Genomics of drug sensitivity in bladder cancer: an integrated resource for pharmacogenomic analysis in bladder cancer.


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.


BMC Med Genomics


BMC medical genomics


Ansari AA,Park I,Kim I,Park S,Ahn SM,Lee JL




Has Abstract


2018-10-03 00:00:00












  • Blood signatures for second stage human African trypanosomiasis: a transcriptomic approach.

    abstract:BACKGROUND:Rhodesiense sleeping sickness is caused by infection with T. b rhodesiense parasites resulting in an acute disease that is fatal if not treated in time. The aim of this study was to understand the global impact of active T. b rhodesiense infection on the patient's immune response in the early and late stages...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Mulindwa J,Matovu E,Enyaru J,Clayton C

    更新日期:2020-01-30 00:00:00

  • 12q14 microduplication: a new clinical entity reciprocal to the microdeletion syndrome?

    abstract:BACKGROUND:12q14 microdeletion syndrome is characterized by low birth weight and failure to thrive, proportionate short stature and developmental delay. The opposite syndrome (microduplication) has not yet been characterized. Our main objective is the recognition of a new clinical entity - 12q14 microduplication syndro...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Dória S,Alves D,Pinho MJ,Pinto J,Leão M

    更新日期:2020-01-03 00:00:00

  • Birt-Hogg-Dubé renal tumors are genetically distinct from other renal neoplasias and are associated with up-regulation of mitochondrial gene expression.

    abstract:BACKGROUND:Germline mutations in the folliculin (FLCN) gene are associated with the development of Birt-Hogg-Dubé syndrome (BHDS), a disease characterized by papular skin lesions, a high occurrence of spontaneous pneumothorax, and the development of renal neoplasias. The majority of renal tumors that arise in BHDS-affe...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Klomp JA,Petillo D,Niemi NM,Dykema KJ,Chen J,Yang XJ,Sääf A,Zickert P,Aly M,Bergerheim U,Nordenskjöld M,Gad S,Giraud S,Denoux Y,Yonneau L,Méjean A,Vasiliu V,Richard S,MacKeigan JP,Teh BT,Furge KA

    更新日期:2010-12-16 00:00:00

  • MySeq: privacy-protecting browser-based personal Genome analysis for genomics education and exploration.

    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


    authors: Linderman MD,McElroy L,Chang L

    更新日期:2019-11-27 00:00:00

  • Using gene expression signatures to identify novel treatment strategies in gulf war illness.

    abstract:BACKGROUND:Gulf War Illness (GWI) is a complex multi-symptom disorder that affects up to one in three veterans of this 1991 conflict and for which no effective treatment has been found. Discovering novel treatment strategies for such a complex chronic illness is extremely expensive, carries a high probability of failur...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Craddock TJ,Harvey JM,Nathanson L,Barnes ZM,Klimas NG,Fletcher MA,Broderick G

    更新日期:2015-07-09 00:00:00

  • The similarity of inherited diseases (II): clinical and biological similarity between the phenotypic series.

    abstract:BACKGROUND:Despite being caused by mutations in different genes, diseases in the same phenotypic series are clinically similar, as reported in Part I of this study. Here, in Part II, we hypothesized that the phenotypic series too might be clinically similar. Furthermore, on the assumption that gene mutations indirectly...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Gamba A,Salmona M,Cantù L,Bazzoni G

    更新日期:2020-09-24 00:00:00

  • Identification of exon skipping events associated with Alzheimer's disease in the human hippocampus.

    abstract:BACKGROUND:At least 90% of human genes are alternatively spliced. Alternative splicing has an important function regulating gene expression and miss-splicing can contribute to risk for human diseases, including Alzheimer's disease (AD). METHODS:We developed a splicing decision model as a molecular mechanism to identif...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Han S,Miller JE,Byun S,Kim D,Risacher SL,Saykin AJ,Lee Y,Nho K,for Alzheimer’s Disease Neuroimaging Initiative.

    更新日期:2019-01-31 00:00:00

  • Evaluation of the imputation performance of the program IMPUTE in an admixed sample from Mexico City using several model designs.

    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


    authors: Krithika S,Valladares-Salgado A,Peralta J,Escobedo-de La Peña J,Kumate-Rodríguez J,Cruz M,Parra EJ

    更新日期:2012-05-01 00:00:00

  • Key genes for modulating information flow play a temporal role as breast tumor coexpression networks are dynamically rewired by letrozole.

    abstract:BACKGROUND:Genes do not act in isolation but instead as part of complex regulatory networks. To understand how breast tumors adapt to the presence of the drug letrozole, at the molecular level, it is necessary to consider how the expression levels of genes in these networks change relative to one another. METHODS:Usin...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Penrod NM,Moore JH

    更新日期:2013-01-01 00:00:00

  • LDSplitDB: a database for studies of meiotic recombination hotspots in MHC using human genomic data.

    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


    authors: Guo J,Chen H,Yang P,Lee YT,Wu M,Przytycka TM,Kwoh CK,Zheng J

    更新日期:2018-04-20 00:00:00

  • CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations.

