate is limited by...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-35
更新日期:2008-08-11 00:00:00
abstract:BACKGROUND:To explore long-non-coding RNA (lncRNA), microRNA (miRNA) and messenger RNA (mRNA) expression profiles and their biological functions in the urine samples in calcium oxalate (CaOx) patients. METHODS:Five CaOx kidney stone patients were recruited in CaOx stone group and six healthy people were included as co...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0502-y
更新日期:2019-04-29 00:00:00
abstract:BACKGROUND:Gastric emptying is impaired in patients with gastroparesis whereas it is either unchanged or accelerated in obese individuals. The goal of the current study was to identify changes in gene expression in the stomach muscularis that may be contributing to altered gastric motility in idiopathic gastroparesis a...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0550-3
更新日期:2019-06-20 00:00:00
abstract:BACKGROUND:The complexity of genome informatics is a recurring challenge for genome exploration and analysis by students and other non-experts. This complexity creates a barrier to wider implementation of experiential genomics education, even in settings with substantial computational resources and expertise. Reducing ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0615-3
更新日期:2019-11-27 00:00:00
abstract:BACKGROUND:Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulation could lead to serio...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0351-0
更新日期:2018-04-20 00:00:00
abstract:BACKGROUND:2q37 deletion syndrome is a rare congenital disorder that is characterized by facial dysmorphism, obesity, vascular and skeletal malformations, and a variable degree of intellectual disability. To date, common but variable phenotypes, such as skeletal or digit malformations and obesity, have been associated ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-7-19
更新日期:2014-04-22 00:00:00
abstract:BACKGROUND:Preeclampsia (PE) is a pregnancy-related condition that affects both the infant and the mother. Although the role of various inflammatory molecules in PE has been demonstrated, the importance of pro-inflammatory molecules such as IL-17A, IL-23 is not well understood. In the present investigation, a potential...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-00840-8
更新日期:2021-01-06 00:00:00
abstract:BACKGROUND:We explored the imputation performance of the program IMPUTE in an admixed sample from Mexico City. The following issues were evaluated: (a) the impact of different reference panels (HapMap vs. 1000 Genomes) on imputation; (b) potential differences in imputation performance between single-step vs. two-step (...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-5-12
更新日期:2012-05-01 00:00:00
abstract:BACKGROUND:With the introduction of increasingly powerful mass spectrometry (MS) techniques for clinical research, several recent large-scale MS proteomics studies have sought to characterize the entire human plasma proteome with a general objective for identifying thousands of proteins leaked from tissues in the circu...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-12
更新日期:2008-04-25 00:00:00
abstract:BACKGROUND:The noninvasive prenatal diagnosis procedures that are currently used to detect genetic diseases do not achieve desirable levels of sensitivity and specificity. Recently, fetal methylated DNA biomarkers in maternal peripheral blood have been explored for the noninvasive prenatal detection of genetic disorder...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-5-26
更新日期:2012-06-18 00:00:00
abstract:BACKGROUND:Reliability of real-time PCR (RT-qPCR) data is dependent on the use of appropriate reference gene(s) for normalization. To date, no validated reference genes have been reported for normalizing gene expression in human myocardium. This study aimed to identify validated reference genes for use in gene expressi...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-64
更新日期:2008-12-29 00:00:00
abstract:BACKGROUND:Epithelial to mesenchymal transition, and mimicking processes, contribute to cancer invasion and metastasis, and are known to be responsible for resistance to various therapeutic agents in many cancers. While a number of studies have proposed molecular signatures that characterize the spectrum of such transi...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-017-0252-7
更新日期:2017-03-09 00:00:00
abstract:BACKGROUND:Recent advances in whole-genome association studies (WGASs) for human cancer risk are beginning to provide the part lists of low-penetrance susceptibility genes. However, statistical analysis in these studies is complicated by the vast number of genetic variants examined and the weak effects observed, as a r...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-62
更新日期:2008-12-18 00:00:00
abstract:BACKGROUND:Childhood asthma is a syndrome composed of heterogeneous phenotypes; furthermore, intrinsic biologic variation among racial/ethnic populations suggests possible genetic ancestry variation in childhood asthma. The objective of the study is to identify clinically homogeneous asthma subphenotypes in a diverse s...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0367-5
更新日期:2018-05-31 00:00:00
abstract:BACKGROUND:The rapid adoption of next-generation sequencing provides an efficient system for detecting somatic alterations in neoplasms. The detection of such alterations requires a matched non-neoplastic sample for adequate filtering of non-somatic events such as germline polymorphisms. Non-neoplastic tissue adjacent ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-016-0226-1
更新日期:2016-10-19 00:00:00
abstract:BACKGROUND:Novel tuberculosis (TB) vaccines recently tested in humans have been designed to boost immunity induced by the current vaccine, Mycobacterium bovis Bacille Calmette-Guérin (BCG). Because BCG vaccination is used extensively in infants, this population group is likely to be the first in which efficacy trials o...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-2-10
更新日期:2009-02-24 00:00:00
abstract:BACKGROUND:Detection of copy number variants (CNVs) is an important aspect of clinical testing for several disorders, including Duchenne muscular dystrophy, and is often performed using multiplex ligation-dependent probe amplification (MLPA). However, since many genetic carrier screens depend instead on next-generation...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0404-4
更新日期:2018-10-20 00:00:00
abstract:BACKGROUND:The right dataset is essential to obtain the right insights in data science; therefore, it is important for data scientists to have a good understanding of the availability of relevant datasets as well as the content, structure, and existing analyses of these datasets. While a number of efforts are underway ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0411-5
更新日期:2018-11-20 00:00:00
abstract:BACKGROUND:Loss of heterozygosity (LOH) is a common genetic event in cancer development, and is known to be involved in the somatic loss of wild-type alleles in many inherited cancer syndromes. The wider involvement of LOH in cancer is assumed to relate to unmasking a somatically mutated tumour suppressor gene through ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-015-0123-z
更新日期:2015-08-01 00:00:00
abstract:BACKGROUND:The majority of copy number callers requires high read coverage data that is often achieved with elevated material input, which increases the heterogeneity of tissue samples. However, to gain insights into smaller areas within a tissue sample, e.g. a cancerous area in a heterogeneous tissue sample, less mate...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-00731-y
更新日期:2020-06-01 00:00:00
abstract:BACKGROUND:Alterations in gene expression in peripheral blood cells have been shown to be sensitive to the presence and extent of coronary artery disease (CAD). A non-invasive blood test that could reliably assess obstructive CAD likelihood would have diagnostic utility. RESULTS:Microarray analysis of RNA samples from...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-26
更新日期:2011-03-28 00:00:00
abstract::This editorial summarizes eight research articles included in this supplement issue for the 2020 International Conference on Intelligent Biology and Medicine (ICIBM 2020) conference, that was held on August 9-10, 2020 (virtual conference), with a topic on data-driven analytics in biomedical genomics. These articles co...
journal_title:BMC medical genomics
pub_type: 社论
doi:10.1186/s12920-020-00833-7
更新日期:2020-12-28 00:00:00
abstract:BACKGROUND:Chiari Type I Malformation (CMI) is characterized by herniation of the cerebellar tonsils through the foramen magnum at the base of the skull, resulting in significant neurologic morbidity. As CMI patients display a high degree of clinical variability and multiple mechanisms have been proposed for tonsillar ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-7-39
更新日期:2014-06-25 00:00:00
abstract:BACKGROUND:Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignancies in humans. The average 5-year survival rate is one of the lowest among aggressive cancers, showing no significant improvement in recent years. When detected early, HNSCC has a good prognosis, but most patients present metast...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-56
更新日期:2008-11-11 00:00:00
abstract:BACKGROUND:Genomic copy number alterations are widely associated with a broad range of human tumors and offer the potential to be used as a diagnostic tool. Especially in the emerging era of personalized medicine medical informatics tools that allow the fast visualization and analysis of genomic alterations of a patien...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-3-11
更新日期:2010-04-09 00:00:00
abstract:BACKGROUND:Primary microcephaly represents an example of clinically and genetically heterogeneous condition. Here we describe a case of primary microcephaly from the Karachay-Cherkess Republic, which was initially diagnosed with Seckel syndrome. CASE PRESENTATION:Clinical exome sequencing of the proband revealed a nov...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0326-1
更新日期:2018-02-13 00:00:00
abstract:BACKGROUND:DNA methylation levels will be important for detection of epigenetic effects. However, there are few reports showing sex-related differences in the sensitivity to DNA methylation. To evaluate their sex-related individual differences in the sensitivity to methylation rigorously, we performed a systematic anal...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-016-0217-2
更新日期:2016-08-26 00:00:00
abstract:BACKGROUND:Intra-tumor heterogeneity stems from genetic, epigenetic, functional, and environmental differences among tumor cells. A major source of genetic heterogeneity comes from DNA sequence differences and/or whole chromosome and focal copy number variations (CNVs). Whole chromosome CNVs are caused by chromosomal i...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0532-5
更新日期:2019-05-31 00:00:00
abstract:BACKGROUND:Rapid advances in scientific research have led to an increase in public awareness of genetic testing and pharmacogenetics. Direct-to-consumer (DTC) genetic testing companies, such as 23andMe, allow consumers to access their genetic information directly through an online service without the involvement of hea...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-017-0283-0
更新日期:2017-06-19 00:00:00