    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


    authors: Kotliarov Y,Bozdag S,Cheng H,Wuchty S,Zenklusen JC,Fine HA

    更新日期:2010-04-09 00:00:00

  • DNA methylation differences in monozygotic twin pairs discordant for schizophrenia identifies psychosis related genes and networks.

    abstract:BACKGROUND:Despite their singular origin, monozygotic twin pairs often display discordance for complex disorders including schizophrenia. It is a common (1%) and often familial disease with a discordance rate of ~50% in monozygotic twins. This high discordance is often explained by the role of yet unknown environmental...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Castellani CA,Laufer BI,Melka MG,Diehl EJ,O'Reilly RL,Singh SM

    更新日期:2015-05-06 00:00:00

  • Logistic regression over encrypted data from fully homomorphic encryption.

    abstract:BACKGROUND:One of the tasks in the 2017 iDASH secure genome analysis competition was to enable training of logistic regression models over encrypted genomic data. More precisely, given a list of approximately 1500 patient records, each with 18 binary features containing information on specific mutations, the idea was f...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Chen H,Gilad-Bachrach R,Han K,Huang Z,Jalali A,Laine K,Lauter K

    更新日期:2018-10-11 00:00:00

  • Characterization of global transcription profile of normal and HPV-immortalized keratinocytes and their response to TNF treatment.

    abstract:BACKGROUND:Persistent infection by high risk HPV types (e.g. HPV-16, -18, -31, and -45) is the main risk factor for development of cervical intraepithelial neoplasia and cervical cancer. Tumor necrosis factor (TNF) is a key mediator of epithelial cell inflammatory response and exerts a potent cytostatic effect on norma...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Termini L,Boccardo E,Esteves GH,Hirata R Jr,Martins WK,Colo AE,Neves EJ,Villa LL,Reis LF

    更新日期:2008-06-27 00:00:00

  • Primary microcephaly case from the Karachay-Cherkess Republic poses an additional support for microcephaly and Seckel syndrome spectrum disorders.

    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


    authors: Marakhonov AV,Konovalov FA,Makaov AK,Vasilyeva TA,Kadyshev VV,Galkina VA,Dadali EL,Kutsev SI,Zinchenko RA

    更新日期:2018-02-13 00:00:00

  • Screening significantly hypermethylated genes in fetal tissues compared with maternal blood using a methylated-CpG island recovery assay-based microarray.

    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


    authors: Yin A,Zhang X,Wu J,Du L,He T,Zhang X

    更新日期:2012-06-18 00:00:00

  • LncRNA-miRNA-mRNA expression variation profile in the urine of calcium oxalate stone patients.

    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


    authors: Liang X,Lai Y,Wu W,Chen D,Zhong F,Huang J,Zeng T,Duan X,Huang Y,Zhang S,Li S,Wu W

    更新日期:2019-04-29 00:00:00

  • Gene profiling of the erythro- and megakaryoblastic leukaemias induced by the Graffi murine retrovirus.

    abstract:BACKGROUND:Acute erythro- and megakaryoblastic leukaemias are associated with very poor prognoses and the mechanism of blastic transformation is insufficiently elucidated. The murine Graffi leukaemia retrovirus induces erythro- and megakaryoblastic leukaemias when inoculated into NFS mice and represents a good model to...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Voisin V,Legault P,Ospina DP,Ben-David Y,Rassart E

    更新日期:2010-01-26 00:00:00

  • Developing a healthcare dataset information resource (DIR) based on Semantic Web.

    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


    authors: Shi J,Zheng M,Yao L,Ge Y

    更新日期:2018-11-20 00:00:00

  • Pan-cancer analysis of differential DNA methylation patterns.

    abstract:BACKGROUND:DNA methylation is a key epigenetic regulator contributing to cancer development. To understand the role of DNA methylation in tumorigenesis, it is important to investigate and compare differential methylation (DM) patterns between normal and case samples across different cancer types. However, current pan-c...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Shi M,Tsui SK,Wu H,Wei Y

    更新日期:2020-10-22 00:00:00

  • Genome-wide DNA methylome reveals the dysfunction of intronic microRNAs in major psychosis.

    abstract:BACKGROUND:DNA methylation is thought to be extensively involved in the pathogenesis of many diseases, including major psychosis. However, most studies focus on DNA methylation alteration at promoters of protein-coding genes, despite the poor correlation between DNA methylation and gene expression. METHODS:We analyzed...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Zhao H,Xu J,Pang L,Zhang Y,Fan H,Liu L,Liu T,Yu F,Zhang G,Lan Y,Bai J,Li X,Xiao Y

    更新日期:2015-10-14 00:00:00

  • Molecular conservation of estrogen-response associated with cell cycle regulation, hormonal carcinogenesis and cancer in zebrafish and human cancer cell lines.

    abstract:BACKGROUND:The zebrafish is recognized as a versatile cancer and drug screening model. However, it is not known whether the estrogen-responsive genes and signaling pathways that are involved in estrogen-dependent carcinogenesis and human cancer are operating in zebrafish. In order to determine the potential of zebrafis...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Lam SH,Lee SG,Lin CY,Thomsen JS,Fu PY,Murthy KR,Li H,Govindarajan KR,Nick LC,Bourque G,Gong Z,Lufkin T,Liu ET,Mathavan S

    更新日期:2011-05-16 00:00:00

  • DNA methylation differences at growth related genes correlate with birth weight: a molecular signature linked to developmental origins of adult disease?

    abstract:BACKGROUND:Infant birth weight is a complex quantitative trait associated with both neonatal and long-term health outcomes. Numerous studies have been published in which candidate genes (IGF1, IGF2, IGF2R, IGF binding proteins, PHLDA2 and PLAGL1) have been associated with birth weight, but these studies are difficult t...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Turan N,Ghalwash MF,Katari S,Coutifaris C,Obradovic Z,Sapienza C

    更新日期:2012-04-12 00:00:00

  • New insights into DNA methylation signatures: SMARCA2 variants in Nicolaides-Baraitser syndrome.

    abstract:BACKGROUND:Nicolaides-Baraitser syndrome (NCBRS) is a neurodevelopmental disorder caused by pathogenic sequence variants in SMARCA2 which encodes the catalytic component of the chromatin remodeling BAF complex. Pathogenic variants in genes that encode epigenetic regulators have been associated with genome-wide changes ...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Chater-Diehl E,Ejaz R,Cytrynbaum C,Siu MT,Turinsky A,Choufani S,Goodman SJ,Abdul-Rahman O,Bedford M,Dorrani N,Engleman K,Flores-Daboub J,Genevieve D,Mendoza-Londono R,Meschino W,Perrin L,Safina N,Townshend S,Scherer S

    更新日期:2019-07-09 00:00:00

  • Gene expression signatures in childhood acute leukemias are largely unique and distinct from those of normal tissues and other malignancies.

    abstract:BACKGROUND:Childhood leukemia is characterized by the presence of balanced chromosomal translocations or by other structural or numerical chromosomal changes. It is well know that leukemias with specific molecular abnormalities display profoundly different global gene expression profiles. However, it is largely unknown...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Andersson A,Edén P,Olofsson T,Fioretos T

    更新日期:2010-03-08 00:00:00

  • Identification of sequence variants associated with severe microtia-astresia by targeted sequencing.

    abstract:BACKGROUND:Microtia-atresia is characterized by abnormalities of the auricle (microtia) and aplasia or hypoplasia of the external auditory canal, often associated with middle ear abnormalities. To date, no causal genetic mutations or genes have been identified in microtia-atresia patients. METHODS:We designed a panel ...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Wang P,Wang Y,Fan X,Liu Y,Fan Y,Liu T,Chen C,Zhang S,Chen X

    更新日期:2019-01-28 00:00:00

  • What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations.

    abstract:BACKGROUND:Testing strategies is crucial for genetics clinics and testing laboratories. In this study, we tried to compare the hit rate between solo and trio and trio plus testing and between trio and sibship testing. Finally, we studied the impact of extended family analysis, mainly in complex and unsolved cases. MET...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Alfares A,Alsubaie L,Aloraini T,Alaskar A,Althagafi A,Alahmad A,Rashid M,Alswaid A,Alothaim A,Eyaid W,Ababneh F,Albalwi M,Alotaibi R,Almutairi M,Altharawi N,Alsamer A,Abdelhakim M,Kafkas S,Mineta K,Cheung N,Abdall

    更新日期:2020-07-17 00:00:00

  • The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: genomics meets medicine.

    abstract::During June 10-12, 2018, the International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held in Los Angeles, California, USA. The conference included 11 scientific sessions, four tutorials, one poster session, four keynote talks and four eminent scholar talks that covered a wide range of topics rang...

    journal_title:BMC medical genomics

    pub_type: 社论


    authors: Zhi D,Zhao Z,Li F,Wu Z,Liu X,Wang K

    更新日期:2019-01-31 00:00:00

  • Transcriptional profiling of mycobacterial antigen-induced responses in infants vaccinated with BCG at birth.

    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


    authors: Fletcher HA,Keyser A,Bowmaker M,Sayles PC,Kaplan G,Hussey G,Hill AV,Hanekom WA

    更新日期:2009-02-24 00:00:00

  • Study design and data analysis considerations for the discovery of prognostic molecular biomarkers: a case study of progression free survival in advanced serous ovarian cancer.

    abstract:BACKGROUND:Accurate discovery of molecular biomarkers that are prognostic of a clinical outcome is an important yet challenging task, partly due to the combination of the typically weak genomic signal for a clinical outcome and the frequently strong noise due to microarray handling effects. Effective strategies to reso...

    journal_title:BMC medical genomics

    pub_type: 杂志文章


    authors: Qin LX,Levine DA

    更新日期:2016-06-10 00:00:00